Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate 7024323 Shewana3_1515 tryptophan synthase subunit alpha (RefSeq)
Query= uniprot:H0BV16 (269 letters) >FitnessBrowser__ANA3:7024323 Length = 278 Score = 162 bits (411), Expect = 6e-45 Identities = 97/267 (36%), Positives = 150/267 (56%), Gaps = 7/267 (2%) Query: 3 RIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMADGP 62 R + FS L+A+GR A +P+VT G P +++ ++ +V+ GAD +ELG PFSDP+ADGP Sbjct: 15 RYHAAFSRLKAEGRGAFVPFVTLGDPSPELSLKIIDTLVQNGADALELGFPFSDPLADGP 74 Query: 63 VIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVRDS 122 VIQ A +AL+ G Q + + + R + P+ L+ YAN V +G AF + Sbjct: 75 VIQGANLRALAAGTTPTQCFNLLAQIRAKYPELPIGLLLYANLV----FANGIDAFYAKA 130 Query: 123 AAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYYVS 182 AGVD VLI D P EE F + +AHG+ IF+ P + E + +V++ GY Y +S Sbjct: 131 QQAGVDSVLIADVPVEEAAPFIQAAKAHGIAPIFIAPPNADSETLEKVSQSGEGYTYLLS 190 Query: 183 LKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKV-ADAVVIGSRII 241 GVTG+ VE++L +++ P +GFGI + A A K A + GS ++ Sbjct: 191 RAGVTGTDTKAGTPVEEILAKLQAFNAPPPLLGFGIAEPAQVSAAIKAGAAGAISGSAVV 250 Query: 242 QLIE--DQEHAKVVPLTIDFLRGIRKA 266 ++IE Q+ AK++ +F R ++ A Sbjct: 251 KIIEAHQQDEAKLLSTLGEFTRAMKAA 277 Lambda K H 0.321 0.137 0.389 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: 13 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: 269 Length of database: 278 Length adjustment: 25 Effective length of query: 244 Effective length of database: 253 Effective search space: 61732 Effective search space used: 61732 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 (21.8 bits) S2: 47 (22.7 bits)
Align candidate 7024323 Shewana3_1515 (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.5522.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.3e-104 333.8 0.0 2.6e-104 333.6 0.0 1.0 1 lcl|FitnessBrowser__ANA3:7024323 Shewana3_1515 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__ANA3:7024323 Shewana3_1515 tryptophan synthase subunit alpha (RefSeq) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 333.6 0.0 2.6e-104 2.6e-104 1 256 [] 20 275 .. 20 275 .. 0.99 Alignments for each domain: == domain 1 score: 333.6 bits; conditional E-value: 2.6e-104 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekalel 77 f lk+++ afvpFvt+gdP+ e sl+ii+tlv++GadalElG+pfsDPlaDGp+iq a+lRAl+ag++++++++l lcl|FitnessBrowser__ANA3:7024323 20 FSRLKAEGRGAFVPFVTLGDPSPELSLKIIDTLVQNGADALELGFPFSDPLADGPVIQGANLRALAAGTTPTQCFNL 96 6789999********************************************************************** PP TIGR00262 78 lkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPtaeee 154 l+++r+k+++ Pi+ll+y+nl+f++g+++Fyaka++agvd+vl+aD+P+eea+ +++aak hg+++if+++P+a++e lcl|FitnessBrowser__ANA3:7024323 97 LAQIRAKYPELPIGLLLYANLVFANGIDAFYAKAQQAGVDSVLIADVPVEEAAPFIQAAKAHGIAPIFIAPPNADSE 173 ***************************************************************************** PP TIGR00262 155 rlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvivGsAlv 231 +l+k+++++eG++Yl+s+aGvtg+ +++ + v+e+++k++a+++ P l+GFGi+++ qv +++++ga+g+i+GsA+v lcl|FitnessBrowser__ANA3:7024323 174 TLEKVSQSGEGYTYLLSRAGVTGTDTKAGTPVEEILAKLQAFNAPPPLLGFGIAEPAQVSAAIKAGAAGAISGSAVV 250 ***************************************************************************** PP TIGR00262 232 kiieeklddeekaleeleefvkelk 256 kiie + +de k+l l ef++++k lcl|FitnessBrowser__ANA3:7024323 251 KIIEAHQQDEAKLLSTLGEFTRAMK 275 **********************997 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (278 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 0.01s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 6.97 // [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