GO Annotations

Steven Roberts 2025-03-21

Want to start with grabbing protein with specific GOs

see also https://www.ebi.ac.uk/QuickGO/annotations

Variables

# Global R options
knitr::opts_chunk$set(echo = TRUE)

# Define key paths and tool directories
 
OUT_DIR <- "../output/27-Apul-pheno-annot/"
evalue <- "1E-20"
fasta <- "../data/Apulchra-genome.pep.faa"

# Export these as environment variables for bash chunks.
Sys.setenv(
  OUT_DIR = OUT_DIR,
  evalue = evalue,
  fasta =fasta
)

Aerobic respiration (GO:0009060)

GO="0009060"

curl -H "Accept: text/plain" "https://rest.uniprot.org/uniprotkb/stream?format=fasta&query=%28%28go%3A"${GO}"%29%29+AND+%28reviewed%3Atrue%29" -o "${OUT_DIR}"SwissProt-GO:"${GO}".fa

head "${OUT_DIR}"SwissProt-GO:"${GO}".fa

echo "Number of Proteins"
grep -c ">" "${OUT_DIR}"SwissProt-GO:"${GO}".fa

/home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \
-in "${OUT_DIR}"SwissProt-GO:"${GO}".fa \
-dbtype prot \
-out "${OUT_DIR}"SwissProt-GO:"${GO}"


/home/shared/ncbi-blast-2.15.0+/bin/blastp \
-query $fasta \
-db "${OUT_DIR}"SwissProt-GO:"${GO}" \
-out "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab \
-evalue "${evalue}" \
-num_threads 42 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6 \
2> "${OUT_DIR}"blast_warnings"${GO}".txt

head "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab

echo "Number of hits"

wc -l "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
100  673k    0  673k    0     0   378k      0 --:--:--  0:00:01 --:--:--  377k
100 2157k    0 2157k    0     0   768k      0 --:--:--  0:00:02 --:--:--  768k
100 3305k    0 3305k    0     0   868k      0 --:--:--  0:00:03 --:--:--  868k
100 4953k    0 4953k    0     0  1015k      0 --:--:--  0:00:04 --:--:-- 1015k
100 5219k    0 5219k    0     0  1064k      0 --:--:--  0:00:04 --:--:-- 1346k
>sp|A0A096P8D3|IDH_OSTTA Isocitrate dehydrogenase (NAD(+)), mitochondrial OS=Ostreococcus tauri OX=70448 GN=IDH PE=1 SV=1
MTRVERGRVLARAIERAVAHRASARRWTTTTRTPAWMVTGWMGGRGVDRSTAMTRFERCG
STASSKITAAPMVYVRGEEMTAYVMDLIRSRWIEPRVDVGGWETFDLRAKNRDDTEDRVL
RDVIEAGKRIKAIFKEPTVTPTADQVKRLGLRKSWGSPNGAMRRGWNGITISRDTIHIDG
VELGYKKPVLFERHAVGGEYSAGYKNVGKGKLTTTFTPSEGPDAGKTVVVDEREIVDEEA
AVVTYHNPYDNVHDLARFFFGRCLEAKVTPYVVTKKTVFKWQEPFWQIMRTVFDEEFKAQ
FVAAGVMKEGEELVHLLSDAATMKLVQWRQGGFGMAAHNYDGDVLTDELAQVHKSPGFIT
SNLVGVHEDGTLIKEFEASHGTVADMDEARLRGEETSLNPLGMVEGLIGAMNHAADVHNI
DRDRTHAFTTKMRTVIHQLFREGKGTRDLCGPSGLTTEQFIDAVAERLDA
>sp|A0A0D2Y5A7|ODP2_FUSO4 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial OS=Fusarium oxysporum f. sp. lycopersici (strain 4287 / CBS 123668 / FGSC 9935 / NRRL 34936) OX=426428 GN=LAT1 PE=1 SV=1
Number of Proteins
10978


Building a new DB, current time: 03/21/2025 12:49:44
New DB name:   /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0009060
New DB title:  ../output/27-Apul-pheno-annot/SwissProt-GO:0009060.fa
Sequence type: Protein
Deleted existing Protein BLAST database named /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0009060
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 10978 sequences in 0.179029 seconds.


FUN_000047-T1   sp|Q757N1|H3_EREGS  88.971  136 15  0   4   139 1   136 2.14e-86    246
FUN_000049-T1   sp|Q757N1|H3_EREGS  92.079  101 8   0   1   101 1   101 1.61e-63    190
FUN_000051-T1   sp|Q757N1|H3_EREGS  92.079  101 8   0   1   101 1   101 1.61e-63    190
FUN_000053-T1   sp|Q757N1|H3_EREGS  92.079  101 8   0   1   101 1   101 1.61e-63    190
FUN_000055-T1   sp|Q757N1|H3_EREGS  92.079  101 8   0   1   101 1   101 1.61e-63    190
FUN_000057-T1   sp|Q757N1|H3_EREGS  92.079  101 8   0   1   101 1   101 1.61e-63    190
FUN_000059-T1   sp|Q757N1|H3_EREGS  92.079  101 8   0   1   101 1   101 1.61e-63    190
FUN_000061-T1   sp|Q757N1|H3_EREGS  92.079  101 8   0   1   101 1   101 1.61e-63    190
FUN_000063-T1   sp|Q757N1|H3_EREGS  92.079  101 8   0   1   101 1   101 1.61e-63    190
FUN_000065-T1   sp|Q757N1|H3_EREGS  88.971  136 15  0   4   139 1   136 2.14e-86    246
Number of hits
616 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0009060_out.tab

