Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 202599 SO3496 aldehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__MR1:202599 Length = 498 Score = 233 bits (595), Expect = 9e-66 Identities = 159/478 (33%), Positives = 246/478 (51%), Gaps = 17/478 (3%) Query: 8 KNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKT--WSKVAV 65 K +INGE+ ++ + D ++P +L V D + A A E F + WSK A Sbjct: 22 KAFINGEYRDASSGNTFDCISPIDGRLLAPVASCDLMDANIAVANAREVFDSGVWSKAAP 81 Query: 66 PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGD 125 +R +++ F +LL ++ ELA L T++ GK + + G +G + D Sbjct: 82 VKRKQVMIRFAELLEENANELALLETLDMGKPIRFSKAVDVAGAARAIRWSGEAIDKLYD 141 Query: 126 SLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLT 185 LA A + R P+GVV I P+NFP+++ CW A+ GN+ ILKPSE++PL Sbjct: 142 ELAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALVTGNSVILKPSEKSPLTA 201 Query: 186 EKLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVG-EYVYKKGSEN 243 ++ EL +AG+PKGV NV+ G H V + H ++ + F GS + + + G N Sbjct: 202 IRIAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGESN 261 Query: 244 LKRVQSLTGAKNHTIVLNDA-NLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMA 302 +KRV G K+ IV NDA +L+ A + GE C A + + VE G+ DE + Sbjct: 262 MKRVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIGFNQGEVCTAGSRLLVESGVKDELVG 321 Query: 303 KLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSD-DG 361 + E++A + G+ L+ G V+ + LSYI+ G EGA LV G++ +++ G Sbjct: 322 LIAEELASWQPGHPLEPTTVSGAVVDKQQLDTILSYIKAGQNEGASLVYGGQQVLAETGG 381 Query: 362 YFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNA 421 +V PT+F NV +M I +EIF PVLSVI ++EAI IAN + + A ++T++ + Sbjct: 382 VYVQPTVFSNVKNQMKIASEEIFGPVLSVIEFNGMEEAIAIANDTIYGLAAGVWTADISK 441 Query: 422 IRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKD----SVDFYTRKK 475 + + +GM+ IN M PF G+K S NG+D S D YT K Sbjct: 442 AHKTAKALRSGMVWINHYDGGDMT-APFGGYKQS------GNGRDKSLHSFDKYTEIK 492 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: 582 Number of extensions: 31 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