Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_013075706.1 BTUS_RS08525 tryptophan synthase subunit alpha
Query= uniprot:M4NLA4 (266 letters) >NCBI__GCF_000092905.1:WP_013075706.1 Length = 273 Score = 182 bits (461), Expect = 9e-51 Identities = 104/260 (40%), Positives = 151/260 (58%), Gaps = 10/260 (3%) Query: 12 KAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMADGPVIQHASERA 71 + TG IPF+TAGDP+ E V + LV AGAD +E+G+P+SDP+ADGP IQ ASERA Sbjct: 13 RRGGETGFIPFITAGDPTMEVTVEAVRRLVRAGADAVEIGMPYSDPLADGPTIQAASERA 72 Query: 72 IAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQAGVDGVLLVDC 131 + G + D+ R+ + P+V Y NP+ G+ FA + +AG GV++ D Sbjct: 73 LRGGFQMPDLFRLGPILREAAGEVPLVAFTYANPVYRWGWQTFAEDLAKAGYAGVIVPDL 132 Query: 132 PLEESAVLQPLRD-AGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVSFAGITGAAHLSTG 190 P+EE+ L+ D AG+ + L APT+ R+ ++C +A GF+Y VS G+TG Sbjct: 133 PMEEATPLREAADRAGVALVPLVAPTSH-GRIERICRTARGFVYAVSSTGVTGVRKRMPE 191 Query: 191 DIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVDRLAGAT----DAG 246 ++ + D+R P+ VGFGI +A A+A ADAV++GSALV LA T DAG Sbjct: 192 HLSRFIDDIRRCTDLPIGVGFGIGTPEAAAAVAETADAVIVGSALVRILAAITEEGKDAG 251 Query: 247 EITRRTQAF----LAPIRAA 262 ++ + F +AP+R A Sbjct: 252 DVLDDLETFARTLVAPLRRA 271 Lambda K H 0.322 0.136 0.394 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: 254 Number of extensions: 9 Number of successful extensions: 1 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: 266 Length of database: 273 Length adjustment: 25 Effective length of query: 241 Effective length of database: 248 Effective search space: 59768 Effective search space used: 59768 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 (21.9 bits) S2: 47 (22.7 bits)
Align candidate WP_013075706.1 BTUS_RS08525 (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.4325.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 5.2e-84 267.1 0.0 6.1e-84 266.9 0.0 1.0 1 lcl|NCBI__GCF_000092905.1:WP_013075706.1 BTUS_RS08525 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000092905.1:WP_013075706.1 BTUS_RS08525 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 266.9 0.0 6.1e-84 6.1e-84 4 255 .. 12 264 .. 9 265 .. 0.96 Alignments for each domain: == domain 1 score: 266.9 bits; conditional E-value: 6.1e-84 TIGR00262 4 lkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagvkve 72 ++ +e+ f+pF+tagdP++e+++e+++ lv+aGada+E+G+p+sDPlaDGptiqaa+ RAl+ g+++ lcl|NCBI__GCF_000092905.1:WP_013075706.1 12 RRRGGETGFIPFITAGDPTMEVTVEAVRRLVRAGADAVEIGMPYSDPLADGPTIQAASERALRGGFQMP 80 56778999************************************************************* PP TIGR00262 73 kalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakkhgv 141 + ++l +re a ++P+v +ty+n++++ g ++F + +++ag gv+v+DlP+eea l+eaa + gv lcl|NCBI__GCF_000092905.1:WP_013075706.1 81 DLFRLGPILREAAGEVPLVAFTYANPVYRWGWQTFAEDLAKAGYAGVIVPDLPMEEATPLREAADRAGV 149 ********************************************************************* PP TIGR00262 142 kqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGiskk 210 + + lvaPt++ r+++i ++++GfvY+vs++Gvtg+r+r+ e+++++i ++++++ P+ vGFGi + lcl|NCBI__GCF_000092905.1:WP_013075706.1 150 ALVPLVAPTSH-GRIERICRTARGFVYAVSSTGVTGVRKRMPEHLSRFIDDIRRCTDLPIGVGFGIGTP 217 *********98.9******************************************************** PP TIGR00262 211 eqvkelkelgadgvivGsAlvkiieekld...deekaleeleefvkel 255 e + ++ e+ ad+vivGsAlv+i++ + d +l++le+f+++l lcl|NCBI__GCF_000092905.1:WP_013075706.1 218 EAAAAVAET-ADAVIVGSALVRILAAITEegkDAGDVLDDLETFARTL 264 ******999.899*********987665544478899*******9987 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (273 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: 00:00:00.00 # Mc/sec: 7.41 // [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