Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate 8501003 DvMF_1740 tryptophan synthase subunit alpha (RefSeq)
Query= uniprot:H0BV16 (269 letters) >FitnessBrowser__Miya:8501003 Length = 270 Score = 181 bits (458), Expect = 2e-50 Identities = 106/245 (43%), Positives = 147/245 (60%), Gaps = 5/245 (2%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 +SR+ + +A A GR AL+P++TAGFP D M G+ GADVIE+GVPFSDP+AD Sbjct: 18 VSRLEARVTAANAAGRPALVPFLTAGFPTLDRFWEEMDGLDRGGADVIEIGVPFSDPVAD 77 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 GPV++ A +AL G+ + +LD ++ R +VLMGY NP +Y G Sbjct: 78 GPVVEAASLRALENGVTLRWILDGLKA-RAGRYEAELVLMGYYNPFLQY----GLENLAA 132 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 D+AAAGV G ++ D P EE A L A G+DLI L+ P +++ERMAE A VASGYVY Sbjct: 133 DAAAAGVAGFIVPDLPLEEDAEMRALLAARGIDLIALVGPNTSEERMAEYAAVASGYVYV 192 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 VS+ G+TG V Q L R R+ +P+ +GFGI++ + DAVV GS + Sbjct: 193 VSVLGITGVREGLPPEVPQTLARARKAFRLPLALGFGIKEPKQLEGFPDRPDAVVFGSAL 252 Query: 241 IQLIE 245 ++ I+ Sbjct: 253 LRHID 257 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: 217 Number of extensions: 10 Number of successful extensions: 4 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: 270 Length adjustment: 25 Effective length of query: 244 Effective length of database: 245 Effective search space: 59780 Effective search space used: 59780 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 8501003 DvMF_1740 (tryptophan synthase subunit alpha (RefSeq))
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.6384.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-66 210.3 0.0 1.3e-66 210.1 0.0 1.0 1 lcl|FitnessBrowser__Miya:8501003 DvMF_1740 tryptophan synthase su Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Miya:8501003 DvMF_1740 tryptophan synthase subunit alpha (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 210.1 0.0 1.3e-66 1.3e-66 6 246 .. 30 267 .. 25 270 .] 0.95 Alignments for each domain: == domain 1 score: 210.1 bits; conditional E-value: 1.3e-66 TIGR00262 6 kkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalellkkvr 82 +++ a+vpF+tag P+l++ e ++ l + Gad++E+GvpfsDP+aDGp++ aa+lRAl++gv+++ +l+ lk+ r lcl|FitnessBrowser__Miya:8501003 30 AAGRPALVPFLTAGFPTLDRFWEEMDGLDRGGADVIEIGVPFSDPVADGPVVEAASLRALENGVTLRWILDGLKA-R 105 566779**************************************************************9997765.6 PP TIGR00262 83 ekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeeerlkki 159 + + ++ +vl+ yyn+ +++g+e+ a a++agv g +v+DlPlee ++++ + +g++ i lv P+++eer+ + lcl|FitnessBrowser__Miya:8501003 106 AGRYEAELVLMGYYNPFLQYGLENLAADAAAAGVAGFIVPDLPLEEDAEMRALLAARGIDLIALVGPNTSEERMAEY 182 66699************************************************************************ PP TIGR00262 160 aekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAlvkiiee 236 a ++G+vY+vsv+G+tg+re + ev + ++++++ + P ++GFGi ++ q++ + d+v+ GsAl++ i+ lcl|FitnessBrowser__Miya:8501003 183 AAVASGYVYVVSVLGITGVREGLPPEVPQTLARARKAFRLPLALGFGIKEPKQLEGFPDR-PDAVVFGSALLRHIDA 258 ***********************************************************9.788***********99 PP TIGR00262 237 klddeekale 246 + e +l+ lcl|FitnessBrowser__Miya:8501003 259 G-NSAESFLA 267 8.66777776 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (270 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: 9.57 // [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