Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate RR42_RS14350 RR42_RS14350 tryptophan synthase alpha chain
Query= uniprot:H0BV16 (269 letters) >FitnessBrowser__Cup4G11:RR42_RS14350 Length = 265 Score = 329 bits (843), Expect = 4e-95 Identities = 168/269 (62%), Positives = 207/269 (76%), Gaps = 4/269 (1%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 MSRI +TF+AL AQ +K LIP++TAG P +T ALMH +V GADVIELGVPFSDPMAD Sbjct: 1 MSRIKTTFAALAAQNKKGLIPFITAGDPEPGLTVALMHALVAGGADVIELGVPFSDPMAD 60 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 GPVIQ+A E+AL+ G+ + +VL V EFR+ N TPVVLMGYANP+ER GE F + Sbjct: 61 GPVIQRASERALAQGVTLTKVLAWVAEFRQTNAATPVVLMGYANPIERM----GEETFAK 116 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 + AAGVDGVL+VDYPPEECE+FAA +RA+ MD IFLLAPTSTD+R+ VA++ASGY+YY Sbjct: 117 AARAAGVDGVLVVDYPPEECESFAAQMRANEMDPIFLLAPTSTDDRIEAVAKLASGYLYY 176 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 VSLKGVTGS +D +V +P I++H +PVGVGFGIRDA TA+ IG VADAVVIGSR+ Sbjct: 177 VSLKGVTGSATIDLDSVAARIPLIKRHANLPVGVGFGIRDAQTARTIGSVADAVVIGSRL 236 Query: 241 IQLIEDQEHAKVVPLTIDFLRGIRKALDA 269 +QL+ED + V F+ IR+ALDA Sbjct: 237 VQLLEDAPRGQAVQSLQSFIAEIRQALDA 265 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: 237 Number of extensions: 10 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: 265 Length adjustment: 25 Effective length of query: 244 Effective length of database: 240 Effective search space: 58560 Effective search space used: 58560 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 RR42_RS14350 RR42_RS14350 (tryptophan synthase alpha chain)
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.7896.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5e-79 250.8 0.1 5.7e-79 250.6 0.1 1.0 1 lcl|FitnessBrowser__Cup4G11:RR42_RS14350 RR42_RS14350 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Cup4G11:RR42_RS14350 RR42_RS14350 tryptophan synthase alpha chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 250.6 0.1 5.7e-79 5.7e-79 1 255 [. 8 259 .. 8 260 .. 0.98 Alignments for each domain: == domain 1 score: 250.6 bits; conditional E-value: 5.7e-79 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f++l ++++k ++pF+tagdP+ ++ +++ lv Gad++ElGvpfsDP+aDGp+iq+a+ RAl++gv lcl|FitnessBrowser__Cup4G11:RR42_RS14350 8 FAALAAQNKKGLIPFITAGDPEPGLTVALMHALVAGGADVIELGVPFSDPMADGPVIQRASERALAQGV 76 6788999************************************************************** PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 +++k+l+ ++++r+++ + P+vl+ y+n+i ++g+e+F + a++agvdgvlv+D P ee +++ + + lcl|FitnessBrowser__Cup4G11:RR42_RS14350 77 TLTKVLAWVAEFRQTNAATPVVLMGYANPIERMGEETFAKAARAAGVDGVLVVDYPPEECESFAAQMRA 145 ********************************************************************* PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 +++++ifl aPt+ ++r++++a+ ++G+ Y vs Gvtg + ++v + i +k++++ Pv vGFGi lcl|FitnessBrowser__Cup4G11:RR42_RS14350 146 NEMDPIFLLAPTSTDDRIEAVAKLASGYLYYVSLKGVTGSATIDLDSVAARIPLIKRHANLPVGVGFGI 214 ******************************************9999*********************** PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkel 255 ++ ++++ ++ ad+v++Gs lv+++e+ + +a+++l++f+ e+ lcl|FitnessBrowser__Cup4G11:RR42_RS14350 215 RDAQTARTIGSV-ADAVVIGSRLVQLLEDA--PRGQAVQSLQSFIAEI 259 ***999999999.899*************9..789********99876 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (265 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: 5.90 // [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