Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 7025944 Shewana3_3092 succinate semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__ANA3:7025944 Length = 482 Score = 235 bits (599), Expect = 3e-66 Identities = 138/450 (30%), Positives = 235/450 (52%), Gaps = 3/450 (0%) Query: 10 YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRA 69 YING+W ++++ + + NPAT V+ VP+ + + A A A W + R Sbjct: 14 YINGQWCDAQSKETVAIANPATGAVIASVPVMGQAETQAAIAAAEAALPAWRALTAKERG 73 Query: 70 RILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLAS 129 L + +LL+++ ++LA ++T E GK EA GEV +E+ A + GD++ Sbjct: 74 VKLRRWFELLNENSDDLALMMTSEQGKPLAEAKGEVTYAASFIEWFAEEAKRVYGDTIPG 133 Query: 130 IATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLV 189 D + P+GV I P+NFP + A+A G T ++KP+ +TP L Sbjct: 134 HQGDKRIMVIKQPVGVTAAITPWNFPAAMITRKAAPALAAGCTMVVKPAPQTPFTALALA 193 Query: 190 ELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRVQ 248 L E+AG+P GVF+V+ G A + N + +P ++ +SF GS VG + ++ + LK++ Sbjct: 194 VLAERAGIPAGVFSVITGDAIGIGNEMCSNPVVRKLSFTGSTQVGIKLMEQCAPTLKKLS 253 Query: 249 SLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKV 308 G IV +DAN++ V + A + +AG+ C+ + V+ G+ DEF KL V Sbjct: 254 LELGGNAPFIVFDDANIDAAVEGAMIAKYRNAGQTCVCANRIYVQAGVYDEFARKLSIAV 313 Query: 309 ADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPTI 368 +K+G G+ +GV GP+I ++ S++E L +GA +V G+ + S G F PT+ Sbjct: 314 GKLKVGEGIGEGVTTGPLINCAAVEKVQSHLEDALSKGATVVAGGKPH-SLGGNFFEPTV 372 Query: 369 FDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFREN 428 NV + M + ++E F P+ + + ++ + I+ AN +EF A + + + + E Sbjct: 373 LTNVDSSMRVAREETFGPLAPLFKFTDVDDVIKQANDTEFGLAAYFYGRDISLVWKVTEA 432 Query: 429 IDAGMLGINLGVPAPMAFFPFSGWKSSFFG 458 ++ GM+G+N G+ PF G KSS G Sbjct: 433 LEYGMVGVNTGL-ISTEVAPFGGMKSSGLG 461 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: 558 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: 482 Length adjustment: 34 Effective length of query: 453 Effective length of database: 448 Effective search space: 202944 Effective search space used: 202944 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