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_086508312.1 BZY95_RS01885 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
Query= SwissProt::Q02253 (535 letters) >NCBI__GCF_002151265.1:WP_086508312.1 Length = 499 Score = 560 bits (1443), Expect = e-164 Identities = 270/485 (55%), Positives = 356/485 (73%) Query: 36 SVPTVKLFIDGKFVESKSDKWIDIHNPATNEVVGRVPQSTKAEMEAAVAACKRAFPAWAD 95 S+ + ++IDG+ V S+S +W D+ NPAT EVV RVP T E++ AVA+ K AF W Sbjct: 2 SIREIPMYIDGQAVPSQSQEWRDVINPATQEVVARVPFCTAEEVDRAVASAKEAFKTWRK 61 Query: 96 TSILSRQQVLLRYQQLIKENLKEIARLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLM 155 T + R +++L Q LI+E+ +E+A LIT E GKTL DA G+V RGL+VVEHACS+TSL Sbjct: 62 TPLAKRMRIMLTLQALIREHTEELAALITEEHGKTLPDAAGEVGRGLEVVEHACSITSLQ 121 Query: 156 LGETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVP 215 LGE + ++D+Y+ PLGV AGI FNFP M+P +MFP+A+ GNTF++KPSE+ P Sbjct: 122 LGELAENAANEVDVYTLNQPLGVGAGITAFNFPIMLPCFMFPLAIATGNTFVLKPSEQDP 181 Query: 216 GATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNQAGEYIFERGSR 275 +TM L +L ++G P G LN++HG + N ICDHPDIKA+SF+GS G +I+ R S Sbjct: 182 SSTMRLVELAHEAGVPAGVLNVVHGGPDVANQICDHPDIKALSFIGSTNVGTHIYRRASE 241 Query: 276 NGKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLPE 335 GKRVQ+ MGAKNH VVMPDAN+ +N L+G+AFGAAGQRCMA S VLVGEA +WL + Sbjct: 242 AGKRVQSMMGAKNHCVVMPDANRSQAINNLLGSAFGAAGQRCMANSVVVLVGEANQWLDD 301 Query: 336 LVERAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGAKEGASILLDGRKIKVKGYEN 395 +VE A+N++V G Q ADLGPL++ A++RV LID+G KEGA +L+DGR +V+GY + Sbjct: 302 IVEGARNMKVGPGTQRDADLGPLVSKAARDRVVRLIDAGEKEGARLLVDGRGYQVEGYPD 361 Query: 396 GNFVGPTIISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAIFTTNGA 455 GNFVG T+ ++VKP MT Y+EEIFGPVL V+ +TLDEAI +N NP GNGT+IFT +G Sbjct: 362 GNFVGATVFADVKPEMTIYREEIFGPVLCVVSVDTLDEAIAFINANPNGNGTSIFTNSGW 421 Query: 456 IARKYAHMVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQ 515 +AR++ +DVGQVG+NVPIPVP+ FSFTGSR S GD GKQ IQF+TQ KT+T++ Sbjct: 422 VARRFETDIDVGQVGINVPIPVPVAYFSFTGSRGSKLGDLGPNGKQAIQFWTQTKTVTAR 481 Query: 516 WKEED 520 W E + Sbjct: 482 WFEPE 486 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: 700 Number of extensions: 37 Number of successful extensions: 1 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: 499 Length adjustment: 35 Effective length of query: 500 Effective length of database: 464 Effective search space: 232000 Effective search space used: 232000 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