Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_086508781.1 BZY95_RS04480 tryptophan synthase subunit alpha
Query= uniprot:M4NLA4 (266 letters) >NCBI__GCF_002151265.1:WP_086508781.1 Length = 271 Score = 277 bits (709), Expect = 1e-79 Identities = 146/267 (54%), Positives = 180/267 (67%), Gaps = 2/267 (0%) Query: 1 MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60 M+RID+RFA LKA R LIPF+TAGDP+P++ V MHALV+AGAD+IELGVPFSDPMAD Sbjct: 1 MNRIDKRFAELKAQGRRALIPFITAGDPAPQYTVGFMHALVEAGADVIELGVPFSDPMAD 60 Query: 61 GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120 GPVIQ A ERA+ V L + V FRQ D+DTP+VLMGYLNP+E G FA +A Sbjct: 61 GPVIQKACERALKHNVRLTHLFEMVREFRQRDSDTPVVLMGYLNPVERIGLEAFADQAAA 120 Query: 121 AGVDGVLLVDCPLEESAVLQP-LRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFA 179 AG+DGVL VD P EE+ P L+ GL I L APTT R A +C EG+LYYV+ Sbjct: 121 AGIDGVLTVDMPPEEADEFGPILKQRGLASIFLVAPTTSSERAATICAHGEGYLYYVALK 180 Query: 180 GITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRL 239 G+TGAA L+ D+A +A +R + P+ VGFGIRD ASA + AD V++GSALV R+ Sbjct: 181 GVTGAATLNAADVAEHLAPLRGLTELPLCVGFGIRDGASAAEVGKVADGVIVGSALVSRI 240 Query: 240 AGATDAGE-ITRRTQAFLAPIRAALDA 265 A + E I +A L +R ALDA Sbjct: 241 ADNAERPEAIADELKAVLGEMRQALDA 267 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: 255 Number of extensions: 9 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: 271 Length adjustment: 25 Effective length of query: 241 Effective length of database: 246 Effective search space: 59286 Effective search space used: 59286 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_086508781.1 BZY95_RS04480 (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.32325.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2e-82 261.9 0.0 2.3e-82 261.7 0.0 1.0 1 lcl|NCBI__GCF_002151265.1:WP_086508781.1 BZY95_RS04480 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508781.1 BZY95_RS04480 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 261.7 0.0 2.3e-82 2.3e-82 1 256 [] 8 262 .. 8 262 .. 0.99 Alignments for each domain: == domain 1 score: 261.7 bits; conditional E-value: 2.3e-82 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f++lk+++ +a++pF+tagdP + ++ +++ lv+aGad++ElGvpfsDP+aDGp+iq+a RAlk+ v lcl|NCBI__GCF_002151265.1:WP_086508781.1 8 FAELKAQGRRALIPFITAGDPAPQYTVGFMHALVEAGADVIELGVPFSDPMADGPVIQKACERALKHNV 76 7899***************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 ++++ +e+++++r++ s+ P+vl+ y n++ + g+e+F ++a++ag+dgvl +D+P eead++ k+ lcl|NCBI__GCF_002151265.1:WP_086508781.1 77 RLTHLFEMVREFRQRDSDTPVVLMGYLNPVERIGLEAFADQAAAAGIDGVLTVDMPPEEADEFGPILKQ 145 ********************************************************************* PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 +g++ iflvaPt+++er +i ++eG+ Y v+ Gvtga + +++v e ++ ++ l++ P +vGFGi lcl|NCBI__GCF_002151265.1:WP_086508781.1 146 RGLASIFLVAPTTSSERAATICAHGEGYLYYVALKGVTGAATLNAADVAEHLAPLRGLTELPLCVGFGI 214 ********************************************************************* PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkelk 256 + e+ ++ adgvivGsAlv +i+++ + +e++ +el+++ e++ lcl|NCBI__GCF_002151265.1:WP_086508781.1 215 RDGASAAEVGKV-ADGVIVGSALVSRIADNAERPEAIADELKAVLGEMR 262 *********999.9****************************9999885 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (271 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: 9.50 // [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