Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_092481605.1 BM299_RS01050 tryptophan synthase subunit alpha
Query= uniprot:M4NLA4 (266 letters) >NCBI__GCF_900115975.1:WP_092481605.1 Length = 274 Score = 193 bits (491), Expect = 3e-54 Identities = 112/267 (41%), Positives = 158/267 (59%), Gaps = 2/267 (0%) Query: 1 MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60 M++I++R + A GLI ++TAGDP V L A+ +AGAD++ELGVPFSDP+AD Sbjct: 1 MNKIEKRLREVLARGEKGLIAYITAGDPDLATTVELAVAMGEAGADVLELGVPFSDPVAD 60 Query: 61 GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120 GP IQ AS+RA+A GV + ++ V R+ +D P+VLM Y NP+ +G RFA +A + Sbjct: 61 GPAIQAASQRALAGGVTVRGIIRAVEQIRRR-SDIPLVLMTYYNPVYQYGPGRFAADAAR 119 Query: 121 AGVDGVLLVDCPLEESA-VLQPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFA 179 AG +G+++ D P EES +L+ D + I L P T R+ + G A GF+Y VS Sbjct: 120 AGANGLIVPDLPPEESGPLLEAAGDNQIDLIPLVTPNTPARRLPVITGRARGFIYCVSVT 179 Query: 180 GITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRL 239 G+TG D+AA VR+ PVAVGFGI A A A+A DAVV+GSALV+ + Sbjct: 180 GVTGERESIMTDLAAMTDGVRSVTPLPVAVGFGISRPAQAAAVARHCDAVVVGSALVNTV 239 Query: 240 AGATDAGEITRRTQAFLAPIRAALDAR 266 A + + + ++ AL AR Sbjct: 240 AQKAGTPGLIKAVCEQVRELKEALTAR 266 Lambda K H 0.322 0.136 0.394 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: 188 Number of extensions: 12 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: 266 Length of database: 274 Length adjustment: 25 Effective length of query: 241 Effective length of database: 249 Effective search space: 60009 Effective search space used: 60009 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_092481605.1 BM299_RS01050 (tryptophan synthase subunit alpha)
to HMM TIGR00262 (trpA: tryptophan synthase, alpha 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/TIGR00262.hmm # target sequence database: /tmp/gapView.22074.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00262 [M=256] Accession: TIGR00262 Description: trpA: tryptophan synthase, alpha 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.3e-81 257.6 0.0 5.1e-81 257.3 0.0 1.0 1 lcl|NCBI__GCF_900115975.1:WP_092481605.1 BM299_RS01050 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900115975.1:WP_092481605.1 BM299_RS01050 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.3 0.0 5.1e-81 5.1e-81 5 246 .. 12 250 .. 8 264 .. 0.94 Alignments for each domain: == domain 1 score: 257.3 bits; conditional E-value: 5.1e-81 TIGR00262 5 kkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvek 73 +++ek +++++tagdPdl++++e++ + +aGad+lElGvpfsDP+aDGp+iqaa++RAl+ gv+v+ lcl|NCBI__GCF_900115975.1:WP_092481605.1 12 LARGEKGLIAYITAGDPDLATTVELAVAMGEAGADVLELGVPFSDPVADGPAIQAASQRALAGGVTVRG 80 67899**************************************************************** PP TIGR00262 74 alellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvk 142 +++ ++++r++ s+iP+vl+tyyn+++++g F a a+ ag +g++v+DlP ee++ lleaa ++++ lcl|NCBI__GCF_900115975.1:WP_092481605.1 81 IIRAVEQIRRR-SDIPLVLMTYYNPVYQYGPGRFAADAARAGANGLIVPDLPPEESGPLLEAAGDNQID 148 **********9.********************************************************* PP TIGR00262 143 qiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskke 211 i lv+P+++ rl i+ +++Gf+Y+vsv+Gvtg+re + +++ ++ v++++ Pv+vGFGis++ lcl|NCBI__GCF_900115975.1:WP_092481605.1 149 LIPLVTPNTPARRLPVITGRARGFIYCVSVTGVTGERESIMTDLAAMTDGVRSVTPLPVAVGFGISRPA 217 ********************************************************************* PP TIGR00262 212 qvkelkelgadgvivGsAlvkiieeklddeekale 246 q+ ++ d+v+vGsAlv+++++k +++ +++ lcl|NCBI__GCF_900115975.1:WP_092481605.1 218 QAAAVARH-CDAVVVGSALVNTVAQKAGTPG-LIK 250 ***99998.788*************988653.333 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (274 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: 00:00:00.00 # Mc/sec: 7.35 // [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