Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011383248.1 AMB_RS04115 5-carboxymethyl-2-hydroxymuconate semialdehyde dehydrogenase
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000009985.1:WP_011383248.1 Length = 485 Score = 249 bits (636), Expect = 1e-70 Identities = 159/483 (32%), Positives = 256/483 (53%), Gaps = 25/483 (5%) Query: 7 LKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVP 66 +K+ ING VES + +NPA EV+CQ+ + ++ A A EAF W+ + Sbjct: 2 IKHLINGRQVESASTIAN--LNPANNEVICQIAAGGEAEVAQAVAAAKEAFPKWAGLPAS 59 Query: 67 RRARILFNFQQLLSQHKEELAHLITIENGKN---TKEALGEVGRGIENVEFAAGAPSLMM 123 +RA++L L++QH +E+A L +++ G++ TK+ L V R +N F A + Sbjct: 60 QRAKLLRKVGDLINQHVDEIAKLESLDTGQSYWRTKKML--VPRAADNFYFFADTCCHVD 117 Query: 124 GDSLASIATDVEAANYRY--PIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERT 181 G++ + + NY P+GVVG I+P+N P M W +A GNT +LK SE + Sbjct: 118 GETYPTN----DHLNYTLYQPVGVVGLISPWNVPFMTATWKTAPCLAFGNTAVLKMSELS 173 Query: 182 PLLTEKLVELFEKAGLPKGVFNVVYGAHDVVN-GILEHPEIKAISFVGSKPVGEYVYKKG 240 PL ++L +L +AG+P GVFN+V+G V +++HP+++ +SF GS G + + G Sbjct: 174 PLSADRLGQLILEAGIPAGVFNIVHGYGSAVGEALVKHPDVRGVSFTGSTATGNRIIQSG 233 Query: 241 SENLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEF 300 LK+ G K+ I+ +D + E V + A +G+ GE C + V++G+ D F Sbjct: 234 G--LKKYSMELGGKSPNIIFDDCDFERAVDAAIVAVYGNNGESCTNGTRILVQDGLYDRF 291 Query: 301 MAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVS-- 358 +A L E+ + +G+ LD+ +GP+I D+ K+ SYIE G+ EGAR+V G Sbjct: 292 VAALAERTRKVVVGDPLDEATNVGPMITRDHWKKVTSYIELGISEGARVVAGGLGTPEGL 351 Query: 359 ----DDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACL 414 +G FV PT+ +V + ++EIF PV VIR K+ EA++IAN + + + + Sbjct: 352 APHLKNGNFVRPTVLADVDNSWRVAQEEIFGPVACVIRFKDEAEALKIANATSYGLASYV 411 Query: 415 FTSNSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRK 474 +T N E I+AG++ +N + PF G K S GT G S + + Sbjct: 412 WTENGARAIRMAEGIEAGLVFVNSQNVRDLR-QPFGGIKGS--GTGREGGHYSYEAFLEV 468 Query: 475 KVV 477 K V Sbjct: 469 KNV 471 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: 576 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: 485 Length adjustment: 34 Effective length of query: 453 Effective length of database: 451 Effective search space: 204303 Effective search space used: 204303 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