Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate Ga0059261_3677 Ga0059261_3677 methylmalonic acid semialdehyde dehydrogenase
Query= BRENDA::Q97UA1 (478 letters) >FitnessBrowser__Korea:Ga0059261_3677 Length = 503 Score = 244 bits (624), Expect = 4e-69 Identities = 149/473 (31%), Positives = 244/473 (51%), Gaps = 13/473 (2%) Query: 14 GSGEEYLDINPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGE 73 G+G D+ + V A++ L + D+ A+ AV W+ T +R ++ Sbjct: 19 GTGTRRSDVFDPNTGAVQAQVTLGAQADLDAAMANAVRAQISWAATNPQRRARVMFNFKA 78 Query: 74 LMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIF 133 L+E+ +E A L++ E GK + D+ ++ R +++F + + G+ A P ++ Sbjct: 79 LIEKNMEELAHLLSSEHGKVIADAKGDIQRGLEVIEFVCGIPHVLKGEYTQGAGPGIDVY 138 Query: 134 TVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAGL 193 ++++PLGVVA ITP+NFP IP+W A+A GN ++KP+ + P + +L E++ +AGL Sbjct: 139 SMRQPLGVVAGITPFNFPAMIPMWMFGVAIACGNAFILKPSERDPSVPVRLAELMLEAGL 198 Query: 194 PEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYK--LVGNKNRMTRIQLELG 251 PEGV+ +V G E+ D I+ I AVSF GS+++ +Y+ + K R+Q G Sbjct: 199 PEGVLQVVQG-DKEMVDAILDHPEIKAVSFVGSSDIAHYVYRRGVAAGK----RVQAMGG 253 Query: 252 GKNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLI-INKDVYTQFKQRLLERVKKW 310 KN V ADL FG G+ C A ++ + + +LL ++ Sbjct: 254 AKNHGIVMPDADLDQVVNDLAGAAFGSAGERCMALPVVVPVGDKTADALRAKLLPAIEAL 313 Query: 311 RVGPGTE-DVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGN--IIPG--KGYFLEPTI 365 RVG T+ GPVV K YI+ G + GA+L+ G + G +G+F+ PT+ Sbjct: 314 RVGVSTDAGAHYGPVVTAAHKAKIESYIQMGVDEGAELVVDGRGFTLQGHEQGFFVGPTL 373 Query: 366 FEGVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSR 425 F+ VT M+ ++EEIFGPVL + A D + A+RL + YG+ I + A EF +R Sbjct: 374 FDRVTPQMQSYQEEIFGPVLQIVRAPDFETALRLPSEHQYGNGVAIFTRNGHAAREFAAR 433 Query: 426 VEAGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYEGW 478 V G++ +N P FGG+K S + G + ++F+ K KTV + W Sbjct: 434 VNVGMVGINVPIPVPVAYHTFGGWKRSAFGDTNQHGMEGIKFFTKVKTVTQRW 486 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: 564 Number of extensions: 35 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: 503 Length adjustment: 34 Effective length of query: 444 Effective length of database: 469 Effective search space: 208236 Effective search space used: 208236 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 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