Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate GFF482 PGA1_c04930 tryptophan synthase alpha chain
Query= uniprot:M4NLA4 (266 letters) >FitnessBrowser__Phaeo:GFF482 Length = 263 Score = 215 bits (548), Expect = 7e-61 Identities = 111/249 (44%), Positives = 156/249 (62%), Gaps = 1/249 (0%) Query: 1 MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60 M+RID +FA LKAA++ + +V AGDP + + L+ L AG D+IELG+PF+DPMAD Sbjct: 1 MTRIDAKFAELKAADKKAFVAYVMAGDPDFDTSLELVKGLPAAGVDVIELGLPFTDPMAD 60 Query: 61 GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120 GP IQ A +RA+ G+ L L FR+ D TPIV+MGY NPI + G F +A + Sbjct: 61 GPTIQLAGQRALEAGMTLQRTLDLARTFREEDNTTPIVMMGYYNPIYSRGVETFLKDAKE 120 Query: 121 AGVDGVLLVDCPLEE-SAVLQPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFA 179 AG+DG+++VD P EE S + P + AGL I LA PTT+ R+ ++ + GF+YYVS Sbjct: 121 AGIDGLIVVDLPPEEDSELCLPAQQAGLNFIRLATPTTDDKRLPRVLQNTSGFVYYVSIT 180 Query: 180 GITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRL 239 GITGAA ++ VA ++++ PV VGFGI ++AIA AD V+GSA+V ++ Sbjct: 181 GITGAAEAEATNVGPEVARIKSQTDLPVIVGFGINTPEKSQAIASVADGAVVGSAIVSQI 240 Query: 240 AGATDAGEI 248 GE+ Sbjct: 241 GAGKPVGEV 249 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: 219 Number of extensions: 7 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: 263 Length adjustment: 25 Effective length of query: 241 Effective length of database: 238 Effective search space: 57358 Effective search space used: 57358 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 GFF482 PGA1_c04930 (tryptophan synthase alpha chain)
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.20281.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-84 268.6 0.1 2.2e-84 268.3 0.1 1.0 1 lcl|FitnessBrowser__Phaeo:GFF482 PGA1_c04930 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Phaeo:GFF482 PGA1_c04930 tryptophan synthase alpha chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 268.3 0.1 2.2e-84 2.2e-84 1 236 [. 8 242 .. 8 258 .. 0.97 Alignments for each domain: == domain 1 score: 268.3 bits; conditional E-value: 2.2e-84 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalel 77 f++lk++++kafv++v agdPd+++sle++k l aG+d++ElG+pf DP+aDGptiq a +RAl+ag++++++l+l lcl|FitnessBrowser__Phaeo:GFF482 8 FAELKAADKKAFVAYVMAGDPDFDTSLELVKGLPAAGVDVIELGLPFTDPMADGPTIQLAGQRALEAGMTLQRTLDL 84 7899************************************************************************* PP TIGR00262 78 lkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeee 154 ++ +re+ ++ Piv++ yyn+i+++gve+F++ akeag+dg++v+DlP ee ++l a++ g++ i l++Pt++++ lcl|FitnessBrowser__Phaeo:GFF482 85 ARTFREEDNTTPIVMMGYYNPIYSRGVETFLKDAKEAGIDGLIVVDLPPEEDSELCLPAQQAGLNFIRLATPTTDDK 161 ***************************************************************************** PP TIGR00262 155 rlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAlv 231 rl ++ ++++GfvY vs +G+tga e +++v ++++k+ ++ Pv+vGFGi +e+ +++ ++ adg++vGsA+v lcl|FitnessBrowser__Phaeo:GFF482 162 RLPRVLQNTSGFVYYVSITGITGAAEAEATNVGPEVARIKSQTDLPVIVGFGINTPEKSQAIASV-ADGAVVGSAIV 237 ***********************************************************999999.99********* PP TIGR00262 232 kiiee 236 i lcl|FitnessBrowser__Phaeo:GFF482 238 SQIGA 242 99965 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (263 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: 10.13 // [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