Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_006748160.1 THITH_RS10410 tryptophan synthase subunit alpha
Query= uniprot:H0BV16 (269 letters) >NCBI__GCF_000227685.2:WP_006748160.1 Length = 277 Score = 269 bits (688), Expect = 4e-77 Identities = 140/245 (57%), Positives = 180/245 (73%), Gaps = 4/245 (1%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 MSRIA F+ ++A GR AL+PY+TAG P +T LMH +V AGA+++ELGVPFSDPMAD Sbjct: 1 MSRIAERFAEIRAAGRAALVPYITAGDPAPGVTVPLMHDLVAAGAEMLELGVPFSDPMAD 60 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 GPVIQ+A E+AL+ G + VL+ VREFR++++ TPV+LMGY NPVER G AF Sbjct: 61 GPVIQQACERALAHGTSLRDVLEMVREFRQQDSRTPVILMGYLNPVERM----GAEAFAA 116 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 ++AAAGVDGVL+VD PPEE A L G+D IFLLAPT++ ER+ VA A G++YY Sbjct: 117 EAAAAGVDGVLVVDLPPEESGDLTAVLEPAGIDPIFLLAPTTSGERVQHVAAAARGFIYY 176 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 VSLKGVTGS ALD A+ L IR +P+GVGFGIRDA TA + +VADAVV+GS + Sbjct: 177 VSLKGVTGSQALDADALGARLDSIRGLTALPLGVGFGIRDADTAAKVARVADAVVVGSAL 236 Query: 241 IQLIE 245 ++L++ Sbjct: 237 VRLVD 241 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: 281 Number of extensions: 13 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: 277 Length adjustment: 25 Effective length of query: 244 Effective length of database: 252 Effective search space: 61488 Effective search space used: 61488 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 WP_006748160.1 THITH_RS10410 (tryptophan synthase subunit alpha)
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.2581524.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-78 248.9 0.0 2.2e-78 248.7 0.0 1.0 1 NCBI__GCF_000227685.2:WP_006748160.1 Domain annotation for each sequence (and alignments): >> NCBI__GCF_000227685.2:WP_006748160.1 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 248.7 0.0 2.2e-78 2.2e-78 1 255 [. 8 261 .. 8 262 .. 0.97 Alignments for each domain: == domain 1 score: 248.7 bits; conditional E-value: 2.2e-78 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvek 73 f+++++++ a+vp++tagdP +++ +++ lv aGa++lElGvpfsDP+aDGp+iq+a RAl++g+++++ NCBI__GCF_000227685.2:WP_006748160.1 8 FAEIRAAGRAALVPYITAGDPAPGVTVPLMHDLVAAGAEMLELGVPFSDPMADGPVIQQACERALAHGTSLRD 80 678899999**************************************************************** PP TIGR00262 74 alellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqifl 146 +le+++++r++ s P++l+ y n++ ++g e+F a+a++agvdgvlv+DlP ee++dl+ + + g+++ifl NCBI__GCF_000227685.2:WP_006748160.1 81 VLEMVREFRQQDSRTPVILMGYLNPVERMGAEAFAAEAAAAGVDGVLVVDLPPEESGDLTAVLEPAGIDPIFL 153 ************************************************************************* PP TIGR00262 147 vaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkel 219 aPt++ er++++a ++Gf+Y vs Gvtg + ++++ + + ++ l++ P vGFGi ++ + ++ + NCBI__GCF_000227685.2:WP_006748160.1 154 LAPTTSGERVQHVAAAARGFIYYVSLKGVTGSQALDADALGARLDSIRGLTALPLGVGFGIRDADTAAKVARV 226 ************************************************************************9 PP TIGR00262 220 gadgvivGsAlvkiieeklddeekaleeleefvkel 255 ad+v+vGsAlv+++++ +d++ + + ++ v+e+ NCBI__GCF_000227685.2:WP_006748160.1 227 -ADAVVVGSALVRLVDQYPGDPDGFRSAAAATVREM 261 .899************99988887777777666666 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (277 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: 13.71 // [ok]
This GapMind analysis is from Jul 25 2024. The underlying query database was built on Jul 25 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