Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011383730.1 AMB_RS06710 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000009985.1:WP_011383730.1 Length = 485 Score = 231 bits (589), Expect = 4e-65 Identities = 141/451 (31%), Positives = 232/451 (51%), Gaps = 4/451 (0%) Query: 10 YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRA 69 YING WV +++ + V NPA ++ +VP + A + A A+ W R+ Sbjct: 15 YINGSWVAAQSGERLAVTNPADGSLIIRVPAMGAAETRQAIEAADRAWGPWKAKTAKERS 74 Query: 70 RILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLAS 129 +L + +L+ + +LA L+T E GK EA GEV G VE+ A + GD++ Sbjct: 75 AVLRRWFELIMAAQNDLAKLMTAEQGKPLAEAKGEVAYGASFVEWFAEEAKRVYGDTIPE 134 Query: 130 IATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLV 189 + PIGVV I P+NFP+ + A+A G ++KP+E TPL L Sbjct: 135 HMPGRRIVVVKEPIGVVAAITPWNFPLAMITRKCAPALAAGCPVVVKPAEDTPLSALALA 194 Query: 190 ELFEKAGLPKGVFNVVYGAHDVVNG--ILEHPEIKAISFVGSKPVGEYVYKKGSENLKRV 247 EL E+AG P GVFNV+ G + +P+++ +SF GS VG+ + + + +K++ Sbjct: 195 ELAERAGFPPGVFNVITAGDPKAVGFELTANPKVRKLSFTGSTEVGKLLMAQCAATVKKL 254 Query: 248 QSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEK 307 G +V +DA+L+ V + + + + G+ C+ + V++GI D F A+L E Sbjct: 255 SLELGGNAPFMVFDDADLDAAVAGAMASKYRNTGQTCVCANRLLVQDGIYDAFTARLAEA 314 Query: 308 VADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPT 367 VA +K+G GL+ GP+I E+ ++ +I + +GAR+V G+ + + G F PT Sbjct: 315 VAALKVGPGLEGDFQQGPLINEEAVRKVERHIADAVAKGARVVMGGKRH-ARGGTFFEPT 373 Query: 368 IFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFRE 427 I +VT +M ++E F PV + R K +EA+ +AN +EF A ++ + + Sbjct: 374 ILADVTPDMAPAREETFGPVAPLFRFKTEEEAVRMANDTEFGLAAYFYSRDVGRVWRVSR 433 Query: 428 NIDAGMLGINLGVPAPMAFFPFSGWKSSFFG 458 ++ G++GIN G+ PF G K S G Sbjct: 434 ALEYGIVGINEGL-ISTEVAPFGGVKESGLG 463 Lambda K H 0.318 0.136 0.396 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: 532 Number of extensions: 24 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: 487 Length of database: 485 Length adjustment: 34 Effective length of query: 453 Effective length of database: 451 Effective search space: 204303 Effective search space used: 204303 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
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