Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate GFF62 Psest_0062 tryptophan synthase, alpha subunit
Query= uniprot:M4NLA4 (266 letters) >FitnessBrowser__psRCH2:GFF62 Length = 269 Score = 219 bits (559), Expect = 4e-62 Identities = 117/243 (48%), Positives = 153/243 (62%), Gaps = 1/243 (0%) Query: 1 MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60 MSR+ RFA LK NR L+ FVTAGDP +A++ L DAGAD+IELG+PF+DPMAD Sbjct: 1 MSRLQSRFAELKEQNRAALVTFVTAGDPDYATSLAILKGLPDAGADVIELGMPFTDPMAD 60 Query: 61 GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120 GP IQ A+ RA+A L L V FR+ +A TP+VLMGY NPI +G RF +A + Sbjct: 61 GPAIQLANIRALAAKQNLPKTLQMVREFRESNASTPLVLMGYYNPIFAYGVERFVADAKE 120 Query: 121 AGVDGVLLVDCPLEESAVL-QPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFA 179 AGVDG+++VD P E + L P + G+ I L PTT+ R+ + + GF+YYVS A Sbjct: 121 AGVDGLIVVDLPPEHNDELCDPAQAVGIDFIRLTTPTTDDKRLPTVLNGSSGFVYYVSVA 180 Query: 180 GITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRL 239 G+TGA + + VA ++ PV VGFGIR A AIA D VV+GSAL+D++ Sbjct: 181 GVTGAGSATMEHVEEAVARLKRHTDIPVCVGFGIRTPEQAAAIARLTDGVVVGSALIDQI 240 Query: 240 AGA 242 A A Sbjct: 241 ASA 243 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: 230 Number of extensions: 7 Number of successful extensions: 4 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: 269 Length adjustment: 25 Effective length of query: 241 Effective length of database: 244 Effective search space: 58804 Effective search space used: 58804 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 GFF62 Psest_0062 (tryptophan synthase, alpha subunit)
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.3698965.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 9.4e-87 276.1 0.0 1.1e-86 275.9 0.0 1.0 1 FitnessBrowser__psRCH2:GFF62 Domain annotation for each sequence (and alignments): >> FitnessBrowser__psRCH2:GFF62 # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 275.9 0.0 1.1e-86 1.1e-86 1 246 [. 8 251 .. 8 261 .. 0.96 Alignments for each domain: == domain 1 score: 275.9 bits; conditional E-value: 1.1e-86 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalellkkv 81 f++lk+++ a+v+FvtagdPd+++sl i+k l +aGad++ElG+pf DP+aDGp+iq a+ RAl+a ++ k+l++++++ FitnessBrowser__psRCH2:GFF62 8 FAELKEQNRAALVTFVTAGDPDYATSLAILKGLPDAGADVIELGMPFTDPMADGPAIQLANIRALAAKQNLPKTLQMVREF 88 7899***************************************************************************** PP TIGR00262 82 rekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeeerlkkiaek 162 re++ + P+vl+ yyn+if++gve F+a akeagvdg++v+DlP e +d+l + a+ g++ i l +Pt++++rl ++ + FitnessBrowser__psRCH2:GFF62 89 RESNASTPLVLMGYYNPIFAYGVERFVADAKEAGVDGLIVVDLPPEHNDELCDPAQAVGIDFIRLTTPTTDDKRLPTVLNG 169 ********************************************************************************* PP TIGR00262 163 seGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAlvkiieeklddeek 243 s+GfvY vsvaGvtga + e+v+e+++++k+++++Pv+vGFGi +eq+ ++ l +dgv+vGsAl++ i+ + ++ FitnessBrowser__psRCH2:GFF62 170 SSGFVYYVSVAGVTGAGSATMEHVEEAVARLKRHTDIPVCVGFGIRTPEQAAAIARL-TDGVVVGSALIDQIASAKS-PQD 248 *******************************************************99.9*************99854.555 PP TIGR00262 244 ale 246 a+e FitnessBrowser__psRCH2:GFF62 249 AVE 251 555 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (269 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: 16.98 // [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