Oxidative phosphorylation (GO:0006119)

GO="0006119"

curl -H "Accept: text/plain" "https://rest.uniprot.org/uniprotkb/stream?format=fasta&query=%28%28go%3A"${GO}"%29%29+AND+%28reviewed%3Atrue%29" -o "${OUT_DIR}"SwissProt-GO:"${GO}".fa

head "${OUT_DIR}"SwissProt-GO:"${GO}".fa

echo "Number of Proteins"
grep -c ">" "${OUT_DIR}"SwissProt-GO:"${GO}".fa

/home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \
-in "${OUT_DIR}"SwissProt-GO:"${GO}".fa \
-dbtype prot \
-out "${OUT_DIR}"SwissProt-GO:"${GO}"


/home/shared/ncbi-blast-2.15.0+/bin/blastp \
-query $fasta \
-db "${OUT_DIR}"SwissProt-GO:"${GO}" \
-out "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab \
-evalue "${evalue}" \
-num_threads 42 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6 \
2> "${OUT_DIR}"blast_warnings"${GO}".txt

head "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab

echo "Number of hits"

wc -l "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100  479k    0  479k    0     0   285k      0 --:--:--  0:00:01 --:--:--  285k
100 2632k    0 2632k    0     0   969k      0 --:--:--  0:00:02 --:--:--  969k
100 2675k    0 2675k    0     0   984k      0 --:--:--  0:00:02 --:--:--  983k
>sp|A0A1D8PHA3|CYT1_CANAL Cytochrome b-c1 complex catalytic subunit, mitochondrial OS=Candida albicans (strain SC5314 / ATCC MYA-2876) OX=237561 GN=CYT1 PE=1 SV=1
MFRTAYKTMNQSMVQKFIAGGVGVTGLTASYLLYQDSMTADAMTAAEHGLHPPAYNWPHN
GMFETFDHASIRRGFQVYREVCAACHSLDRIAWRNLVGVSHTTSEAKAMAEELEYDDEPD
DEGKPRKRPGKLADYIPGPYENEQAARAANQGAYPPDLSLIVKARHGGSDYIFSLLTGYP
DEPPAGVVLPEGSNYNPYFPGGAIAMGRVLFDDLVEYEDGTPATTSQMAKDVSTFLNWAS
EPEHDDRKKWGLKALVVLSSLYLLSIWVKRFKWTPIKNRKFRFDPPKK
>sp|A0A1D8PJX3|RIP1_CANAL Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Candida albicans (strain SC5314 / ATCC MYA-2876) OX=237561 GN=RIP1 PE=1 SV=1
MSSLAFRTLRNGLGLKSSVRALSTTTTTLSNYQQPDYSSYLNNKSGQGSRNFTYFMVGSM
GLLSAAGAKSTVEAFLSSFAASADVLAMAKVEVKLGAIPEGKNVIIKWQGKPVFIRHRTA
DEIEEANQVDIKTLRDPQNDADRVKKPEWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGS
Number of Proteins
6140


Building a new DB, current time: 03/21/2025 12:50:54
New DB name:   /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0006119
New DB title:  ../output/27-Apul-pheno-annot/SwissProt-GO:0006119.fa
Sequence type: Protein
Deleted existing Protein BLAST database named /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0006119
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 6140 sequences in 0.103551 seconds.


FUN_000943-T1   sp|Q791V5|MTCH2_MOUSE   41.549  284 162 2   24  305 8   289 2.00e-80    243
FUN_000977-T1   sp|Q6XHB2|ROCO4_DICDI   30.035  283 163 10  589 848 1023    1293    6.93e-28    119
FUN_001181-T1   sp|O52683|HYDA_THEMA    29.902  408 237 17  115 515 184 549 5.65e-40    151
FUN_001463-T1   sp|Q6XHB2|ROCO4_DICDI   27.059  340 219 14  1552    1876    954 1279    1.37e-23    107
FUN_001483-T1   sp|Q6CFT7|ATPB_YARLI    25.301  415 280 10  45  448 52  447 3.17e-29    117
FUN_001648-T1   sp|P24539|AT5F1_HUMAN   39.691  194 108 3   15  207 62  247 2.52e-38    130
FUN_001648-T2   sp|P24539|AT5F1_HUMAN   40.314  191 105 3   47  236 62  244 2.48e-38    131
FUN_003901-T1   sp|P29410|KAD2_RAT  34.314  204 105 5   30  204 20  223 9.03e-29    105
FUN_004027-T1   sp|Q05752|NDUA7_BOVIN   53.947  76  34  1   1   75  1   76  6.67e-23    83.2
FUN_004095-T1   sp|Q6XHB2|ROCO4_DICDI   28.975  283 175 10  37  301 1015    1289    2.80e-21    96.3
Number of hits
130 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0006119_out.tab

Canonical glycolysis (GO:0061621)

