Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_086509869.1 BZY95_RS10455 aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_002151265.1:WP_086509869.1 Length = 502 Score = 252 bits (643), Expect = 2e-71 Identities = 161/477 (33%), Positives = 257/477 (53%), Gaps = 18/477 (3%) Query: 10 YINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFK--TWSKVAVPR 67 +I+ +V +++ + NPAT E+L QV + D A A AF WS++A + Sbjct: 28 FIDDSFVAAESGATFESRNPATGEILAQVASCDEPDAARAVAVARRAFADGAWSRLAPGK 87 Query: 68 RARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSL 127 R + L + L+ HK ELA + T++ GK +LG++ I + + A + G+ + Sbjct: 88 RKKTLLHLADLMEAHKHELALIDTLDMGKPIASSLGDMAGAIACIRYQAECIDKLYGE-V 146 Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187 A + A R PIGVV I P+NFP+M+ W A+A GN+ ILKPSE++PL + Sbjct: 147 APTGEETLALVLREPIGVVAAIVPWNFPLMMTAWKIAPALAAGNSVILKPSEKSPLSALR 206 Query: 188 LVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYK-KGSENLK 245 L +L ++AG+P+GVF V+ G H V + E+ ++F GS VG+ + + G NLK Sbjct: 207 LAQLAQEAGIPRGVFQVLPGFGHTVGKALALSMEVDCLAFTGSTAVGKQLMQYAGQSNLK 266 Query: 246 RVQSLTGAKNHTIVLNDANLEDTVTNIVGAA-FGSAGERCMACAVVTVEEGIADEFMAKL 304 RV G K+ +V D DTV + AA F + GE C+A + + VE I D+F+ ++ Sbjct: 267 RVYLECGGKSPNLVFADCKDLDTVASHAAAAIFHNQGEVCIAGSRLLVENTIRDDFVERV 326 Query: 305 QEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFV 364 + +++ G+ LD F+G ++ E +R L YI +G+EEGARL G + + G F+ Sbjct: 327 LKAAENMQPGDPLDPDSFMGAIVDEAQHRRILDYIRQGVEEGARLRTGG-QAIDGPGLFI 385 Query: 365 GPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRY 424 PT+FD VT +MTI ++EIF PVL+V+ +EA+ +AN + + A L++ + + I Sbjct: 386 PPTVFDGVTPQMTIGREEIFGPVLAVLGFDTEEEAVAMANDTPYGLAAGLWSQDIDRIMR 445 Query: 425 FRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKD----SVDFYTRKKVV 477 + +G + +N PF G K S NG+D S++ Y+ K V Sbjct: 446 VTRRLQSGQVFVNNWAGGDQT-MPFGGVKQS------GNGRDKSHHSLEEYSELKSV 495 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: 522 Number of extensions: 23 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: 502 Length adjustment: 34 Effective length of query: 453 Effective length of database: 468 Effective search space: 212004 Effective search space used: 212004 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 24 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