Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate BWI76_RS10695 BWI76_RS10695 aldehyde dehydrogenase PuuC
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Koxy:BWI76_RS10695 Length = 495 Score = 384 bits (987), Expect = e-111 Identities = 202/474 (42%), Positives = 289/474 (60%), Gaps = 4/474 (0%) Query: 38 QIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMD 97 ++FIN E+ A F T++P+ + + +VA G K DVD+AV+AAR F G W + Sbjct: 21 RLFINGEYSAAADNSVFATIDPAAQQTLAEVARGKKADVDRAVQAARGVFDRGD-WSQAS 79 Query: 98 ASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYH 157 + R +L + ADL++ R LA LETLD GKP S D+ + +R+YA DK + Sbjct: 80 PAQRKAVLTKFADLMDAHREELALLETLDTGKPIRHSLRDDIPGAARAIRWYAEAIDKVY 139 Query: 158 GKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLT 217 G+ P G+ + EP+GV ++PWNFPLL+ WKLGPALA+GN VV+K +E++PLT Sbjct: 140 GEVAPTGGNELAMIVREPIGVIAAVVPWNFPLLLACWKLGPALASGNSVVLKPSEKSPLT 199 Query: 218 ALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSS 277 AL +A L K+AG P GV N+V GFG AG A+A H DV+ + FTGST + + AG S Sbjct: 200 ALRLAGLAKQAGLPDGVFNVVSGFGHEAGQALALHPDVEVITFTGSTRTAKQLLKDAGDS 259 Query: 278 NLKRVTLELGGKSPNIIMSDA-DMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFV 336 N+KRV LE GGKS NI+ +D D+ AV +F+NQGQ C AG+R ++E I D F+ Sbjct: 260 NMKRVWLEAGGKSANIVFADCPDLQKAVNATAGGIFYNQGQVCIAGTRLLLEESIADRFL 319 Query: 337 ERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGY 396 + +AK GNP D T G +D T + +I G+ LL G Sbjct: 320 DLLKEQAKGWQPGNPLDPNTTMGMLIDNTHADSVHSFIRAGEAHSTLLLDGRKNPWPAA- 378 Query: 397 FIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKA 456 + PT+F DV +++EEIFGPV+ + +FK E+ + AN+S YGL AAV+T+DL +A Sbjct: 379 -VGPTIFVDVDPASPLSQEEIFGPVLVVTRFKNEEQALALANDSRYGLGAAVWTRDLSRA 437 Query: 457 NYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTV 510 + +S+ L+AG+V+VN Y+ PFGGYK SG+GR+ + L+ +TE+KT+ + Sbjct: 438 HRVSRRLKAGSVFVNNYNDGDMTVPFGGYKQSGNGRDKSLHALEKFTELKTIWI 491 Lambda K H 0.319 0.136 0.409 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: 610 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: 517 Length of database: 495 Length adjustment: 34 Effective length of query: 483 Effective length of database: 461 Effective search space: 222663 Effective search space used: 222663 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