Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate Ga0059261_0239 Ga0059261_0239 tryptophan synthase, alpha chain (EC 4.2.1.20)
Query= uniprot:M4NLA4 (266 letters) >FitnessBrowser__Korea:Ga0059261_0239 Length = 266 Score = 214 bits (544), Expect = 2e-60 Identities = 120/263 (45%), Positives = 159/263 (60%), Gaps = 5/263 (1%) Query: 1 MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60 M+R+ FAA A +R L+ FVTAGD A++ ALV GAD+IELG+PF+DPMAD Sbjct: 1 MTRLTSAFAAAVAQHRATLVTFVTAGDGDT---AAILDALVAGGADVIELGMPFTDPMAD 57 Query: 61 GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120 GP IQ A+ R++AKG ADVL AAFRQ D P+VLMGY N + FA +A + Sbjct: 58 GPAIQAANLRSLAKGTRTADVLAIAAAFRQRHPDVPLVLMGYANTMTRPTPGAFAQKAGE 117 Query: 121 AGVDGVLLVDCPLEESAVLQPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFAG 180 AG+DG ++VD P EE+ + P G+ I LA PTT+ R+ + A GF+YYVS AG Sbjct: 118 AGIDGTIIVDIPPEEADEIAPFAAHGIATIRLATPTTDAGRLPAVLSGATGFVYYVSVAG 177 Query: 181 ITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRLA 240 ITG + I A VA ++A PVAVGFG+R A AI AD VV+GSA++D + Sbjct: 178 ITGLQQAAQDSIEAAVAKLKAATDLPVAVGFGVRTPEQAAAIGRVADGVVVGSAIIDLI- 236 Query: 241 GATDAGEITRRTQAFLAPIRAAL 263 A + + Q ++ + AAL Sbjct: 237 -AANGADAPAAVQTYIQSLSAAL 258 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: 235 Number of extensions: 9 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: 266 Length adjustment: 25 Effective length of query: 241 Effective length of database: 241 Effective search space: 58081 Effective search space used: 58081 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 Ga0059261_0239 Ga0059261_0239 (tryptophan synthase, alpha chain (EC 4.2.1.20))
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.10478.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-71 225.7 0.9 2.6e-71 225.5 0.9 1.0 1 lcl|FitnessBrowser__Korea:Ga0059261_0239 Ga0059261_0239 tryptophan syntha Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Korea:Ga0059261_0239 Ga0059261_0239 tryptophan synthase, alpha chain (EC 4.2.1.20) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 225.5 0.9 2.6e-71 2.6e-71 6 245 .. 13 247 .. 8 258 .. 0.93 Alignments for each domain: == domain 1 score: 225.5 bits; conditional E-value: 2.6e-71 TIGR00262 6 kkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkveka 74 +++ ++v+Fvtagd d ++ i++ lv Gad++ElG+pf DP+aDGp+iqaa+lR l++g++++++ lcl|FitnessBrowser__Korea:Ga0059261_0239 13 AQHRATLVTFVTAGDGD---TAAILDALVAGGADVIELGMPFTDPMADGPAIQAANLRSLAKGTRTADV 78 567789*********87...567999******************************************* PP TIGR00262 75 lellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkq 143 l++++++r++++++P+vl+ y+n + + +F +ka eag+dg +++D+P eead++ a hg+++ lcl|FitnessBrowser__Korea:Ga0059261_0239 79 LAIAAAFRQRHPDVPLVLMGYANTMTRPTPGAFAQKAGEAGIDGTIIVDIPPEEADEIAPFA-AHGIAT 146 *********************************************************98876.69**** PP TIGR00262 144 iflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeq 212 i l++Pt++ rl ++ + ++GfvY vsvaG+tg ++ ++++++++++k+ka ++ Pv+vGFG+ +eq lcl|FitnessBrowser__Korea:Ga0059261_0239 147 IRLATPTTDAGRLPAVLSGATGFVYYVSVAGITGLQQAAQDSIEAAVAKLKAATDLPVAVGFGVRTPEQ 215 ********************************************************************* PP TIGR00262 213 vkelkelgadgvivGsAlvkiieeklddeekal 245 + ++ + adgv+vGsA++++i+ + d +a+ lcl|FitnessBrowser__Korea:Ga0059261_0239 216 AAAIGRV-ADGVVVGSAIIDLIAANGADAPAAV 247 *999998.9*************99855443333 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (266 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: 8.67 // [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