Align methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_011373513.1 SUDEN_RS09855 aldehyde dehydrogenase family protein
Query= BRENDA::P42412 (487 letters) >NCBI__GCF_000012965.1:WP_011373513.1 Length = 471 Score = 187 bits (475), Expect = 7e-52 Identities = 133/437 (30%), Positives = 210/437 (48%), Gaps = 11/437 (2%) Query: 27 VNPATKEVLCQVPISTKEDIDYAAQTAAEAFKTWSKVAVPRRARILFNFQQLLSQHKEEL 86 VNP EV + +D A A A K SK + +R L + L+Q+KE++ Sbjct: 21 VNPYNGEVASEFVTCNADDAKKALNIALLASKEASKTTIAQRCSWLLDVASKLAQNKEDI 80 Query: 87 AHLITIENGKNTKEALGEVGRGIENVEFAAGAPSLMMGDSLAS--IATDVEAANY--RYP 142 A IT E GK + EV R IE V AA M G+++ + A+ + ++ R P Sbjct: 81 AKTITDEVGKPITYSRIEVERCIETVTLAAETMRTMHGETVNTDAFASGKKTISFFSRVP 140 Query: 143 IGVVGGIAPFNFPMMVPCWMFPMAIALGNTFILKPSERTPLLTEKLVELF-EKAGLPKGV 201 GVV I PFNFP+ + A+ GN ILKP+ PL K +LF E K Sbjct: 141 CGVVVAITPFNFPLNLIAHKIAPALVAGNAVILKPTPEAPLTAYKFAKLFIESEFAIKDA 200 Query: 202 FNVVYGAHDVVNGILEHPEIKAISFVGSKPVGEYVYKKGSENLKRVQSLTGAKNHTIVLN 261 +VVYG DV ++ + ISF GS VGE + K S +K+V G T + Sbjct: 201 LSVVYGDADVGGTLVTSEIPRVISFTGSVGVGEIITK--SAGIKKVSLELGGNAATFIDK 258 Query: 262 DANLEDTVTNIVGAAFGSAGERCMACAVVTVEEGIADEFMAKLQEKVADIKIGNGLDDGV 321 ANL+ AF ++G+ C++ + V + I EF K+ E + +G+ ++ Sbjct: 259 SANLDLAAQRCAIGAFVNSGQVCISLQRIYVHKDIYSEFALKIAEATKKLVVGSPYEEDT 318 Query: 322 FLGPVIREDNKKRTLSYIEKGLEEGARLVCDGRENVSDDGYFVGPTIFDNVTTEMTIWKD 381 F+GP++ ++ KR + +++ ++EGA + + R +G P + +V +M I Sbjct: 319 FMGPLVNDEAAKRAMEWVQSAIKEGATPILEPRV----EGRVFYPCVMADVKEDMAIVCQ 374 Query: 382 EIFAPVLSVIRVKNLKEAIEIANKSEFANGACLFTSNSNAIRYFRENIDAGMLGINLGVP 441 E+FAP++S+I VK+ EA+ + N S + +FT++ N + +DAG + IN Sbjct: 375 EVFAPIVSLIEVKDFDEALPMMNNSPYGLQFSIFTNDLNLTKRAINELDAGGIVINDMPT 434 Query: 442 APMAFFPFSGWKSSFFG 458 P+ G K S G Sbjct: 435 LRFDIQPYGGVKLSGVG 451 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: 494 Number of extensions: 27 Number of successful extensions: 4 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: 471 Length adjustment: 34 Effective length of query: 453 Effective length of database: 437 Effective search space: 197961 Effective search space used: 197961 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: 51 (24.3 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