Align long-chain-aldehyde dehydrogenase (EC 1.2.1.48) (characterized)
to candidate 8501918 DvMF_2633 Aldehyde Dehydrogenase (RefSeq)
Query= BRENDA::P51648 (485 letters) >FitnessBrowser__Miya:8501918 Length = 460 Score = 224 bits (571), Expect = 5e-63 Identities = 146/464 (31%), Positives = 235/464 (50%), Gaps = 22/464 (4%) Query: 9 RQAFL-SGRSRPLRFRLQQLEALRRMVQEREKDILTAIAADLCKSEFNVYSQEVITVLGE 67 ++AF+ SG P R+ L LR VQ + AI AD + E +EV+ VL E Sbjct: 8 QKAFIASGAVLPSGARVDALRRLREGVQGYRDRLADAIRADYGRPEHPFLVREVVPVLHE 67 Query: 68 IDFMLENLPEWVTAKPVKKNVLTMLDEAYIQPQPLGVVLIIGAWNYPFVLTIQPLIGAIA 127 ID++++ +P + + V ++ +Y++ QPLG V+ W PF + PL AI Sbjct: 68 IDWLIKAVPGFCGGRRVLPSLGQFKARSYVRRQPLGRVVAYAHWADPFRSLLVPLADAIG 127 Query: 128 AGNAVIIKPSELSENTAKILAKLLPQYLDQDLYIVINGGVEETTELLKQRFDHIFYTGNT 187 AGNAV+++PS + TA+++ +++ QY + + V+ GG E LL D ++Y G+ Sbjct: 128 AGNAVVLRPSAEAPATAEMVTRMVRQYFEPEHVAVVGGGAETDEALLATAPDFVWYDGDA 187 Query: 188 AVGKIVMEAAAKHLTPVTLELGGKSPCYIDKDCDLDIVCRRITWGKYMNCGQTCIAPDYI 247 + + AA LTP GG S + D D+ + RRI W K+++ GQ APD + Sbjct: 188 RGARTIAVLAAPTLTPYAAITGGPSAALVHGDADMAMAARRIVWAKFLHAGQLRAAPDVL 247 Query: 248 LCEASLQNQIVWKIKETVKEFYGENIKESPDYERIINLRHFKRILSLLE-GQKIAFG--- 303 L + ++ ++++ ++ ++ +G + S D+ R+++ F R L G+ + FG Sbjct: 248 LVQRTVLDRVLDALRTELERAFGPQPRTSADFGRMVSAAGFARQAERLAIGRALPFGPGD 307 Query: 304 --GETDEATRYIAPTVLTDVDPKTKVMQEEIFGPILPIVPVKNVDEAINFINEREKPLAL 361 + D A+ Y+ PT+LTDV + V++EE FGP+L + P +DEA F+ AL Sbjct: 308 AANQPDRASLYVPPTLLTDVPDDSPVLREEGFGPVLVVRPYTRLDEATAFLAGLPALTAL 367 Query: 362 YVFSHNHKLIKRMIDETSSGGVTGNDVIMHFTLNSFPFGGVGSSGMGAYHGKHSFDTFSH 421 Y F+ H +R+++ T +G V ND H P GGVG +G GA G TFS Sbjct: 368 YAFTTAHARGERLMENTRAGAVLINDAATHLANPRLPQGGVGETGHGAMAGPAGLATFSA 427 Query: 422 QRPCLLKSLKREGAN----KLRYPPNSQSKVDWGKFFLLKRFNK 461 R + G+N LR+ P S K+ +LKR K Sbjct: 428 PRATAV------GSNFFDIPLRFAPGSDLKLK-----VLKRLYK 460 Lambda K H 0.321 0.139 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: 419 Number of extensions: 19 Number of successful extensions: 2 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: 485 Length of database: 460 Length adjustment: 33 Effective length of query: 452 Effective length of database: 427 Effective search space: 193004 Effective search space used: 193004 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 (21.9 bits) S2: 51 (24.3 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