Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_029000327.1 H537_RS0126820 tryptophan synthase subunit alpha
Query= uniprot:H0BV16 (269 letters) >NCBI__GCF_000430725.1:WP_029000327.1 Length = 276 Score = 366 bits (940), Expect = e-106 Identities = 188/266 (70%), Positives = 220/266 (82%), Gaps = 4/266 (1%) Query: 3 RIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMADGP 62 RIA+TF L++QGRKALIPYVTAG P+AD+TPALM + + GADVIELGVPFSDPMADGP Sbjct: 7 RIAATFERLKSQGRKALIPYVTAGDPYADVTPALMRALADGGADVIELGVPFSDPMADGP 66 Query: 63 VIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVRDS 122 VIQ+A E+AL+ GIGM QVLD VR+FR+ ++ TPVVLMGYANPVERY G FV D+ Sbjct: 67 VIQQAAERALAKGIGMAQVLDIVRDFRRSDDVTPVVLMGYANPVERY----GVERFVADA 122 Query: 123 AAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYYVS 182 AGVDGVLIVDYPPEECE FAA L+A GMD IFLLAPTST+ RMA V R+ASGYVYYVS Sbjct: 123 RDAGVDGVLIVDYPPEECEVFAAQLQAAGMDPIFLLAPTSTEARMAHVGRIASGYVYYVS 182 Query: 183 LKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRIIQ 242 LKGVTG+G LDT+AV M+PRIR HV++PVGVGFGIRDAATA+A+G+VADAVVIGSR++Q Sbjct: 183 LKGVTGAGHLDTSAVAAMVPRIRAHVSVPVGVGFGIRDAATARAVGEVADAVVIGSRLVQ 242 Query: 243 LIEDQEHAKVVPLTIDFLRGIRKALD 268 L++ Q +VV F+ IR ALD Sbjct: 243 LLQGQPRDEVVATGRRFMAEIRAALD 268 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: 307 Number of extensions: 10 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: 276 Length adjustment: 25 Effective length of query: 244 Effective length of database: 251 Effective search space: 61244 Effective search space used: 61244 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_029000327.1 H537_RS0126820 (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.28996.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.2e-76 240.6 0.1 7.6e-76 240.4 0.1 1.0 1 lcl|NCBI__GCF_000430725.1:WP_029000327.1 H537_RS0126820 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000430725.1:WP_029000327.1 H537_RS0126820 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 240.4 0.1 7.6e-76 7.6e-76 1 243 [. 12 251 .. 12 265 .. 0.96 Alignments for each domain: == domain 1 score: 240.4 bits; conditional E-value: 7.6e-76 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 fe lk+++ ka++p+vtagdP ++++ +++ l++ Gad++ElGvpfsDP+aDGp+iq+a+ RAl++g+ lcl|NCBI__GCF_000430725.1:WP_029000327.1 12 FERLKSQGRKALIPYVTAGDPYADVTPALMRALADGGADVIELGVPFSDPMADGPVIQQAAERALAKGI 80 7999***************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 ++++l++++ +r++ P+vl+ y+n++ ++gve F+a a++agvdgvl++D P ee + + + + lcl|NCBI__GCF_000430725.1:WP_029000327.1 81 GMAQVLDIVRDFRRSDDVTPVVLMGYANPVERYGVERFVADARDAGVDGVLIVDYPPEECEVFAAQLQA 149 ********************************************************************* PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 g+++ifl aPt+ e r+ ++ + ++G+vY vs Gvtga + +++v +++ +++a+ ++Pv vGFGi lcl|NCBI__GCF_000430725.1:WP_029000327.1 150 AGMDPIFLLAPTSTEARMAHVGRIASGYVYYVSLKGVTGAGHLDTSAVAAMVPRIRAHVSVPVGVGFGI 218 ********************************************************************* PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeek 243 + ++++ e+ ad+v++Gs lv++++ + +++ lcl|NCBI__GCF_000430725.1:WP_029000327.1 219 RDAATARAVGEV-ADAVVIGSRLVQLLQGQ--PRDE 251 ***********9.899**********9987..3444 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (276 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: 7.53 // [ok]
This GapMind analysis is from Apr 10 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