Align homoserine O-succinyltransferase (EC 2.3.1.46) (characterized)
to candidate BWI76_RS01655 BWI76_RS01655 homoserine O-succinyltransferase
Query= BRENDA::P07623 (309 letters) >FitnessBrowser__Koxy:BWI76_RS01655 Length = 309 Score = 602 bits (1553), Expect = e-177 Identities = 290/309 (93%), Positives = 298/309 (96%) Query: 1 MPIRVPDELPAVNFLREENVFVMTTSRASGQEIRPLKVLILNLMPKKIETENQFLRLLSN 60 MPIRV DELPAVNFLR ENVFVMTT+RA+ QEIRPLKVLILNLMPKKIETENQFLRLLSN Sbjct: 1 MPIRVQDELPAVNFLRNENVFVMTTTRATTQEIRPLKVLILNLMPKKIETENQFLRLLSN 60 Query: 61 SPLQVDIQLLRIDSRESRNTPAEHLNNFYCNFEDIQDQNFDGLIVTGAPLGLVEFNDVAY 120 SPLQ+DIQLLRID+RESRNTPAEHLNNFYCNFEDI DQNFDGLIVTGAPLGLVEFNDVAY Sbjct: 61 SPLQLDIQLLRIDARESRNTPAEHLNNFYCNFEDICDQNFDGLIVTGAPLGLVEFNDVAY 120 Query: 121 WPQIKQVLEWSKDHVTSTLFVCWAVQAALNILYGIPKQTRTEKLSGVYEHHILHPHALLT 180 WPQIKQVLEW+KDHVTSTLFVCWAVQAALNILYGIPKQTR+EK+SGVYEHHIL PHALLT Sbjct: 121 WPQIKQVLEWAKDHVTSTLFVCWAVQAALNILYGIPKQTRSEKISGVYEHHILQPHALLT 180 Query: 181 RGFDDSFLAPHSRYADFPAALIRDYTDLEILAETEEGDAYLFASKDKRIAFVTGHPEYDA 240 RGFDDSFLAPHSRYADFPAALIRDYTDLEILAETEEGDAYLFASKDKRIAFVTGHPEYDA Sbjct: 181 RGFDDSFLAPHSRYADFPAALIRDYTDLEILAETEEGDAYLFASKDKRIAFVTGHPEYDA 240 Query: 241 QTLAQEFFRDVEAGLDPDVPYNYFPHNDPQNTPRASWRSHGNLLFTNWLNYYVYQITPYD 300 TLA EFFRDVEAGLDP VPYNYFP NDPQN PRA+WRSHGNLLF NWLNYYVYQITPYD Sbjct: 241 NTLASEFFRDVEAGLDPQVPYNYFPQNDPQNKPRATWRSHGNLLFINWLNYYVYQITPYD 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: 486 Number of extensions: 12 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 BWI76_RS01655 BWI76_RS01655 (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.19465.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-167 542.5 0.2 1.9e-167 542.3 0.2 1.0 1 lcl|FitnessBrowser__Koxy:BWI76_RS01655 BWI76_RS01655 homoserine O-succi Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__Koxy:BWI76_RS01655 BWI76_RS01655 homoserine O-succinyltransferase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 542.3 0.2 1.9e-167 1.9e-167 1 301 [] 1 302 [. 1 302 [. 1.00 Alignments for each domain: == domain 1 score: 542.3 bits; conditional E-value: 1.9e-167 TIGR01001 1 mpirvpdelpavellkeenifvmtekrashqdirplevlilnlmpkkietenqllrllsnsplqvditllr 71 mpirv delpav++l++en+fvmt+ ra++q+irpl+vlilnlmpkkietenq+lrllsnsplq+di+llr lcl|FitnessBrowser__Koxy:BWI76_RS01655 1 MPIRVQDELPAVNFLRNENVFVMTTTRATTQEIRPLKVLILNLMPKKIETENQFLRLLSNSPLQLDIQLLR 71 9********************************************************************** PP TIGR01001 72 idsrkskntpiehlekfykeleevkdrkfdGlivtGapvellefedvayweelkeilewskenvtstlyic 142 id+r+s+ntp+ehl++fy+++e++ d++fdGlivtGap++l+ef+dvayw+++k++lew+k++vtstl++c lcl|FitnessBrowser__Koxy:BWI76_RS01655 72 IDARESRNTPAEHLNNFYCNFEDICDQNFDGLIVTGAPLGLVEFNDVAYWPQIKQVLEWAKDHVTSTLFVC 142 *********************************************************************** PP TIGR01001 143 waaqaalkllygipkrtleeklsGvykhdiv.kedlllrgfddkflaphsryadldeeliaeltdleilae 212 wa+qaal++lygipk+t++ek+sGvy+h+i+ +++ll+rgfdd+flaphsryad++++li+++tdleilae lcl|FitnessBrowser__Koxy:BWI76_RS01655 143 WAVQAALNILYGIPKQTRSEKISGVYEHHILqPHALLTRGFDDSFLAPHSRYADFPAALIRDYTDLEILAE 213 ******************************989999*********************************** PP TIGR01001 213 sdeagvylaaskdernifvtGhpeydketlrqeyvrdvgeglkvdipknyypkddpektpiaswrshanll 283 ++e+++yl+askd+r++fvtGhpeyd++tl+ e++rdv++gl++++p+ny+p++dp+++p+a+wrsh+nll lcl|FitnessBrowser__Koxy:BWI76_RS01655 214 TEEGDAYLFASKDKRIAFVTGHPEYDANTLASEFFRDVEAGLDPQVPYNYFPQNDPQNKPRATWRSHGNLL 284 *********************************************************************** PP TIGR01001 284 fanwlnyavyqktpydle 301 f nwlny+vyq+tpydl+ lcl|FitnessBrowser__Koxy:BWI76_RS01655 285 FINWLNYYVYQITPYDLR 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: 0.01u 0.00s 00:00:00.01 Elapsed: 00:00:00.01 # Mc/sec: 7.52 // [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