Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_077280014.1 B1C78_RS15180 tryptophan synthase subunit alpha
Query= uniprot:M4NLA4 (266 letters) >NCBI__GCF_002000365.1:WP_077280014.1 Length = 266 Score = 268 bits (685), Expect = 9e-77 Identities = 142/265 (53%), Positives = 181/265 (68%), Gaps = 2/265 (0%) Query: 1 MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60 MSR+ RF AL+AA R LIP+VTAGDP+P++ V LMHA+V+AG D+IELGVPFSDPMAD Sbjct: 1 MSRLAPRFEALRAAGRKALIPYVTAGDPNPDNTVPLMHAMVEAGVDIIELGVPFSDPMAD 60 Query: 61 GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120 GPVIQ A ERA+ V L V+G V FR+ D DTP+VLMGYLNP+E GY FA A Sbjct: 61 GPVIQQACERALRHHVSLRQVIGMVKTFREKDGDTPVVLMGYLNPVEIMGYEAFADAASS 120 Query: 121 AGVDGVLLVDCPLEES-AVLQPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFA 179 AGVDG+L VD P EE ++Q LR + I L APT+ +R+ ++C +A GF+YYVS Sbjct: 121 AGVDGLLTVDLPPEEGHDLVQALRARDIDPIYLLAPTSHEARIRRICAAASGFVYYVSLK 180 Query: 180 GITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRL 239 G+TGAA L ++ +VA +R+ PV VGFGI DA SA ++ ADAV++GSALV R+ Sbjct: 181 GVTGAATLDVDEVGRKVAAIRSHTDLPVGVGFGIGDAESAARVSAVADAVIVGSALVRRI 240 Query: 240 AGATDAGEITRR-TQAFLAPIRAAL 263 A + E RR LA +R A+ Sbjct: 241 AEHENDPEAGRRAVSELLAGMRKAM 265 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: 242 Number of extensions: 10 Number of successful extensions: 2 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: 266 Length adjustment: 25 Effective length of query: 241 Effective length of database: 241 Effective search space: 58081 Effective search space used: 58081 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_077280014.1 B1C78_RS15180 (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.13646.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-81 259.1 0.0 1.6e-81 258.9 0.0 1.0 1 lcl|NCBI__GCF_002000365.1:WP_077280014.1 B1C78_RS15180 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002000365.1:WP_077280014.1 B1C78_RS15180 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 258.9 0.0 1.6e-81 1.6e-81 1 255 [. 8 261 .. 8 262 .. 0.98 Alignments for each domain: == domain 1 score: 258.9 bits; conditional E-value: 1.6e-81 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 fe+l++++ ka++p+vtagdP+ ++++ +++ +v+aG+d++ElGvpfsDP+aDGp+iq+a RAl++ v lcl|NCBI__GCF_002000365.1:WP_077280014.1 8 FEALRAAGRKALIPYVTAGDPNPDNTVPLMHAMVEAGVDIIELGVPFSDPMADGPVIQQACERALRHHV 76 8999***************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 ++++++ ++k +rek + P+vl+ y n++ +g e+F + a +agvdg+l +DlP ee +dl++a + lcl|NCBI__GCF_002000365.1:WP_077280014.1 77 SLRQVIGMVKTFREKDGDTPVVLMGYLNPVEIMGYEAFADAASSAGVDGLLTVDLPPEEGHDLVQALRA 145 ********************************************************************* PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 +++++i+l aPt++e r+++i ++GfvY vs Gvtga + +ev + ++ ++++++ Pv vGFGi lcl|NCBI__GCF_002000365.1:WP_077280014.1 146 RDIDPIYLLAPTSHEARIRRICAAASGFVYYVSLKGVTGAATLDVDEVGRKVAAIRSHTDLPVGVGFGI 214 ******************************************999************************ PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkel 255 +e + ++ ++ ad+vivGsAlv++i+e+ +d+e+ +++ e+ + lcl|NCBI__GCF_002000365.1:WP_077280014.1 215 GDAESAARVSAV-ADAVIVGSALVRRIAEHENDPEAGRRAVSELLAGM 261 *********998.899*******************9999999888776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (266 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.00 # Mc/sec: 8.70 // [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