Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate YP_002827648.1 NGR_c31610 homoserine O-succinyltransferase
Query= SwissProt::G4RES5 (306 letters) >NCBI__GCF_000018545.1:YP_002827648.1 Length = 307 Score = 387 bits (994), Expect = e-112 Identities = 175/307 (57%), Positives = 234/307 (76%), Gaps = 2/307 (0%) Query: 1 MPIRIPDQLPARKTLETEGVVVMDQSRSARQDIRPLQFGLLNLMPNKQRTETQFARLIAS 60 MPI+IPD LPA +TL EGV VM ++ + RQDIRPLQ GLLNLMPNK +TE Q ARLI + Sbjct: 1 MPIKIPDTLPAFETLVNEGVRVMTETAAVRQDIRPLQIGLLNLMPNKIKTEIQIARLIGA 60 Query: 61 TPLQIDLTLVRVADPLSKSTPEDYLQNFYSTWEDVRAKKFDGFVVTGAPIANMPFEDVRY 120 TPLQ++LTLVR+ K+TPE++L FY TWE+V+ +KFDGF++TGAP+ + +E+V Y Sbjct: 61 TPLQVELTLVRIGGYRPKNTPEEHLFAFYETWEEVKGRKFDGFIITGAPVETLDYEEVTY 120 Query: 121 WPEMLEIMDWTQTNVHHTMFICWGAQAALHHLHGVKRYRMEHKAFGVYRHKVLDTRHPFL 180 W E+ I +WT+T+VH T+ +CWGA AA++H HGV +Y ++ KAFGVYRH+ L +L Sbjct: 121 WDELKSIFEWTETHVHSTLNVCWGAMAAIYHFHGVPKYPLKEKAFGVYRHQNLKPSSVYL 180 Query: 181 RGFSDDLAVPVSRYNDIDRQSLS--PDLDILIDSDEVGICMLDDRKYRAAYMLNHLEYDN 238 GFSDD AVPVSR+ ++ R + P L+IL++S E+G+C++ ++K YM NH+EYD+ Sbjct: 181 NGFSDDFAVPVSRWTEVRRADIDRVPSLEILMESKEMGVCLVHEKKGNRLYMFNHVEYDS 240 Query: 239 TSLADEYHRDIEAGLDTPLPVNLFPGNDPSRMPENRWRSHAHLLFQNWINEIYQTTPYEL 298 TSL+DEY RD++AG+ LP + FP ND P+NRWRSHAHL F NWINE+YQTTPYEL Sbjct: 241 TSLSDEYFRDVDAGVPIKLPHDYFPHNDADLPPQNRWRSHAHLFFGNWINEMYQTTPYEL 300 Query: 299 EKVGTGE 305 EK+GTG+ Sbjct: 301 EKIGTGD 307 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: 357 Number of extensions: 14 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: 307 Length adjustment: 27 Effective length of query: 279 Effective length of database: 280 Effective search space: 78120 Effective search space used: 78120 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 YP_002827648.1 NGR_c31610 (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.3167.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-118 381.8 0.0 1.6e-118 381.6 0.0 1.0 1 lcl|NCBI__GCF_000018545.1:YP_002827648.1 NGR_c31610 homoserine O-succinyl Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000018545.1:YP_002827648.1 NGR_c31610 homoserine O-succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 381.6 0.0 1.6e-118 1.6e-118 1 301 [] 1 301 [. 1 301 [. 0.99 Alignments for each domain: == domain 1 score: 381.6 bits; conditional E-value: 1.6e-118 TIGR01001 1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditl 69 mpi++pd lpa e l +e++ vmte a qdirpl++ +lnlmp+ki+te+q+ rl++ +plqv++tl lcl|NCBI__GCF_000018545.1:YP_002827648.1 1 MPIKIPDTLPAFETLVNEGVRVMTETAAVRQDIRPLQIGLLNLMPNKIKTEIQIARLIGATPLQVELTL 69 9******************************************************************** PP TIGR01001 70 lridsrkskntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtst 138 +ri +++kntp+ehl fy+++eevk rkfdG+i+tGapve l++e+v yw+elk i+ew+ ++v st lcl|NCBI__GCF_000018545.1:YP_002827648.1 70 VRIGGYRPKNTPEEHLFAFYETWEEVKGRKFDGFIITGAPVETLDYEEVTYWDELKSIFEWTETHVHST 138 ********************************************************************* PP TIGR01001 139 lyicwaaqaalkllygipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltd 206 l +cw+a+aa++ ++g+pk+ l+ek +Gvy+h+ + ++++ l+gf d f +p sr++++ +++i+ ++ lcl|NCBI__GCF_000018545.1:YP_002827648.1 139 LNVCWGAMAAIYHFHGVPKYPLKEKAFGVYRHQNLkPSSVYLNGFSDDFAVPVSRWTEVRRADIDRVPS 207 *********************************9978999***************************** PP TIGR01001 207 leilaesdeagvylaaskdernifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpias 275 leil+es+e+gv l+ +k+ ++++ h eyd +l +ey+rdv++g+ ++ p++y+p++d + p lcl|NCBI__GCF_000018545.1:YP_002827648.1 208 LEILMESKEMGVCLVHEKKGNRLYMFNHVEYDSTSLSDEYFRDVDAGVPIKLPHDYFPHNDADLPPQNR 276 ********************************************************************* PP TIGR01001 276 wrshanllfanwlnyavyqktpydle 301 wrsha+l+f nw+n +yq+tpy+le lcl|NCBI__GCF_000018545.1:YP_002827648.1 277 WRSHAHLFFGNWIN-EMYQTTPYELE 301 **************.68*******96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (301 nodes) Target sequences: 1 (307 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: 00:00:00.00 # Mc/sec: 9.52 // [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