Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate RR42_RS28560 RR42_RS28560 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::Q02252 (535 letters) >FitnessBrowser__Cup4G11:RR42_RS28560 Length = 506 Score = 596 bits (1536), Expect = e-175 Identities = 282/496 (56%), Positives = 380/496 (76%), Gaps = 1/496 (0%) Query: 29 SASSFSSSVPTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKR 88 SA + +++ PTVKL I G++VES + ++ + NPAT +V+ +VP AT AE++AA+ + R Sbjct: 2 SAQNPNAAAPTVKLLINGEWVESAATEFRPVVNPATQQVLAQVPLATAAEVNAAVGAAHR 61 Query: 89 AFPAWADTSVLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHA 148 AF W T + +R +++L+YQ LI+E+ K IA ++T EQGKTLADAEGD+FRGL+VVEHA Sbjct: 62 AFATWRHTPLGARLRIMLKYQALIREHSKRIAAILTAEQGKTLADAEGDIFRGLEVVEHA 121 Query: 149 CSVTSLMMGETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLM 208 CS+ +L G ++ +D Y+ + P+GVCAGI PFNFPAMIPLWMFPMA+VCGNTF++ Sbjct: 122 CSIGTLQQGGFAENVAATVDTYTLQQPIGVCAGITPFNFPAMIPLWMFPMAIVCGNTFVL 181 Query: 209 KPSERVPGATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEY 268 KPSE+ P +TM L KL ++G P G LN++HG E V+ +C HPDIKA+SFVGS G + Sbjct: 182 KPSEQDPLSTMELVKLAIEAGVPAGVLNVVHGAREVVDALCTHPDIKAVSFVGSTAVGTH 241 Query: 269 IFERGSRHGKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGE 328 ++ HGKRVQ+ MGAKNH VV+PDA++E+TLN L GAAFGAAGQRCMA S AVLVG Sbjct: 242 VYNLAGAHGKRVQSMMGAKNHAVVLPDAHREHTLNALAGAAFGAAGQRCMATSVAVLVGA 301 Query: 329 AKKWLPELVEHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKI 388 A++WLPELV+ A L+V AG++PG D+ P+++ A++RV LI++G +EGA++ LDGR + Sbjct: 302 AREWLPELVKKAATLKVGAGNEPGTDVCPVVSVAARQRVLGLIEAGEREGATLALDGRNV 361 Query: 389 KVKGYENGNFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTA 448 +V GY GNF+GPT+ ++V M+ Y +EIFGPVLVV+ ETLDEAI +VN NP+GNGT Sbjct: 362 QVAGYPEGNFIGPTVFADVTTEMSIYTQEIFGPVLVVIGVETLDEAIALVNRNPFGNGTG 421 Query: 449 IFTTNGATARKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQ 508 IFT +GA ARK+ +DVGQVG+N+PIPVP+P FSFTGSR S GD YGKQ +QFYTQ Sbjct: 422 IFTQSGAAARKFQSEIDVGQVGINIPIPVPVPYFSFTGSRGSKLGDLGPYGKQVVQFYTQ 481 Query: 509 LKTITSQWKEEDATLS 524 KT+T++W +DAT++ Sbjct: 482 TKTVTARW-FDDATVN 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: 684 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: 506 Length adjustment: 35 Effective length of query: 500 Effective length of database: 471 Effective search space: 235500 Effective search space used: 235500 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