Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate SMc03797 SMc03797 homoserine O-succinyltransferase
Query= SwissProt::G4RES5 (306 letters) >FitnessBrowser__Smeli:SMc03797 Length = 331 Score = 386 bits (991), Expect = e-112 Identities = 179/307 (58%), Positives = 233/307 (75%), Gaps = 2/307 (0%) Query: 1 MPIRIPDQLPARKTLETEGVVVMDQSRSARQDIRPLQFGLLNLMPNKQRTETQFARLIAS 60 MPI+IPD LPA +TL EGV +M ++ + RQDIRPLQ GLLNLMPNK +TE Q ARLI + Sbjct: 24 MPIKIPDTLPAFETLVHEGVRLMTETEAIRQDIRPLQIGLLNLMPNKIKTEIQMARLIGA 83 Query: 61 TPLQIDLTLVRVADPLSKSTPEDYLQNFYSTWEDVRAKKFDGFVVTGAPIANMPFEDVRY 120 TPLQ++LTLVRV K+TPE++L FY T+E+V A+KFDGF++TGAPI + +E+V Y Sbjct: 84 TPLQVELTLVRVNGHRPKNTPEEHLLAFYETFEEVEARKFDGFIITGAPIETLEYEEVTY 143 Query: 121 WPEMLEIMDWTQTNVHHTMFICWGAQAALHHLHGVKRYRMEHKAFGVYRHKVLDTRHPFL 180 W E+ I DWT TNVH T+ +CWG AA++H HGV +Y ++ KAFGVYRH+ L +L Sbjct: 144 WKELQRIFDWTTTNVHSTLNVCWGGMAAVYHFHGVPKYPLKEKAFGVYRHQNLQPSSVYL 203 Query: 181 RGFSDDLAVPVSRYNDIDRQSLS--PDLDILIDSDEVGICMLDDRKYRAAYMLNHLEYDN 238 GFSDD AVPVSR+ ++ R + PDL+IL++S EVG+C++ ++K YM NH+EYD+ Sbjct: 204 NGFSDDFAVPVSRWTEVRRADIDRVPDLEILMESKEVGVCLVHEKKGNRLYMFNHVEYDS 263 Query: 239 TSLADEYHRDIEAGLDTPLPVNLFPGNDPSRMPENRWRSHAHLLFQNWINEIYQTTPYEL 298 TSL++EY RD++AG+ LP + FP ND + P+NRWRSHAHL F NWINEIYQTTPYEL Sbjct: 264 TSLSEEYFRDVDAGVPIKLPHDYFPHNDSALPPQNRWRSHAHLFFGNWINEIYQTTPYEL 323 Query: 299 EKVGTGE 305 K+GTGE Sbjct: 324 AKIGTGE 330 Lambda K H 0.321 0.137 0.431 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: 363 Number of extensions: 17 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: 306 Length of database: 331 Length adjustment: 27 Effective length of query: 279 Effective length of database: 304 Effective search space: 84816 Effective search space used: 84816 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: 48 (23.1 bits)
Align candidate SMc03797 SMc03797 (homoserine O-succinyltransferase)
to HMM TIGR01001 (metA: homoserine O-succinyltransferase (EC 2.3.1.46))
# 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/TIGR01001.hmm # target sequence database: /tmp/gapView.13823.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR01001 [M=301] Accession: TIGR01001 Description: metA: homoserine O-succinyltransferase 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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.4e-117 378.6 0.0 1.6e-117 378.4 0.0 1.0 1 lcl|FitnessBrowser__Smeli:SMc03797 SMc03797 homoserine O-succinyltr Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Smeli:SMc03797 SMc03797 homoserine O-succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 378.4 0.0 1.6e-117 1.6e-117 1 300 [. 24 323 .. 24 324 .. 0.99 Alignments for each domain: == domain 1 score: 378.4 bits; conditional E-value: 1.6e-117 TIGR01001 1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditllridsr 75 mpi++pd lpa e l +e++ +mte a+ qdirpl++ +lnlmp+ki+te+q+ rl++ +plqv++tl+r++ + lcl|FitnessBrowser__Smeli:SMc03797 24 MPIKIPDTLPAFETLVHEGVRLMTETEAIRQDIRPLQIGLLNLMPNKIKTEIQMARLIGATPLQVELTLVRVNGH 98 9************************************************************************** PP TIGR01001 76 kskntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtstlyicwaaqaalk 150 ++kntp+ehl fy+++eev+ rkfdG+i+tGap+e le+e+v yw+el+ i++w+ +nv stl +cw+ +aa++ lcl|FitnessBrowser__Smeli:SMc03797 99 RPKNTPEEHLLAFYETFEEVEARKFDGFIITGAPIETLEYEEVTYWKELQRIFDWTTTNVHSTLNVCWGGMAAVY 173 *************************************************************************** PP TIGR01001 151 llygipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltdleilaesdeagvylaask 224 ++g+pk+ l+ek +Gvy+h+ + ++++ l+gf d f +p sr++++ +++i+ ++dleil+es+e+gv l+ +k lcl|FitnessBrowser__Smeli:SMc03797 174 HFHGVPKYPLKEKAFGVYRHQNLqPSSVYLNGFSDDFAVPVSRWTEVRRADIDRVPDLEILMESKEVGVCLVHEK 248 *********************997999************************************************ PP TIGR01001 225 dernifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpiaswrshanllfanwlnyavyqktpyd 299 + ++++ h eyd +l +ey+rdv++g+ ++ p++y+p++d+ p wrsha+l+f nw+n +yq+tpy+ lcl|FitnessBrowser__Smeli:SMc03797 249 KGNRLYMFNHVEYDSTSLSEEYFRDVDAGVPIKLPHDYFPHNDSALPPQNRWRSHAHLFFGNWIN-EIYQTTPYE 322 ****************************************************************9.79******9 PP TIGR01001 300 l 300 l lcl|FitnessBrowser__Smeli:SMc03797 323 L 323 8 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (301 nodes) Target sequences: 1 (331 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: 7.68 // [ok]
This GapMind analysis is from Apr 09 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