Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate WP_077279116.1 B1C78_RS10500 methylmalonate-semialdehyde dehydrogenase (CoA acylating)
Query= BRENDA::Q97UA1 (478 letters) >NCBI__GCF_002000365.1:WP_077279116.1 Length = 507 Score = 272 bits (696), Expect = 2e-77 Identities = 162/471 (34%), Positives = 256/471 (54%), Gaps = 10/471 (2%) Query: 14 GSGEEYLDI-NPADKDHVLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAG 72 G+ + + ++ NPA + V A++ L + DV+EA+ A A W+ T +R +L + Sbjct: 25 GANDRFGEVFNPATGE-VTARVPLAGQADVEEALTAATAALPGWADTSPLRRARVLFRFK 83 Query: 73 ELMEQEAQEFALLMTLEEGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRI 132 EL+E+ A E L+T E GK L D+ E TR +++F + + G+ Sbjct: 84 ELLEKNADELTALITHEHGKVLSDARGEFTRGLEVVEFACGIPHLLKGEYSDQVGTGIDS 143 Query: 133 FTVKEPLGVVALITPWNFPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKAG 192 +++++P+GV A ITP+NFP+ +P+W A+A GNT V+KP+ + P L E+L +AG Sbjct: 144 YSLRQPVGVCAGITPFNFPVMVPMWMFPVAIACGNTFVLKPSERDPGPALMLAELLREAG 203 Query: 193 LPEGVVNLVVGKGSEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGG 252 LP GV N++ G +E + +++D +AAVSF GST + + IY + R+Q G Sbjct: 204 LPNGVFNVLNG-DAEAVNALLTDPRVAAVSFVGSTPIAQHIYSTGAAHGK--RVQALGGA 260 Query: 253 KNALYVDKSADLTLAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRV 312 KN + V ADL A + V +G G+ C A S + DV R+ +RV+K R+ Sbjct: 261 KNHMVVMPDADLEQAVDALVGAAYGSAGERCMAISVAVAVGDVADALVARVADRVRKLRI 320 Query: 313 GPGTE-DVDMGPVVDEGQFKKDLEYIEYGKNVGAKLIYGGN--IIPGK--GYFLEPTIFE 367 GPGT+ + DMGP++ ++ Y++ G + GA+L+ G + G G+FL +F+ Sbjct: 321 GPGTDPEADMGPLITRAHLERVTGYVDLGVSEGAELVVDGRGFRVEGHEGGFFLGGCLFD 380 Query: 368 GVTSDMRLFKEEIFGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSRVE 427 V MR+++EEIFGPVLSV DLD AI LVNA ++G+ + + EF R+ Sbjct: 381 RVEPSMRIYREEIFGPVLSVVRVPDLDHAISLVNAHEFGNGVAVFTRNGGVAREFTRRIS 440 Query: 428 AGVIKVNKPTVGLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKTVYEGW 478 AG++ +N P FGG+K+S G + + FY + KTV W Sbjct: 441 AGMVGINVPIPVPLAFHSFGGWKHSLFGDHAIHGPEGVHFYTRLKTVTSRW 491 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: 587 Number of extensions: 30 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: 478 Length of database: 507 Length adjustment: 34 Effective length of query: 444 Effective length of database: 473 Effective search space: 210012 Effective search space used: 210012 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