Align threonine synthase (EC 4.2.3.1) (characterized)
to candidate WP_026607323.1 METAC_RS0112695 threonine synthase
Query= BRENDA::Q8YFS0 (463 letters) >NCBI__GCF_000427445.1:WP_026607323.1 Length = 472 Score = 549 bits (1415), Expect = e-161 Identities = 281/464 (60%), Positives = 337/464 (72%), Gaps = 2/464 (0%) Query: 1 MKYVSTRGEAPVLGFSDALLAGLARDGGLYLPQEYPQFTAEQIRALRGKSYVEVALAVLT 60 M+Y+STRGEAP L F++ LLAGLA+DGGLYLP+ YP A++I GK Y +VALAV++ Sbjct: 1 MRYISTRGEAPPLSFTETLLAGLAQDGGLYLPETYPSLGADEIAGFAGKPYADVALAVIS 60 Query: 61 PFTGGEIPAADFERMVREAYGTFRHDAVCPLVQTDANEFVLELFHGPTLAFKDVAMQLLA 120 PF GEI RM+ EAY FRH AV PL Q D+N F LELFHGPTLAFKDVAMQLLA Sbjct: 61 PFVAGEIETGALRRMIEEAYAGFRHPAVAPLAQIDSNLFALELFHGPTLAFKDVAMQLLA 120 Query: 121 RMMDYVLAQRGERATIVGATSGDTGGAAIEAFGGRDNTDIFILFPNGRVSPVQQRQMTSS 180 R++D+ L RG+RATIVGATSGDTG AAIEAF G D D+FIL+P+GRVS VQ+RQMT+ Sbjct: 121 RLIDHALKARGQRATIVGATSGDTGAAAIEAFRGLDQVDVFILYPHGRVSDVQRRQMTTV 180 Query: 181 GFSNVHALSIEGNFDDCQNLVKGMFNDLEFCDALSLSGVNSINWARIMPQVVYYFTAALS 240 NVHA+++EGNFDD Q VK MFN F D L GVNSINWARI+ Q VYYFT+A Sbjct: 181 AADNVHAIALEGNFDDAQARVKAMFNHRAFRDEFGLCGVNSINWARIVAQTVYYFTSAAV 240 Query: 241 LGAPDRAVSFTVPTGNFGDIFAGYVAKRMGLPIEQLIIATNDNDILSRTLESGAYEMRGV 300 LG P R VSF PTGNFGDIFAG++AKRMGLPI++LIIA N NDIL R L S +Y + V Sbjct: 241 LGGPLRPVSFATPTGNFGDIFAGWIAKRMGLPIDRLIIAANANDILPRALASASYALGEV 300 Query: 301 AQTTSPSMDIQISSNFERLLFEAHGRDAAAVRGLMQGLKQSGGFTISEKPLSAIRSEFSA 360 T SPSMDIQ+SSNFERLLFEA+GRD AVRG M L QSG F+I PL+AIRSEF A Sbjct: 301 QATQSPSMDIQVSSNFERLLFEAYGRDPRAVRGKMASLLQSGAFSIDRGPLAAIRSEFDA 360 Query: 361 GRSTVDETAATIESVLSKDGYLLDPHSAIGVKVAR--EKASGTAPMVVLATAHPAKFPDA 418 + ET I + GYL+DPH+A+G++ AR + P +VLATAHPAKFPDA Sbjct: 361 FSTGEAETTQEIGNTWRGSGYLVDPHTAVGLRAARLAQPRDPLIPHIVLATAHPAKFPDA 420 Query: 419 VKAACGVEPQLPAWLCDLMQRKESFTVLHNELKIVEEYVRHHSR 462 ++ A G P LPA L DL++R E F+V+ N+ VE ++R +R Sbjct: 421 IERATGARPGLPAHLSDLLERDERFSVVANDQSEVERFIRARAR 464 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: 571 Number of extensions: 14 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: 472 Length adjustment: 33 Effective length of query: 430 Effective length of database: 439 Effective search space: 188770 Effective search space used: 188770 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_026607323.1 METAC_RS0112695 (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.18609.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 4.6e-82 261.8 0.0 6e-82 261.5 0.0 1.0 1 lcl|NCBI__GCF_000427445.1:WP_026607323.1 METAC_RS0112695 threonine syntha Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000427445.1:WP_026607323.1 METAC_RS0112695 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 261.5 0.0 6e-82 6e-82 17 334 .. 74 427 .. 64 432 .. 0.90 Alignments for each domain: == domain 1 score: 261.5 bits; conditional E-value: 6e-82 TIGR00260 17 dlaegstelfrspkla..eevgaenlyvkelfhgPtlaFKDrglqfvavlltkalelgne..tvlcAts 81 ++e ++ fr p++a +++ + nl+ +elfhgPtlaFKD+++q +a l+ +al++ + t+++Ats lcl|NCBI__GCF_000427445.1:WP_026607323.1 74 RMIEEAYAGFRHPAVAplAQIDS-NLFALELFHGPTLAFKDVAMQLLARLIDHALKARGQraTIVGATS 141 6778899999***9997788888.*****************************988655456******* PP TIGR00260 82 GdtgaaaaealagkanvkvvvLyPkgkispv.keklvtalaenakvlaikGdFDdaqdlvkeifedke. 148 Gdtgaaa+ea++g v+v++LyP+g++s v +++t+ a n++ +a +G+FDdaq+ vk++f+++ lcl|NCBI__GCF_000427445.1:WP_026607323.1 142 GDTGAAAIEAFRGLDQVDVFILYPHGRVSDVqRRQMTTVAADNVHAIALEGNFDDAQARVKAMFNHRAf 210 *******************************99********************************7777 PP TIGR00260 149 ..klklnsvNsinparieaqktyafeiveqlgkespdkvvvpvpsgnfgailkGflekkelglpiekla 215 + +l vNsin+ari aq +y+f ++ lg+ v ++ p gnfg+i++G+ +k+++ lpi+ l lcl|NCBI__GCF_000427445.1:WP_026607323.1 211 rdEFGLCGVNSINWARIVAQTVYYFTSAAVLGGP-LRPVSFATPTGNFGDIFAGWIAKRMG-LPIDRLI 277 88******************************54.567****************9999999.******* PP TIGR00260 216 iaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnledlke.......... 274 iaa+ + di++r l s e ++T s++mdi +sn+er+l+ a+ + + k lcl|NCBI__GCF_000427445.1:WP_026607323.1 278 IAANAN-DILPRALASASYALGEVQATQSPSMDIQVSSNFERLLFEAYGRDPRAVRGKMasllqsgafs 345 **9998.**********88889999******************9844433333322222556669**** PP TIGR00260 275 ................svsdeeileaikklaeeegyllephtavavaalkklvekg......vsatadp 321 s ++e++++i + + gyl++phtav+++a + + v ata+p lcl|NCBI__GCF_000427445.1:WP_026607323.1 346 idrgplaairsefdafSTGEAETTQEIGNTWRGSGYLVDPHTAVGLRAARLAQPRDpliphiVLATAHP 414 ***************9999*****************************9887777787765444***** PP TIGR00260 322 aKFeevvealtgn 334 aKF++++e+ tg lcl|NCBI__GCF_000427445.1:WP_026607323.1 415 AKFPDAIERATGA 427 *******998886 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (472 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: 00:00:00.01 # Mc/sec: 13.00 // [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