Align Threonine synthase; TS; EC 4.2.3.1 (uncharacterized)
to candidate WP_005454968.1 SACCYDRAFT_RS07335 threonine synthase
Query= curated2:Q58860 (405 letters) >NCBI__GCF_000244975.1:WP_005454968.1 Length = 420 Score = 248 bits (634), Expect = 2e-70 Identities = 138/358 (38%), Positives = 210/358 (58%), Gaps = 10/358 (2%) Query: 27 LEIIYDYEEIKDKVSEEKLRKREIGVWRYLEYLPVKDESKIVSLCEGG-TPLYRCNNLEK 85 LE+ YD+ +V E + +WRY + LPV + + E G T L R + L K Sbjct: 45 LEVAYDF----GRVRREDIESGPRNIWRYKKLLPVPSNVEEIPNTEPGCTRLVRADRLAK 100 Query: 86 ELGIKELYVKNEGANPTGSFKDRGMTVGVTRANELGVEVVGCASTGNTSASLAAYSARSG 145 ELG++ L+VK++ NPT SFKDR + V + A E G + + C STGN + ++AA +AR+G Sbjct: 101 ELGVRRLWVKDDTGNPTHSFKDRVVAVALAAAREFGFDTLACPSTGNLANAVAAAAARAG 160 Query: 146 KKCIVLLPEGKVALGKLAQAMFYGAKVIQVKGNFDDALDMVKQLAKEKLIYLLNSIN--P 203 + +VL+P L A++ GA +I V GN+DD + +LA E + ++N P Sbjct: 161 WRSVVLIPSSLERAKVLTTAVYDGA-LIAVDGNYDDVNRLATELAAEHESWAFVNVNVRP 219 Query: 204 FRLEGQKTIAFEICDQLNWQVPDRVIVPVGNAGNISAIWKGFKEFEITGIIDELP-KMTG 262 + EG KT+AFE+ +QL W++P++++VP+ + ++ + KGF+E G++D ++ G Sbjct: 220 YYSEGSKTLAFEVAEQLGWRLPEQIVVPIASGSQLTKVDKGFRELGELGLVDAASYRVFG 279 Query: 263 IQADGAKPIVEAFRKRAKDIIPYKNPETIATAIRIGNPVNAPKALDAIYSSGGYAEAVTD 322 QA G P+ AFR D++ P+TIA ++ IGNP + P LD + +GG V+D Sbjct: 280 AQATGCSPVSAAFRD-GHDVVRPVRPDTIARSLAIGNPADGPYVLDTVRRTGGAISDVSD 338 Query: 323 EEIVEAQKLLARKEGIFVEPASASSIAGLKKLLEEGIIDRDERIVCITTGHGLKDPDA 380 +E+VE +LLAR EGIF E A ++A KKLLE G +D D V + TG GLK DA Sbjct: 339 DEVVEGIRLLARTEGIFTETAGGVTVATAKKLLEAGKLDPDAETVLLITGDGLKTLDA 396 Lambda K H 0.317 0.137 0.395 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: 454 Number of extensions: 24 Number of successful extensions: 5 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: 405 Length of database: 420 Length adjustment: 31 Effective length of query: 374 Effective length of database: 389 Effective search space: 145486 Effective search space used: 145486 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 50 (23.9 bits)
Align candidate WP_005454968.1 SACCYDRAFT_RS07335 (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.20194.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-87 279.7 0.0 1.9e-87 279.5 0.0 1.0 1 lcl|NCBI__GCF_000244975.1:WP_005454968.1 SACCYDRAFT_RS07335 threonine syn Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000244975.1:WP_005454968.1 SACCYDRAFT_RS07335 threonine synthase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 279.5 0.0 1.9e-87 1.9e-87 1 339 [. 66 394 .. 66 395 .. 0.97 Alignments for each domain: == domain 1 score: 279.5 bits; conditional E-value: 1.9e-87 TIGR00260 1 vvryreilevt..ekdlvdlaegstelfrspklaeevgaenlyvkelfhgPtlaFKDrglqfvavlltk 67 ++ry+++l+v+ +++ + + g t+l+r+++la+e+g+++l+vk++ +Pt +FKDr+ vav+l++ lcl|NCBI__GCF_000244975.1:WP_005454968.1 66 IWRYKKLLPVPsnVEEIPNTEPGCTRLVRADRLAKELGVRRLWVKDDTGNPTHSFKDRV---VAVALAA 131 8*********9766677788999************************************...******* PP TIGR00260 68 alelgnetvlcAtsGdtgaaaaealagkanvkvvvLyPkgkispvkeklvtalaenakvlaikGdFDda 136 a+e g +t++c ++G++++a+a a a++a+ + vvL+P+ ++ k++t+ ++ ++a++G++Dd+ lcl|NCBI__GCF_000244975.1:WP_005454968.1 132 AREFGFDTLACPSTGNLANAVA-AAAARAGWRSVVLIPSS-LE--RAKVLTTAVYDGALIAVDGNYDDV 196 **********************.****************9.88..9*********************** PP TIGR00260 137 qdlvkeifedkeklklnsvNsinparieaqktyafeiveqlgkespdkvvvpvp.sgnfgailkGflek 204 ++l +e++ ++e + +++vN + p++ e++kt+afe++eqlg++ p+++vvp++ ++ ++++ kGf e+ lcl|NCBI__GCF_000244975.1:WP_005454968.1 197 NRLATELAAEHESWAFVNVN-VRPYYSEGSKTLAFEVAEQLGWRLPEQIVVPIAsGSQLTKVDKGFREL 264 ********************.55*******************************7789*********** PP TIGR00260 205 kelg....lpieklaiaaegaadivrrflksgdlepkedkeTlstAmdignpsnveralelarrslgnl 269 elg + + +++a+g++++ +f+ + d++ +++T++ +++ignp++ +++l+ +rr++g + lcl|NCBI__GCF_000244975.1:WP_005454968.1 265 GELGlvdaASYRVFGAQATGCSPVSAAFRDGHDVVRPVRPDTIARSLAIGNPADGPYVLDTVRRTGGAI 333 ****9999777999**************9999************************************* PP TIGR00260 270 edlkesvsdeeileaikklaeeegyllephtavavaalkklvekgvsatadpaKFeevvealtgnklkd 338 d+ sd+e++e i++la++eg+++e++++v+va kkl+e+g ++dp+ +e+v+ +tg +lk+ lcl|NCBI__GCF_000244975.1:WP_005454968.1 334 SDV----SDDEVVEGIRLLARTEGIFTETAGGVTVATAKKLLEAG---KLDPD--AETVLLITGDGLKT 393 ***....**************************************...*****..************98 PP TIGR00260 339 p 339 lcl|NCBI__GCF_000244975.1:WP_005454968.1 394 L 394 5 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (340 nodes) Target sequences: 1 (420 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: 12.33 // [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