Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 3607686 Dshi_1095 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P42412 (487 letters) >FitnessBrowser__Dino:3607686 Length = 506 Score = 213 bits (541), Expect = 2e-59 Identities = 154/485 (31%), Positives = 240/485 (49%), Gaps = 19/485 (3%) Query: 9 NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68 N+I G++V +Y D V P T EV+ Q+ S+ D++ A A A W K +V R Sbjct: 21 NFIGGKFVPPVEGRYFDNVTPITGEVVGQIARSSAADVELALDAAHAAKDAWGKTSVTER 80 Query: 69 ARILFNFQQLLSQHKEELAHLITIENGKNTKEA-LGEVGRGIENVEFAAGAPSLMMGDSL 127 A I+ + ++ + +A T +NGK +E L ++ +++ + AG G S+ Sbjct: 81 ANIVLKIADRIEENLDIIAKAETWDNGKPIRETTLADIPLAVDHFRYFAGVLRGQEG-SM 139 Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187 + I D A ++ P+GVVG I P+NF +++ W AIA GN +LKP+E+TP Sbjct: 140 SEIDNDTVAYHFHEPLGVVGQIIPWNFSILMAAWKLAPAIAAGNCIVLKPAEQTPAAIMV 199 Query: 188 LVELFEKAGLPKGVFNVVYGAHDVVNGILEHPE-IKAISFVGSKPVGEYVYKKGSENLKR 246 LVEL LP GV N+V G V L + I I+F GS G + + + NL Sbjct: 200 LVELISDL-LPAGVLNIVNGYGGEVGAALATSDRIAKIAFTGSTATGRKIMEAATVNLIP 258 Query: 247 VQSLTGAKNHTIVLNDANLED------TVTNIVGAAFGSAGERCMACAVVTVEEGIADEF 300 V G K+ I D ED V V AF + GE C + + E I +EF Sbjct: 259 VTLELGGKSPNIFFKDVMAEDDAFLDKAVEGFVLFAF-NQGEVCTCPSRALIHEDIYEEF 317 Query: 301 MAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGR-ENVSD 359 +A+ +V I G+ +G ++ K + LSY + G+EEGA ++ G+ +VSD Sbjct: 318 IARAIARVKAIVQGDPRKMETMVGAQASKEQKDKILSYFQIGVEEGAEVLTGGKVADVSD 377 Query: 360 ---DGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFT 416 DG+++ PTI +M ++++EIF PV+SV K +EA+E+AN + + GA +++ Sbjct: 378 DLKDGFYIEPTILKG-HNKMRVFQEEIFGPVVSVTTFKTEEEALELANDTMYGLGAGVWS 436 Query: 417 SNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKV 476 + N F + AG + +N A A F G+K S G N K +D Y + K Sbjct: 437 RDQNTCYRFGRGVQAGRVWVN-NYHAYPAHAAFGGYKQSGIG--RENHKMMLDHYQQTKN 493 Query: 477 VTARY 481 + Y Sbjct: 494 MLVSY 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: 582 Number of extensions: 36 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 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