Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_086508981.1 BZY95_RS05575 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_002151265.1:WP_086508981.1 Length = 464 Score = 458 bits (1179), Expect = e-133 Identities = 250/467 (53%), Positives = 319/467 (68%), Gaps = 10/467 (2%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 M+Y+STRG+AP L F + +L G+A DGGLY+P+ PQ + E++ + G SY EVA V+ Sbjct: 1 MRYISTRGQAPALSFEEVVLTGMASDGGLYVPETIPQLSREELAGMAGLSYAEVAFRVMR 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PF GEI F +VR+AY TF HDAV PL Q DAN F+LELFHGPTLAFKDVA+QLL Sbjct: 61 PFVNGEIDDETFRGIVRDAYATFSHDAVVPLNQLDANHFLLELFHGPTLAFKDVALQLLG 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R++D+ LA+RGERA I+GATSGDTG AAIE DN DIFIL P+ RVS VQ+RQMTS Sbjct: 121 RILDHFLAKRGERAVIMGATSGDTGSAAIEGCRHCDNLDIFILHPHNRVSEVQRRQMTSV 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 NV ++IEGNFDD Q +VK F D F L VNSINWARIM Q+VYY A ++ Sbjct: 181 LADNVFNIAIEGNFDDAQAMVKASFADQGFLGGTRLVAVNSINWARIMAQIVYYVAAGVA 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LGAP R VSF VP+ NFG++FAGY+A RMGLP++Q IIATN NDIL RT+ + + + Sbjct: 241 LGAPHRQVSFCVPSANFGNVFAGYMAYRMGLPVKQFIIATNANDILHRTIADNDFSKQEL 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 T +PSMDI +SSNFERLLFEA+ RD AAV L+ G QS ++E PL +R+ F++ Sbjct: 301 KATLAPSMDIVVSSNFERLLFEAYERDGAAVAALL-GRFQSEPTALAEAPLERLRALFAS 359 Query: 361 GRSTVDETAATIESVLSKDGY----LLDPHSAIGVKVA-REKASGTAPMVVLATAHPAKF 415 +VD+ ATI V+ + + +LDPH+A G + A R +A PM+ LATAHPAKF Sbjct: 360 --HSVDD--ATILEVIREAHHRTKEVLDPHTATGYRAAERARADAETPMITLATAHPAKF 415 Query: 416 PDAVKAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSR 462 +AV A LP + DL++R+E +TVL EL V+ +V + R Sbjct: 416 AEAVVKAGFPGVPLPPHMDDLLEREERYTVLPAELAKVQAFVAENRR 462 Lambda K H 0.320 0.135 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: 534 Number of extensions: 22 Number of successful extensions: 3 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: 463 Length of database: 464 Length adjustment: 33 Effective length of query: 430 Effective length of database: 431 Effective search space: 185330 Effective search space used: 185330 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: 51 (24.3 bits)
Align candidate WP_086508981.1 BZY95_RS05575 (threonine synthase)
to HMM TIGR00260 (thrC: threonine synthase (EC 4.2.3.1))
# 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/TIGR00260.hmm # target sequence database: /tmp/gapView.11413.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR00260 [M=340] Accession: TIGR00260 Description: thrC: threonine synthase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.1e-81 258.7 0.1 7.3e-81 257.9 0.1 1.3 1 lcl|NCBI__GCF_002151265.1:WP_086508981.1 BZY95_RS05575 threonine synthase Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_002151265.1:WP_086508981.1 BZY95_RS05575 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 257.9 0.1 7.3e-81 7.3e-81 22 329 .. 79 420 .. 64 423 .. 0.91 Alignments for each domain: == domain 1 score: 257.9 bits; conditional E-value: 7.3e-81 TIGR00260 22 stelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAtsGdtga 86 +++f +++ +++ a n +++elfhgPtlaFKD++lq ++ +l ++l + e ++++AtsGdtg+ lcl|NCBI__GCF_002151265.1:WP_086508981.1 79 AYATFSHDAVVplNQLDA-NHFLLELFHGPTLAFKDVALQLLGRILDHFLAKRGEraVIMGATSGDTGS 146 678888888877788888.9****************************987655556************ PP TIGR00260 87 aaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke...klk 151 aa+e+ + n+++++L P+ ++s v +++ +la n+ +ai+G+FDdaq++vk+ f d+ + lcl|NCBI__GCF_002151265.1:WP_086508981.1 147 AAIEGCRHCDNLDIFILHPHNRVSEVqRRQMTSVLADNVFNIAIEGNFDDAQAMVKASFADQGflgGTR 215 **************************99*******************************977779999* PP TIGR00260 152 lnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpieklaiaaeg 220 l++vNsin+ari aq++y+ + +lg +v + vps+nfg++++G+++++++ lp+ k +i a++ lcl|NCBI__GCF_002151265.1:WP_086508981.1 216 LVAVNSINWARIMAQIVYYVAAGVALG-APHRQVSFCVPSANFGNVFAGYMAYRMG-LPV-KQFIIATN 281 ****************99999999999.78889**********************9.**5.55666666 PP TIGR00260 221 aadivrrflksgdlepkedkeTlstAmdignpsnverale.larrslgnledlke.............. 274 a+di++r + + d++++e k+Tl+++mdi +sn+er+l+ + +r ++ + +l lcl|NCBI__GCF_002151265.1:WP_086508981.1 282 ANDILHRTIADNDFSKQELKATLAPSMDIVVSSNFERLLFeAYERDGAAVAAL-Lgrfqseptalaeap 349 66*************************************96666666677776.358************ PP TIGR00260 275 ...........svsdeeileaikklaeeegyllephtavavaalkklvekg...vs..atadpaKFeev 327 sv d+ ile i+++ ++ + +l+phta++++a ++ ++ + ata+paKF+e+ lcl|NCBI__GCF_002151265.1:WP_086508981.1 350 lerlralfashSVDDATILEVIREAHHRTKEVLDPHTATGYRAAERARADAetpMItlATAHPAKFAEA 418 **********************************************999886551157**********9 PP TIGR00260 328 ve 329 v+ lcl|NCBI__GCF_002151265.1:WP_086508981.1 419 VV 420 96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (464 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: 0.00u 0.00s 00:00:00.00 Elapsed: 00:00:00.01 # Mc/sec: 11.41 // [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