Align tryptophan synthase subunit α (EC 4.1.2.8) (characterized)
to candidate 6938001 Sama_2134 tryptophan synthase subunit alpha (RefSeq)
Query= metacyc::MONOMER-3561 (251 letters) >FitnessBrowser__SB2B:6938001 Length = 266 Score = 157 bits (398), Expect = 2e-43 Identities = 84/250 (33%), Positives = 144/250 (57%), Gaps = 5/250 (2%) Query: 4 KGSLIPYLTAGDPSVEKTLEFLLA-VEEFAGLIELGIPFSDPMADGKTIQESHYRALRNG 62 +G+ +P++T GDP ++++L + A VE A +ELG PFSDP+ADG IQ ++ RAL G Sbjct: 16 RGAFVPFVTLGDPGIDESLAIIDALVEGGADCLELGFPFSDPLADGPVIQGANIRALAAG 75 Query: 63 FKLDDTFRILREFR-RHSSTPVILMTYYNPVFRTGVKKFLGEAKASGADGILVVDLPVSH 121 D F+++ + R ++ P+ L+ Y N VF G++ F AKA+G D +L+ D+P Sbjct: 76 TTPDTCFKMIEQIRAKYPELPIGLLLYANLVFANGIEAFYQRAKAAGVDSVLIADVPAEE 135 Query: 122 AGEFLDAAKEEGLKTVFLAAPNTPDERLREIDKASTGFVYLISLYGTTGARDRLPETAFE 181 + F+ AA+ EG+ +F+A PN + LR + G+ YL+S G TGA ++ Sbjct: 136 SAPFVAAARAEGIAPIFIAPPNASADTLRLVASLGEGYTYLLSRAGVTGADNKAGMPLDS 195 Query: 182 FVRRARKICNNKLAVGFGVSRREQVEELLKAGADGVVVGSALIELISRSENPVEELRRKV 241 + ++ +GFG++ QV+E + AGA G + GSA+++ R E +++ + + Sbjct: 196 VLSALKEFNAPPPLLGFGIAEPSQVQEAIAAGAAGAISGSAVVK---RIEALKDDMPKLL 252 Query: 242 AELSGYSRAL 251 EL ++ A+ Sbjct: 253 TELKSFASAM 262 Lambda K H 0.319 0.138 0.386 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: 188 Number of extensions: 8 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 251 Length of database: 266 Length adjustment: 24 Effective length of query: 227 Effective length of database: 242 Effective search space: 54934 Effective search space used: 54934 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 (21.7 bits) S2: 47 (22.7 bits)
Align candidate 6938001 Sama_2134 (tryptophan synthase subunit alpha (RefSeq))
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.8025.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.5e-99 317.3 0.0 2.9e-99 317.1 0.0 1.0 1 lcl|FitnessBrowser__SB2B:6938001 Sama_2134 tryptophan synthase su Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__SB2B:6938001 Sama_2134 tryptophan synthase subunit alpha (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 317.1 0.0 2.9e-99 2.9e-99 1 256 [] 8 263 .. 8 263 .. 0.99 Alignments for each domain: == domain 1 score: 317.1 bits; conditional E-value: 2.9e-99 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalel 77 f+ lk+ + afvpFvt+gdP +++sl ii+ lv+ Gad lElG+pfsDPlaDGp+iq a+ RAl+ag++++ ++++ lcl|FitnessBrowser__SB2B:6938001 8 FARLKAGSRGAFVPFVTLGDPGIDESLAIIDALVEGGADCLELGFPFSDPLADGPVIQGANIRALAAGTTPDTCFKM 84 678999999******************************************************************** PP TIGR00262 78 lkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeee 154 ++++r+k+++ Pi+ll+y+nl+f++g+e+Fy++ak+agvd+vl+aD+P ee++ ++ aa+ +g+++if+++P+a+ + lcl|FitnessBrowser__SB2B:6938001 85 IEQIRAKYPELPIGLLLYANLVFANGIEAFYQRAKAAGVDSVLIADVPAEESAPFVAAARAEGIAPIFIAPPNASAD 161 ***************************************************************************** PP TIGR00262 155 rlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAlv 231 +l+ +a+ +eG++Yl+s+aGvtga +++ +++++ +k++++ P l+GFGi+++ qv+e++++ga+g+i+GsA+v lcl|FitnessBrowser__SB2B:6938001 162 TLRLVASLGEGYTYLLSRAGVTGADNKAGMPLDSVLSALKEFNAPPPLLGFGIAEPSQVQEAIAAGAAGAISGSAVV 238 ***************************************************************************** PP TIGR00262 232 kiieeklddeekaleeleefvkelk 256 k+ie +dd k+l el++f++++k lcl|FitnessBrowser__SB2B:6938001 239 KRIEALKDDMPKLLTELKSFASAMK 263 *********************9997 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.26 // [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