GO="0061621"

curl -H "Accept: text/plain" "https://rest.uniprot.org/uniprotkb/stream?format=fasta&query=%28%28go%3A"${GO}"%29%29+AND+%28reviewed%3Atrue%29" -o "${OUT_DIR}"SwissProt-GO:"${GO}".fa

head "${OUT_DIR}"SwissProt-GO:"${GO}".fa

echo "Number of Proteins"
grep -c ">" "${OUT_DIR}"SwissProt-GO:"${GO}".fa

/home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \
-in "${OUT_DIR}"SwissProt-GO:"${GO}".fa \
-dbtype prot \
-out "${OUT_DIR}"SwissProt-GO:"${GO}"


/home/shared/ncbi-blast-2.15.0+/bin/blastp \
-query $fasta \
-db "${OUT_DIR}"SwissProt-GO:"${GO}" \
-out "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab \
-evalue "${evalue}" \
-num_threads 42 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6 \
2> "${OUT_DIR}"blast_warnings"${GO}".txt

head "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab

echo "Number of hits"

wc -l "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:--  0:00:01 --:--:--     0
100  208k    0  208k    0     0   117k      0 --:--:--  0:00:01 --:--:--  117k
>sp|A1A4J1|PFKAL_BOVIN ATP-dependent 6-phosphofructokinase, liver type OS=Bos taurus OX=9913 GN=PFKL PE=2 SV=1
MASVDLEKLRTTGAGKAIGVLTSGGDAQGMNAAVRAVTRMGIYVGAKVFLIYEGYEGLVE
GGENIKQANWLSVSNIIQLGGTVIGSARCKAFTTREGRRAAAYNLVQRGITNLCVIGGDG
SLTGANIFRSEWGSLLEELVSEGKISEGTAQTYSHLNIAGLVGSIDNDFCGTDMTIGTDS
ALHRIMEVIDAITTTAQSHQRTFVLEVMGRHCGYLALVSALASGADWLFIPEAPPEDGWE
NFMCERLGETRSRGSRLNIIIIAEGAIDRNGKPISSRYVKDLVVQRLGFDTRVTVLGHVQ
RGGTPSAFDRILSSKMGMEAVMALLEATPDTPACVVSLSGNQSVRLPLMECVQMTKEVQK
AMDEKRFDEAIQLRGGSFENNWNIYKLLSHQKISKEKTNFSLAILNVGAPAAGMNAAVRS
AVRSGISQGHTVYVVHDGFEGLAKNQVQEVSWHDVAGWLGRGGSMLGTKRTLPKGFMEKI
VENIRLHNIHALLVIGGFEAYEGVLQLVEARGRYEELCIVMCVIPATISNNVPGTDFSLG
Number of Proteins
394


Building a new DB, current time: 03/21/2025 12:51:31
New DB name:   /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0061621
New DB title:  ../output/27-Apul-pheno-annot/SwissProt-GO:0061621.fa
Sequence type: Protein
Deleted existing Protein BLAST database named /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0061621
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 394 sequences in 0.0159671 seconds.


FUN_005030-T1   sp|P85037|FOXK1_HUMAN   51.000  100 48  1   95  194 302 400 4.38e-26    103
FUN_005036-T1   sp|P42128|FOXK1_MOUSE   48.454  97  50  0   30  126 290 386 1.70e-27    105
FUN_005159-T1   sp|Q3UCQ1|FOXK2_MOUSE   52.041  98  45  1   95  190 247 344 7.57e-28    108
FUN_008233-T1   sp|Q7ZX03|FOXK2_XENLA   43.066  137 75  1   37  173 188 321 1.35e-33    125
FUN_009301-T1   sp|Q867C9|PFKAM_HORSE   58.634  776 300 4   70  833 13  779 0.0 935
FUN_010519-T1   sp|P00940|TPIS_CHICK    69.672  244 74  0   3   246 4   247 1.09e-126   353
FUN_012871-T1   sp|P00940|TPIS_CHICK    69.672  244 74  0   3   246 4   247 1.09e-126   353
FUN_013147-T1   sp|Q7ZX03|FOXK2_XENLA   46.939  98  50  1   143 238 215 312 3.77e-24    96.3
FUN_013305-T1   sp|P42128|FOXK1_MOUSE   42.202  109 61  1   47  153 287 395 2.42e-22    86.7
FUN_015434-T1   sp|P05064|ALDOA_MOUSE   72.269  357 97  1   5   359 8   364 0.0 528
Number of hits
37 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0061621_out.tab

Tricarboxylic Acid Cycle (GO:0006099)

GO="0006099"

curl -H "Accept: text/plain" "https://rest.uniprot.org/uniprotkb/stream?format=fasta&query=%28%28go%3A"${GO}"%29%29+AND+%28reviewed%3Atrue%29" -o "${OUT_DIR}"SwissProt-GO:"${GO}".fa

head "${OUT_DIR}"SwissProt-GO:"${GO}".fa

echo "Number of Proteins"
grep -c ">" "${OUT_DIR}"SwissProt-GO:"${GO}".fa

/home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \
-in "${OUT_DIR}"SwissProt-GO:"${GO}".fa \
-dbtype prot \
-out "${OUT_DIR}"SwissProt-GO:"${GO}"


