Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__PV4:5208455 Length = 498 Score = 232 bits (591), Expect = 3e-65 Identities = 156/476 (32%), Positives = 248/476 (52%), Gaps = 17/476 (3%) Query: 10 YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKT--WSKVAVPR 67 +INGE+ + ++ D ++P VL QV D + A A E F+ WS++ + Sbjct: 24 FINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANRAVANAREVFERGDWSQLPPVK 83 Query: 68 RARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSL 127 R +++ F LL +++ELA L T++ GK + + G +G + D + Sbjct: 84 RKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDVAGAARALRWSGEAVDKIYDEI 143 Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187 A A + R P+GVV I P+NFP+++ CW A+A GN+ +LKPSE++PL + Sbjct: 144 APTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALATGNSVVLKPSEKSPLTAIR 203 Query: 188 LVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVG-EYVYKKGSENLK 245 + +L +AG+PKGV NV+ G H V + H ++ + F GS + + + G N+K Sbjct: 204 MAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGESNMK 263 Query: 246 RVQSLTGAKNHTIVLNDA-NLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKL 304 RV G K+ IV NDA NL++ A + GE C A + + VE G+ +E + + Sbjct: 264 RVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEVCTAGSRLLVESGVKEELINLI 323 Query: 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSD-DGYF 363 + ++ + G+ LD G V+ + + L YI G+ EGA+L G++ +++ G + Sbjct: 324 EAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRAGVAEGAQLRQGGQQVLAETGGVY 383 Query: 364 VGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIR 423 V PTIF NV EMTI K+EIF PVLSVI ++EAI I N + + A ++TS+ + Sbjct: 384 VAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAIRIGNDTIYGLAAGVWTSDISKAH 443 Query: 424 YFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKD----SVDFYTRKK 475 + + +GM+ IN M PF G+K S NG+D + D YT K Sbjct: 444 KTAKALRSGMVWINHYDGGDMT-APFGGYKQS------GNGRDKSLHAFDKYTEIK 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: 574 Number of extensions: 35 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 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