Align malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18) (characterized)
to candidate WP_007152784.1 MDG893_RS05705 CoA-acylating methylmalonate-semialdehyde dehydrogenase
Query= BRENDA::Q9EQ20 (535 letters) >NCBI__GCF_000170835.1:WP_007152784.1 Length = 496 Score = 563 bits (1451), Expect = e-165 Identities = 264/482 (54%), Positives = 359/482 (74%) Query: 40 VKLFIDGKFVESKSDKWIDIHNPATNEVVGRVPQSTKAEMDAAVESCKRAFPAWADTSIL 99 V L+I G+FV+S++D+WID+ +PATNEV+ R P +T AEM A+E+ F W + + Sbjct: 4 VPLYIAGEFVQSQTDQWIDVTDPATNEVIARAPCTTDAEMRRAIENAGEVFKTWKEVPVS 63 Query: 100 SRQQVLLRYQQLIKENLKEIARLITLEQGKTLADAEGDVFRGLQVVEHACSVTSLMLGET 159 R +V++RYQ L+KE+ EIA +++ E GKT DA+GDV+RG++VVEHA ++ SLM+GET Sbjct: 64 ERARVMMRYQALLKEHHDEIAEILSSETGKTFEDAKGDVWRGIEVVEHAANIPSLMMGET 123 Query: 160 MPSITKDMDLYSYRLPLGVCAGIAPFNFPAMIPLWMFPMAMVCGNTFLMKPSERVPGATM 219 + ++ +++D YSY PLGVCAGI PFNFPAMIPLWMFPMA+ GNTF++KPSE+ P M Sbjct: 124 VENVAREIDTYSYTQPLGVCAGITPFNFPAMIPLWMFPMAIASGNTFILKPSEQDPLTPM 183 Query: 220 LLAKLLQDSGAPDGTLNIIHGQHDAVNFICDHPDIKAISFVGSNQAGEYIFERGSRNGKR 279 LA+L +++GAP G L ++HG + V+ + P IKA+SFVGS G YI+E G+RN KR Sbjct: 184 RLAELFEEAGAPKGVLQVVHGGKEQVDVLLTDPAIKAVSFVGSVPVGRYIYETGTRNMKR 243 Query: 280 VQANMGAKNHGVVMPDANKENTLNQLVGAAFGAAGQRCMALSTAILVGEAKKWLPELVDR 339 VQ+ GAKNH V++PDA+K + LVGA+ GAAGQRCMA+S A+ VGEA++W+PE+ + Sbjct: 244 VQSFAGAKNHMVILPDADKNQVVKALVGASVGAAGQRCMAISVAVFVGEAQEWIPEVKEA 303 Query: 340 AKNLRVNAGDQPGADLGPLITPQAKERVCNLIDSGTKEGASILLDGRRIKVKGYENGNFV 399 +R A + A GP+I+ QAK+RV +LI G +EGA +LLDGR V G +GN+V Sbjct: 304 LAAVRPGAWNDKEASYGPIISKQAKQRVESLITRGEEEGAKLLLDGRNCTVDGLPDGNWV 363 Query: 400 GPTIISNVKPSMTCYKEEIFGPVLVVLETETLDEAIKIVNDNPYGNGTAIFTTNGATARK 459 GPT+ + VKP M YKEEIFGPVL +E +TL++AI +VND+PYGNGT+IFT++G AR+ Sbjct: 364 GPTLFAGVKPEMDVYKEEIFGPVLACMEVDTLEDAINLVNDSPYGNGTSIFTSSGGAARR 423 Query: 460 YAHMVDVGQVGVNVPIPVPLPMFSFTGSRSSFRGDTNFYGKQGIQFYTQLKTITSQWKEE 519 Y H ++VGQVG+NVPIPVPLP FSFTG + SF GD + YGKQ ++FYT+ KTIT +W Sbjct: 424 YQHEIEVGQVGINVPIPVPLPFFSFTGWKGSFYGDQHAYGKQAVKFYTETKTITCRWFSS 483 Query: 520 DA 521 DA Sbjct: 484 DA 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: 727 Number of extensions: 25 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: 496 Length adjustment: 35 Effective length of query: 500 Effective length of database: 461 Effective search space: 230500 Effective search space used: 230500 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 24 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