/home/shared/ncbi-blast-2.15.0+/bin/blastp \
-query $fasta \
-db "${OUT_DIR}"SwissProt-GO:"${GO}" \
-out "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab \
-evalue "${evalue}" \
-num_threads 42 \
-max_target_seqs 1 \
-max_hsps 1 \
-outfmt 6 \
2> "${OUT_DIR}"blast_warnings"${GO}".txt

head "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab

echo "Number of hits"

wc -l "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab

  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed

  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
100 31776    0 31776    0     0  26928      0 --:--:--  0:00:01 --:--:-- 26906
100 1726k    0 1726k    0     0   889k      0 --:--:--  0:00:01 --:--:--  889k
>sp|A0A096P8D3|IDH_OSTTA Isocitrate dehydrogenase (NAD(+)), mitochondrial OS=Ostreococcus tauri OX=70448 GN=IDH PE=1 SV=1
MTRVERGRVLARAIERAVAHRASARRWTTTTRTPAWMVTGWMGGRGVDRSTAMTRFERCG
STASSKITAAPMVYVRGEEMTAYVMDLIRSRWIEPRVDVGGWETFDLRAKNRDDTEDRVL
RDVIEAGKRIKAIFKEPTVTPTADQVKRLGLRKSWGSPNGAMRRGWNGITISRDTIHIDG
VELGYKKPVLFERHAVGGEYSAGYKNVGKGKLTTTFTPSEGPDAGKTVVVDEREIVDEEA
AVVTYHNPYDNVHDLARFFFGRCLEAKVTPYVVTKKTVFKWQEPFWQIMRTVFDEEFKAQ
FVAAGVMKEGEELVHLLSDAATMKLVQWRQGGFGMAAHNYDGDVLTDELAQVHKSPGFIT
SNLVGVHEDGTLIKEFEASHGTVADMDEARLRGEETSLNPLGMVEGLIGAMNHAADVHNI
DRDRTHAFTTKMRTVIHQLFREGKGTRDLCGPSGLTTEQFIDAVAERLDA
>sp|A0A3Q0KQY7|FUMC_SCHMA Fumarate hydratase OS=Schistosoma mansoni OX=6183 GN=Smp_158240 PE=1 SV=2
Number of Proteins
2837


Building a new DB, current time: 03/21/2025 12:51:40
New DB name:   /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0006099
New DB title:  ../output/27-Apul-pheno-annot/SwissProt-GO:0006099.fa
Sequence type: Protein
Deleted existing Protein BLAST database named /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0006099
Keep MBits: T
Maximum file size: 3000000000B
Adding sequences from FASTA; added 2837 sequences in 0.0586021 seconds.


FUN_000960-T1   sp|P21399|ACOHC_HUMAN   70.588  867 255 0   24  890 21  887 0.0 1312
FUN_001356-T1   sp|A0QMB9|GABD1_MYCA1   30.787  445 291 4   79  508 7   449 5.73e-62    214
FUN_003898-T1   sp|Q9V0D5|MDH_PYRAB 41.694  307 173 3   6   310 7   309 2.54e-71    224
FUN_003899-T1   sp|Q9V0D5|MDH_PYRAB 37.110  353 215 5   28  377 9   357 2.79e-73    229
FUN_004736-T1   sp|Q9VWH4|IDH3A_DROME   72.892  332 89  1   40  371 47  377 0.0 514
FUN_004752-T1   sp|A0QMB9|GABD1_MYCA1   34.848  462 284 6   426 879 3   455 5.01e-74    248
FUN_006329-T1   sp|P09624|DLDH_YEAST    56.557  488 199 7   30  508 15  498 0.0 540
FUN_006649-T1   sp|A4SFT4|MDH_CHLPM 36.093  302 182 4   24  322 2   295 4.65e-64    202
FUN_006864-T1   sp|Q73TP5|GABD1_MYCPA   35.141  461 285 7   65  519 5   457 6.75e-76    244
FUN_006864-T2   sp|Q73TP5|GABD1_MYCPA   35.141  461 285 7   65  519 5   457 2.18e-76    245
Number of hits
82 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0006099_out.tab

Summary of blast hits

wc -l "${OUT_DIR}"*tab

   82 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0006099_out.tab
  130 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0006119_out.tab
  616 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0009060_out.tab
   37 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0061621_out.tab
  865 total

