Align lactaldehyde dehydrogenase (EC 1.2.1.22); 2,5-dioxovalerate dehydrogenase (EC 1.2.1.26) (characterized)
to candidate CA265_RS19780 CA265_RS19780 aldehyde dehydrogenase family protein
Query= BRENDA::Q97UA1 (478 letters) >FitnessBrowser__Pedo557:CA265_RS19780 Length = 513 Score = 249 bits (636), Expect = 2e-70 Identities = 151/455 (33%), Positives = 246/455 (54%), Gaps = 17/455 (3%) Query: 30 VLAKIRLYTKDDVKEAINKAVAKFDEWSRTPAPKRGSILLKAGELMEQEAQEFALLMTLE 89 ++A ++ T DD + KA F W PAPKRG I+ + G+ + + L++ E Sbjct: 46 LIASAKIATADDYDAVVLKAQEAFTAWRSVPAPKRGEIVRQFGDALRENKDALGTLVSYE 105 Query: 90 EGKTLKDSMFEVTRSYNLLKFYGALAFKISGKTLPSADPNTRIFTVKEPLGVVALITPWN 149 GK+L++ EV ++ F L+ ++ G T+ S P+ R++ PLG+V +I+ +N Sbjct: 106 MGKSLQEGFGEVQEMIDICDFAVGLSRQLYGLTMHSERPSHRMYEQWHPLGIVGIISAFN 165 Query: 150 FPLSIPVWKLAPALAAGNTAVIKPATKTPLMVAKLVEVLSKA----GLPEGVVNLVVGKG 205 FP+++ W A AL GN + KP+ KTPL +++K + EGV NL++G Sbjct: 166 FPVAVWSWNTALALVCGNVCIWKPSEKTPLTAIACQHIIAKVFKDNDIAEGVCNLILG-D 224 Query: 206 SEVGDTIVSDDNIAAVSFTGSTEVGKRIYKLVGNKNRMTRIQLELGGKNALYVDKSADLT 265 EVG+ + +D I +S TGST +GK + VG R+ + LELGG NA+ + + ADL Sbjct: 225 REVGERMTNDGRIPLISATGSTRMGKAVGAAVG--ARLGKSLLELGGNNAIIISEHADLD 282 Query: 266 LAAELAVRGGFGLTGQSCTATSRLIINKDVYTQFKQRLLERVKKWRVG-PGTEDVDMGPV 324 ++ AV G G GQ CT+T RLII++ VY F +L++ + R+G P ++ +GP+ Sbjct: 283 MSLIGAVFGAVGTAGQRCTSTRRLIIHESVYDAFTAKLVKAYGQLRIGDPLDQNNHVGPL 342 Query: 325 VDEGQFKKDLEYIEYGKNVGAKLIYGGNIIPGKGY----FLEPTIFEGVTSDMRLFKEEI 380 +D L+ I K G + G ++ G Y +++P I E V +D ++ + E Sbjct: 343 IDTDAVAAYLDSIAKCKAEGGNFVVEGGVLSGDAYTSGCYVKPCIAE-VQNDFKIVQHET 401 Query: 381 FGPVLSVTEAKDLDEAIRLVNAVDYGHTAGIVASDIKAINEFVSR--VEAGVIKVNKPTV 438 F P+L + + K LDEAI L N V G ++ I+ +++ +F+S + G+ VN T Sbjct: 402 FAPILYLIKYKTLDEAIALQNGVPQGLSSAIMTLNLREAEQFLSAKGSDCGIANVNIGTS 461 Query: 439 GLELQAPFGGFKNSGATTWKEMGEDALEFYLKEKT 473 G E+ FGG K +G +E G DA Y++ +T Sbjct: 462 GAEIGGAFGGEKETGG--GRESGSDAWRAYMRRQT 494 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: 602 Number of extensions: 33 Number of successful extensions: 4 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: 513 Length adjustment: 34 Effective length of query: 444 Effective length of database: 479 Effective search space: 212676 Effective search space used: 212676 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