Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate SMc02765 SMc02765 tryptophan synthase subunit alpha
Query= uniprot:M4NLA4 (266 letters) >FitnessBrowser__Smeli:SMc02765 Length = 279 Score = 213 bits (542), Expect = 4e-60 Identities = 116/253 (45%), Positives = 160/253 (63%), Gaps = 2/253 (0%) Query: 2 SRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMADG 61 +R+++RFA + A R L+ + GDP + +A+M AL AGAD+IELGVPFSDPMADG Sbjct: 3 ARMEQRFADVAAEGRPVLVTYFMGGDPDFDTSLAIMKALRQAGADIIELGVPFSDPMADG 62 Query: 62 PVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQA 121 P IQ A +RA+ G LA L FR D TPIVLMGY NPI +G RF +A++A Sbjct: 63 PAIQLAGQRALKAGQSLAKTLELARLFRAEDQRTPIVLMGYYNPIYIYGVERFLADALEA 122 Query: 122 GVDGVLLVDCPLE-ESAVLQPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFAG 180 GVDG+++VD P E + + P + G+ I LA PTT+ R+ ++ + GF+YYVS G Sbjct: 123 GVDGLIVVDLPPEMDDELCIPALEKGISFIRLATPTTDDRRLPKVLENTSGFVYYVSMTG 182 Query: 181 ITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRLA 240 ITG+A IA VA ++A PV VGFG++ A A+AI AD VV+G+A+V+++A Sbjct: 183 ITGSALPDPSLIAGAVARIKAHTPLPVCVGFGVKTADHARAIGASADGVVVGTAIVNQIA 242 Query: 241 GA-TDAGEITRRT 252 + T+ G T T Sbjct: 243 SSLTEEGRATEAT 255 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: 219 Number of extensions: 11 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: 266 Length of database: 279 Length adjustment: 25 Effective length of query: 241 Effective length of database: 254 Effective search space: 61214 Effective search space used: 61214 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 SMc02765 SMc02765 (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.5082.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.5e-79 250.9 0.0 5.2e-79 250.7 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc02765 SMc02765 tryptophan synthase sub Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc02765 SMc02765 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 250.7 0.0 5.2e-79 5.2e-79 6 247 .. 14 254 .. 9 266 .. 0.95 Alignments for each domain: == domain 1 score: 250.7 bits; conditional E-value: 5.2e-79 TIGR00262 6 kkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalellkk 80 +++ +v+++ gdPd+++sl i+k l +aGad++ElGvpfsDP+aDGp+iq a +RAlkag +++k+lel++ lcl|FitnessBrowser__Smeli:SMc02765 14 AEGRPVLVTYFMGGDPDFDTSLAIMKALRQAGADIIELGVPFSDPMADGPAIQLAGQRALKAGQSLAKTLELARL 88 5566689******************************************************************** PP TIGR00262 81 vrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeeer 155 +r++ + Pivl+ yyn+i+ +gve F+a a eagvdg++v+DlP e d+l a ++g++ i l++Pt+++ r lcl|FitnessBrowser__Smeli:SMc02765 89 FRAEDQRTPIVLMGYYNPIYIYGVERFLADALEAGVDGLIVVDLPPEMDDELCIPALEKGISFIRLATPTTDDRR 163 *************************************************************************** PP TIGR00262 156 lkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAl 230 l k+ e+++GfvY vs++G+tg + + +++++ka++ Pv+vGFG+ +++++++ ++adgv+vG A+ lcl|FitnessBrowser__Smeli:SMc02765 164 LPKVLENTSGFVYYVSMTGITGSALPDPSLIAGAVARIKAHTPLPVCVGFGVKTADHARAIG-ASADGVVVGTAI 237 ************************999999***************************99775.56********** PP TIGR00262 231 vkiieeklddeekalee 247 v+ i+ +l +e +a+e+ lcl|FitnessBrowser__Smeli:SMc02765 238 VNQIASSLTEEGRATEA 254 *******9988877765 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (279 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: 9.78 // [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