Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_036262823.1 DL86_RS14335 aldehyde dehydrogenase family protein
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000746085.1:WP_036262823.1 Length = 506 Score = 213 bits (541), Expect = 2e-59 Identities = 151/484 (31%), Positives = 240/484 (49%), Gaps = 17/484 (3%) Query: 9 NYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRR 68 N+I G+WV + Q + ++P V+C V S+ ED++ A A A W + + R Sbjct: 21 NFIGGKWVPAVKGQTFENISPIDGRVICTVARSSAEDVELALDAAHAARGAWGRTSPAER 80 Query: 69 ARILFNFQQLLSQHKEELAHLITIENGKNTKEA-LGEVGRGIENVEFAAGAPSLMMGDSL 127 + L + Q + LA + TI+NGK +E ++ +++ + AG G + Sbjct: 81 SLALLRIADRIEQKLDMLAMVETIDNGKPIRETKAADLPLAVDHFRYFAGCLRAQEG-GI 139 Query: 128 ASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEK 187 + I D A ++ P+GVV I P+NFP+++ W A+A GN ILKP+E+TP+ Sbjct: 140 SEIDHDTVAYHFHEPLGVVAQIIPWNFPLLMAVWKLAPALAAGNCVILKPAEQTPMSVMV 199 Query: 188 LVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKR 246 LV++ LP GV NV+ G + + ++ I ++F G G + + SEN+ Sbjct: 200 LVDMIGDL-LPPGVLNVINGFGVEAGKPLAQNKRIAKVAFTGETTTGRLIMQYASENIIP 258 Query: 247 VQSLTGAKNHTIVLND-ANLEDTVTNIVGAAFG----SAGERCMACAVVTVEEGIADEFM 301 V G K+ I D A+ +D + F + GE C + V+E I D FM Sbjct: 259 VTLELGGKSPNIFFADVADEDDDFFDKALEGFSMFALNQGEVCTCPSRALVQEKIYDRFM 318 Query: 302 AKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVC-DGRENVSDD 360 + +V IK GN LD +G D ++ LSY++ G +EGA+++ GR +V + Sbjct: 319 ERAVARVKKIKQGNPLDPATMIGAQASNDQLEKILSYLDIGRQEGAKVLAGGGRADVGPE 378 Query: 361 ---GYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTS 417 G++V PTI + +M I+++EIF PVLSV K+ +EA+EIAN + + GA ++T Sbjct: 379 LAGGFYVQPTILEG-HNKMRIFQEEIFGPVLSVTSFKDDEEALEIANDTLYGLGAGVWTR 437 Query: 418 NSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477 N F I+AG + N P A F G+K S G N K +D Y + K + Sbjct: 438 NGTRAYRFGRAIEAGRVWTNCYHLYP-AHAAFGGYKQSGIG--RENHKMMLDHYQKTKNM 494 Query: 478 TARY 481 Y Sbjct: 495 LVSY 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: 546 Number of extensions: 20 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