Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_085771646.1 B1812_RS11095 tryptophan synthase subunit alpha
Query= uniprot:M4NLA4 (266 letters) >NCBI__GCF_002117405.1:WP_085771646.1 Length = 296 Score = 217 bits (552), Expect = 3e-61 Identities = 119/245 (48%), Positives = 153/245 (62%), Gaps = 1/245 (0%) Query: 2 SRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMADG 61 +RID+RFA LKA R GL+ F+ AGDP + ++ +L AGAD+IE+G+PF+DPMADG Sbjct: 3 TRIDQRFAQLKAEGRAGLVTFLMAGDPDLGTSLEILKSLPAAGADVIEVGMPFTDPMADG 62 Query: 62 PVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQA 121 P IQ A RA+ G L L V +FR D TPIVLMGY NPI +G RF A QA Sbjct: 63 PAIQAAGLRALKAGTTLKKTLALVESFRALDRTTPIVLMGYYNPIYVYGVERFLQAAKQA 122 Query: 122 GVDGVLLVDCPLEESAVL-QPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFAG 180 GVDG+++VD P EE L P R AGL I LA PTT+ R+ ++ + GF+YYVS G Sbjct: 123 GVDGLIVVDLPPEEDDELCLPARAAGLNFIRLATPTTDDRRLPKVLENTSGFVYYVSLTG 182 Query: 181 ITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRLA 240 ITGAA + A V ++ P+AVGFG++ A A +A AD VV+G+ALV+ L Sbjct: 183 ITGAALADYSGVEAAVTRIKRHTNLPIAVGFGVKTAEGASQVARAADGVVVGTALVNALK 242 Query: 241 GATDA 245 DA Sbjct: 243 ETLDA 247 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: 232 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: 296 Length adjustment: 26 Effective length of query: 240 Effective length of database: 270 Effective search space: 64800 Effective search space used: 64800 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_085771646.1 B1812_RS11095 (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.13297.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.7e-82 260.2 0.0 8.1e-82 259.9 0.0 1.0 1 lcl|NCBI__GCF_002117405.1:WP_085771646.1 B1812_RS11095 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002117405.1:WP_085771646.1 B1812_RS11095 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 259.9 0.0 8.1e-82 8.1e-82 1 247 [. 9 254 .. 9 266 .. 0.96 Alignments for each domain: == domain 1 score: 259.9 bits; conditional E-value: 8.1e-82 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f++lk+++ +v+F+ agdPdl +slei+k+l aGad++E+G+pf DP+aDGp+iqaa lRAlkag+ lcl|NCBI__GCF_002117405.1:WP_085771646.1 9 FAQLKAEGRAGLVTFLMAGDPDLGTSLEILKSLPAAGADVIEVGMPFTDPMADGPAIQAAGLRALKAGT 77 7899999************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 +++k+l+l++ +r+ + Pivl+ yyn+i+ +gve F++ ak+agvdg++v+DlP ee d+l a+ lcl|NCBI__GCF_002117405.1:WP_085771646.1 78 TLKKTLALVESFRALDRTTPIVLMGYYNPIYVYGVERFLQAAKQAGVDGLIVVDLPPEEDDELCLPARA 146 ********************************************************************* PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 g++ i l++Pt+++ rl k+ e+++GfvY vs +G+tga + v++++ ++k++++ P++vGFG+ lcl|NCBI__GCF_002117405.1:WP_085771646.1 147 AGLNFIRLATPTTDDRRLPKVLENTSGFVYYVSLTGITGAALADYSGVEAAVTRIKRHTNLPIAVGFGV 215 ********************************************************************* PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeekalee 247 +e + ++ + adgv+vG Alv+ ++e+ld e++a + lcl|NCBI__GCF_002117405.1:WP_085771646.1 216 KTAEGASQVARA-ADGVVVGTALVNALKETLDAENRAAPQ 254 *********998.9******************88876543 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (296 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 0.00s 00:00:00.01 Elapsed: 00:00:00.00 # Mc/sec: 8.08 // [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