Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate AO353_05990 AO353_05990 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::Q02252 (535 letters) >lcl|FitnessBrowser__pseudo3_N2E3:AO353_05990 AO353_05990 methylmalonate-semialdehyde dehydrogenase Length = 507 Score = 606 bits (1562), Expect = e-178 Identities = 287/487 (58%), Positives = 376/487 (77%) Query: 35 SSVPTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWA 94 ++V VKL I G++VES++ +W DI NPAT +V+ +VP AT AE+DAAI++ RAF W Sbjct: 9 TTVQKVKLLIDGQWVESQTTEWHDIVNPATQQVLAKVPFATPAEVDAAISAAHRAFQTWK 68 Query: 95 DTSVLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSL 154 T + +R +++L+ Q LI+E+ K IA +++ EQGKT+ADAEGD+FRGL+VVEHACS+ SL Sbjct: 69 LTPIGARMRIMLKLQALIREHSKRIAVVLSAEQGKTIADAEGDIFRGLEVVEHACSIGSL 128 Query: 155 MMGETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERV 214 MGE ++ +D Y+ R P+GVCAGI PFNFPAMIPLWMFPMA+ CGNTF++KPSE+ Sbjct: 129 QMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQD 188 Query: 215 PGATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERGS 274 P +TMLL +L ++G P G LN++HG + V+ +C H DIKA+SFVGS G ++++ Sbjct: 189 PMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVYDLAG 248 Query: 275 RHGKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLP 334 +HGKRVQ+ MGAKNH VV+PDAN+E LN LVGA FGAAGQRCMA S VLVG AK+WLP Sbjct: 249 KHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGAAKQWLP 308 Query: 335 ELVEHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYE 394 +L A+ L+VNAG +PG D+GP+I+ +AK R+ +LI+SG KEGA + LDGR I V GYE Sbjct: 309 DLKALAQKLKVNAGSEPGTDVGPVISKRAKARILDLIESGIKEGAKLELDGRDITVPGYE 368 Query: 395 NGNFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNG 454 GNFVGPT+ S V +M Y +EIFGPVLVVLE +TLD+AI +VN NP+GNGT +FT +G Sbjct: 369 KGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVDTLDQAIALVNANPFGNGTGLFTQSG 428 Query: 455 ATARKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITS 514 A ARK+ + +DVGQVG+N+PIPVP+P FSFTGSR S GD YGKQ +QFYTQ KT+TS Sbjct: 429 AAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTS 488 Query: 515 QWKEEDA 521 +W ++D+ Sbjct: 489 RWFDDDS 495 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: 666 Number of extensions: 29 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: 507 Length adjustment: 35 Effective length of query: 500 Effective length of database: 472 Effective search space: 236000 Effective search space used: 236000 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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