Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011766665.1 AZO_RS14770 aldehyde dehydrogenase family protein
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000061505.1:WP_011766665.1 Length = 506 Score = 226 bits (575), Expect = 2e-63 Identities = 161/485 (33%), Positives = 235/485 (48%), Gaps = 19/485 (3%) Query: 9 NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68 N+I G+WV QY D + P T + CQV ST+EDI+ A A A W + +V R Sbjct: 21 NFIGGKWVAPVRGQYMDNITPITGKPFCQVARSTEEDINLALDAAHAAADKWGRTSVIER 80 Query: 69 ARILFNFQQLLSQHKEELAHLITIENGKNTKEAL-GEVGRGIENVEFAAGAPSLMMGDSL 127 A L L Q+ E +A+ T++NGK +E + ++ I++ + AG G SL Sbjct: 81 ANTLCRIADRLEQNLELIAYAETVDNGKPIRETMAADIPLAIDHFRYFAGCIRAQEG-SL 139 Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187 A + + A ++ P+GVVG I P+NFP+++ W A+A GN +LKP+E TP+ Sbjct: 140 AELDENTVAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNVVVLKPAESTPVGILV 199 Query: 188 LVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKR 246 + EL LP GV N+V G + + I I+F GS G + + S+N+ Sbjct: 200 IAELIADL-LPAGVLNIVNGLGREAGVPLATSSRIAKIAFTGSTTTGRLIMQAASQNIIP 258 Query: 247 VQSLTGAKNHTIVLNDANLED------TVTNIVGAAFGSAGERCMACAVVTVEEGIADEF 300 V G K+ I D D V V A + GE C + + E I D F Sbjct: 259 VTLELGGKSPNIFFQDVAAADDEFFDKAVEGFVLFAL-NQGEVCTCPSRALIHESIYDRF 317 Query: 301 MAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRE----N 356 M + +V IK GN LD +G + K+ LSYIE G EEGA+L+ G E Sbjct: 318 MDRALARVKAIKQGNPLDTETMIGAQASTEQMKKILSYIELGKEEGAQLLAGGGEAKFGG 377 Query: 357 VSDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFT 416 +GY+V PT+F +M I+++EIF PVLSV K+ EA+ IAN + + GA +++ Sbjct: 378 ELAEGYYVQPTVFKG-HNKMRIFQEEIFGPVLSVTTFKDEAEALSIANDTLYGLGAGVWS 436 Query: 417 SNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKV 476 + + NI AG + N P A F G+K S G K +D Y + K Sbjct: 437 RDGSTAYRMGRNIKAGRVWTNCYHLYP-AHAAFGGYKQSGIG--RETHKMMLDHYQQTKN 493 Query: 477 VTARY 481 + Y Sbjct: 494 LLVSY 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: 555 Number of extensions: 29 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: 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 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