Align Homoserine O-succinyltransferase; HST; Homoserine transsuccinylase; HTS; EC 2.3.1.46 (characterized)
to candidate 200841 SO1676 homoserine O-succinyltransferase (NCBI ptt file)
Query= SwissProt::A6WLE9 (313 letters) >FitnessBrowser__MR1:200841 Length = 313 Score = 625 bits (1612), Expect = 0.0 Identities = 299/313 (95%), Positives = 307/313 (98%) Query: 1 MPVRIPDHLPAAEVLESENIFVMSETRAANQDIRPMKVLILNLMPNKIETETQLLRLLGN 60 MPV+IPDHLPAA +LESENIFVMSETRAANQDIRPMKVLILNLMPNKIETETQLLRLLGN Sbjct: 1 MPVKIPDHLPAAGILESENIFVMSETRAANQDIRPMKVLILNLMPNKIETETQLLRLLGN 60 Query: 61 TPLQVDVDLLRIHDKESKHTSIDHMNTFYRDFEAVRHKNYDGLIITGAPLGQIDFEDVVY 120 TPLQVDVDLLRIHDKESKHTSIDHMNTFYRDFE VRHKNYDGLIITGAPLGQIDFEDV Y Sbjct: 61 TPLQVDVDLLRIHDKESKHTSIDHMNTFYRDFEDVRHKNYDGLIITGAPLGQIDFEDVTY 120 Query: 121 WDHIREIIDWSQEHVTSVLFLCWAAHAGLYHLYGLNRKILQQKRSGVFVHRRTSQHFPLL 180 WDHIREIIDWSQ+HVTSVLFLCWAAHAGLYHLYGLNRKIL+QKRSGVFVHRRT QHFPLL Sbjct: 121 WDHIREIIDWSQQHVTSVLFLCWAAHAGLYHLYGLNRKILEQKRSGVFVHRRTCQHFPLL 180 Query: 181 RGFDDEFFAPHSRFAEMDVEEIRQHPQLQLLAESDEAGAYLVLSRNNRNLFVMGHPEYQK 240 RGFDDEFFAPHSRFAEMDVEEIRQHPQLQLLAESDEAGAYLVLSRNNRNLFVMGHPEYQK Sbjct: 181 RGFDDEFFAPHSRFAEMDVEEIRQHPQLQLLAESDEAGAYLVLSRNNRNLFVMGHPEYQK 240 Query: 241 STLNEEYQRDLSQGLDPNVPQNYYRNDDPKADAIARWHSHGSLLVSNWLNYYVYQLTPYD 300 STLN+EY RDL+Q L+PNVPQNYYRNDDPKADAIARWHSHGSLLVSNWLNYYVYQLTPYD Sbjct: 241 STLNDEYHRDLAQSLNPNVPQNYYRNDDPKADAIARWHSHGSLLVSNWLNYYVYQLTPYD 300 Query: 301 LSDMTAMTPWESR 313 LSDMTAMTPWES+ Sbjct: 301 LSDMTAMTPWESQ 313 Lambda K H 0.321 0.136 0.419 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: 507 Number of extensions: 16 Number of successful extensions: 1 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: 313 Length of database: 313 Length adjustment: 27 Effective length of query: 286 Effective length of database: 286 Effective search space: 81796 Effective search space used: 81796 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 200841 SO1676 (homoserine O-succinyltransferase (NCBI ptt file))
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.7136.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 1.7e-144 466.9 0.5 1.9e-144 466.8 0.5 1.0 1 lcl|FitnessBrowser__MR1:200841 SO1676 homoserine O-succinyltran Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__MR1:200841 SO1676 homoserine O-succinyltransferase (NCBI ptt file) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 466.8 0.5 1.9e-144 1.9e-144 1 300 [. 1 301 [. 1 302 [. 0.99 Alignments for each domain: == domain 1 score: 466.8 bits; conditional E-value: 1.9e-144 TIGR01001 1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditllridsrkskn 79 mp+++pd+lpa +l+ enifvm+e ra +qdirp++vlilnlmp+kiete+qllrll+n+plqvd++llri++++sk+ lcl|FitnessBrowser__MR1:200841 1 MPVKIPDHLPAAGILESENIFVMSETRAANQDIRPMKVLILNLMPNKIETETQLLRLLGNTPLQVDVDLLRIHDKESKH 79 9****************************************************************************** PP TIGR01001 80 tpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtstlyicwaaqaalkllygipkr 158 t i+h+++fy+++e+v+++++dGli+tGap+++++fedv yw++++ei++ws+++vts l++cwaa+a+l+ lyg++++ lcl|FitnessBrowser__MR1:200841 80 TSIDHMNTFYRDFEDVRHKNYDGLIITGAPLGQIDFEDVTYWDHIREIIDWSQQHVTSVLFLCWAAHAGLYHLYGLNRK 158 ******************************************************************************* PP TIGR01001 159 tleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltdleilaesdeagvylaaskdernifvtGhpe 236 le+k sGv+ h+ + ++ +llrgfdd+f+aphsr+a++d e+i+++++l++laesdeag+yl++s+++rn+fv+Ghpe lcl|FitnessBrowser__MR1:200841 159 ILEQKRSGVFVHRRTcQHFPLLRGFDDEFFAPHSRFAEMDVEEIRQHPQLQLLAESDEAGAYLVLSRNNRNLFVMGHPE 237 *************9978999*********************************************************** PP TIGR01001 237 ydketlrqeyvrdvgeglkvdipknyypkddpektpiaswrshanllfanwlnyavyqktpydl 300 y+k tl++ey rd+ ++l++++p+nyy +ddp+ ia w+sh+ ll +nwlny+vyq tpydl lcl|FitnessBrowser__MR1:200841 238 YQKSTLNDEYHRDLAQSLNPNVPQNYYRNDDPKADAIARWHSHGSLLVSNWLNYYVYQLTPYDL 301 **************************************************************98 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (301 nodes) Target sequences: 1 (313 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: 11.24 // [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