Align tryptophan synthase (EC 4.2.1.20) (characterized)
to candidate WP_019896003.1 A377_RS0109025 tryptophan synthase subunit beta
Query= BRENDA::Q97TX6 (429 letters) >NCBI__GCF_000384235.1:WP_019896003.1 Length = 401 Score = 119 bits (298), Expect = 2e-31 Identities = 112/371 (30%), Positives = 174/371 (46%), Gaps = 35/371 (9%) Query: 67 EVLERYLQ--VGRPTPIIRAKRLEEYLGNNIKIYLKMESYTYTGSHKINSALAHVYYAKL 124 E L R Q VGRPTP+ A+R + LG KIYLK E +TG+HKIN+ + AK Sbjct: 49 EALTRDYQDYVGRPTPLYLAERWSDALGG-AKIYLKREDLNHTGAHKINNTIGQALLAKK 107 Query: 125 DNAKFVTTETGAGQWGSSVALASALFRMKAHIFMVRTSYYAKPYRKYMMQMYGAEVHPSP 184 + ETGAGQ G + A +A ++ ++M + M+M GA+V P Sbjct: 108 LGKTRIIAETGAGQHGVASATVAARLGLECVVYMGAEDVKRQAPNVARMRMLGAKVVP-- 165 Query: 185 SDLTEFGRQLLAKDSNHPGSLGIAISDAVEYAHKNGGKYVVGSVVNSDIM------FKTI 238 E G + L KD +L A+ D V + + Y++G+V F+ I Sbjct: 166 ---VESGTRTL-KD-----ALNEAMRDWV--TNVDDTFYIIGTVSGPHPYPMMVRDFQAI 214 Query: 239 AGMEAKKQ-MELIGEDPDYIIGVVGGGSNYAALAYPFLGDE---LRSGKVRRKYIASGSS 294 G EAK+Q +E PD ++ VGGGSN + + FL D+ L + +ASG Sbjct: 215 MGREAKRQHLEKENRLPDAVVACVGGGSNAIGIFHDFLADDSVKLVGVEAGGHGLASGQH 274 Query: 295 EVPKMTKGVYKYDYPDTAKLLPMLKMYTIGSDFVPPPVYAGGLRYHGVAPTLSLLISKGI 354 P + +G + + ++ +G+ + + GL Y GV P + L G Sbjct: 275 AAP-LCQGKPGVLHGNRTYIMEDENGQILGTHSI-----SAGLDYPGVGPEHAWLKDIGR 328 Query: 355 VQARDYSQEESFKWAKLFSELEGYIPAPETSHALPILAEIAEEAKKSGERKTVLVSFSGH 414 V+ +E+ + + + EG IPA ETSHA LA A+ A + ++++V+ SG Sbjct: 329 VEYVAIEDDEAMQGCRDLTRFEGIIPALETSHA---LAHAAKMAVEMTPEQSIIVNLSGR 385 Query: 415 GLLDLGNYASV 425 G D+ A++ Sbjct: 386 GDKDMNTIAAI 396 Lambda K H 0.316 0.135 0.392 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: 422 Number of extensions: 25 Number of successful extensions: 5 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: 429 Length of database: 401 Length adjustment: 31 Effective length of query: 398 Effective length of database: 370 Effective search space: 147260 Effective search space used: 147260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_019896003.1 A377_RS0109025 (tryptophan synthase subunit beta)
to HMM TIGR00263 (trpB: tryptophan synthase, beta subunit (EC 4.2.1.20))
# 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/TIGR00263.hmm # target sequence database: /tmp/gapView.32503.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00263 [M=385] Accession: TIGR00263 Description: trpB: tryptophan synthase, beta subunit 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3e-192 624.7 0.3 3.5e-192 624.6 0.3 1.0 1 lcl|NCBI__GCF_000384235.1:WP_019896003.1 A377_RS0109025 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000384235.1:WP_019896003.1 A377_RS0109025 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 624.6 0.3 3.5e-192 3.5e-192 1 383 [. 13 395 .. 13 397 .. 0.99 Alignments for each domain: == domain 1 score: 624.6 bits; conditional E-value: 3.5e-192 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg +GG + pe+l++al+el+++y+++k+d++f++ l++ ++y+grptpl+ a++ s +lggakiy lcl|NCBI__GCF_000384235.1:WP_019896003.1 13 GHFGVYGGVFAPETLMSALSELTEQYQSLKNDPAFVEALTRDYQDYVGRPTPLYLAERWSDALGGAKIY 81 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahkinn++gqallak+lGk+riiaetGaGqhGva+at+aa+lglec+vymGaedv+rq+ lcl|NCBI__GCF_000384235.1:WP_019896003.1 82 LKREDLNHTGAHKINNTIGQALLAKKLGKTRIIAETGAGQHGVASATVAARLGLECVVYMGAEDVKRQA 150 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 +nv rm++lgakvvpv+sG++tlkda+nea+rdWvt+v+dt+y++G++ GphP+P +vr+fq+++g+e+ lcl|NCBI__GCF_000384235.1:WP_019896003.1 151 PNVARMRMLGAKVVPVESGTRTLKDALNEAMRDWVTNVDDTFYIIGTVSGPHPYPMMVRDFQAIMGREA 219 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 k+q leke+rlPdav+acvGGGsnaiGif++f+ d++v+l+gveagG+G+++ +haa l +Gk+GvlhG lcl|NCBI__GCF_000384235.1:WP_019896003.1 220 KRQHLEKENRLPDAVVACVGGGSNAIGIFHDFLADDSVKLVGVEAGGHGLASGQHAAPLCQGKPGVLHG 288 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 ++t+++ de+Gqi +hs+saGldypgvgPeha+l+++gr+ey+ai+d+ea+++ + l++ eGiipale lcl|NCBI__GCF_000384235.1:WP_019896003.1 289 NRTYIMEDENGQILGTHSISAGLDYPGVGPEHAWLKDIGRVEYVAIEDDEAMQGCRDLTRFEGIIPALE 357 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 +shala++ k+a +++ ++ ++vnlsGrGdkd++t+a lcl|NCBI__GCF_000384235.1:WP_019896003.1 358 TSHALAHAAKMAVEMTPEQSIIVNLSGRGDKDMNTIAA 395 ***********************************985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (401 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: 8.53 // [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