Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_014147966.1 MEALZ_RS07245 tryptophan synthase subunit alpha
Query= uniprot:H0BV16 (269 letters) >NCBI__GCF_000968535.2:WP_014147966.1 Length = 267 Score = 257 bits (656), Expect = 2e-73 Identities = 133/270 (49%), Positives = 181/270 (67%), Gaps = 6/270 (2%) Query: 1 MSRIASTFSALQAQGRKALIPYVTAGFPFADITPALMHGMVEAGADVIELGVPFSDPMAD 60 MSR+A+ F L GRKALIP++TAG P + T +MH MVEAG D+IELGVPFSDPMAD Sbjct: 1 MSRLAAKFDELSKSGRKALIPFLTAGDPHPNFTVPMMHAMVEAGVDIIELGVPFSDPMAD 60 Query: 61 GPVIQKAGEKALSLGIGMVQVLDHVREFRKRNNTTPVVLMGYANPVERYDQKHGEGAFVR 120 GPVIQKA E+AL+ + + +VL+ V EFR++++ TPVVLMGY NP+E G F Sbjct: 61 GPVIQKASERALAHKMSLRKVLNIVAEFRRKDDQTPVVLMGYLNPIEAM----GYEDFAN 116 Query: 121 DSAAAGVDGVLIVDYPPEECEAFAASLRAHGMDLIFLLAPTSTDERMAEVARVASGYVYY 180 + +DGVL VD PPEE + + L G+D +FLLAP S +ER+ ++ SGY+YY Sbjct: 117 AAQRVEIDGVLTVDLPPEEADFCVSLLNERGIDPVFLLAPNSNEERIRKMDAAGSGYIYY 176 Query: 181 VSLKGVTGSGALDTAAVEQMLPRIRQHVTIPVGVGFGIRDAATAQAIGKVADAVVIGSRI 240 VSLKGVTG+G L+TA VE+ L IR + +P+G+GFG++DA TA+ + + D VV+GS + Sbjct: 177 VSLKGVTGAGHLNTADVEERLKLIRANTRLPIGIGFGVKDAETAKTVAHLGDGVVVGSAL 236 Query: 241 IQLIED--QEHAKVVPLTIDFLRGIRKALD 268 I IE + +D L+ +R A+D Sbjct: 237 ISKIEANLDNPEQACSEIVDLLKAMRAAMD 266 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: 248 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: 267 Length adjustment: 25 Effective length of query: 244 Effective length of database: 242 Effective search space: 59048 Effective search space used: 59048 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 WP_014147966.1 MEALZ_RS07245 (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.11740.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.7e-83 264.7 0.0 3.1e-83 264.6 0.0 1.0 1 lcl|NCBI__GCF_000968535.2:WP_014147966.1 MEALZ_RS07245 tryptophan synthas Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000968535.2:WP_014147966.1 MEALZ_RS07245 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 264.6 0.0 3.1e-83 3.1e-83 1 256 [] 8 262 .. 8 262 .. 0.99 Alignments for each domain: == domain 1 score: 264.6 bits; conditional E-value: 3.1e-83 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f++l k++ ka++pF+tagdP+ + ++ +++ +v+aG+d++ElGvpfsDP+aDGp+iq+a+ RAl++ + lcl|NCBI__GCF_000968535.2:WP_014147966.1 8 FDELSKSGRKALIPFLTAGDPHPNFTVPMMHAMVEAGVDIIELGVPFSDPMADGPVIQKASERALAHKM 76 77899999************************************************************* PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 +++k+l++++++r+k + P+vl+ y n+i ++g e F + a+ + +dgvl +DlP eead ++ ++ lcl|NCBI__GCF_000968535.2:WP_014147966.1 77 SLRKVLNIVAEFRRKDDQTPVVLMGYLNPIEAMGYEDFANAAQRVEIDGVLTVDLPPEEADFCVSLLNE 145 ********************************************************************* PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 +g++++fl aP+++eer++k++ ++G++Y vs Gvtga + +++v+e +k ++a ++ P+ +GFG+ lcl|NCBI__GCF_000968535.2:WP_014147966.1 146 RGIDPVFLLAPNSNEERIRKMDAAGSGYIYYVSLKGVTGAGHLNTADVEERLKLIRANTRLPIGIGFGV 214 ********************************************************************* PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeekaleeleefvkelk 256 +e +k++ +lg dgv+vGsAl+ +ie +ld++e+a e+ ++ k+++ lcl|NCBI__GCF_000968535.2:WP_014147966.1 215 KDAETAKTVAHLG-DGVVVGSALISKIEANLDNPEQACSEIVDLLKAMR 262 ************6.78***************************999985 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (267 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: 8.82 // [ok]
This GapMind analysis is from Apr 10 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