Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_058929223.1 AU252_RS01555 aldehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_001484605.1:WP_058929223.1 Length = 508 Score = 248 bits (632), Expect = 5e-70 Identities = 152/478 (31%), Positives = 247/478 (51%), Gaps = 10/478 (2%) Query: 5 RKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKT--WSK 62 R I+G WV+S + + V+P +VP +T ED+D A + A AF W + Sbjct: 19 RSYSMLIDGAWVQSSSGETFACVDPYDNASWGRVPAATVEDVDRAVRAARRAFDEGGWPQ 78 Query: 63 VAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLM 122 +RA +L F LL+++ +ELA ENGK E + ++ + AG + Sbjct: 79 TLPSQRAALLRRFADLLTENADELARGQIHENGKLIGEMTWGALQMGQHAHYVAGLAETI 138 Query: 123 MGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTP 182 G ++ S + A +R PIGVV I P+N P+M+ W A+A GNT ++KPSE TP Sbjct: 139 QGRTIESNWPNTAAFTFREPIGVVAMITPWNSPLMLLSWKLFAALAAGNTVVIKPSEATP 198 Query: 183 LLTEKLVELFEKAGLPKGVFNVVYG-AHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGS 241 T ++ EL +AG P GV NVV G + +++H + I+F GS G + K+ + Sbjct: 199 TSTLRMAELAMEAGFPPGVINVVTGFGQPTGSALVDHRGVDKIAFTGSTSAGRAINKQAA 258 Query: 242 ENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFM 301 E RV G K+ I+ +DA++++ V + FG+ G+ CM + V V++ I D+F+ Sbjct: 259 ERFARVTLELGGKSPNIIFSDADIDNAVHGAMAGIFGATGQTCMGGSRVLVQDSIYDDFV 318 Query: 302 AKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVS--- 358 ++ + +G+ LD V +GPV ++ + Y++ G EGA +V G ++ Sbjct: 319 DRMARATQALTLGDPLDPTVDMGPVSNRAQFQKVIDYVDLGQSEGAEVVAGGARCMTTSE 378 Query: 359 -DDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTS 417 G F PT+F NV+ E + ++EIF PV S+IR ++ EA++IAN S+F A ++T+ Sbjct: 379 LSKGLFFEPTVFANVSNESRLAQEEIFGPVASIIRFRDEDEAVKIANASDFGLAAGVWTN 438 Query: 418 NSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKK 475 + + + +G + +N PF G+K S G G D++D YT K Sbjct: 439 DVSRAHRMIRRVRSGTVWVNT-YRLTNYSVPFGGFKQSGIG--RELGPDALDAYTEVK 493 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: 541 Number of extensions: 29 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: 508 Length adjustment: 34 Effective length of query: 453 Effective length of database: 474 Effective search space: 214722 Effective search space used: 214722 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