Align homoserine O-succinyltransferase (EC 2.3.1.46) (characterized)
to candidate 18041 b4013 homoserine O-succinyltransferase (NCBI)
Query= BRENDA::P07623 (309 letters) >FitnessBrowser__Keio:18041 Length = 309 Score = 640 bits (1650), Expect = 0.0 Identities = 309/309 (100%), Positives = 309/309 (100%) Query: 1 MPIRVPDELPAVNFLREENVFVMTTSRASGQEIRPLKVLILNLMPKKIETENQFLRLLSN 60 MPIRVPDELPAVNFLREENVFVMTTSRASGQEIRPLKVLILNLMPKKIETENQFLRLLSN Sbjct: 1 MPIRVPDELPAVNFLREENVFVMTTSRASGQEIRPLKVLILNLMPKKIETENQFLRLLSN 60 Query: 61 SPLQVDIQLLRIDSRESRNTPAEHLNNFYCNFEDIQDQNFDGLIVTGAPLGLVEFNDVAY 120 SPLQVDIQLLRIDSRESRNTPAEHLNNFYCNFEDIQDQNFDGLIVTGAPLGLVEFNDVAY Sbjct: 61 SPLQVDIQLLRIDSRESRNTPAEHLNNFYCNFEDIQDQNFDGLIVTGAPLGLVEFNDVAY 120 Query: 121 WPQIKQVLEWSKDHVTSTLFVCWAVQAALNILYGIPKQTRTEKLSGVYEHHILHPHALLT 180 WPQIKQVLEWSKDHVTSTLFVCWAVQAALNILYGIPKQTRTEKLSGVYEHHILHPHALLT Sbjct: 121 WPQIKQVLEWSKDHVTSTLFVCWAVQAALNILYGIPKQTRTEKLSGVYEHHILHPHALLT 180 Query: 181 RGFDDSFLAPHSRYADFPAALIRDYTDLEILAETEEGDAYLFASKDKRIAFVTGHPEYDA 240 RGFDDSFLAPHSRYADFPAALIRDYTDLEILAETEEGDAYLFASKDKRIAFVTGHPEYDA Sbjct: 181 RGFDDSFLAPHSRYADFPAALIRDYTDLEILAETEEGDAYLFASKDKRIAFVTGHPEYDA 240 Query: 241 QTLAQEFFRDVEAGLDPDVPYNYFPHNDPQNTPRASWRSHGNLLFTNWLNYYVYQITPYD 300 QTLAQEFFRDVEAGLDPDVPYNYFPHNDPQNTPRASWRSHGNLLFTNWLNYYVYQITPYD Sbjct: 241 QTLAQEFFRDVEAGLDPDVPYNYFPHNDPQNTPRASWRSHGNLLFTNWLNYYVYQITPYD 300 Query: 301 LRHMNPTLD 309 LRHMNPTLD Sbjct: 301 LRHMNPTLD 309 Lambda K H 0.321 0.138 0.424 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: 513 Number of extensions: 11 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: 309 Length of database: 309 Length adjustment: 27 Effective length of query: 282 Effective length of database: 282 Effective search space: 79524 Effective search space used: 79524 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 (21.8 bits) S2: 48 (23.1 bits)
Align candidate 18041 b4013 (homoserine O-succinyltransferase (NCBI))
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.15722.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 ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 3.9e-173 561.0 0.1 4.4e-173 560.8 0.1 1.0 1 lcl|FitnessBrowser__Keio:18041 b4013 homoserine O-succinyltrans Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Keio:18041 b4013 homoserine O-succinyltransferase (NCBI) # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 560.8 0.1 4.4e-173 4.4e-173 1 301 [] 1 302 [. 1 302 [. 1.00 Alignments for each domain: == domain 1 score: 560.8 bits; conditional E-value: 4.4e-173 TIGR01001 1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditllridsrkskn 79 mpirvpdelpav++l+een+fvmt++ras+q+irpl+vlilnlmpkkietenq+lrllsnsplqvdi+llridsr+s+n lcl|FitnessBrowser__Keio:18041 1 MPIRVPDELPAVNFLREENVFVMTTSRASGQEIRPLKVLILNLMPKKIETENQFLRLLSNSPLQVDIQLLRIDSRESRN 79 9****************************************************************************** PP TIGR01001 80 tpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtstlyicwaaqaalkllygipkr 158 tp+ehl++fy+++e+++d++fdGlivtGap++l+ef+dvayw+++k++lewsk++vtstl++cwa+qaal++lygipk+ lcl|FitnessBrowser__Keio:18041 80 TPAEHLNNFYCNFEDIQDQNFDGLIVTGAPLGLVEFNDVAYWPQIKQVLEWSKDHVTSTLFVCWAVQAALNILYGIPKQ 158 ******************************************************************************* PP TIGR01001 159 tleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltdleilaesdeagvylaaskdernifvtGhpe 236 t++eklsGvy+h+i+ +++ll+rgfdd+flaphsryad++++li+++tdleilae++e+++yl+askd+r++fvtGhpe lcl|FitnessBrowser__Keio:18041 159 TRTEKLSGVYEHHILhPHALLTRGFDDSFLAPHSRYADFPAALIRDYTDLEILAETEEGDAYLFASKDKRIAFVTGHPE 237 **************98999************************************************************ PP TIGR01001 237 ydketlrqeyvrdvgeglkvdipknyypkddpektpiaswrshanllfanwlnyavyqktpydle 301 yd++tl+qe++rdv++gl++d+p+ny+p++dp++tp+aswrsh+nllf+nwlny+vyq+tpydl+ lcl|FitnessBrowser__Keio:18041 238 YDAQTLAQEFFRDVEAGLDPDVPYNYFPHNDPQNTPRASWRSHGNLLFTNWLNYYVYQITPYDLR 302 ***************************************************************96 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (301 nodes) Target sequences: 1 (309 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: 10.80 // [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