Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate PP_0082 PP_0082 tryptophan synthase alpha chain
Query= uniprot:H0BV16 (269 letters) >FitnessBrowser__Putida:PP_0082 Length = 269 Score = 226 bits (575), Expect = 5e-64 Identities = 124/271 (45%), Positives = 167/271 (61%), Gaps = 9/271 (3%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 MSR+ F+ L+A+GR AL+ +VTAG P D + ++ G+ AGADVIELG+PF+DPMAD Sbjct: 1 MSRLEQRFAELKAEGRSALVTFVTAGDPGYDASLQILKGLPAAGADVIELGMPFTDPMAD 60 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 G IQ A +AL G +V+ L VREFR N TTP+VLMGY NP+ R+ G FV Sbjct: 61 GVAIQLATLRALEAGQTLVKTLQMVREFRVDNQTTPIVLMGYYNPIHRF----GVDTFVT 116 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 + AGVDG++IVD PPE A +A G+D I L PT+ D R+ V +SG+VYY Sbjct: 117 QAKEAGVDGLIIVDLPPEHDAELATPAQAAGIDFIRLTTPTTDDARLPRVLERSSGFVYY 176 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 VS+ GVTG+G+ T V + + R+R+H +P+ VGFGIR A I ++AD VV+GS + Sbjct: 177 VSVAGVTGAGSATTEHVTEAIARLRRHTDLPISVGFGIRTPEQAANIARLADGVVVGSAL 236 Query: 241 IQLI-----EDQEHAKVVPLTIDFLRGIRKA 266 + I DQ V+ L G+R A Sbjct: 237 VDKIAQAKSADQAVTDVLSLCSALAEGVRGA 267 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: 243 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: 269 Length adjustment: 25 Effective length of query: 244 Effective length of database: 244 Effective search space: 59536 Effective search space used: 59536 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 PP_0082 PP_0082 (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.20721.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.1e-86 275.9 0.0 1.2e-86 275.7 0.0 1.0 1 lcl|FitnessBrowser__Putida:PP_0082 PP_0082 tryptophan synthase alph Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Putida:PP_0082 PP_0082 tryptophan synthase alpha chain # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 275.7 0.0 1.2e-86 1.2e-86 1 252 [. 8 257 .. 8 261 .. 0.96 Alignments for each domain: == domain 1 score: 275.7 bits; conditional E-value: 1.2e-86 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkvekal 75 f++lk+++ a+v+FvtagdP ++ sl+i+k l aGad++ElG+pf DP+aDG +iq a+lRAl+ag ++ k+l lcl|FitnessBrowser__Putida:PP_0082 8 FAELKAEGRSALVTFVTAGDPGYDASLQILKGLPAAGADVIELGMPFTDPMADGVAIQLATLRALEAGQTLVKTL 82 7899*********************************************************************** PP TIGR00262 76 ellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgvkqiflvaPt 150 ++++++r ++++ Pivl+ yyn+i++ gv++F+++akeagvdg++++DlP e ++l a+ g++ i l +Pt lcl|FitnessBrowser__Putida:PP_0082 83 QMVREFRVDNQTTPIVLMGYYNPIHRFGVDTFVTQAKEAGVDGLIIVDLPPEHDAELATPAQAAGIDFIRLTTPT 157 *************************************************************************** PP TIGR00262 151 aeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskkeqvkelkelgadgvi 225 +++ rl ++ e+s+GfvY vsvaGvtga + +e+v+e+i++++++++ P+ vGFGi +eq+ ++ l adgv+ lcl|FitnessBrowser__Putida:PP_0082 158 TDDARLPRVLERSSGFVYYVSVAGVTGAGSATTEHVTEAIARLRRHTDLPISVGFGIRTPEQAANIARL-ADGVV 231 *********************************************************************.99*** PP TIGR00262 226 vGsAlvkiieeklddeekaleeleefv 252 vGsAlv++i++ + ++a+ ++ +++ lcl|FitnessBrowser__Putida:PP_0082 232 VGSALVDKIAQAKS-ADQAVTDVLSLC 257 ***********965.666666666655 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (269 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: 00:00:00.00 # Mc/sec: 9.48 // [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