--- title: "Getting to GO with Phenotype" description: "A short list for machine learning" categories: [e5, GO] #citation: date: 03-21-2025 image: http://gannet.fish.washington.edu/seashell/snaps/2025-03-21_12-56-06.png # finding a good image author: - name: Steven Roberts url: orcid: 0000-0001-8302-1138 affiliation: Professor, UW - School of Aquatic and Fishery Sciences affiliation-url: https://robertslab.info #url: # self-defined draft: false # setting this to `true` will prevent your post from appearing on your listing page until you're ready! format: html: code-fold: FALSE code-tools: true code-copy: true highlight-style: github code-overflow: wrap --- # GO Annotations Steven Roberts 2025-03-21 - [Variables](#variables) - [Aerobic respiration (GO:0009060)](#aerobic-respiration-go0009060) - [Oxidative phosphorylation (GO:0006119)](#oxidative-phosphorylation-go0006119) - [Canonical glycolysis (GO:0061621)](#canonical-glycolysis-go0061621) - [Tricarboxylic Acid Cycle (GO:0006099)](#tricarboxylic-acid-cycle-go0006099) - [Summary of blast hits](#summary-of-blast-hits) Want to start with grabbing protein with specific GOs see also https://www.ebi.ac.uk/QuickGO/annotations # Variables ``` r # Global R options knitr::opts_chunk$set(echo = TRUE) # Define key paths and tool directories OUT_DIR <- "../output/27-Apul-pheno-annot/" evalue <- "1E-20" fasta <- "../data/Apulchra-genome.pep.faa" # Export these as environment variables for bash chunks. Sys.setenv( OUT_DIR = OUT_DIR, evalue = evalue, fasta =fasta ) ``` # Aerobic respiration (GO:0009060) ``` bash GO="0009060" curl -H "Accept: text/plain" "https://rest.uniprot.org/uniprotkb/stream?format=fasta&query=%28%28go%3A"${GO}"%29%29+AND+%28reviewed%3Atrue%29" -o "${OUT_DIR}"SwissProt-GO:"${GO}".fa head "${OUT_DIR}"SwissProt-GO:"${GO}".fa echo "Number of Proteins" grep -c ">" "${OUT_DIR}"SwissProt-GO:"${GO}".fa /home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \ -in "${OUT_DIR}"SwissProt-GO:"${GO}".fa \ -dbtype prot \ -out "${OUT_DIR}"SwissProt-GO:"${GO}" /home/shared/ncbi-blast-2.15.0+/bin/blastp \ -query $fasta \ -db "${OUT_DIR}"SwissProt-GO:"${GO}" \ -out "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab \ -evalue "${evalue}" \ -num_threads 42 \ -max_target_seqs 1 \ -max_hsps 1 \ -outfmt 6 \ 2> "${OUT_DIR}"blast_warnings"${GO}".txt head "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab echo "Number of hits" wc -l "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab ``` % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0 100 673k 0 673k 0 0 378k 0 --:--:-- 0:00:01 --:--:-- 377k 100 2157k 0 2157k 0 0 768k 0 --:--:-- 0:00:02 --:--:-- 768k 100 3305k 0 3305k 0 0 868k 0 --:--:-- 0:00:03 --:--:-- 868k 100 4953k 0 4953k 0 0 1015k 0 --:--:-- 0:00:04 --:--:-- 1015k 100 5219k 0 5219k 0 0 1064k 0 --:--:-- 0:00:04 --:--:-- 1346k >sp|A0A096P8D3|IDH_OSTTA Isocitrate dehydrogenase (NAD(+)), mitochondrial OS=Ostreococcus tauri OX=70448 GN=IDH PE=1 SV=1 MTRVERGRVLARAIERAVAHRASARRWTTTTRTPAWMVTGWMGGRGVDRSTAMTRFERCG STASSKITAAPMVYVRGEEMTAYVMDLIRSRWIEPRVDVGGWETFDLRAKNRDDTEDRVL RDVIEAGKRIKAIFKEPTVTPTADQVKRLGLRKSWGSPNGAMRRGWNGITISRDTIHIDG VELGYKKPVLFERHAVGGEYSAGYKNVGKGKLTTTFTPSEGPDAGKTVVVDEREIVDEEA AVVTYHNPYDNVHDLARFFFGRCLEAKVTPYVVTKKTVFKWQEPFWQIMRTVFDEEFKAQ FVAAGVMKEGEELVHLLSDAATMKLVQWRQGGFGMAAHNYDGDVLTDELAQVHKSPGFIT SNLVGVHEDGTLIKEFEASHGTVADMDEARLRGEETSLNPLGMVEGLIGAMNHAADVHNI DRDRTHAFTTKMRTVIHQLFREGKGTRDLCGPSGLTTEQFIDAVAERLDA >sp|A0A0D2Y5A7|ODP2_FUSO4 Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial OS=Fusarium oxysporum f. sp. lycopersici (strain 4287 / CBS 123668 / FGSC 9935 / NRRL 34936) OX=426428 GN=LAT1 PE=1 SV=1 Number of Proteins 10978 Building a new DB, current time: 03/21/2025 12:49:44 