Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_086510804.1 BZY95_RS15485 NAD-dependent succinate-semialdehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_002151265.1:WP_086510804.1 Length = 481 Score = 256 bits (655), Expect = 9e-73 Identities = 157/478 (32%), Positives = 245/478 (51%), Gaps = 8/478 (1%) Query: 2 AEIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWS 61 A+I K +I G+W ++ ++ DV NPA E L VP + +D A A A+ W Sbjct: 5 ADIFSDKAFIGGQWRDA--ERRFDVTNPANGETLASVPDLSADDARDAVAAAEAAWPAWR 62 Query: 62 KVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSL 121 + +RA +L + + H+E LA ++T+E GK E+ GEV G VEF A Sbjct: 63 RQTAKQRAALLRAWFDAIMAHQESLARMMTLEQGKPLAESRGEVAYGASFVEFYAEQAKR 122 Query: 122 MMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERT 181 M G++L S D +R P+GVV I P+NFP+ + A+A G ++KP+E T Sbjct: 123 MAGETLPSHGADKRILVFREPVGVVAAITPWNFPLAMITRKCAPALAAGCPVVIKPAEAT 182 Query: 182 PLLTEKLVELFEKAGLPKGVFNVVYGAHDVVNG--ILEHPEIKAISFVGSKPVGEYVYKK 239 PL L L E+ G P GV NVV + G + P ++ +SF GS VG+ + + Sbjct: 183 PLTALALARLAEQVGFPAGVLNVVTASRPAEIGEVLTSDPRVRKVSFTGSTAVGKRLLAQ 242 Query: 240 GSENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADE 299 + +K+ G IV +DA+L+ V V + + ++G+ C+ + V+ G+ + Sbjct: 243 CAGTVKKASMELGGNAPFIVFDDADLDAAVEGAVASKYRNSGQTCVCTNRLLVQSGVYEA 302 Query: 300 FMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSD 359 F+ KL +VA +K+GNGLD+GV GP+I + + S+I L +GARLVC G + Sbjct: 303 FVEKLAARVAQLKVGNGLDEGVVQGPLINQAAVDKVQSHIADALAKGARLVCGGEPHAL- 361 Query: 360 DGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNS 419 G F PT+ +VT EM + ++E F P+ V R + ++AI +AN +EF A + + Sbjct: 362 GGTFFQPTVVADVTDEMRVAREETFGPLAPVFRFDSDEQAIAMANATEFGLAAYFYARDY 421 Query: 420 NAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477 I + E ++ GM+ +N G+ PF G K S G +D +T K V Sbjct: 422 RRIWHVMEGLEYGMVAVNEGI-LSTELAPFGGVKESGLG--REGSHHGLDEFTELKYV 476 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: 525 Number of extensions: 25 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: 481 Length adjustment: 34 Effective length of query: 453 Effective length of database: 447 Effective search space: 202491 Effective search space used: 202491 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 24 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