Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 6937206 Sama_1376 methylmalonate-semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::Q02252 (535 letters) >FitnessBrowser__SB2B:6937206 Length = 497 Score = 556 bits (1432), Expect = e-163 Identities = 266/484 (54%), Positives = 350/484 (72%) Query: 37 VPTVKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWADT 96 + VK +I G+F + ++ I + NPA N+ I V A+ E+ AIAS K AF +W + Sbjct: 2 ITQVKHYIDGEFTTGQGERIITVTNPANNQPIAEVRCASDEEVHGAIASAKAAFQSWKEV 61 Query: 97 SVLSRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMM 156 V R +V+LRYQ L+KE+ E+A ++ E GKT DA+GDV+RG++V EHAC++ SL+M Sbjct: 62 PVSERARVMLRYQALLKEHHDELATILAKETGKTFEDAKGDVWRGIEVAEHACNIASLLM 121 Query: 157 GETMPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPG 216 GET+ ++ + +D YSY PLGVCAGI PFNFPAMIPLWMFP+A+ CGNTF++KPSE+ P Sbjct: 122 GETVENVARKIDTYSYTQPLGVCAGITPFNFPAMIPLWMFPLAVACGNTFVLKPSEQDPM 181 Query: 217 ATMLLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERGSRH 276 + LA+L + +GAP G L ++HG AV+ + HPDIKAISFVGS G+Y+++ G+ + Sbjct: 182 TPLRLAELFEQAGAPKGVLQLVHGDKSAVDILLTHPDIKAISFVGSVGVGQYVYKTGTDN 241 Query: 277 GKRVQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLPEL 336 KRVQA GAKNH V+MPDANK+ +N LVGA+ GAAGQRCMA+S AV VG AK+W+PEL Sbjct: 242 LKRVQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMAISVAVFVGAAKEWIPEL 301 Query: 337 VEHAKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYENG 396 E +R D A GPLI+P AK RV LI+ G EGA LLDG V GYE+G Sbjct: 302 KEALAKVRPGLWDDKDAGYGPLISPAAKARVLKLIEQGKAEGAECLLDGSDFTVPGYESG 361 Query: 397 NFVGPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNGAT 456 N+VGPT+ V +M+ YKEEIFGPVL +E + L++AI++VN +PYGNGT+IFT +GA Sbjct: 362 NWVGPTMFDKVTTDMSIYKEEIFGPVLCCMEVDELEDAIELVNKSPYGNGTSIFTASGAA 421 Query: 457 ARKYAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQW 516 ARKY H ++VGQVG+NVPIPVPLP FSFTG + SF GD + YGKQ I+F+T+ KTIT +W Sbjct: 422 ARKYQHEIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAIRFFTETKTITCRW 481 Query: 517 KEED 520 E+D Sbjct: 482 FEDD 485 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: 710 Number of extensions: 27 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: 497 Length adjustment: 35 Effective length of query: 500 Effective length of database: 462 Effective search space: 231000 Effective search space used: 231000 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 Apr 09 2024. 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