Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate AO356_07870 AO356_07870 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::Q02252 (535 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_07870 Length = 508 Score = 609 bits (1571), Expect = e-179 Identities = 289/493 (58%), Positives = 378/493 (76%) Query: 29 SASSFSSSVPTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKR 88 S + +++ TV+L I G++VES+S +W DI NPAT +V+ +VP AT +E+DAAIA+ +R Sbjct: 4 SLTPSDTALQTVRLLIDGEWVESQSSEWHDIVNPATQQVLAKVPFATASEVDAAIAAAQR 63 Query: 89 AFPAWADTSVLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHA 148 AF W T + +R +++L+ Q LI+E+ K IA +++ EQGKT+ADAEGD+FRGL+VVEHA Sbjct: 64 AFQTWKLTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVVEHA 123 Query: 149 CSVTSLMMGETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLM 208 CS+ +L MGE ++ +D Y+ R P+GVCAGI PFNFPAMIPLWMFPMA+ CGNTF++ Sbjct: 124 CSIGTLQMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVL 183 Query: 209 KPSERVPGATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEY 268 KPSE+ P +TMLL +L ++G P G LN++HG + V+ +C H DIKA+SFVGS G + Sbjct: 184 KPSEQDPLSTMLLVELAIEAGVPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTH 243 Query: 269 IFERGSRHGKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGE 328 +++ RHGKRVQ+ MGAKNH VV+PDAN+E TLN LVGA FGAAGQRCMA S VLVG Sbjct: 244 VYDLAGRHGKRVQSMMGAKNHAVVLPDANREQTLNALVGAGFGAAGQRCMATSVVVLVGA 303 Query: 329 AKKWLPELVEHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKI 388 AK+WLPEL A+ L+VNAG +PG D+GP+I+ +AK R+ LI+SG KEGA + LDGR I Sbjct: 304 AKQWLPELKALAQKLKVNAGSEPGTDVGPVISKRAKARILELIESGVKEGAKLELDGRGI 363 Query: 389 KVKGYENGNFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTA 448 V G+E GNFVGPT+ S V M Y EEIFGPVLVVLE +TLD+AI +VN NP+GNGT Sbjct: 364 SVPGFEQGNFVGPTLFSGVTTEMRIYTEEIFGPVLVVLEVDTLDQAIALVNANPFGNGTG 423 Query: 449 IFTTNGATARKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQ 508 +FT +GA ARK+ +DVGQVG+N+PIPVP+P FSFTGSR S GD YGKQ +QFYTQ Sbjct: 424 LFTQSGAAARKFQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQ 483 Query: 509 LKTITSQWKEEDA 521 KT+T++W ++D+ Sbjct: 484 TKTVTARWFDDDS 496 Lambda K H 0.318 0.133 0.391 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: 654 Number of extensions: 28 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: 508 Length adjustment: 35 Effective length of query: 500 Effective length of database: 473 Effective search space: 236500 Effective search space used: 236500 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