Align Methylmalonate-semialdehyde dehydrogenase [acylating], mitochondrial; MMSDH; Malonate-semialdehyde dehydrogenase [acylating]; Aldehyde dehydrogenase family 6 member A1; EC 1.2.1.18; EC 1.2.1.27 (characterized)
to candidate WP_057687530.1 ABB28_RS16890 betaine-aldehyde dehydrogenase
Query= SwissProt::Q02253 (535 letters) >NCBI__GCF_001431535.1:WP_057687530.1 Length = 490 Score = 229 bits (585), Expect = 1e-64 Identities = 149/485 (30%), Positives = 245/485 (50%), Gaps = 14/485 (2%) Query: 35 SSVPTVKLFIDGKFVESKSDKWIDIHNPATNEVVGRVPQSTKAEMEAAVAACKRAFPAWA 94 S++P +L+I GK V++ S K NPAT +V+ V + +A++E AVA+ WA Sbjct: 2 STLPLQQLYIHGKLVDATSGKTFQSINPATGKVIAEVQIANQADVERAVASAAEGQKVWA 61 Query: 95 DTSILSRQQVLLRYQQLIKENLKEIARLITLEQGKTLADAEG-DVFRGLQVVEHACSVTS 153 + + R ++L R L++E +A+L TL+ GK L++ D+ G V+E+ + + Sbjct: 62 AMTAMERSRILRRAVDLLRERNDALAQLETLDTGKALSETTTVDIVTGADVLEYYAGLAT 121 Query: 154 LMLGETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSER 213 + G +P + + Y+ R PLGV AGI +N+P I LW A+ GN + KPSE Sbjct: 122 AIEGNQVP-LRESSFFYTRREPLGVVAGIGAWNYPVQIALWKSAPALAAGNAMVFKPSEV 180 Query: 214 VPGATMLLAKLLQDSGAPDGTLNIIHGQ-HEAVNFICDHPDIKAISFVGSNQAGEYIFER 272 P + LAK+ ++G PDG N++ G E ++ +HP I+ ISF G + G+ + Sbjct: 181 TPLTVIELAKIYTEAGVPDGVFNVVQGPGREVGQWLTEHPVIEKISFTGGVETGKKVMAS 240 Query: 273 GSRNG-KRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKK 331 + + K V +G K+ V+ DA E + V A F ++GQ C T V V Sbjct: 241 AASSSLKEVTMELGGKSPLVICDDAQLERAADIAVMANFFSSGQVCTN-GTRVFVPRPML 299 Query: 332 WLPE--LVERAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGAKEGASILLDGRKIK 389 E +VER K +R+ + GP+ + + V LI++G +EGA +L G + Sbjct: 300 AAFEAAVVERVKRIRIGDPQDAQTNFGPMTSFAHMDNVLRLIETGKREGARLLTGGGRAT 359 Query: 390 VKGYENGNFVGPTIISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAI 449 G +V PT+ S+ + MT +EEIFGPV+ +L + +E I ND +G + Sbjct: 360 DGALAKGAYVLPTVFSDCRDDMTIVREEIFGPVMSILAYDDEEEVIARANDTHFGLAAGV 419 Query: 450 FTTNGAIARKYAHMVDVGQVGVNV--PIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYT 507 + + A A + H ++ G +N P +P+ G + S G N G + YT Sbjct: 420 VSNDIARAHRIIHRLEAGICWINTWGESPAEMPV---GGYKQSGVGREN--GISTLAHYT 474 Query: 508 QLKTI 512 ++K++ Sbjct: 475 RIKSV 479 Lambda K H 0.318 0.133 0.389 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: 517 Number of extensions: 27 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: 535 Length of database: 490 Length adjustment: 35 Effective length of query: 500 Effective length of database: 455 Effective search space: 227500 Effective search space used: 227500 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