Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_085772518.1 B1812_RS16250 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_002117405.1:WP_085772518.1 Length = 498 Score = 251 bits (641), Expect = 4e-71 Identities = 155/473 (32%), Positives = 241/473 (50%), Gaps = 9/473 (1%) Query: 12 IKGSGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKA 71 + G+ E + D +++ L ++ +V AI A A W+ +R +L K Sbjct: 13 VAGTSERFCDGYEPMSGATISRTPLASRAEVAAAIASAEAAQPAWAAFSPQRRARVLTKF 72 Query: 72 GELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTR 131 E + QEA A L++ E GKT+ D+ ++ R +++F + + G+ D Sbjct: 73 VERVTQEADSLASLLSREHGKTIGDARGDIQRGLEVVEFAIGVPHFLKGEYSDGGDRGID 132 Query: 132 IFTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKA 191 ++++++PLGV A TP+NFP +P+W APA+A GN V+KP+ + + +L E++ +A Sbjct: 133 LYSMRQPLGVAAGATPFNFPAMLPMWMFAPAIACGNAFVLKPSERDASVPLRLAELMMEA 192 Query: 192 GLPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELG 251 GLP GV+N+V G E D ++ + A SF GST V + +Y + R+Q G Sbjct: 193 GLPAGVLNVVNG-DKEAVDALLDHAGVRAFSFVGSTAVAQYVYARGAASGK--RMQCFGG 249 Query: 252 GKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLI-INKDVYTQFKQRLLERVKKW 310 KN + V ADL A E V +G G+ C A S + + +RL+ RVK Sbjct: 250 AKNHMIVMPDADLDQAVEALVGSAYGAAGERCMAISVAVPVGNAAAEALIERLVPRVKTL 309 Query: 311 RVGPGTE-DVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPGKGY----FLEPTI 365 ++GP T+ + D GP+V + ++ YI G+ GA L+ G +GY +L + Sbjct: 310 KIGPSTDAEADFGPLVTQAHLERVCSYIGLGEREGASLLVDGRNFGLQGYEQGFYLGGCL 369 Query: 366 FEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSR 425 + VT MR+++EEIFGPVL V A D EA+ LVN +YG+ I D +FVSR Sbjct: 370 LDRVTRGMRVYQEEIFGPVLVVLRAADYAEALALVNDHEYGNGVAIFTRDGGVARDFVSR 429 Query: 426 VEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYEGW 478 G++ VN P FGG+K S + G D++ FY K KTV W Sbjct: 430 ARVGMVGVNVPIPVPLAHYSFGGWKRSFFGDLGQHGPDSMRFYTKTKTVTSRW 482 Lambda K H 0.316 0.135 0.389 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: 544 Number of extensions: 29 Number of successful extensions: 6 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: 478 Length of database: 498 Length adjustment: 34 Effective length of query: 444 Effective length of database: 464 Effective search space: 206016 Effective search space used: 206016 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 (21.6 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