Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate 209407 DVU0471 tryptophan synthase, alpha subunit
Query= uniprot:M4NLA4 (266 letters) >MicrobesOnline__882:209407 Length = 257 Score = 176 bits (446), Expect = 4e-49 Identities = 105/250 (42%), Positives = 143/250 (57%), Gaps = 2/250 (0%) Query: 2 SRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMADG 61 SR++RR +AA R LIPF+TAG P+ E + AL AGAD+IE+GVPFSDP+ADG Sbjct: 4 SRLERRIREAQAAGRPALIPFLTAGFPTKERFWDELEALDAAGADIIEVGVPFSDPVADG 63 Query: 62 PVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQA 121 PV+ AS+RA+ GV L ++ +AA R+ +VLMGYLNP +G+ RF +A A Sbjct: 64 PVVAAASQRALESGVTLRWIMDGLAA-RKGRLRAGLVLMGYLNPFMQYGFERFVSDAADA 122 Query: 122 GVDGVLLVDCPLEESAVLQPLRDA-GLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFAG 180 GV G ++ D PL+E A L+ L A + I L P T RM + A G++Y VS G Sbjct: 123 GVAGCIIPDLPLDEDADLRALLAARDMDLIALVGPNTGEGRMREYAAVASGYVYVVSVMG 182 Query: 181 ITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRLA 240 TG ++A +A R PVA+GFGI A + ++ DAV+ GSAL+ L Sbjct: 183 TTGVRDGLPVEVADTLARARQCFSIPVALGFGISRPAQLEGLSHPPDAVIFGSALLRHLD 242 Query: 241 GATDAGEITR 250 DA + Sbjct: 243 AGGDAASFMK 252 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: 217 Number of extensions: 11 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: 266 Length of database: 257 Length adjustment: 25 Effective length of query: 241 Effective length of database: 232 Effective search space: 55912 Effective search space used: 55912 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 209407 DVU0471 (tryptophan synthase, alpha subunit)
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.32121.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 7e-66 207.7 0.0 8.1e-66 207.5 0.0 1.0 1 lcl|MicrobesOnline__882:209407 DVU0471 tryptophan synthase, alp Domain annotation for each sequence (and alignments): >> lcl|MicrobesOnline__882:209407 DVU0471 tryptophan synthase, alpha subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 207.5 0.0 8.1e-66 8.1e-66 6 237 .. 15 244 .. 10 256 .. 0.94 Alignments for each domain: == domain 1 score: 207.5 bits; conditional E-value: 8.1e-66 TIGR00262 6 kkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalellkkvrek 84 +++ a++pF+tag P+ e+ + ++ l aGad++E+GvpfsDP+aDGp++ aa++RAl++gv+++ +++ l++ + lcl|MicrobesOnline__882:209407 15 AAGRPALIPFLTAGFPTKERFWDELEALDAAGADIIEVGVPFSDPVADGPVVAAASQRALESGVTLRWIMDGLAARK-G 92 566779*************************************************************9998776655.5 PP TIGR00262 85 asniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeeerlkkiaeks 163 + + +vl+ y n+ +++g e F++ a++agv g +++DlPl+e +dl+ + ++++ i lv P++ e r+++ a + lcl|MicrobesOnline__882:209407 93 RLRAGLVLMGYLNPFMQYGFERFVSDAADAGVAGCIIPDLPLDEDADLRALLAARDMDLIALVGPNTGEGRMREYAAVA 171 599**************************************************************************** PP TIGR00262 164 eGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAlvkiieek 237 +G+vY+vsv+G tg+r+ + ev + +++++++ ++Pv++GFGis++ q++ l + d+vi GsAl++ ++ lcl|MicrobesOnline__882:209407 172 SGYVYVVSVMGTTGVRDGLPVEVADTLARARQCFSIPVALGFGISRPAQLEGLSHP-PDAVIFGSALLRHLDAG 244 ****************************************************9887.889*********99877 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (257 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: 7.09 // [ok]
This GapMind analysis is from Apr 09 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