New DB name: /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0009060 New DB title: ../output/27-Apul-pheno-annot/SwissProt-GO:0009060.fa Sequence type: Protein Deleted existing Protein BLAST database named /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0009060 Keep MBits: T Maximum file size: 3000000000B Adding sequences from FASTA; added 10978 sequences in 0.179029 seconds. FUN_000047-T1 sp|Q757N1|H3_EREGS 88.971 136 15 0 4 139 1 136 2.14e-86 246 FUN_000049-T1 sp|Q757N1|H3_EREGS 92.079 101 8 0 1 101 1 101 1.61e-63 190 FUN_000051-T1 sp|Q757N1|H3_EREGS 92.079 101 8 0 1 101 1 101 1.61e-63 190 FUN_000053-T1 sp|Q757N1|H3_EREGS 92.079 101 8 0 1 101 1 101 1.61e-63 190 FUN_000055-T1 sp|Q757N1|H3_EREGS 92.079 101 8 0 1 101 1 101 1.61e-63 190 FUN_000057-T1 sp|Q757N1|H3_EREGS 92.079 101 8 0 1 101 1 101 1.61e-63 190 FUN_000059-T1 sp|Q757N1|H3_EREGS 92.079 101 8 0 1 101 1 101 1.61e-63 190 FUN_000061-T1 sp|Q757N1|H3_EREGS 92.079 101 8 0 1 101 1 101 1.61e-63 190 FUN_000063-T1 sp|Q757N1|H3_EREGS 92.079 101 8 0 1 101 1 101 1.61e-63 190 FUN_000065-T1 sp|Q757N1|H3_EREGS 88.971 136 15 0 4 139 1 136 2.14e-86 246 Number of hits 616 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0009060_out.tab # Oxidative phosphorylation (GO:0006119) ``` bash GO="0006119" curl -H "Accept: text/plain" "https://rest.uniprot.org/uniprotkb/stream?format=fasta&query=%28%28go%3A"${GO}"%29%29+AND+%28reviewed%3Atrue%29" -o "${OUT_DIR}"SwissProt-GO:"${GO}".fa head "${OUT_DIR}"SwissProt-GO:"${GO}".fa echo "Number of Proteins" grep -c ">" "${OUT_DIR}"SwissProt-GO:"${GO}".fa /home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \ -in "${OUT_DIR}"SwissProt-GO:"${GO}".fa \ -dbtype prot \ -out "${OUT_DIR}"SwissProt-GO:"${GO}" /home/shared/ncbi-blast-2.15.0+/bin/blastp \ -query $fasta \ -db "${OUT_DIR}"SwissProt-GO:"${GO}" \ -out "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab \ -evalue "${evalue}" \ -num_threads 42 \ -max_target_seqs 1 \ -max_hsps 1 \ -outfmt 6 \ 2> "${OUT_DIR}"blast_warnings"${GO}".txt head "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab echo "Number of hits" wc -l "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab ``` % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 479k 0 479k 0 0 285k 0 --:--:-- 0:00:01 --:--:-- 285k 100 2632k 0 2632k 0 0 969k 0 --:--:-- 0:00:02 --:--:-- 969k 100 2675k 0 2675k 0 0 984k 0 --:--:-- 0:00:02 --:--:-- 983k >sp|A0A1D8PHA3|CYT1_CANAL Cytochrome b-c1 complex catalytic subunit, mitochondrial OS=Candida albicans (strain SC5314 / ATCC MYA-2876) OX=237561 GN=CYT1 PE=1 SV=1 MFRTAYKTMNQSMVQKFIAGGVGVTGLTASYLLYQDSMTADAMTAAEHGLHPPAYNWPHN GMFETFDHASIRRGFQVYREVCAACHSLDRIAWRNLVGVSHTTSEAKAMAEELEYDDEPD DEGKPRKRPGKLADYIPGPYENEQAARAANQGAYPPDLSLIVKARHGGSDYIFSLLTGYP DEPPAGVVLPEGSNYNPYFPGGAIAMGRVLFDDLVEYEDGTPATTSQMAKDVSTFLNWAS EPEHDDRKKWGLKALVVLSSLYLLSIWVKRFKWTPIKNRKFRFDPPKK >sp|A0A1D8PJX3|RIP1_CANAL Cytochrome b-c1 complex subunit Rieske, mitochondrial OS=Candida albicans (strain SC5314 / ATCC MYA-2876) OX=237561 GN=RIP1 PE=1 SV=1 MSSLAFRTLRNGLGLKSSVRALSTTTTTLSNYQQPDYSSYLNNKSGQGSRNFTYFMVGSM GLLSAAGAKSTVEAFLSSFAASADVLAMAKVEVKLGAIPEGKNVIIKWQGKPVFIRHRTA DEIEEANQVDIKTLRDPQNDADRVKKPEWLIMLGICTHLGCVPIGEAGDFGGWFCPCHGS Number of Proteins 6140 Building a new DB, current time: 03/21/2025 12:50:54 New DB name: /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0006119 New DB title: ../output/27-Apul-pheno-annot/SwissProt-GO:0006119.fa Sequence type: Protein Deleted existing Protein BLAST database named /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0006119 Keep MBits: T Maximum file size: 3000000000B Adding sequences from FASTA; added 6140 sequences in 0.103551 seconds. FUN_000943-T1 sp|Q791V5|MTCH2_MOUSE 41.549 284 162 2 24 305 