Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate BWI76_RS10695 BWI76_RS10695 aldehyde dehydrogenase PuuC
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Koxy:BWI76_RS10695 Length = 495 Score = 237 bits (604), Expect = 8e-67 Identities = 156/462 (33%), Positives = 244/462 (52%), Gaps = 14/462 (3%) Query: 10 YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKT--WSKVAVPR 67 +INGE+ + + ++PA ++ L +V K D+D A Q A F WS+ + + Sbjct: 23 FINGEYSAAADNSVFATIDPAAQQTLAEVARGKKADVDRAVQAARGVFDRGDWSQASPAQ 82 Query: 68 RARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAGAPSLMMGDS 126 R +L F L+ H+EELA L T++ GK + +L ++ + + A A + G+ Sbjct: 83 RKAVLTKFADLMDAHREELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVYGE- 141 Query: 127 LASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTE 186 +A + A R PIGV+ + P+NFP+++ CW A+A GN+ +LKPSE++PL Sbjct: 142 VAPTGGNELAMIVREPIGVIAAVVPWNFPLLLACWKLGPALASGNSVVLKPSEKSPLTAL 201 Query: 187 KLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYK-KGSENL 244 +L L ++AGLP GVFNVV G H+ + HP+++ I+F GS + + K G N+ Sbjct: 202 RLAGLAKQAGLPDGVFNVVSGFGHEAGQALALHPDVEVITFTGSTRTAKQLLKDAGDSNM 261 Query: 245 KRVQSLTGAKNHTIVLNDA-NLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAK 303 KRV G K+ IV D +L+ V G F + G+ C+A + +EE IAD F+ Sbjct: 262 KRVWLEAGGKSANIVFADCPDLQKAVNATAGGIFYNQGQVCIAGTRLLLEESIADRFLDL 321 Query: 304 LQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYF 363 L+E+ + GN LD +G +I + S+I G E + L+ DGR+N Sbjct: 322 LKEQAKGWQPGNPLDPNTTMGMLIDNTHADSVHSFIRAG-EAHSTLLLDGRKNPWPAA-- 378 Query: 364 VGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIR 423 VGPTIF +V + ++EIF PVL V R KN ++A+ +AN S + GA ++T + + Sbjct: 379 VGPTIFVDVDPASPLSQEEIFGPVLVVTRFKNEEQALALANDSRYGLGAAVWTRDLSRAH 438 Query: 424 YFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFG---TLHA 462 + AG + +N M PF G+K S G +LHA Sbjct: 439 RVSRRLKAGSVFVNNYNDGDMT-VPFGGYKQSGNGRDKSLHA 479 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: 509 Number of extensions: 32 Number of successful extensions: 7 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: 495 Length adjustment: 34 Effective length of query: 453 Effective length of database: 461 Effective search space: 208833 Effective search space used: 208833 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