Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate PfGW456L13_5146 Methylmalonate-semialdehyde dehydrogenase (EC 1.2.1.27)
Query= BRENDA::Q02252 (535 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_5146 Length = 508 Score = 607 bits (1565), Expect = e-178 Identities = 288/487 (59%), Positives = 375/487 (77%) Query: 35 SSVPTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWA 94 ++V VKL I G++VESK+ +W DI NPAT +V+ +VP AT E+DAAI++ RAF W Sbjct: 10 TTVQKVKLLIDGQWVESKTTEWHDIINPATQQVLAKVPFATAEEVDAAISAAHRAFQTWK 69 Query: 95 DTSVLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSL 154 T + +R +++L+ Q LI+E+ K IA +++ EQGKT+ADAEGD+FRGL+VVEHACS+ SL Sbjct: 70 LTPIGARMRIMLKLQALIREHSKRIAAVLSAEQGKTIADAEGDIFRGLEVVEHACSIGSL 129 Query: 155 MMGETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERV 214 MGE ++ +D Y+ R P+GVCAGI PFNFPAMIPLWMFPMA+ CGNTF++KPSE+ Sbjct: 130 QMGEFAENVAGGVDTYTLRQPIGVCAGITPFNFPAMIPLWMFPMAIACGNTFVLKPSEQD 189 Query: 215 PGATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERGS 274 P +TMLL +L ++G P G LN++HG + V+ +C H DIKA+SFVGS G ++++ Sbjct: 190 PMSTMLLVELAIEAGIPAGVLNVVHGGKDVVDGLCTHKDIKAVSFVGSTAVGTHVYDLAG 249 Query: 275 RHGKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLP 334 +HGKRVQ+ MGAKNH VV+PDAN+E LN LVGA FGAAGQRCMA S VLVG AK+WLP Sbjct: 250 KHGKRVQSMMGAKNHAVVLPDANREQALNALVGAGFGAAGQRCMATSVVVLVGAAKQWLP 309 Query: 335 ELVEHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYE 394 +L A+ L+VNAG +PG D+GP+I+ +AK R+ +LI+SG KEGA + LDGR+I V GYE Sbjct: 310 DLKALAQKLKVNAGSEPGTDVGPVISKKAKARILDLIESGIKEGAKLELDGREISVPGYE 369 Query: 395 NGNFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNG 454 GNFVGPT+ S V +M Y +EIFGPVLVVLE TLDEAI +VN NP+GNGT +FT +G Sbjct: 370 KGNFVGPTLFSGVTTDMQIYTQEIFGPVLVVLEVNTLDEAIALVNANPFGNGTGLFTQSG 429 Query: 455 ATARKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITS 514 A ARK+ + +DVGQVG+N+PIPVP+P FSFTGSR S GD YGKQ +QFYTQ KT+TS Sbjct: 430 AAARKFQNEIDVGQVGINIPIPVPVPFFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTS 489 Query: 515 QWKEEDA 521 +W ++D+ Sbjct: 490 RWFDDDS 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: 668 Number of extensions: 32 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