Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate HSERO_RS16470 HSERO_RS16470 tryptophan synthase subunit alpha
Query= uniprot:H0BV16 (269 letters) >FitnessBrowser__HerbieS:HSERO_RS16470 Length = 265 Score = 308 bits (789), Expect = 8e-89 Identities = 157/269 (58%), Positives = 198/269 (73%), Gaps = 4/269 (1%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 MSRI +TFS L Q RKALI ++TAG P ++T L+H +V G D++ELGVPFSDPMA+ Sbjct: 1 MSRIQTTFSQLAEQKRKALITFITAGDPAPELTVPLLHALVAGGVDILELGVPFSDPMAE 60 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 GPVIQ+A E+AL GI VL +VREFRK N TP+VLMGYANP+ER+ G AF+ Sbjct: 61 GPVIQRACERALKFGISTHDVLGYVREFRKTNTHTPIVLMGYANPIERF----GVDAFIA 116 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 ++ AGVDG ++VDYPPEECE FA ++A GMD IFLLAPTS+ ER+ +VA V+SG+ YY Sbjct: 117 AASEAGVDGTIVVDYPPEECEEFAQKMQAKGMDPIFLLAPTSSQERIRQVAAVSSGFCYY 176 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 VSLKGVTG+G +DTA V + + IRQHV +P+ VGFGIRD ATA+ +G VADAVVIGSRI Sbjct: 177 VSLKGVTGAGHIDTAEVAERIAAIRQHVKLPIAVGFGIRDGATARTVGSVADAVVIGSRI 236 Query: 241 IQLIEDQEHAKVVPLTIDFLRGIRKALDA 269 I +E+ + F+ IR+ALDA Sbjct: 237 IAELENTPQDQACDAVQAFVTDIRQALDA 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: 247 Number of extensions: 7 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 HSERO_RS16470 HSERO_RS16470 (tryptophan synthase subunit alpha)
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.1739.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.2e-77 246.3 0.1 1.4e-77 246.1 0.1 1.0 1 lcl|FitnessBrowser__HerbieS:HSERO_RS16470 HSERO_RS16470 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__HerbieS:HSERO_RS16470 HSERO_RS16470 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 246.1 0.1 1.4e-77 1.4e-77 1 255 [. 8 259 .. 8 260 .. 0.97 Alignments for each domain: == domain 1 score: 246.1 bits; conditional E-value: 1.4e-77 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkag 68 f +l +++ ka+++F+tagdP e ++ +++ lv G+d+lElGvpfsDP+a+Gp+iq+a RAlk g lcl|FitnessBrowser__HerbieS:HSERO_RS16470 8 FSQLAEQKRKALITFITAGDPAPELTVPLLHALVAGGVDILELGVPFSDPMAEGPVIQRACERALKFG 75 678999************************************************************** PP TIGR00262 69 vkvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaa 136 ++++++l ++++r+++++ Pivl+ y+n+i + gv++F+a a eagvdg +v+D P ee +++ ++ lcl|FitnessBrowser__HerbieS:HSERO_RS16470 76 ISTHDVLGYVREFRKTNTHTPIVLMGYANPIERFGVDAFIAAASEAGVDGTIVVDYPPEECEEFAQKM 143 ******************************************************************** PP TIGR00262 137 kkhgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvG 204 + +g+++ifl aPt+++er++++a s+Gf Y vs Gvtga + ++ev e i+ ++++ k P++vG lcl|FitnessBrowser__HerbieS:HSERO_RS16470 144 QAKGMDPIFLLAPTSSQERIRQVAAVSSGFCYYVSLKGVTGAGHIDTAEVAERIAAIRQHVKLPIAVG 211 ******************************************************************** PP TIGR00262 205 FGiskkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkel 255 FGi ++++ ++ ad+v++Gs ++ +e++ +++a +++++fv+++ lcl|FitnessBrowser__HerbieS:HSERO_RS16470 212 FGIRDGATARTVGSV-ADAVVIGSRIIAELENT--PQDQACDAVQAFVTDI 259 ************999.899***********999..6789999999998765 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 0.00s 00:00:00.01 Elapsed: 00:00:00.06 # Mc/sec: 1.06 // [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