Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_010937164.1 DET_RS07630 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000011905.1:WP_010937164.1 Length = 399 Score = 139 bits (350), Expect = 2e-37 Identities = 124/361 (34%), Positives = 176/361 (48%), Gaps = 38/361 (10%) Query: 73 GRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTETG 132 GRPTPL+ A+RL E+L ARIY K E TG+HKIN A+ Q A G + V+ ETG Sbjct: 58 GRPTPLYLAERLTEHLGG-ARIYLKREDLAHTGAHKINNALGQGLLALHMGKKRVIAETG 116 Query: 133 AGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKIL 192 AGQ G A A +M ++ ++M + +++ + M+L G V + G + L Sbjct: 117 AGQHGVATAAVCAMLGLECIVYMGEDDIKRQALNVFRMKLMGTEVRS-----VSSGSRTL 171 Query: 193 ETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ- 243 + A++EA+ + N Y++GSV+ +V Q+VIGQET Q Sbjct: 172 KD----------AINEAMRDWVSNPETTYYIIGSVVGPRPYPAMVRDFQAVIGQETKAQS 221 Query: 244 LDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAEIPKFSKGEYKYDFPDS 303 L LG D ++ CVGGGSN G Y FI + + R I V +A S G K+ S Sbjct: 222 LRQLGGLPDCIVACVGGGSNAMGIFYDFIPD-QSVRLIGVEAAG-SGISTG--KHSATLS 277 Query: 304 AGLLPLV--KMITLGKD----YVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNEREI 357 AG + ++ M L +D + + GL Y GV P S L VE+ + E Sbjct: 278 AGKVGILHGAMSYLLQDEHGQVIETHSISAGLDYPGVGPEHSYLKDNKRVEYVSVTDEEA 337 Query: 358 FEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDLSNYESM 417 K+ +GI+PA ES+HAI + A+ KN K IV NLSG G D+ + Sbjct: 338 LNGFKLLCSLEGIMPALESSHAIAHALKIAVGMPKN---KNIVINLSGRGDKDMDIVQKA 394 Query: 418 M 418 M Sbjct: 395 M 395 Lambda K H 0.318 0.138 0.403 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: 411 Number of extensions: 19 Number of successful extensions: 4 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: 425 Length of database: 399 Length adjustment: 31 Effective length of query: 394 Effective length of database: 368 Effective search space: 144992 Effective search space used: 144992 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 (21.7 bits) S2: 50 (23.9 bits)
Align candidate WP_010937164.1 DET_RS07630 (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.5679.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7.1e-196 636.7 0.4 8e-196 636.5 0.4 1.0 1 lcl|NCBI__GCF_000011905.1:WP_010937164.1 DET_RS07630 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000011905.1:WP_010937164.1 DET_RS07630 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 636.5 0.4 8e-196 8e-196 1 384 [. 11 394 .. 11 395 .. 1.00 Alignments for each domain: == domain 1 score: 636.5 bits; conditional E-value: 8e-196 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg++GGq+vpe+l++ l+ele+aye+akkde+f++ l++l ++++grptpl+ a++l+++lgga+iy lcl|NCBI__GCF_000011905.1:WP_010937164.1 11 GYFGKYGGQFVPEILVPVLNELEQAYEQAKKDETFQSRLKSLSNTFSGRPTPLYLAERLTEHLGGARIY 79 79******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl htGahkinnalgq lla ++Gkkr+iaetGaGqhGvata+++a+lglec vymG++d++rq+ lcl|NCBI__GCF_000011905.1:WP_010937164.1 80 LKREDLAHTGAHKINNALGQGLLALHMGKKRVIAETGAGQHGVATAAVCAMLGLECIVYMGEDDIKRQA 148 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 lnvfrm+l+g++v +v+sGs+tlkda+nea+rdWv++ e+t+y++Gs+vGp P+P++vr+fq+vig+e+ lcl|NCBI__GCF_000011905.1:WP_010937164.1 149 LNVFRMKLMGTEVRSVSSGSRTLKDAINEAMRDWVSNPETTYYIIGSVVGPRPYPAMVRDFQAVIGQET 217 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 k+q l++ g lPd ++acvGGGsna+Gif++fi d++v+ligvea+G+Gi+t kh+atls+Gk+G+lhG lcl|NCBI__GCF_000011905.1:WP_010937164.1 218 KAQSLRQLGGLPDCIVACVGGGSNAMGIFYDFIPDQSVRLIGVEAAGSGISTGKHSATLSAGKVGILHG 286 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 a+++llqde+Gq+ e+hs+saGldypgvgPeh++l++++r+ey+++tdeeal+++kll+ eGi+pale lcl|NCBI__GCF_000011905.1:WP_010937164.1 287 AMSYLLQDEHGQVIETHSISAGLDYPGVGPEHSYLKDNKRVEYVSVTDEEALNGFKLLCSLEGIMPALE 355 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 ssha+a++ k+a ++k++ +v+nlsGrGdkd++ v+ka lcl|NCBI__GCF_000011905.1:WP_010937164.1 356 SSHAIAHALKIAVGMPKNKNIVINLSGRGDKDMDIVQKA 394 ***********************************9986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (399 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 9.77 // [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