Align Aldehyde dehydrogenase family 2 member B7, mitochondrial; ALDH2b; EC 1.2.1.3 (characterized)
to candidate N515DRAFT_0379 N515DRAFT_0379 Acyl-CoA reductase
Query= SwissProt::Q8S528 (534 letters) >FitnessBrowser__Dyella79:N515DRAFT_0379 Length = 476 Score = 225 bits (574), Expect = 3e-63 Identities = 154/462 (33%), Positives = 238/462 (51%), Gaps = 23/462 (4%) Query: 74 LDPRNGEVIAQVSEGDAEDVNRAVAAARKAFDEGPWPKMTAYERSKILFRFADLIEKHND 133 LD +G+V +V+ DA+ +A+AAA KA + P + +ER +L + D Sbjct: 24 LDKYSGKVATRVAVPDAKATEQAIAAAVKAAE--PMRQFKPWERQAVLQHCVQRFTERRD 81 Query: 134 EIAALETWDNGKPYEQSAQIEVPMLARVFRYYAGWADKIHGMTMPGD-----GPHHVQTL 188 E+A + GKP + SA EV L F A A + +G T+ + +H T Sbjct: 82 ELAYALCVEAGKPIKDSAG-EVTRLIETFGIAAEEAVRTNGETINLEIAKRLNGYHGYTR 140 Query: 189 HEPIGVAGQIIPWNFPLLMLSWKLGPALACGNTVVLKTAEQTPLSALLVGKLLHEAGLPD 248 P+G I P+NFPL +++ K+ PA+A G VLK AE+TP+ AL++G++L E LP Sbjct: 141 RVPLGPVSFITPFNFPLNLVAHKVAPAIAAGCPFVLKPAERTPIGALIIGEVLAETDLPK 200 Query: 249 GVVNIVSGFGATAGAAIASHMDVDKVAFTGSTDVGKIILELASKSNLKAVTLELGGKSPF 308 G +I++ G A + + ++FTGS +I +L +++ K VTLELGG + Sbjct: 201 GAFSILNLDGKHA-SPLVEDPRFKLLSFTGS----QIGWDLKTRAGHKKVTLELGGNAAC 255 Query: 309 IVCEDAD----VDQAVELAHFALFFNQGQCCCAGSRTFVHERVYDEFVEKAKARALKRNV 364 IV DAD +D +E F F+ GQ C + R + HE +YDE ++ A Sbjct: 256 IV--DADQLPRLDHVIERLVFGAFYQSGQSCISVQRIYAHESLYDELKKRLVAAVKGLKA 313 Query: 365 GDPFKSGIEQGPQVDSEQFNKILKYIKHGVEAGATLQAGGDRLGSKGYYIQPTVFSDVKD 424 GDP K GP +D ++ +I+ + G + GG R KG ++ T+ +V+ Sbjct: 314 GDPKKKETFLGPMIDEAAAERLHGWIEEARKGGGKVLCGGKR---KGPMLEATLMENVRG 370 Query: 425 DMLIATDEIFGPVQTILKFKDLDEVIARANNSRYGLAAGVFTQNLDTAHRLMRALRVGTV 484 D + E+FGP + FK LDE IA N+S YGL AG+FT +L A R L G V Sbjct: 371 DAKVNRQEVFGPFALLAPFKSLDEAIAMTNDSDYGLQAGIFTDSLANAMRAWNELEQGGV 430 Query: 485 WINCFDVLDA-SIPFGGYKMSGIGREKGIYSLNNYLQVKAVV 525 +N ++P+GG K+SG GRE Y++ + +++ +V Sbjct: 431 IVNDVPSFRVDNMPYGGVKLSGAGREGVRYAIEDMTEIRLMV 472 Lambda K H 0.319 0.135 0.401 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: 612 Number of extensions: 31 Number of successful extensions: 7 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: 534 Length of database: 476 Length adjustment: 34 Effective length of query: 500 Effective length of database: 442 Effective search space: 221000 Effective search space used: 221000 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 (21.8 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