Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate 350055 BT0527 tryptophan synthase alpha chain (NCBI ptt file)
Query= uniprot:A0A3N7DTH5 (255 letters) >FitnessBrowser__Btheta:350055 Length = 256 Score = 268 bits (684), Expect = 1e-76 Identities = 127/242 (52%), Positives = 178/242 (73%), Gaps = 1/242 (0%) Query: 1 MNRINKLFQE-KKNILSIYYTAGYPNLGDTVAIAEELERSGADLLEIGFPYSDPVADGPV 59 MNRIN+LF KK+ILSIY+ AG P L TV + LE+ G ++E+G P+SDP+ADG V Sbjct: 1 MNRINQLFNSNKKDILSIYFCAGNPTLDGTVNVIRTLEKHGVSMIEVGIPFSDPMADGIV 60 Query: 60 IQASSKTALDGGMTLKLLFEQLKDLRKTVNIPVLLMGYVNPMLQYGVENFCKSCAEVGVD 119 IQ ++ AL GM+LK+LFEQL+++R+ V+IP++ MGY+NP++Q+G ENFC+ C E G+D Sbjct: 61 IQNAATQALRNGMSLKILFEQLRNIRQEVSIPLVFMGYLNPIMQFGFENFCRKCVECGID 120 Query: 120 GCIVPDLPMVEYEELYSGVFEANGLTNIFLVTPQTSTERIRKIDGLSNGFIYLLSSSATT 179 G I+PDLP +Y++ Y + E G+ I L+TP+TS ER+R+ID ++GFIY++SS+ATT Sbjct: 121 GVIIPDLPFRDYQDHYRIIAERYGIKVIMLITPETSEERVREIDAHTDGFIYMVSSAATT 180 Query: 180 GQNLQVSENTEAYFSRIAEMKLNNPTMIGFGISSKETFDKACQYANGAIIGSAFVKSLKS 239 G +E AYF +I +M L NP M+GFGIS+K TF AC++A+GAIIGS FV L+ Sbjct: 181 GAQQDFNEQKRAYFKKIEDMNLRNPLMVGFGISNKATFQAACEHASGAIIGSRFVTLLEE 240 Query: 240 GK 241 K Sbjct: 241 EK 242 Lambda K H 0.317 0.135 0.382 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: 228 Number of extensions: 8 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: 255 Length of database: 256 Length adjustment: 24 Effective length of query: 231 Effective length of database: 232 Effective search space: 53592 Effective search space used: 53592 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 bits)
Align candidate 350055 BT0527 (tryptophan synthase alpha chain (NCBI ptt file))
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.9569.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 8e-74 233.7 0.0 9.2e-74 233.5 0.0 1.0 1 lcl|FitnessBrowser__Btheta:350055 BT0527 tryptophan synthase alpha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Btheta:350055 BT0527 tryptophan synthase alpha chain (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 233.5 0.0 9.2e-74 9.2e-74 5 250 .. 9 253 .. 5 256 .] 0.93 Alignments for each domain: == domain 1 score: 233.5 bits; conditional E-value: 9.2e-74 TIGR00262 5 kkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalellkk 80 +++++ + ++ ag+P+l+ ++++i+tl k+G++++E+G+pfsDP+aDG++iq+a++ Al++g++++ +e l++ lcl|FitnessBrowser__Btheta:350055 9 NSNKKDILSIYFCAGNPTLDGTVNVIRTLEKHGVSMIEVGIPFSDPMADGIVIQNAATQALRNGMSLKILFEQLRN 84 5556667778999*************************************************************** PP TIGR00262 81 vrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlle.aakkhgvkqiflvaPtaeeer 155 +r++ ++iP+v++ y n+i++ g e+F +k+ e+g+dgv+++DlP+ + +d ++ a+++g+k i+l++P ++eer lcl|FitnessBrowser__Btheta:350055 85 IRQE-VSIPLVFMGYLNPIMQFGFENFCRKCVECGIDGVIIPDLPFRDYQDHYRiIAERYGIKVIMLITPETSEER 159 ****.*****************************************997766552799****************** PP TIGR00262 156 lkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkals.kkPvlvGFGiskkeqvkelkelgadgvivGsAl 230 +++i+ +++Gf+Y+vs+a tga++ ++e+ ++ kk+ +++ + P +vGFGis+k +++ e a g+i+Gs + lcl|FitnessBrowser__Btheta:350055 160 VREIDAHTDGFIYMVSSAATTGAQQDFNEQKRAYFKKIEDMNlRNPLMVGFGISNKATFQAACEH-ASGAIIGSRF 234 ***************************************998579*******************9.788******* PP TIGR00262 231 vkiieeklddeekaleelee 250 v ++ee++d +eka+ +l++ lcl|FitnessBrowser__Btheta:350055 235 VTLLEEEKD-PEKAILKLKD 253 *******76.7777777765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (256 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: 8.73 // [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