Align Tryptophan synthase beta chain 1; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_027456316.1 K420_RS0100475 tryptophan synthase subunit beta
Query= uniprot:P50383 (425 letters) >NCBI__GCF_000519045.1:WP_027456316.1 Length = 403 Score = 140 bits (353), Expect = 7e-38 Identities = 115/362 (31%), Positives = 168/362 (46%), Gaps = 52/362 (14%) Query: 72 IGRPTPLFRAKRLEEYLKTPARIYFKYEGATPTGSHKINTAIPQAYFAKEEGIEHVVTET 131 +GRP+P++ AKR + L A+IY K E TG+HK+N I QA AK G V+ ET Sbjct: 61 VGRPSPIYHAKRWSDLLGG-AQIYLKREDLNHTGAHKVNNCIGQAMLAKRMGKPRVIAET 119 Query: 132 GAGQWGTAVALAASMYNMKSTIFMVKVSYEQKPMRRSIMQLYGANVYASPTNLTEYGRKI 191 GAGQ G A A A+ Y M+ ++M +++ M+L GA V E G K Sbjct: 120 GAGQHGVATATVAARYGMECVVYMGSEDVKRQAANVYRMKLLGAKVVP-----VESGSKT 174 Query: 192 LETNPQHPGSLGIAMSEAIEYALKNEFRYLVGSVLD------VVLLHQSVIGQETITQL- 244 L+ +L AM + + + N F Y++G+V +V Q +IG+E +TQ+ Sbjct: 175 LK------DALNEAMRDWVT-NIHNTF-YIIGTVAGPHPYPMLVRDFQKIIGEECLTQMP 226 Query: 245 DLLGEDADILIGCVGGGSNFGGFTYPFIGNKKGKRYIAVS---------------SAEIP 289 ++ G D +I VGGGSN G YP+I N +G R I V +A +P Sbjct: 227 EMAGRQPDAVIAAVGGGSNAMGIFYPYI-NVEGVRLIGVEAAGSGIETGKHAASLTAGVP 285 Query: 290 KFSKGEYKYDFPDSAGLLPLVKMITLGKDYVPPPIYAGGLRYHGVAPTLSLLTKEGIVEW 349 G Y D G + + + GL Y GV P + L G E+ Sbjct: 286 GVLHGNRTYLLQDKDGQI------------IETHSVSAGLDYPGVGPEHAWLKDIGRAEY 333 Query: 350 REYNEREIFEAAKIFIENQGIVPAPESAHAIRAVVDEAIEARKNNERKVIVFNLSGHGLL 409 + + E EA +GI+PA ES+HA+ A K+ K+++ NLSG G Sbjct: 334 QPITDAEALEAFHNLCRLEGIIPALESSHALAYAAKLAPTLGKD---KILLVNLSGRGDK 390 Query: 410 DL 411 D+ Sbjct: 391 DM 392 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: 395 Number of extensions: 18 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: 403 Length adjustment: 31 Effective length of query: 394 Effective length of database: 372 Effective search space: 146568 Effective search space used: 146568 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_027456316.1 K420_RS0100475 (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.31671.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1e-193 629.6 0.4 1.2e-193 629.4 0.4 1.0 1 lcl|NCBI__GCF_000519045.1:WP_027456316.1 K420_RS0100475 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000519045.1:WP_027456316.1 K420_RS0100475 tryptophan synthase subunit beta # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 629.4 0.4 1.2e-193 1.2e-193 1 384 [. 15 398 .. 15 399 .. 1.00 Alignments for each domain: == domain 1 score: 629.4 bits; conditional E-value: 1.2e-193 TIGR00263 1 gkfgefGGqyvpevllealeelekayekakkdeefkkeleellkeyagrptpltfaknlskklggakiy 69 g+fg +GG +v+e+l+ al+el++ay a++d++f++e+e+ lk+++grp+p+++ak+ s lgga+iy lcl|NCBI__GCF_000519045.1:WP_027456316.1 15 GHFGPYGGVFVAETLFGALDELKAAYAAAQADPAFHAEYEYELKHFVGRPSPIYHAKRWSDLLGGAQIY 83 68******************************************************************* PP TIGR00263 70 lkredllhtGahkinnalgqallakrlGkkriiaetGaGqhGvatataaallglecevymGaedverqk 138 lkredl+htGahk+nn +gqa+lakr+Gk r+iaetGaGqhGvatat+aa+ g+ec+vymG+edv+rq+ lcl|NCBI__GCF_000519045.1:WP_027456316.1 84 LKREDLNHTGAHKVNNCIGQAMLAKRMGKPRVIAETGAGQHGVATATVAARYGMECVVYMGSEDVKRQA 152 ********************************************************************* PP TIGR00263 139 lnvfrmellgakvvpvtsGsktlkdavnealrdWvtsvedthyvlGsavGphPfPeivrefqsvigeev 207 nv+rm+llgakvvpv+sGsktlkda+nea+rdWvt++++t+y++G+++GphP+P +vr+fq++igee+ lcl|NCBI__GCF_000519045.1:WP_027456316.1 153 ANVYRMKLLGAKVVPVESGSKTLKDALNEAMRDWVTNIHNTFYIIGTVAGPHPYPMLVRDFQKIIGEEC 221 ********************************************************************* PP TIGR00263 208 keqilekegrlPdaviacvGGGsnaiGifaafiedeeveligveagGkGidtekhaatlskGkeGvlhG 276 +q+ e++gr Pdavia+vGGGsna+Gif+++i+ e v+ligvea+G+Gi+t khaa+l++G +GvlhG lcl|NCBI__GCF_000519045.1:WP_027456316.1 222 LTQMPEMAGRQPDAVIAAVGGGSNAMGIFYPYINVEGVRLIGVEAAGSGIETGKHAASLTAGVPGVLHG 290 ********************************************************************* PP TIGR00263 277 aktkllqdedGqieeahsvsaGldypgvgPehaalaetgraeyeaitdeealealkllskeeGiipale 345 ++t+llqd+dGqi e+hsvsaGldypgvgPeha+l+++graey+ itd+ealea+++l++ eGiipale lcl|NCBI__GCF_000519045.1:WP_027456316.1 291 NRTYLLQDKDGQIIETHSVSAGLDYPGVGPEHAWLKDIGRAEYQPITDAEALEAFHNLCRLEGIIPALE 359 ********************************************************************* PP TIGR00263 346 sshalaaleklapklkkdeivvvnlsGrGdkdletvaka 384 sshala++ klap+l kd+i++vnlsGrGdkd++tva++ lcl|NCBI__GCF_000519045.1:WP_027456316.1 360 SSHALAYAAKLAPTLGKDKILLVNLSGRGDKDMHTVAEK 398 ************************************986 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (385 nodes) Target sequences: 1 (403 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: 00:00:00.02 # Mc/sec: 6.86 // [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