Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_003543755.1 RLEG_RS20465 homoserine O-succinyltransferase
Query= SwissProt::G4RES5 (306 letters) >NCBI__GCF_000023185.1:WP_003543755.1 Length = 307 Score = 391 bits (1005), Expect = e-114 Identities = 176/305 (57%), Positives = 238/305 (78%), Gaps = 2/305 (0%) Query: 1 MPIRIPDQLPARKTLETEGVVVMDQSRSARQDIRPLQFGLLNLMPNKQRTETQFARLIAS 60 MPI+IPD LPA +TL EGV VM ++ + RQDIRPLQ GLLNLMPNK +TE Q ARL+ + Sbjct: 1 MPIKIPDTLPAFETLVQEGVRVMTETLAIRQDIRPLQIGLLNLMPNKIKTELQMARLVGA 60 Query: 61 TPLQIDLTLVRVADPLSKSTPEDYLQNFYSTWEDVRAKKFDGFVVTGAPIANMPFEDVRY 120 +PLQ++L+L+R+ +K+T ED+L FY TWE+V+ +KFDGF++TGAPI +P+EDV Y Sbjct: 61 SPLQVELSLIRIGGHKAKNTSEDHLLAFYQTWEEVKHRKFDGFIITGAPIELLPYEDVTY 120 Query: 121 WPEMLEIMDWTQTNVHHTMFICWGAQAALHHLHGVKRYRMEHKAFGVYRHKVLDTRHPFL 180 WPEM EI+DWT+TNVH TM +CWGA AA++H HGV +Y ++ KAFGVYRH+ L +L Sbjct: 121 WPEMQEILDWTETNVHSTMNVCWGAMAAVYHFHGVPKYELKEKAFGVYRHRNLKPSSIYL 180 Query: 181 RGFSDDLAVPVSRYNDIDRQSL--SPDLDILIDSDEVGICMLDDRKYRAAYMLNHLEYDN 238 GFSD+ VPVSR+ ++ R + S L+IL++S E+G+C++ +++ R YM NH+EYD+ Sbjct: 181 NGFSDNFEVPVSRWTEVRRADIEKSESLEILMESSEMGVCLVHEKRGRRLYMFNHVEYDS 240 Query: 239 TSLADEYHRDIEAGLDTPLPVNLFPGNDPSRMPENRWRSHAHLLFQNWINEIYQTTPYEL 298 TSL+DEY RD+ AG+ +P N FP NDP+ P+NRWRSHAHLLF NWINEIYQTTP+++ Sbjct: 241 TSLSDEYFRDVNAGVPIKMPHNYFPHNDPALAPQNRWRSHAHLLFGNWINEIYQTTPFDV 300 Query: 299 EKVGT 303 E++GT Sbjct: 301 EEIGT 305 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: 346 Number of extensions: 13 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: 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 WP_003543755.1 RLEG_RS20465 (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.10332.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-119 385.1 0.1 1.6e-119 384.9 0.1 1.0 1 lcl|NCBI__GCF_000023185.1:WP_003543755.1 RLEG_RS20465 homoserine O-succin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000023185.1:WP_003543755.1 RLEG_RS20465 homoserine O-succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 384.9 0.1 1.6e-119 1.6e-119 1 300 [. 1 300 [. 1 301 [. 0.99 Alignments for each domain: == domain 1 score: 384.9 bits; conditional E-value: 1.6e-119 TIGR01001 1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditl 69 mpi++pd lpa e l +e++ vmte a+ qdirpl++ +lnlmp+ki+te q+ rl++ splqv++ l lcl|NCBI__GCF_000023185.1:WP_003543755.1 1 MPIKIPDTLPAFETLVQEGVRVMTETLAIRQDIRPLQIGLLNLMPNKIKTELQMARLVGASPLQVELSL 69 9******************************************************************** PP TIGR01001 70 lridsrkskntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtst 138 +ri +k+knt ++hl fy+++eevk+rkfdG+i+tGap+ell++edv yw+e++eil+w+ +nv st lcl|NCBI__GCF_000023185.1:WP_003543755.1 70 IRIGGHKAKNTSEDHLLAFYQTWEEVKHRKFDGFIITGAPIELLPYEDVTYWPEMQEILDWTETNVHST 138 ********************************************************************* PP TIGR01001 139 lyicwaaqaalkllygipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltd 206 + +cw+a+aa++ ++g+pk++l+ek +Gvy+h+ + ++++ l+gf d+f +p sr++++ +++i++ + lcl|NCBI__GCF_000023185.1:WP_003543755.1 139 MNVCWGAMAAVYHFHGVPKYELKEKAFGVYRHRNLkPSSIYLNGFSDNFEVPVSRWTEVRRADIEKSES 207 *********************************99788999**************************** PP TIGR01001 207 leilaesdeagvylaaskdernifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpias 275 leil+es e+gv l+ +k r++++ h eyd +l +ey+rdv++g+ +++p+ny+p++dp p lcl|NCBI__GCF_000023185.1:WP_003543755.1 208 LEILMESSEMGVCLVHEKRGRRLYMFNHVEYDSTSLSDEYFRDVNAGVPIKMPHNYFPHNDPALAPQNR 276 ********************************************************************* PP TIGR01001 276 wrshanllfanwlnyavyqktpydl 300 wrsha+llf nw+n +yq+tp+d+ lcl|NCBI__GCF_000023185.1:WP_003543755.1 277 WRSHAHLLFGNWIN-EIYQTTPFDV 300 *************9.79******97 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: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.01 # Mc/sec: 6.69 // [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