Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 202599 SO3496 aldehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::Q8BH00 (487 letters) >FitnessBrowser__MR1:202599 Length = 498 Score = 297 bits (760), Expect = 6e-85 Identities = 171/481 (35%), Positives = 264/481 (54%), Gaps = 16/481 (3%) Query: 13 FIGGKFLPCNS--YIDSYDPSTGEVYCKVPNSGKEEIEAAVEAAREAFPA--WSSRSPQE 68 FI G++ +S D P G + V + + AV ARE F + WS +P + Sbjct: 24 FINGEYRDASSGNTFDCISPIDGRLLAPVASCDLMDANIAVANAREVFDSGVWSKAAPVK 83 Query: 69 RSLVLNRLADVLEQSLEELAQAESKDQGKTLTLARTMDIPRSVLNFRFF--ASSNLHHVS 126 R V+ R A++LE++ ELA E+ D GK + ++ +D+ + R+ A L+ Sbjct: 84 RKQVMIRFAELLEENANELALLETLDMGKPIRFSKAVDVAGAARAIRWSGEAIDKLYDEL 143 Query: 127 ECTQMSHLGCMHYTVRTPVGIAGLISPWNLPLYLLTWKIAPAIAAGNTVIAKPSEMTSVT 186 T + +G + R PVG+ I PWN PL + WK+ PA+ GN+VI KPSE + +T Sbjct: 144 APTAHNEIGMI---TREPVGVVAAIVPWNFPLLMACWKLGPALVTGNSVILKPSEKSPLT 200 Query: 187 AWMFCKLLDKAGVPPGVINIVFGTGPRVGEALVSHPEVPLISFTGSQPTAERITQLSAP- 245 A +L +AG+P GV+N++ G G VG+AL H +V + FTGS A+++ + Sbjct: 201 AIRIAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGES 260 Query: 246 HCKKLSLELGGKNPAIIFEDA-NLEECIPATVRSSFANQGEICLCTSRIFVQRSIYSEFL 304 + K++ LE GGK+P I+F DA +L+ A + NQGE+C SR+ V+ + E + Sbjct: 261 NMKRVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIGFNQGEVCTAGSRLLVESGVKDELV 320 Query: 305 KRFVEATRKWKVGVPSDPSANMGALISKAHLEKVRSYVLKAQTEGARILCGEGVDQLSLP 364 E W+ G P +P+ GA++ K L+ + SY+ Q EGA ++ G Sbjct: 321 GLIAEELASWQPGHPLEPTTVSGAVVDKQQLDTILSYIKAGQNEGASLVYGG-----QQV 375 Query: 365 LRNQAGYFMLPTVITDIKDESRCMTEEIFGPVTCVVPFDSEEEVITRANSVRYGLAATVW 424 L G ++ PTV +++K++ + +EEIFGPV V+ F+ EE I AN YGLAA VW Sbjct: 376 LAETGGVYVQPTVFSNVKNQMKIASEEIFGPVLSVIEFNGMEEAIAIANDTIYGLAAGVW 435 Query: 425 SKDVGRIHRVAKKLQSGLVWTNCWLIRELNLPFGGMKSSGIGREGAKDSYDFFTEIKTIT 484 + D+ + H+ AK L+SG+VW N + ++ PFGG K SG GR+ + S+D +TEIK Sbjct: 436 TADISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHSFDKYTEIKATW 495 Query: 485 I 485 I Sbjct: 496 I 496 Lambda K H 0.319 0.134 0.404 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: 545 Number of extensions: 24 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: 487 Length of database: 498 Length adjustment: 34 Effective length of query: 453 Effective length of database: 464 Effective search space: 210192 Effective search space used: 210192 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 Apr 09 2024. 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