Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 202599 SO3496 aldehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__MR1:202599 Length = 498 Score = 392 bits (1008), Expect = e-113 Identities = 209/474 (44%), Positives = 289/474 (60%), Gaps = 4/474 (0%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FIN E+ DA S TF ++P G ++ VA D D + AV AR F G W + Sbjct: 24 FINGEYRDASSGNTFDCISPIDGRLLAPVASCDLMDANIAVANAREVFDSGV-WSKAAPV 82 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R +++ R A+L+E + LA LETLD GKP S VD+ + +R+ DK + + Sbjct: 83 KRKQVMIRFAELLEENANELALLETLDMGKPIRFSKAVDVAGAARAIRWSGEAIDKLYDE 142 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 P + EPVGV I+PWNFPLLM WKLGPAL TGN V++K +E++PLTA+ Sbjct: 143 LAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALVTGNSVILKPSEKSPLTAI 202 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 +A L +AG P GV+N++PG+G T G A+A H DVD + FTGST+I + + + AG SN+ Sbjct: 203 RIAELAVQAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIYAGESNM 262 Query: 280 KRVTLELGGKSPNIIMSDA-DMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338 KRV LE GGKSPNI+ +DA D+ A A A+ FNQG+ C AGSR V+ + DE V Sbjct: 263 KRVWLEAGGKSPNIVFNDAPDLKAAAVAAAEAIGFNQGEVCTAGSRLLVESGVKDELVGL 322 Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGG--IAADRGY 396 S G+P + T G VD+ Q IL YI G+ EGA L+ GG +A G Sbjct: 323 IAEELASWQPGHPLEPTTVSGAVVDKQQLDTILSYIKAGQNEGASLVYGGQQVLAETGGV 382 Query: 397 FIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKA 456 ++QPTVF +V++ M IA EEIFGPV+ +++F +EE + AN++ YGLAA V+T D+ KA Sbjct: 383 YVQPTVFSNVKNQMKIASEEIFGPVLSVIEFNGMEEAIAIANDTIYGLAAGVWTADISKA 442 Query: 457 NYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTV 510 + ++AL++G VW+N YD +PFGGYK SG+GR+ + YTE+K + Sbjct: 443 HKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHSFDKYTEIKATWI 496 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: 591 Number of extensions: 23 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: 498 Length adjustment: 34 Effective length of query: 483 Effective length of database: 464 Effective search space: 224112 Effective search space used: 224112 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