Align malonate-semialdehyde dehydrogenase (EC 1.2.1.15); malonate-semialdehyde dehydrogenase (acetylating) (EC 1.2.1.18); methylmalonate-semialdehyde dehydrogenase (CoA-acylating) (EC 1.2.1.27) (characterized)
to candidate WP_055437407.1 ASC41_RS13180 aldehyde dehydrogenase
Query= BRENDA::A0A081YAY7 (498 letters) >NCBI__GCF_001418085.1:WP_055437407.1 Length = 500 Score = 191 bits (486), Expect = 4e-53 Identities = 146/464 (31%), Positives = 229/464 (49%), Gaps = 18/464 (3%) Query: 6 HLIGGELIADT-GRTADVFNPSTGEAVRKVPLADRETMQQAIDAAKAAFPAWRNTPPAKR 64 + IGG+ + G+ D +P G+ + + +E + A+DAA AFPAW + +R Sbjct: 15 NFIGGKFVDPVKGQYFDNVSPVDGKVFTQAARSTQEDIDLALDAAHEAFPAWSTSSATER 74 Query: 65 AQVLFRFKQLLEANEERIVKLISEEHGKTI-EDAAGELKRGIENVEYATAAPEILKGEYS 123 + +L + Q++E N E + L + ++GK I E A ++ I++ Y +G S Sbjct: 75 SNMLLKIAQVMEDNFEYLATLETIDNGKPIRESRAADIPYCIDHFRYFAGVIRADEGSIS 134 Query: 124 RNVGPNIDAWSDFQPIGVVAGITPFNFPAMVPLWMYPLAIACGNTFILKPSERDPSSTLL 183 + + +P+GVV I P+NFP ++ W A+A G T ++KP+E+ P+S ++ Sbjct: 135 EHDKDTVSIVLH-EPVGVVGEIIPWNFPMLMLAWKIAPALAAGCTAVVKPAEQTPTSVIM 193 Query: 184 IAELFHEAGLPKGVLNVVHG---DKGAVDALIEAPEVKALSFVGSTPIAEYIYSEGTKRG 240 + EL + LP GVLN+V G + GA AL + + LSF GST + + Sbjct: 194 LMELIGDI-LPAGVLNIVTGFGAEAGA--ALATSKRIAKLSFTGSTETGRKVLHNAAENI 250 Query: 241 KRVQALGGAKNHAVLMP---DADLDNAVSALMGAAYGSC--GERCMAISVAVCVGDQIAD 295 V G K+ V P D D D A+ GA S GE C A S + V + IAD Sbjct: 251 IPVTMELGGKSPNVFFPSVADHDDDFFSKAIEGALMFSLNQGEICTAPS-RILVHEDIAD 309 Query: 296 ALVQKLVPQIKGLKIGAGTSCGLDMGPLVTGAARDKVTGYIDTGVAQGAELVVDGRGYKV 355 ++K+ ++K +K G +G V+ DK+ YI G +GAE+V G Sbjct: 310 LFIEKMKVRLKAIKTGNPLDPETMIGSQVSKPQYDKILDYIKIGKDEGAEVVAGGDAGNY 369 Query: 356 AGH-ENGFFLGGTLFDRVTPEMTIYKEEIFGPVLCIVRVNSLEEAMQLINDHEYGNGTCI 414 G G+++ T+ + +M I++EEIFGPV+ + +S EEA+ + ND YG G + Sbjct: 370 EGELSEGYYIQPTVL-KGNNKMRIFQEEIFGPVVALTTFSSTEEAIAIANDTPYGLGAGV 428 Query: 415 FTRDGEAARLFCDEIEVGMVGVNVPLPVPVAYHSFGGWKRSLFG 458 ++RD I+ G V VN P A+ FGG K S FG Sbjct: 429 WSRDAHELYQVPRAIQAGRVWVNQYHTYP-AHAPFGGVKESGFG 471 Lambda K H 0.319 0.137 0.411 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: 605 Number of extensions: 34 Number of successful extensions: 5 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: 498 Length of database: 500 Length adjustment: 34 Effective length of query: 464 Effective length of database: 466 Effective search space: 216224 Effective search space used: 216224 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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