Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate Dsui_3191 Dsui_3191 tryptophan synthase, alpha subunit
Query= uniprot:H0BV16 (269 letters) >FitnessBrowser__PS:Dsui_3191 Length = 267 Score = 299 bits (765), Expect = 5e-86 Identities = 159/269 (59%), Positives = 198/269 (73%), Gaps = 7/269 (2%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 MSRI TF AL+AQG+KALIP++TAG P +T L+H +VEAGADVIELGVPFSDPMAD Sbjct: 1 MSRIQQTFDALKAQGKKALIPFITAGDPHPALTVTLLHTLVEAGADVIELGVPFSDPMAD 60 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 GP IQ+A E+AL+ G+ + QVL V EFR+++ TP+VLMGYANP+E G FV Sbjct: 61 GPTIQRASERALAKGVSLRQVLAMVSEFREKDGETPIVLMGYANPIESM----GMETFVA 116 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 +A AGVDGVL+VDY PEE AF A++ A +D IFLLAPTSTD R+ +V ++A GYVYY Sbjct: 117 AAAEAGVDGVLVVDYTPEESAAFCAAMNARDLDTIFLLAPTSTDARINQVGQLARGYVYY 176 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 VSLKGVTGSGAL+ V + +P+IR+ +PVGVGFGIRDA TA+ I +ADAVV+GSRI Sbjct: 177 VSLKGVTGSGALNFDEVAERIPKIREATGLPVGVGFGIRDAETAKRIAGMADAVVVGSRI 236 Query: 241 IQLIE---DQEHAKVVPLTIDFLRGIRKA 266 I+ +E D A+V L D RG+ A Sbjct: 237 IEEMEKYPDDAVARVKGLVADIRRGVDAA 265 Lambda K H 0.321 0.137 0.389 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: 258 Number of extensions: 11 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: 269 Length of database: 267 Length adjustment: 25 Effective length of query: 244 Effective length of database: 242 Effective search space: 59048 Effective search space used: 59048 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 (21.8 bits) S2: 47 (22.7 bits)
Align candidate Dsui_3191 Dsui_3191 (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.5621.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-81 258.5 0.1 2.6e-81 258.3 0.1 1.0 1 lcl|FitnessBrowser__PS:Dsui_3191 Dsui_3191 tryptophan synthase, a Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__PS:Dsui_3191 Dsui_3191 tryptophan synthase, alpha subunit # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 258.3 0.1 2.6e-81 2.6e-81 1 250 [. 8 253 .. 8 259 .. 0.96 Alignments for each domain: == domain 1 score: 258.3 bits; conditional E-value: 2.6e-81 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalel 77 f++lk++++ka++pF+tagdP+ + ++ +++tlv+aGad++ElGvpfsDP+aDGptiq+a+ RAl++gv+++++l++ lcl|FitnessBrowser__PS:Dsui_3191 8 FDALKAQGKKALIPFITAGDPHPALTVTLLHTLVEAGADVIELGVPFSDPMADGPTIQRASERALAKGVSLRQVLAM 84 7899************************************************************************* PP TIGR00262 78 lkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeee 154 + ++rek + Pivl+ y+n+i ++g+e+F+a a+eagvdgvlv+D ee++ + a + +++++ifl aPt+ + lcl|FitnessBrowser__PS:Dsui_3191 85 VSEFREKDGETPIVLMGYANPIESMGMETFVAAAAEAGVDGVLVVDYTPEESAAFCAAMNARDLDTIFLLAPTSTDA 161 ***************************************************************************** PP TIGR00262 155 rlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAlv 231 r++++ + ++G+vY vs Gvtg +ev e i k+++ + Pv vGFGi +e +k++ + ad+v+vGs ++ lcl|FitnessBrowser__PS:Dsui_3191 162 RINQVGQLARGYVYYVSLKGVTGSGALNFDEVAERIPKIREATGLPVGVGFGIRDAETAKRIAGM-ADAVVVGSRII 237 **************************999************************************.899*******9 PP TIGR00262 232 kiieeklddeekaleelee 250 + +e+ d a+++++ lcl|FitnessBrowser__PS:Dsui_3191 238 EEMEKYPD---DAVARVKG 253 99999855...44444444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (267 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: 00:00:00.01 # Mc/sec: 5.93 // [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