Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate WP_011444345.1 SARO_RS03415 homoserine O-succinyltransferase
Query= SwissProt::G4RES5 (306 letters) >NCBI__GCF_000013325.1:WP_011444345.1 Length = 301 Score = 346 bits (888), Expect = e-100 Identities = 161/304 (52%), Positives = 215/304 (70%), Gaps = 6/304 (1%) Query: 1 MPIRIPDQLPARKTLETEGVVVMDQSRSARQDIRPLQFGLLNLMPNKQRTETQFARLIAS 60 MPIRI D LPAR+TLE EGV+VM ++ +ARQDIRP++ LLNLMP+K TETQ ARL+ + Sbjct: 1 MPIRIADNLPARRTLEAEGVIVMSETEAARQDIRPMRIALLNLMPDKITTETQIARLLGA 60 Query: 61 TPLQIDLTLVRVADPLSKSTPEDYLQNFYSTWEDVRAKKFDGFVVTGAPIANMPFEDVRY 120 TPLQ+DL LVR++D +SK+T ++ FY W+DVRA+K+DG +VTGAP+ +P+E+V Y Sbjct: 61 TPLQVDLELVRISDHVSKNTSAGHISAFYRPWDDVRAEKYDGLIVTGAPVETIPYEEVSY 120 Query: 121 WPEMLEIMDWTQTNVHHTMFICWGAQAALHHLHGVKRYRMEHKAFGVYRHKVLDTRHPFL 180 W E+ I DW+Q+NVH T+ +CWGA AAL+H HG++++ + KA GV+RH P++ Sbjct: 121 WDELRRIFDWSQSNVHRTLSVCWGAMAALYHFHGIEKHGLPTKASGVFRHVNHAPASPWM 180 Query: 181 RGFSDDLAVPVSRYNDIDRQSL--SPDLDILIDSDEVGICMLDDRKYRAAYMLNHLEYDN 238 RG D VPVSR++++ R+ L L +L DS E G+C++DD R +M NHLEYD Sbjct: 181 RGLPDVFDVPVSRWSEVRREDLPEGRGLSVLADSAETGLCLIDDPAMRTLHMFNHLEYDT 240 Query: 239 TSLADEYHRDIEAGLDTPLPVNLFPGNDPSRMPENRWRSHAHLLFQNWINEIYQTTPYEL 298 +LA EY RD LP N FPG+DP MP N WR H HLL+ NWINE YQTTPY+L Sbjct: 241 LTLAGEYARD----EGKYLPRNYFPGDDPQAMPANTWRGHGHLLYGNWINETYQTTPYDL 296 Query: 299 EKVG 302 +G Sbjct: 297 ADIG 300 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: 348 Number of extensions: 15 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: 301 Length adjustment: 27 Effective length of query: 279 Effective length of database: 274 Effective search space: 76446 Effective search space used: 76446 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_011444345.1 SARO_RS03415 (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.31589.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 2.2e-104 335.2 0.0 2.5e-104 335.0 0.0 1.0 1 lcl|NCBI__GCF_000013325.1:WP_011444345.1 SARO_RS03415 homoserine O-succin Domain annotation for each sequence (and alignments): >> lcl|NCBI__GCF_000013325.1:WP_011444345.1 SARO_RS03415 homoserine O-succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 335.0 0.0 2.5e-104 2.5e-104 1 300 [. 1 296 [. 1 297 [. 0.98 Alignments for each domain: == domain 1 score: 335.0 bits; conditional E-value: 2.5e-104 TIGR01001 1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditl 69 mpir+ d+lpa l+ e++ vm+e a qdirp+++ +lnlmp+ki te+q+ rll+ +plqvd++l lcl|NCBI__GCF_000013325.1:WP_011444345.1 1 MPIRIADNLPARRTLEAEGVIVMSETEAARQDIRPMRIALLNLMPDKITTETQIARLLGATPLQVDLEL 69 9******************************************************************** PP TIGR01001 70 lridsrkskntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtst 138 +ri +++sknt + h+ fy+ +++v+ +k+dGlivtGapve +++e+v+yw+el+ i++ws++nv t lcl|NCBI__GCF_000013325.1:WP_011444345.1 70 VRISDHVSKNTSAGHISAFYRPWDDVRAEKYDGLIVTGAPVETIPYEEVSYWDELRRIFDWSQSNVHRT 138 ********************************************************************* PP TIGR01001 139 lyicwaaqaalkllygipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltd 206 l +cw+a+aal+ ++gi+k+ l+ k sGv++h + + ++ +rg+ d f +p sr++++ +e++ e + lcl|NCBI__GCF_000013325.1:WP_011444345.1 139 LSVCWGAMAALYHFHGIEKHGLPTKASGVFRHVNHaPASPWMRGLPDVFDVPVSRWSEVRREDLPEGRG 207 ********************************999899******************************* PP TIGR01001 207 leilaesdeagvylaaskdernifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpias 275 l +la+s e+g l+ r++ + h+eyd tl++ey rd g+ p ny+p ddp+ +p + lcl|NCBI__GCF_000013325.1:WP_011444345.1 208 LSVLADSAETGLCLIDDPAMRTLHMFNHLEYDTLTLAGEYARDEGKY----LPRNYFPGDDPQAMPANT 272 ********************************************765....59**************** PP TIGR01001 276 wrshanllfanwlnyavyqktpydl 300 wr h++ll+ nw+n yq+tpydl lcl|NCBI__GCF_000013325.1:WP_011444345.1 273 WRGHGHLLYGNWIN-ETYQTTPYDL 296 **************.57******98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (301 nodes) Target sequences: 1 (301 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: 00:00:00.00 # Mc/sec: 9.54 // [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