Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate GFF4637 PS417_23725 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::Q02252 (535 letters) >FitnessBrowser__WCS417:GFF4637 Length = 505 Score = 604 bits (1557), Expect = e-177 Identities = 289/490 (58%), Positives = 374/490 (76%) Query: 31 SSFSSSVPTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAF 90 +S SV VKL I G++VESK+ +W DI NPAT EV+ +VP AT E++AAI + RAF Sbjct: 3 ASADISVQQVKLLINGEWVESKTTEWQDIVNPATQEVLAKVPFATADEVNAAIDAAHRAF 62 Query: 91 PAWADTSVLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACS 150 W T + +R +++L+ Q LI+E+ K IA +++ EQGKT+ADAEGD+FRGL+VVEHACS Sbjct: 63 QTWKLTPIGARMRIMLKLQALIREHSKRIAVVLSNEQGKTIADAEGDIFRGLEVVEHACS 122 Query: 151 VTSLMMGETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKP 210 + +L MGE ++ +D Y+ R P+GVCAGI PFNFPAMIPLWMFPMA+ CGNTF++KP Sbjct: 123 IGTLQMGEFSENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKP 182 Query: 211 SERVPGATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIF 270 SE+ P +TMLL +L ++G P G LN++HG + V+ +C H DIKA+SFVGS G +++ Sbjct: 183 SEQDPLSTMLLVELALEAGVPAGVLNVVHGGKDVVDALCTHKDIKAVSFVGSTAVGTHVY 242 Query: 271 ERGSRHGKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAK 330 + +HGKRVQ+ MGAKNH VV+PDAN+E+TLN LVGA FGAAGQRCMA S VLVG +K Sbjct: 243 DLAGKHGKRVQSMMGAKNHAVVLPDANREHTLNALVGAGFGAAGQRCMATSVVVLVGASK 302 Query: 331 KWLPELVEHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKV 390 +WLP+L A+ L+VNAG + G D+GP+I+ +AK R+ LI+SG KEGA + LDGR IKV Sbjct: 303 QWLPDLKALAQKLKVNAGSEAGTDVGPVISKRAKARILELIESGVKEGAKLELDGRDIKV 362 Query: 391 KGYENGNFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIF 450 G+E GNFVGPT+ S V P+M Y +EIFGPVLVVLE TLDEAI +VN NP+GNGT +F Sbjct: 363 PGFEQGNFVGPTLFSGVTPSMQIYTQEIFGPVLVVLEVATLDEAIALVNANPFGNGTGLF 422 Query: 451 TTNGATARKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLK 510 T +GA ARK+ +DVGQVG+N+PIPVP+P FSFTGSR S GD YGKQ +QFYTQ K Sbjct: 423 TQSGAAARKFQSEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTK 482 Query: 511 TITSQWKEED 520 T+TS+W ++D Sbjct: 483 TVTSRWFDDD 492 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: 674 Number of extensions: 31 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: 505 Length adjustment: 35 Effective length of query: 500 Effective length of database: 470 Effective search space: 235000 Effective search space used: 235000 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