Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_012536947.1 AFE_RS09550 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000021485.1:WP_012536947.1 Length = 399 Score = 133 bits (334), Expect = 1e-35 Identities = 114/355 (32%), Positives = 162/355 (45%), Gaps = 38/355 (10%) Query: 72 IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131 +GRP PL+ A RL L A+IY K E TG+HKIN A+ QA A+ G + V+ ET Sbjct: 57 VGRPNPLYHAGRLSRELGG-AQIYLKREDLNHTGAHKINNAVGQALLARRMGKKRVIAET 115 Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191 GAGQ G A A A+ Y M+ ++M + +++ M+L GA V A G + Sbjct: 116 GAGQHGVATATVATRYGMECLVYMGEEDIQRQSSNVFRMRLLGAQVTA-----VSSGTRT 170 Query: 192 LETNPQHPGSLGIAMSEAIEYALKN--EFRYLVGSVLD------VVLLHQSVIGQETITQ 243 L+ A++EA+ + N Y++G+V +V VIG E Q Sbjct: 171 LKD----------ALNEALRDWVTNVESTFYVIGTVAGPHPYPVMVRDFHRVIGDEARAQ 220 Query: 244 -LDLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVSSAEIPKFSKGEYKYDFPD 302 L+L G D LI CVGGGSN G YPFI + R + + E G ++ P Sbjct: 221 CLELTGRLPDCLIACVGGGSNAIGLFYPFIED----RAVRMIGVEAGGLGLGTGQHAAPL 276 Query: 303 SAGLLPLVK------MITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEWREYNERE 356 + G ++ M +P + GL Y GV P + L G E+ + E Sbjct: 277 TTGRPGVLHGNRTYLMEDEDGQILPTHSISAGLDYPGVGPEHAYLKDTGRAEYVAATDEE 336 Query: 357 IFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLLDL 411 A +GI+PA ESAHA+ A R + + I+ NLSG G D+ Sbjct: 337 ALAAFHRLCRTEGIIPALESAHALAHAFRLAPTMRSD---QTIIVNLSGRGDKDI 388 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: 379 Number of extensions: 22 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_012536947.1 AFE_RS09550 (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.25750.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.6e-195 634.4 0.0 4.2e-195 634.2 0.0 1.0 1 lcl|NCBI__GCF_000021485.1:WP_012536947.1 AFE_RS09550 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021485.1:WP_012536947.1 AFE_RS09550 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 634.2 0.0 4.2e-195 4.2e-195 1 383 [. 11 393 .. 11 395 .. 0.99 Alignments for each domain: == domain 1 score: 634.2 bits; conditional E-value: 4.2e-195 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g++g +GG++v+e+l++aleele+ay++a++d+ef++el++ l++++grp pl++a +ls++lgga+iy lcl|NCBI__GCF_000021485.1:WP_012536947.1 11 GHYGPYGGRFVAETLIPALEELERAYQEAQRDPEFRAELHSELRQFVGRPNPLYHAGRLSRELGGAQIY 79 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahkinna+gqalla+r+Gkkr+iaetGaGqhGvatat+a++ g+ec vymG+ed++rq+ lcl|NCBI__GCF_000021485.1:WP_012536947.1 80 LKREDLNHTGAHKINNAVGQALLARRMGKKRVIAETGAGQHGVATATVATRYGMECLVYMGEEDIQRQS 148 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 nvfrm+llga+v++v+sG++tlkda+nealrdWvt+ve+t+yv+G+++GphP+P +vr+f +vig+e+ lcl|NCBI__GCF_000021485.1:WP_012536947.1 149 SNVFRMRLLGAQVTAVSSGTRTLKDALNEALRDWVTNVESTFYVIGTVAGPHPYPVMVRDFHRVIGDEA 217 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 ++q le grlPd +iacvGGGsnaiG+f++fied v++igveagG+G+ t +haa l++G++GvlhG lcl|NCBI__GCF_000021485.1:WP_012536947.1 218 RAQCLELTGRLPDCLIACVGGGSNAIGLFYPFIEDRAVRMIGVEAGGLGLGTGQHAAPLTTGRPGVLHG 286 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 ++t+l+ dedGqi ++hs+saGldypgvgPeha+l++tgraey+a+tdeeal+a+++l+++eGiipale lcl|NCBI__GCF_000021485.1:WP_012536947.1 287 NRTYLMEDEDGQILPTHSISAGLDYPGVGPEHAYLKDTGRAEYVAATDEEALAAFHRLCRTEGIIPALE 355 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvak 383 s+hala++ +lap+++ d++++vnlsGrGdkd++tva lcl|NCBI__GCF_000021485.1:WP_012536947.1 356 SAHALAHAFRLAPTMRSDQTIIVNLSGRGDKDIHTVAA 393 ***********************************985 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: 10.51 // [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