8 289 2.00e-80 243 FUN_000977-T1 sp|Q6XHB2|ROCO4_DICDI 30.035 283 163 10 589 848 1023 1293 6.93e-28 119 FUN_001181-T1 sp|O52683|HYDA_THEMA 29.902 408 237 17 115 515 184 549 5.65e-40 151 FUN_001463-T1 sp|Q6XHB2|ROCO4_DICDI 27.059 340 219 14 1552 1876 954 1279 1.37e-23 107 FUN_001483-T1 sp|Q6CFT7|ATPB_YARLI 25.301 415 280 10 45 448 52 447 3.17e-29 117 FUN_001648-T1 sp|P24539|AT5F1_HUMAN 39.691 194 108 3 15 207 62 247 2.52e-38 130 FUN_001648-T2 sp|P24539|AT5F1_HUMAN 40.314 191 105 3 47 236 62 244 2.48e-38 131 FUN_003901-T1 sp|P29410|KAD2_RAT 34.314 204 105 5 30 204 20 223 9.03e-29 105 FUN_004027-T1 sp|Q05752|NDUA7_BOVIN 53.947 76 34 1 1 75 1 76 6.67e-23 83.2 FUN_004095-T1 sp|Q6XHB2|ROCO4_DICDI 28.975 283 175 10 37 301 1015 1289 2.80e-21 96.3 Number of hits 130 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0006119_out.tab # Canonical glycolysis (GO:0061621) ``` bash GO="0061621" curl -H "Accept: text/plain" "https://rest.uniprot.org/uniprotkb/stream?format=fasta&query=%28%28go%3A"${GO}"%29%29+AND+%28reviewed%3Atrue%29" -o "${OUT_DIR}"SwissProt-GO:"${GO}".fa head "${OUT_DIR}"SwissProt-GO:"${GO}".fa echo "Number of Proteins" grep -c ">" "${OUT_DIR}"SwissProt-GO:"${GO}".fa /home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \ -in "${OUT_DIR}"SwissProt-GO:"${GO}".fa \ -dbtype prot \ -out "${OUT_DIR}"SwissProt-GO:"${GO}" /home/shared/ncbi-blast-2.15.0+/bin/blastp \ -query $fasta \ -db "${OUT_DIR}"SwissProt-GO:"${GO}" \ -out "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab \ -evalue "${evalue}" \ -num_threads 42 \ -max_target_seqs 1 \ -max_hsps 1 \ -outfmt 6 \ 2> "${OUT_DIR}"blast_warnings"${GO}".txt head "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab echo "Number of hits" wc -l "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab ``` % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:01 --:--:-- 0 100 208k 0 208k 0 0 117k 0 --:--:-- 0:00:01 --:--:-- 117k >sp|A1A4J1|PFKAL_BOVIN ATP-dependent 6-phosphofructokinase, liver type OS=Bos taurus OX=9913 GN=PFKL PE=2 SV=1 MASVDLEKLRTTGAGKAIGVLTSGGDAQGMNAAVRAVTRMGIYVGAKVFLIYEGYEGLVE GGENIKQANWLSVSNIIQLGGTVIGSARCKAFTTREGRRAAAYNLVQRGITNLCVIGGDG SLTGANIFRSEWGSLLEELVSEGKISEGTAQTYSHLNIAGLVGSIDNDFCGTDMTIGTDS ALHRIMEVIDAITTTAQSHQRTFVLEVMGRHCGYLALVSALASGADWLFIPEAPPEDGWE NFMCERLGETRSRGSRLNIIIIAEGAIDRNGKPISSRYVKDLVVQRLGFDTRVTVLGHVQ RGGTPSAFDRILSSKMGMEAVMALLEATPDTPACVVSLSGNQSVRLPLMECVQMTKEVQK AMDEKRFDEAIQLRGGSFENNWNIYKLLSHQKISKEKTNFSLAILNVGAPAAGMNAAVRS AVRSGISQGHTVYVVHDGFEGLAKNQVQEVSWHDVAGWLGRGGSMLGTKRTLPKGFMEKI VENIRLHNIHALLVIGGFEAYEGVLQLVEARGRYEELCIVMCVIPATISNNVPGTDFSLG Number of Proteins 394 Building a new DB, current time: 03/21/2025 12:51:31 New DB name: /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0061621 New DB title: ../output/27-Apul-pheno-annot/SwissProt-GO:0061621.fa Sequence type: Protein Deleted existing Protein BLAST database named /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0061621 Keep MBits: T Maximum file size: 3000000000B Adding sequences from FASTA; added 394 sequences in 0.0159671 seconds. FUN_005030-T1 sp|P85037|FOXK1_HUMAN 51.000 100 48 1 95 194 302 400 4.38e-26 103 FUN_005036-T1 sp|P42128|FOXK1_MOUSE 48.454 97 50 0 30 126 290 386 1.70e-27 105 FUN_005159-T1 sp|Q3UCQ1|FOXK2_MOUSE 52.041 98 45 1 95 190 247 344 7.57e-28 108 FUN_008233-T1 sp|Q7ZX03|FOXK2_XENLA 43.066 137 75 1 37 173 188 321 1.35e-33 125 FUN_009301-T1 sp|Q867C9|PFKAM_HORSE 58.634 776 300 4 70 833 13 779 0.0 935 FUN_010519-T1 sp|P00940|TPIS_CHICK 69.672 244 74 0 3 246 4 247 1.09e-126 353 FUN_012871-T1 sp|P00940|TPIS_CHICK 69.672 244 74 0 3 246 4 247 1.09e-126 353 FUN_013147-T1 sp|Q7ZX03|FOXK2_XENLA 46.939 98 50 1 143 238 215 312 3.77e-24 96.3 FUN_013305-T1 sp|P42128|FOXK1_MOUSE 42.202 109 61 1 