Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_092344854.1 BLU87_RS03700 tryptophan synthase subunit alpha
Query= uniprot:M4NLA4 (266 letters) >NCBI__GCF_900107645.1:WP_092344854.1 Length = 268 Score = 240 bits (612), Expect = 3e-68 Identities = 134/266 (50%), Positives = 169/266 (63%), Gaps = 2/266 (0%) Query: 1 MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60 MSRI+ FAAL+ T LIPF+TAGDP + ++ LVDAGADLIELGVPFSDPMAD Sbjct: 1 MSRIEATFAALRQRQETALIPFITAGDPDLKVAAEIILTLVDAGADLIELGVPFSDPMAD 60 Query: 61 GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120 GP IQ +SERA+A G L+ VL VA R+ A P++LMGY NP+ +G RF +AV Sbjct: 61 GPTIQASSERALAAGTTLSGVLQLVAEVRKKTA-VPLILMGYYNPVFCYGVERFVRDAVA 119 Query: 121 AGVDGVLLVDCPLEESAVLQP-LRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFA 179 AGVDG+LLVD P EE+A + P L ++G+ I L APTT RM +L AEG+LYYVS Sbjct: 120 AGVDGLLLVDLPPEEAAEISPLLHESGVALITLLAPTTPRERMQRLAAVAEGYLYYVSMT 179 Query: 180 GITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRL 239 G+TG +S DI V D++ PV VGFGI A A A+ FAD VV+GSALV + Sbjct: 180 GVTGGQKISPEDIRLAVDDLKGMTNVPVGVGFGITTVADACAVGTFADGVVVGSALVKII 239 Query: 240 AGATDAGEITRRTQAFLAPIRAALDA 265 + E+ F+A ++ L A Sbjct: 240 EKYGKSEELLPEVAKFVAELKGGLTA 265 Lambda K H 0.322 0.136 0.394 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: 220 Number of extensions: 10 Number of successful extensions: 3 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: 266 Length of database: 268 Length adjustment: 25 Effective length of query: 241 Effective length of database: 243 Effective search space: 58563 Effective search space used: 58563 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_092344854.1 BLU87_RS03700 (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.22590.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-87 278.2 0.1 2.4e-87 278.0 0.1 1.0 1 lcl|NCBI__GCF_900107645.1:WP_092344854.1 BLU87_RS03700 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_900107645.1:WP_092344854.1 BLU87_RS03700 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 278.0 0.1 2.4e-87 2.4e-87 1 256 [] 8 260 .. 8 260 .. 0.98 Alignments for each domain: == domain 1 score: 278.0 bits; conditional E-value: 2.4e-87 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f++l++++e+a++pF+tagdPdl++++eii tlv+aGad++ElGvpfsDP+aDGptiqa++ RAl+ag+ lcl|NCBI__GCF_900107645.1:WP_092344854.1 8 FAALRQRQETALIPFITAGDPDLKVAAEIILTLVDAGADLIELGVPFSDPMADGPTIQASSERALAAGT 76 789****************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 +++ +l+l+++vr+k +++P++l+ yyn++f +gve F++ a +agvdg+l++DlP eea+++ ++ lcl|NCBI__GCF_900107645.1:WP_092344854.1 77 TLSGVLQLVAEVRKK-TAVPLILMGYYNPVFCYGVERFVRDAVAAGVDGLLLVDLPPEEAAEISPLLHE 144 ***************.***************************************************** PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 gv+ i l aPt++ er++++a +eG+ Y vs++Gvtg ++ e+++ ++ +k ++++Pv vGFGi lcl|NCBI__GCF_900107645.1:WP_092344854.1 145 SGVALITLLAPTTPRERMQRLAAVAEGYLYYVSMTGVTGGQKISPEDIRLAVDDLKGMTNVPVGVGFGI 213 ********************************************************************* PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkelk 256 + + ++ + adgv+vGsAlvkiie+ +++e++l e+++fv elk lcl|NCBI__GCF_900107645.1:WP_092344854.1 214 TTVADACAVGTF-ADGVVVGSALVKIIEKY-GKSEELLPEVAKFVAELK 260 **9999999888.9**************99.99************9997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (268 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: 7.97 // [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