Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_012607209.1 AFE_RS08085 aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000021485.1:WP_012607209.1 Length = 506 Score = 216 bits (550), Expect = 1e-60 Identities = 150/488 (30%), Positives = 236/488 (48%), Gaps = 19/488 (3%) Query: 6 KLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAV 65 K N+I G+WV QY DV+ P + Q ST EDI+ A A W K + Sbjct: 18 KYDNFIGGKWVAPVKGQYFDVITPINGKSYTQAARSTAEDIELALDAAHAIADKWGKTSP 77 Query: 66 PRRARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAGAPSLMMG 124 RA IL + + E LA+ T++NGK +E L ++ +++ + AG G Sbjct: 78 AERANILLKVADRIEANLELLAYAETVDNGKPIRETLNADIPLAVDHFRYFAGCVRAQEG 137 Query: 125 DSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLL 184 ++ I + A ++ P+GVVG I P+NFP+++ W A+ GN +LKP+E TP+ Sbjct: 138 -GISDIDENTVAYHFHEPLGVVGQIIPWNFPILMASWKLAPALGAGNVVVLKPAESTPIS 196 Query: 185 TEKLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSEN 243 L EL LP GV N+V G + + I I+F GS G + + + + Sbjct: 197 ILILAELIADL-LPPGVLNIVNGYGREAGMPLATSKRIAKIAFTGSTTTGRVIAQAAANS 255 Query: 244 LKRVQSLTGAKNHTIVL------NDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIA 297 L G K+ I +D+ L+ + +V AF + GE C + ++E I Sbjct: 256 LIPATLELGGKSPNIFFADVMDKDDSFLDKAIEGLVLFAF-NQGEVCTCPSRALIQESIY 314 Query: 298 DEFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENV 357 D+FM + +++ IK GN LD +G ++ + LSY++ G +EGA+++ G + + Sbjct: 315 DKFMERCLDRIKAIKQGNPLDTNTMIGAQASKEQLTKILSYLDLGKQEGAQVLIGGSQAI 374 Query: 358 ----SDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGAC 413 D GY+V PT+F +M I+++EIF PVL+V K+ EA+ IAN + + GA Sbjct: 375 VDGDLDGGYYVQPTLFKG-HNKMRIFQEEIFGPVLAVTTFKDEAEALSIANDTLYGLGAG 433 Query: 414 LFTSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTR 473 +++ N N I AG + IN P A F G+K S G K +D Y + Sbjct: 434 VWSRNGNVAYRMGRAIKAGRVWINCYHAYP-AHAAFGGYKESGIG--RETHKVMLDHYQQ 490 Query: 474 KKVVTARY 481 K + Y Sbjct: 491 TKNLLVSY 498 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: 559 Number of extensions: 23 Number of successful extensions: 5 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: 506 Length adjustment: 34 Effective length of query: 453 Effective length of database: 472 Effective search space: 213816 Effective search space used: 213816 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