Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_086508780.1 BZY95_RS04475 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_002151265.1:WP_086508780.1 Length = 404 Score = 130 bits (328), Expect = 6e-35 Identities = 114/364 (31%), Positives = 165/364 (45%), Gaps = 55/364 (15%) Query: 72 IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131 +GRP+PL+ A+R + L ARI+ K E TG+HK+N I QA AK G V+ ET Sbjct: 61 VGRPSPLYHAERWSKKLGG-ARIWLKREDLNHTGAHKVNNTIGQALLAKMSGKPRVIAET 119 Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191 GAGQ G A A A+ +K ++M +++ + M+L GANV E G + Sbjct: 120 GAGQHGVATATVAARLGLKCEVYMGAEDVQRQKLNVYRMRLLGANVIP-----VESGTRT 174 Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ 243 L+ AM+EA+ + N + Y++G+V +V +V+G+E Q Sbjct: 175 LKD----------AMNEALRDWVTNVDDTFYIIGTVAGPHPYPMLVRDFNAVVGREARRQ 224 Query: 244 -LDLLGEDADILIGCVGGGSNFGGFTYPFI---------------GNKKGKRYIAVSSAE 287 L+ G+ D LI CVGGGSN G YPF+ G + G+ ++S Sbjct: 225 SLEEFGKLPDALIACVGGGSNAMGLFYPFVEDDEVAMYGVEAGGDGVETGRHAAPLASNA 284 Query: 288 IPKFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIV 347 G Y D G + I+ G D Y GV P +L G V Sbjct: 285 PRGVLHGNRTYLMSDEGGQVSDTHSISAGLD------------YPGVGPEHALWKDVGRV 332 Query: 348 EWREYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHG 407 ++ N+ + EA + +GI+PA ESAHA+ A R + IV NLSG G Sbjct: 333 QYVAANDDAVLEAFRELTRIEGIMPALESAHALAHAKVLAPTMRPDQN---IVVNLSGRG 389 Query: 408 LLDL 411 D+ Sbjct: 390 DKDI 393 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: 358 Number of extensions: 22 Number of successful extensions: 3 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: 404 Length adjustment: 31 Effective length of query: 394 Effective length of database: 373 Effective search space: 146962 Effective search space used: 146962 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_086508780.1 BZY95_RS04475 (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.24116.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.8e-186 604.4 0.0 5.4e-186 604.2 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508780.1 BZY95_RS04475 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508780.1 BZY95_RS04475 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 604.2 0.0 5.4e-186 5.4e-186 1 383 [. 15 398 .. 15 400 .. 0.99 Alignments for each domain: == domain 1 score: 604.2 bits; conditional E-value: 5.4e-186 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg +GG++v+e+l al++lek+y ++++d++f++e+++ l +y+grp+pl++a++ skklgga+i+ lcl|NCBI__GCF_002151265.1:WP_086508780.1 15 GHFGPYGGRFVSETLSFALDDLEKTYMRLRDDPDFQAEFDYDLAHYVGRPSPLYHAERWSKKLGGARIW 83 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahk+nn++gqallak Gk r+iaetGaGqhGvatat+aa+lgl+cevymGaedv+rqk lcl|NCBI__GCF_002151265.1:WP_086508780.1 84 LKREDLNHTGAHKVNNTIGQALLAKMSGKPRVIAETGAGQHGVATATVAARLGLKCEVYMGAEDVQRQK 152 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 lnv+rm+llga+v+pv+sG++tlkda+nealrdWvt+v+dt+y++G+++GphP+P +vr+f +v+g+e+ lcl|NCBI__GCF_002151265.1:WP_086508780.1 153 LNVYRMRLLGANVIPVESGTRTLKDAMNEALRDWVTNVDDTFYIIGTVAGPHPYPMLVRDFNAVVGREA 221 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGk.eGvlh 275 ++q le+ g+lPda+iacvGGGsna+G+f++f+ed+ev+++gveagG G++t +haa l++ Gvlh lcl|NCBI__GCF_002151265.1:WP_086508780.1 222 RRQSLEEFGKLPDALIACVGGGSNAMGLFYPFVEDDEVAMYGVEAGGDGVETGRHAAPLASNApRGVLH 290 ******99***************************************************987658**** PP TIGR00263 276 GaktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipal 344 G++t+l+ de Gq++++hs+saGldypgvgPeha ++ gr++y+a++d+++lea++ l++ eGi+pal lcl|NCBI__GCF_002151265.1:WP_086508780.1 291 GNRTYLMSDEGGQVSDTHSISAGLDYPGVGPEHALWKDVGRVQYVAANDDAVLEAFRELTRIEGIMPAL 359 ********************************************************************* PP TIGR00263 345 esshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 es+hala+++ lap+++ d+ +vvnlsGrGdkd+ tvak lcl|NCBI__GCF_002151265.1:WP_086508780.1 360 ESAHALAHAKVLAPTMRPDQNIVVNLSGRGDKDIMTVAK 398 *************************************97 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (404 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 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 10.70 // [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