Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate 5209190 Shew_1668 methylmalonate-semialdehyde dehydrogenase (RefSeq)
Query= BRENDA::Q02252 (535 letters) >FitnessBrowser__PV4:5209190 Length = 501 Score = 564 bits (1453), Expect = e-165 Identities = 272/481 (56%), Positives = 351/481 (72%) Query: 40 VKLFIGGKFVESKSDKWIDIHNPATNEVIGRVPQATKAEMDAAIASCKRAFPAWADTSVL 99 VK +I G+F+ + I + NPA NEVI + AT E++ AIAS K+AF W + V Sbjct: 5 VKHYIDGQFILGSGQQQISVTNPANNEVIATINAATVEEVETAIASAKQAFATWKEVPVS 64 Query: 100 SRQQVLLRYQQLIKENLKEIAKLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMMGET 159 R +V+ RYQ L+K + EIA ++ E GKT DA+GDV+RG++V EHAC++ SL+MGET Sbjct: 65 ERARVMFRYQHLLKLHHDEIATILAQETGKTFEDAKGDVWRGIEVAEHACNIASLIMGET 124 Query: 160 MPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATM 219 + ++ + +D YSY PLGVCAGI PFNFPAMIPLWMFP+A+ CGNTF++KPSE+ P Sbjct: 125 VENVARSIDTYSYTQPLGVCAGITPFNFPAMIPLWMFPLAIACGNTFVLKPSEQDPLTPQ 184 Query: 220 LLAKLLQDSGAPDGTLNIIHGQHEAVNFICDHPDIKAISFVGSNKAGEYIFERGSRHGKR 279 L +L +++GAP G L ++HG AV+ + H DIKAISFVGS G+YI++ G+ + KR Sbjct: 185 RLVELFEEAGAPKGVLQLVHGDKTAVDVLLSHQDIKAISFVGSVGVGQYIYKTGTDNLKR 244 Query: 280 VQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAVLVGEAKKWLPELVEH 339 VQA GAKNH V+MPDANK+ +N LVGA+ GAAGQRCMALS AV VGEAKKW+PEL + Sbjct: 245 VQAFAGAKNHCVIMPDANKQQVINNLVGASVGAAGQRCMALSVAVFVGEAKKWIPELRDA 304 Query: 340 AKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRKIKVKGYENGNFV 399 +R D A GP+I+P AK RV LI G +EGA LLDG V+GYENGN+V Sbjct: 305 IAKVRPGVWDDKDAAYGPVISPAAKARVLKLIAQGKEEGAECLLDGSDFTVEGYENGNWV 364 Query: 400 GPTIISNVKPNMTCYKEEIFGPVLVVLETETLDEAIQIVNNNPYGNGTAIFTTNGATARK 459 GPT+ +NV +M+ YKEEIFGPVL +E E+L+EAI++VNN+PYGNGT+IFT GA ARK Sbjct: 365 GPTMFTNVTTDMSIYKEEIFGPVLCCMEVESLEEAIELVNNSPYGNGTSIFTACGAAARK 424 Query: 460 YAHLVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQWKEE 519 Y H ++VGQVG+NVPIPVPLP FSFTG + SF GD + YGKQ ++FYT+ KTIT++W E Sbjct: 425 YQHNIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAVRFYTETKTITARWFET 484 Query: 520 D 520 D Sbjct: 485 D 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: 695 Number of extensions: 20 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: 501 Length adjustment: 35 Effective length of query: 500 Effective length of database: 466 Effective search space: 233000 Effective search space used: 233000 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