Align phosphoserine aminotransferase monomer (EC 2.6.1.52; EC 2.6.1.1) (characterized)
to candidate WP_085771168.1 B1812_RS08285 phosphoserine transaminase
Query= metacyc::MONOMER-15918 (370 letters) >NCBI__GCF_002117405.1:WP_085771168.1 Length = 390 Score = 446 bits (1146), Expect = e-130 Identities = 223/375 (59%), Positives = 267/375 (71%), Gaps = 10/375 (2%) Query: 2 KPTRVPKNPCFSSGPCAKHPGYSVEELKDTPFGRSHRSKPGKEKLAEAIKRTRDMLGLPD 61 KP +PKNP FSSGPCAK PG+S + L GRSHR+K GKEKL AI TR++L +PD Sbjct: 7 KPAGLPKNPSFSSGPCAKRPGWSPQNLSAAALGRSHRAKAGKEKLERAIALTREVLRVPD 66 Query: 62 DYFVGIVPASDTGAFEMCLWSMLGCRGVDVLVWESFSKGWATDITKQLKLKDTRVFEAEY 121 DY +GIVPASDTGA EM LWSMLG R VDVL +ESFS GWATD+ KQLKL RV A Y Sbjct: 67 DYRIGIVPASDTGAVEMALWSMLGPRPVDVLAFESFSSGWATDVQKQLKLPQARVLTAPY 126 Query: 122 GKLPDLKKVDFKNDVVFVWNGTTSGVKVPNADWIPDDREGVTLCDATSAIFAMDIPYHKL 181 G+LPDL +V+ +D+VF WNGTTSGV+VPNA +I DR+G+T+CDATS FA + + KL Sbjct: 127 GELPDLAQVNGDHDLVFAWNGTTSGVRVPNAAFIAADRKGLTICDATSGAFAQPLDFAKL 186 Query: 182 DVITFSWQKVLGGEGAHGMLILSPRAVQRLESYTPAWPLPKIFRLTKGGKLNKDIFAGST 241 DV TFSWQK LGGE AHGMLILSPRAV+RLESY P WPLPKIFRLTKG KL + +FAG T Sbjct: 187 DVTTFSWQKCLGGEAAHGMLILSPRAVERLESYVPPWPLPKIFRLTKGSKLIEGVFAGET 246 Query: 242 INTPSMLANEDWLATLKWAESVGGLKQLIRRTNENLAVFEAFVAKNNWIHFLAETKEIRS 301 INTPS+L ED+L L+WA S+GGL L R + N AV + + FLA+ + RS Sbjct: 247 INTPSLLCVEDYLDALQWARSIGGLDALCARADANAAVVAEWTLRQPAFAFLAKQPQTRS 306 Query: 302 STSVCF-----KVDLSDEK-----LKELIKTLEKEKVAYDIGSYRDAPSGLRIWCGATVE 351 +TSVC +V D K K L+ +EKE +D G+YRDAP GLRIWCG TVE Sbjct: 307 NTSVCLEFADPRVIAMDPKARSGLAKALVSLVEKEGAGFDFGAYRDAPPGLRIWCGPTVE 366 Query: 352 KEDLECLCEWIEWAY 366 D+ L +WI+WA+ Sbjct: 367 PADVSLLTDWIDWAF 381 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: 488 Number of extensions: 16 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: 390 Length adjustment: 30 Effective length of query: 340 Effective length of database: 360 Effective search space: 122400 Effective search space used: 122400 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_085771168.1 B1812_RS08285 (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.2004.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.2e-197 641.0 0.0 3.7e-197 640.8 0.0 1.0 1 lcl|NCBI__GCF_002117405.1:WP_085771168.1 B1812_RS08285 phosphoserine tran Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002117405.1:WP_085771168.1 B1812_RS08285 phosphoserine transaminase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 640.8 0.0 3.7e-197 3.7e-197 2 372 .. 12 382 .. 11 384 .. 1.00 Alignments for each domain: == domain 1 score: 640.8 bits; conditional E-value: 3.7e-197 TIGR01365 2 panpefssgpcakrpgysveelknaalgrshrsklgkeklkeaiektrevlevpadyligivaasdtga 70 p+np+fssgpcakrpg+s+++l aalgrshr+k gkekl++ai trevl+vp+dy+igiv+asdtga lcl|NCBI__GCF_002117405.1:WP_085771168.1 12 PKNPSFSSGPCAKRPGWSPQNLSAAALGRSHRAKAGKEKLERAIALTREVLRVPDDYRIGIVPASDTGA 80 99******************************************************************* PP TIGR01365 71 vemalwsllgargvdllafesfgkgwvtdvtkqlklkdvrvleaeygklpdlkkvdfkkdvvftwngtt 139 vemalws+lg r+vd+lafesf++gw+tdv kqlkl++ rvl a+yg+lpdl++v+ ++d+vf+wngtt lcl|NCBI__GCF_002117405.1:WP_085771168.1 81 VEMALWSMLGPRPVDVLAFESFSSGWATDVQKQLKLPQARVLTAPYGELPDLAQVNGDHDLVFAWNGTT 149 ********************************************************************* PP TIGR01365 140 sgvrvpngdfipadreglticdatsaafaqdldyekldvvtfswqkvlggegahgvlilspravarles 208 sgvrvpn+ fi+adr+glticdats afaq ld+ kldv tfswqk lgge ahg+lilsprav+rles lcl|NCBI__GCF_002117405.1:WP_085771168.1 150 SGVRVPNAAFIAADRKGLTICDATSGAFAQPLDFAKLDVTTFSWQKCLGGEAAHGMLILSPRAVERLES 218 ********************************************************************* PP TIGR01365 209 ytpawplpkifrltkggklskdifegetintpsmlavedaldalkwaesigglkalvaraddnlavlea 277 y p wplpkifrltkg+kl++++f getintps+l+ved+ldal+wa+siggl+al arad+n+av+++ lcl|NCBI__GCF_002117405.1:WP_085771168.1 219 YVPPWPLPKIFRLTKGSKLIEGVFAGETINTPSLLCVEDYLDALQWARSIGGLDALCARADANAAVVAE 287 ********************************************************************* PP TIGR01365 278 fvaksswvdflaatkeirsntsvclkvvdpdvaaldedaqadfakelvsalekegvaydigsyrdapag 346 + +++ fla+++++rsntsvcl+++dp v a+d +a++ +ak lvs++ekeg+ +d g+yrdap+g lcl|NCBI__GCF_002117405.1:WP_085771168.1 288 WTLRQPAFAFLAKQPQTRSNTSVCLEFADPRVIAMDPKARSGLAKALVSLVEKEGAGFDFGAYRDAPPG 356 ********************************************************************* PP TIGR01365 347 lriwcgatveksdleallewldwafa 372 lriwcg tve d+ l++w+dwaf+ lcl|NCBI__GCF_002117405.1:WP_085771168.1 357 LRIWCGPTVEPADVSLLTDWIDWAFE 382 *************************7 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (374 nodes) Target sequences: 1 (390 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: 0.02u 0.01s 00:00:00.03 Elapsed: 00:00:00.01 # Mc/sec: 7.78 // [ok]
This GapMind analysis is from Apr 10 2024. The underlying query database was built on Apr 09 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