Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_106719128.1 CU100_RS23855 phosphoserine transaminase
Query= metacyc::MONOMER-15918 (370 letters) >NCBI__GCF_003010935.1:WP_106719128.1 Length = 391 Score = 484 bits (1246), Expect = e-141 Identities = 236/379 (62%), Positives = 280/379 (73%), Gaps = 10/379 (2%) Query: 2 KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61 KP + P NP FSSGPCAK PG+S++ L D P GRSHR+K GK+KL +AI TR++L +P Sbjct: 6 KPAQRPANPNFSSGPCAKRPGWSLDALSDAPLGRSHRAKVGKDKLKQAIDLTREILQVPA 65 Query: 62 DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121 DY +GIVPASDTGA EM LWS+LG RGVD++ WESF GW TD+ KQLKL DTR+ EA Y Sbjct: 66 DYRIGIVPASDTGAVEMALWSLLGERGVDMVAWESFGSGWVTDVIKQLKLGDTRIIEAAY 125 Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKL 181 G LPDL VDF DVVF WNGTTSGV+VP+ D+IP DR+G+T+CDATSA FA + + KL Sbjct: 126 GDLPDLSSVDFDRDVVFTWNGTTSGVRVPDGDFIPADRKGLTICDATSAAFAQRLDFDKL 185 Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGST 241 DV+TFSWQKVLGGEGAHGMLILSPRAV+RL +Y PAWPLPKIFRLT GGKL + IF+G T Sbjct: 186 DVVTFSWQKVLGGEGAHGMLILSPRAVERLLTYKPAWPLPKIFRLTSGGKLIEGIFSGET 245 Query: 242 INTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRS 301 INTPSML ED+L L WA+S+GGL L+ R + N AV +AF+ + WI LA RS Sbjct: 246 INTPSMLCVEDYLDALTWAKSIGGLDGLVGRADRNFAVLDAFIERTPWIANLARVPATRS 305 Query: 302 STSVCFKV----------DLSDEKLKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVE 351 +TSVC + + K L+ LEKE VAYDIG+YRDAPSGLRIW GATVE Sbjct: 306 NTSVCLTIIDPDITALGTEAQANFAKSLVAVLEKEGVAYDIGAYRDAPSGLRIWAGATVE 365 Query: 352 KEDLECLCEWIEWAYNLVK 370 DLE L W+EWA+ K Sbjct: 366 AADLEALTLWLEWAFQSQK 384 Lambda K H 0.319 0.136 0.430 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 470 Number of extensions: 14 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 370 Length of database: 391 Length adjustment: 30 Effective length of query: 340 Effective length of database: 361 Effective search space: 122740 Effective search space used: 122740 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_106719128.1 CU100_RS23855 (phosphoserine transaminase)
to HMM TIGR01365 (phosphoserine aminotransferase (EC 2.6.1.52))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.aa/TIGR01365.hmm # target sequence database: /tmp/gapView.4152971.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01365 [M=374] Accession: TIGR01365 Description: serC_2: phosphoserine aminotransferase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-217 707.2 0.3 2.9e-217 707.0 0.3 1.0 1 NCBI__GCF_003010935.1:WP_106719128.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_003010935.1:WP_106719128.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 707.0 0.3 2.9e-217 2.9e-217 1 373 [. 10 382 .. 10 383 .. 1.00 Alignments for each domain: == domain 1 score: 707.0 bits; conditional E-value: 2.9e-217 TIGR01365 1 rpanpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtgavem 73 rpanp+fssgpcakrpg+s+++l +a+lgrshr+k+gk+klk+ai+ tre+l+vpady+igiv+asdtgavem NCBI__GCF_003010935.1:WP_106719128.1 10 RPANPNFSSGPCAKRPGWSLDALSDAPLGRSHRAKVGKDKLKQAIDLTREILQVPADYRIGIVPASDTGAVEM 82 7************************************************************************ PP TIGR01365 74 alwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngttsgvrvpn 146 alwsllg+rgvd++a+esfg+gwvtdv+kqlkl d r++ea yg+lpdl+ vdf++dvvftwngttsgvrvp+ NCBI__GCF_003010935.1:WP_106719128.1 83 ALWSLLGERGVDMVAWESFGSGWVTDVIKQLKLGDTRIIEAAYGDLPDLSSVDFDRDVVFTWNGTTSGVRVPD 155 ************************************************************************* PP TIGR01365 147 gdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarlesytpawplpkif 219 gdfipadr+glticdatsaafaq+ld++kldvvtfswqkvlggegahg+lilsprav+rl +y+pawplpkif NCBI__GCF_003010935.1:WP_106719128.1 156 GDFIPADRKGLTICDATSAAFAQRLDFDKLDVVTFSWQKVLGGEGAHGMLILSPRAVERLLTYKPAWPLPKIF 228 ************************************************************************* PP TIGR01365 220 rltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavleafvaksswvdflaatk 292 rlt+ggkl+++if getintpsml+ved+ldal wa+siggl+ lv rad n avl+af+++++w+ la + NCBI__GCF_003010935.1:WP_106719128.1 229 RLTSGGKLIEGIFSGETINTPSMLCVEDYLDALTWAKSIGGLDGLVGRADRNFAVLDAFIERTPWIANLARVP 301 ************************************************************************* PP TIGR01365 293 eirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapaglriwcgatveksdlealle 365 ++rsntsvcl ++dpd++al +aqa+fak lv +lekegvaydig+yrdap+glriw gatve+ dleal+ NCBI__GCF_003010935.1:WP_106719128.1 302 ATRSNTSVCLTIIDPDITALGTEAQANFAKSLVAVLEKEGVAYDIGAYRDAPSGLRIWAGATVEAADLEALTL 374 ************************************************************************* PP TIGR01365 366 wldwafal 373 wl+waf+ NCBI__GCF_003010935.1:WP_106719128.1 375 WLEWAFQS 382 ******86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (374 nodes) Target sequences: 1 (391 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 26.32 // [ok]
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 2024.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory