Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate RR42_RS24025 RR42_RS24025 methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::Q02252 (535 letters) >FitnessBrowser__Cup4G11:RR42_RS24025 Length = 507 Score = 619 bits (1596), Expect = 0.0 Identities = 291/483 (60%), Positives = 376/483 (77%) Query: 37 VPTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWADT 96 +PT KL I GKFVES S++W ++ NPAT +VIGRVP AT E+DAAIAS +RAF W +T Sbjct: 12 LPTAKLLIDGKFVESDSNQWGNVVNPATQQVIGRVPFATVEEVDAAIASAQRAFLTWRNT 71 Query: 97 SVLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMM 156 + +R +V+L++Q L++ N++ IA+ +T EQGKTL DA+GD+FRGL+VVEHACSV +L M Sbjct: 72 PLGARLRVMLKFQDLVRRNMERIARTLTAEQGKTLPDAQGDIFRGLEVVEHACSVGTLQM 131 Query: 157 GETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPG 216 GE ++ +D Y+ R P+GVCAGI PFNFP MIPLWMFPMA+VCGNTF++KPSE+ P Sbjct: 132 GEFAENVAGGVDTYTLRQPIGVCAGITPFNFPGMIPLWMFPMAIVCGNTFVLKPSEQDPL 191 Query: 217 ATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERGSRH 276 +TM L +L ++G P G LN++HG V+ +C HPD+KAISFVGS G +++ GS+H Sbjct: 192 STMELVELAMEAGVPPGVLNVVHGGKTVVDMLCTHPDVKAISFVGSTHVGTHVYNLGSKH 251 Query: 277 GKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLPEL 336 GKRVQ+ MGAKNH VV+PDAN++ TLN LVGA FGAAGQRCMA S VLVG+++ WLPEL Sbjct: 252 GKRVQSMMGAKNHAVVLPDANRQQTLNALVGAGFGAAGQRCMATSVVVLVGQSRDWLPEL 311 Query: 337 VEHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYENG 396 VE AK L+VNAG +PG D+GP+++ A RV LI+ G + GA++LLDGR +KV GYE+G Sbjct: 312 VEKAKLLKVNAGHEPGTDVGPVMSKAAHARVTGLIEEGVQAGAALLLDGRDVKVPGYESG 371 Query: 397 NFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNGAT 456 NFVGPTI S V P+M+ Y +EIFGPV+VVLE +TLDEAI +VN NP GNG +FT +GA Sbjct: 372 NFVGPTIFSGVSPDMSIYTQEIFGPVVVVLEVDTLDEAIALVNRNPMGNGVGLFTQSGAA 431 Query: 457 ARKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQW 516 ARK+ +DVGQVG+N+PIPVP+P FSFTGSR S GD YGKQ +QFYTQ KT+T++W Sbjct: 432 ARKFQSEIDVGQVGINIPIPVPVPYFSFTGSRGSKLGDLGPYGKQVVQFYTQTKTVTARW 491 Query: 517 KEE 519 ++ Sbjct: 492 FDD 494 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: 709 Number of extensions: 26 Number of successful extensions: 2 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:
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