47 153 287 395 2.42e-22 86.7 FUN_015434-T1 sp|P05064|ALDOA_MOUSE 72.269 357 97 1 5 359 8 364 0.0 528 Number of hits 37 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0061621_out.tab # Tricarboxylic Acid Cycle (GO:0006099) ``` bash GO="0006099" curl -H "Accept: text/plain" "https://rest.uniprot.org/uniprotkb/stream?format=fasta&query=%28%28go%3A"${GO}"%29%29+AND+%28reviewed%3Atrue%29" -o "${OUT_DIR}"SwissProt-GO:"${GO}".fa head "${OUT_DIR}"SwissProt-GO:"${GO}".fa echo "Number of Proteins" grep -c ">" "${OUT_DIR}"SwissProt-GO:"${GO}".fa /home/shared/ncbi-blast-2.15.0+/bin/makeblastdb \ -in "${OUT_DIR}"SwissProt-GO:"${GO}".fa \ -dbtype prot \ -out "${OUT_DIR}"SwissProt-GO:"${GO}" /home/shared/ncbi-blast-2.15.0+/bin/blastp \ -query $fasta \ -db "${OUT_DIR}"SwissProt-GO:"${GO}" \ -out "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab \ -evalue "${evalue}" \ -num_threads 42 \ -max_target_seqs 1 \ -max_hsps 1 \ -outfmt 6 \ 2> "${OUT_DIR}"blast_warnings"${GO}".txt head "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab echo "Number of hits" wc -l "${OUT_DIR}"Apul_blastp-GO:"${GO}"_out.tab ``` % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 31776 0 31776 0 0 26928 0 --:--:-- 0:00:01 --:--:-- 26906 100 1726k 0 1726k 0 0 889k 0 --:--:-- 0:00:01 --:--:-- 889k >sp|A0A096P8D3|IDH_OSTTA Isocitrate dehydrogenase (NAD(+)), mitochondrial OS=Ostreococcus tauri OX=70448 GN=IDH PE=1 SV=1 MTRVERGRVLARAIERAVAHRASARRWTTTTRTPAWMVTGWMGGRGVDRSTAMTRFERCG STASSKITAAPMVYVRGEEMTAYVMDLIRSRWIEPRVDVGGWETFDLRAKNRDDTEDRVL RDVIEAGKRIKAIFKEPTVTPTADQVKRLGLRKSWGSPNGAMRRGWNGITISRDTIHIDG VELGYKKPVLFERHAVGGEYSAGYKNVGKGKLTTTFTPSEGPDAGKTVVVDEREIVDEEA AVVTYHNPYDNVHDLARFFFGRCLEAKVTPYVVTKKTVFKWQEPFWQIMRTVFDEEFKAQ FVAAGVMKEGEELVHLLSDAATMKLVQWRQGGFGMAAHNYDGDVLTDELAQVHKSPGFIT SNLVGVHEDGTLIKEFEASHGTVADMDEARLRGEETSLNPLGMVEGLIGAMNHAADVHNI DRDRTHAFTTKMRTVIHQLFREGKGTRDLCGPSGLTTEQFIDAVAERLDA >sp|A0A3Q0KQY7|FUMC_SCHMA Fumarate hydratase OS=Schistosoma mansoni OX=6183 GN=Smp_158240 PE=1 SV=2 Number of Proteins 2837 Building a new DB, current time: 03/21/2025 12:51:40 New DB name: /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0006099 New DB title: ../output/27-Apul-pheno-annot/SwissProt-GO:0006099.fa Sequence type: Protein Deleted existing Protein BLAST database named /home/shared/8TB_HDD_03/sr320/github/deep-dive-expression/D-Apul/output/27-Apul-pheno-annot/SwissProt-GO:0006099 Keep MBits: T Maximum file size: 3000000000B Adding sequences from FASTA; added 2837 sequences in 0.0586021 seconds. FUN_000960-T1 sp|P21399|ACOHC_HUMAN 70.588 867 255 0 24 890 21 887 0.0 1312 FUN_001356-T1 sp|A0QMB9|GABD1_MYCA1 30.787 445 291 4 79 508 7 449 5.73e-62 214 FUN_003898-T1 sp|Q9V0D5|MDH_PYRAB 41.694 307 173 3 6 310 7 309 2.54e-71 224 FUN_003899-T1 sp|Q9V0D5|MDH_PYRAB 37.110 353 215 5 28 377 9 357 2.79e-73 229 FUN_004736-T1 sp|Q9VWH4|IDH3A_DROME 72.892 332 89 1 40 371 47 377 0.0 514 FUN_004752-T1 sp|A0QMB9|GABD1_MYCA1 34.848 462 284 6 426 879 3 455 5.01e-74 248 FUN_006329-T1 sp|P09624|DLDH_YEAST 56.557 488 199 7 30 508 15 498 0.0 540 FUN_006649-T1 sp|A4SFT4|MDH_CHLPM 36.093 302 182 4 24 322 2 295 4.65e-64 202 FUN_006864-T1 sp|Q73TP5|GABD1_MYCPA 35.141 461 285 7 65 519 5 457 6.75e-76 244 FUN_006864-T2 sp|Q73TP5|GABD1_MYCPA 35.141 461 285 7 65 519 5 457 2.18e-76 245 Number of hits 82 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0006099_out.tab # Summary of blast hits ``` bash wc -l "${OUT_DIR}"*tab ``` 82 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0006099_out.tab 130 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0006119_out.tab 616 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0009060_out.tab 37 ../output/27-Apul-pheno-annot/Apul_blastp-GO:0061621_out.tab 865 total