Align Tryptophan synthase alpha chain; EC 4.2.1.20 (characterized, see rationale)
to candidate WP_009567136.1 AFE_RS09545 tryptophan synthase subunit alpha
Query= uniprot:M4NLA4 (266 letters) >NCBI__GCF_000021485.1:WP_009567136.1 Length = 272 Score = 248 bits (633), Expect = 1e-70 Identities = 140/266 (52%), Positives = 170/266 (63%), Gaps = 5/266 (1%) Query: 1 MSRIDRRFAALKAANRTGLIPFVTAGDPSPEHMVALMHALVDAGADLIELGVPFSDPMAD 60 MSR+ F L+ A R LIPF+TAGDPS V LMHALV AGAD IELG+PFSDPMAD Sbjct: 1 MSRLAGLFVQLRDAGRAALIPFMTAGDPSLTATVPLMHALVAAGADAIELGMPFSDPMAD 60 Query: 61 GPVIQHASERAIAKGVGLADVLGWVAAFRQHDADTPIVLMGYLNPIETHGYARFAGEAVQ 120 GP IQ ASERA+A+GV L VL WV FR ++ TP++LMGYLNP+E G FA A Sbjct: 61 GPSIQRASERALARGVKLRMVLEWVREFRTTNSHTPVILMGYLNPVEAMGITSFAEAAAT 120 Query: 121 AGVDGVLLVDCPLEE---SAVLQPLRDAGLQRILLAAPTTEPSRMAQLCGSAEGFLYYVS 177 AGVDGV+LVD EE AV+ LR G+ I L APT+ P R+A + GF+YYVS Sbjct: 121 AGVDGVILVDLTPEEGRGEAVV--LRQRGIDPIFLLAPTSGPERVATVRSMGSGFVYYVS 178 Query: 178 FAGITGAAHLSTGDIAARVADVRARAKAPVAVGFGIRDAASAKAIAGFADAVVIGSALVD 237 GITGAA ++ RV + + PVA+GFGIRDAA+ +A ADAVV+GSALVD Sbjct: 179 LRGITGAAQADWAEVLERVQHLHRQLGLPVAIGFGIRDAATVARVATGADAVVVGSALVD 238 Query: 238 RLAGATDAGEITRRTQAFLAPIRAAL 263 +LA E F+ P+ A+ Sbjct: 239 QLAACATDQEAIAAAIRFVEPLAQAV 264 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: 226 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: 266 Length of database: 272 Length adjustment: 25 Effective length of query: 241 Effective length of database: 247 Effective search space: 59527 Effective search space used: 59527 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_009567136.1 AFE_RS09545 (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.23953.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.9e-72 229.2 0.0 2.2e-72 229.0 0.0 1.0 1 lcl|NCBI__GCF_000021485.1:WP_009567136.1 AFE_RS09545 tryptophan synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000021485.1:WP_009567136.1 AFE_RS09545 tryptophan synthase subunit alpha # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 229.0 0.0 2.2e-72 2.2e-72 1 249 [. 8 255 .. 8 261 .. 0.96 Alignments for each domain: == domain 1 score: 229.0 bits; conditional E-value: 2.2e-72 TIGR00262 1 fetlkkkeekafvpFvtagdPdleksleiiktlvkaGadalElGvpfsDPlaDGptiqaaelRAlkagv 69 f +l++++ a++pF+tagdP+l ++ +++ lv aGada+ElG+pfsDP+aDGp+iq+a+ RAl++gv lcl|NCBI__GCF_000021485.1:WP_009567136.1 8 FVQLRDAGRAALIPFMTAGDPSLTATVPLMHALVAAGADAIELGMPFSDPMADGPSIQRASERALARGV 76 567899999************************************************************ PP TIGR00262 70 kvekalellkkvrekasniPivlltyynlifkkgveeFyakakeagvdgvlvaDlPleeaddlleaakk 138 k++ +le ++++r ++s+ P++l+ y n++ ++g+ +F + a+ agvdgv+++Dl ee + ++ lcl|NCBI__GCF_000021485.1:WP_009567136.1 77 KLRMVLEWVREFRTTNSHTPVILMGYLNPVEAMGITSFAEAAATAGVDGVILVDLTPEEGRGEAVVLRQ 145 ***********************************************************999999**** PP TIGR00262 139 hgvkqiflvaPtaeeerlkkiaekseGfvYlvsvaGvtgarerveeevkelikkvkalskkPvlvGFGi 207 +g+++ifl aPt+ +er+ ++ + ++GfvY vs G+tga + +ev e ++++++ Pv++GFGi lcl|NCBI__GCF_000021485.1:WP_009567136.1 146 RGIDPIFLLAPTSGPERVATVRSMGSGFVYYVSLRGITGAAQADWAEVLERVQHLHRQLGLPVAIGFGI 214 ******************************************99999********************** PP TIGR00262 208 skkeqvkelkelgadgvivGsAlvkiieeklddeekaleele 249 + v ++ +gad+v+vGsAlv+ ++ d+e++ ++++ lcl|NCBI__GCF_000021485.1:WP_009567136.1 215 RDAATVARVA-TGADAVVVGSALVDQLAACATDQEAIAAAIR 255 ******9986.68***************99888887777764 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (256 nodes) Target sequences: 1 (272 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: 9.75 // [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