Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011612157.1 TERY_RS12430 aldehyde dehydrogenase family protein
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000014265.1:WP_011612157.1 Length = 490 Score = 261 bits (666), Expect = 5e-74 Identities = 162/483 (33%), Positives = 259/483 (53%), Gaps = 10/483 (2%) Query: 3 EIRKLKNYINGEWVESKTDQYEDVVNPATKEVLCQVPISTKEDIDYAAQTAAEAFKT--W 60 +I K IN EWVES + + + +NPAT EV+C V + D+D A A +AF + W Sbjct: 12 KIGPTKLLINNEWVESASGKRFETINPATGEVICNVAEADAPDVDKAVIAARKAFTSGEW 71 Query: 61 SKVAVPRRARILFNFQQLLSQHKEELAHLITIENGKNTKEALG-EVGRGIENVEFAAGAP 119 K++ +R +L+ L+ ++ EELA L T++NGK K++L ++ I + AG Sbjct: 72 PKISAAKRGELLYKLADLIEKNIEELARLETLDNGKPFKDSLNTDLPLAIACYRYYAGWA 131 Query: 120 SLMMGDSLASIATDVEAANYRYPIGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSE 179 + G ++ I+ P+GVVG I P+NFP+++ W A+A+GNT ++K +E Sbjct: 132 DKVQGKTIP-ISGPYFCYTRHEPVGVVGQIIPWNFPLLMQAWKLAPALAMGNTLVMKTAE 190 Query: 180 RTPLLTEKLVELFEKAGLPKGVFNVVYGAHDVVN-GILEHPEIKAISFVGSKPVGEYVYK 238 +TPL ++ EL +AG P GV N++ G I H +I ++F GS VG + + Sbjct: 191 QTPLSALRVGELVIEAGFPPGVVNILSGYGPTAGAAISHHKDIDKVAFTGSTEVGRLIME 250 Query: 239 KGSE-NLKRVQSLTGAKNHTIVLNDANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIA 297 ++ NLKRV G K+ IV DA+++ + A F + G+ C A + + VEE Sbjct: 251 AAAKSNLKRVTLELGGKSPNIVFADADMDAAIEGSHFALFFNQGQCCCAGSRLFVEEKCY 310 Query: 298 DEFMAKLQEKVADIKIGNGLDDGVFLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENV 357 DEF+ K E+ +G+ + V GP + E+ + +SYIE G ++GA+++C G V Sbjct: 311 DEFVNKSVERAKLRMVGDPFTERVEQGPQVDEEQFNKVMSYIESGQQDGAQMLCGG-SRV 369 Query: 358 SDDGYFVGPTIFDNVTTEMTIWKDEIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTS 417 D GYF+ PT+F +V M I ++EIF PV+S+I+ K++ E +E AN S + A ++T Sbjct: 370 GDRGYFIAPTVFADVQDNMKIAQEEIFGPVMSIIKFKDIDELVERANNSMYGLAAGVWTQ 429 Query: 418 NSNAIRYFRENIDAGMLGINLGVPAPMAFFPFSGWKSSFFGTLHANGKDSVDFYTRKKVV 477 + + AG + +N A PF G+K S G G+ + YT K V Sbjct: 430 DVTKAHTLAHRLRAGTVWVNC-YDVFDAAAPFGGFKQSGLG--RELGEYGLQQYTEIKTV 486 Query: 478 TAR 480 T + Sbjct: 487 TMK 489 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: 556 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: 490 Length adjustment: 34 Effective length of query: 453 Effective length of database: 456 Effective search space: 206568 Effective search space used: 206568 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