Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__SB2B:6938545 Length = 498 Score = 232 bits (591), Expect = 3e-65 Identities = 150/462 (32%), Positives = 241/462 (52%), Gaps = 10/462 (2%) Query: 10 YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKT--WSKVAVPR 67 +ING + ++ + D ++P +L QV + D D A A F++ WS + + Sbjct: 24 FINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADIAVANARAVFESGVWSLQSPVK 83 Query: 68 RARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSL 127 R +++ F +LL H +ELA L T++ GK + G +G + D L Sbjct: 84 RKKVMIRFAELLEAHADELALLETLDMGKPIAHSKAVDVAGAARAIRWSGEAIDKIYDEL 143 Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187 A + R P+GVV I P+NFPM++ CW A+A GN+ +LKPSE++PL + Sbjct: 144 APTPHNEIGMITREPVGVVAAIVPWNFPMLMACWKLGPALATGNSVVLKPSEKSPLTAIR 203 Query: 188 LVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVG-EYVYKKGSENLK 245 + +L ++AGLP GV NV+ G H V + H ++ + F GS + + + G N+K Sbjct: 204 MAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDTLVFTGSTKIAKQLMVYAGQSNMK 263 Query: 246 RVQSLTGAKNHTIVLNDA-NLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL 304 RV G K+ IV NDA +L+ A + GE C A + + VE G+ DE + + Sbjct: 264 RVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEVCTAGSRLLVESGVKDELIKLI 323 Query: 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSD-DGYF 363 +++ + G+ LD G V+ + L YI+ G +EGA+L+C G + +++ G + Sbjct: 324 VKEMEAWQPGHPLDPATTCGAVVDKQQLDTVLGYIKAGHDEGAKLMCGGSQVLAETGGVY 383 Query: 364 VGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIR 423 V PT+FD VT +M I ++EIF PV+SVI + EA+ IAN + + A ++TS+ + Sbjct: 384 VAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAIANDTIYGLAAGVWTSDISKAH 443 Query: 424 YFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFG---TLHA 462 + + +GM+ IN M PF G+K S G +LHA Sbjct: 444 KTAKALRSGMVWINHYDGGDMT-APFGGYKQSGNGRDKSLHA 484 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: 565 Number of extensions: 29 Number of successful extensions: 6 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: 498 Length adjustment: 34 Effective length of query: 453 Effective length of database: 464 Effective search space: 210192 Effective search space used: 210192 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 Apr 09 2024. 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