Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 5208455 Shew_0967 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__PV4:5208455 Length = 498 Score = 398 bits (1022), Expect = e-115 Identities = 214/480 (44%), Positives = 297/480 (61%), Gaps = 4/480 (0%) Query: 34 VFCNQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPW 93 V Q FIN E+ A S TF ++P G V+ QVA D D ++AV AR F+ G W Sbjct: 18 VIQGQAFINGEYCAADSNDTFDCISPIDGRVLTQVASCDLLDANRAVANAREVFERGD-W 76 Query: 94 RRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWA 153 ++ R +++ R ADL+E +R LA LETLD GKP S VD+ + LR+ Sbjct: 77 SQLPPVKRKQVMIRFADLLEANRDELALLETLDMGKPIRYSGAVDVAGAARALRWSGEAV 136 Query: 154 DKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQ 213 DK + + P + EPVGV I+PWNFPLLM WKLGPALATGN VV+K +E+ Sbjct: 137 DKIYDEIAPTAHNEIGMITREPVGVVAAIVPWNFPLLMACWKLGPALATGNSVVLKPSEK 196 Query: 214 TPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVA 273 +PLTA+ +A L EAG P GV+N++PG+G T G A+A H DVD + FTGST+I + + + Sbjct: 197 SPLTAIRMAQLAIEAGIPKGVLNVLPGYGHTVGKALALHMDVDTLVFTGSTKIAKQLMIY 256 Query: 274 AGSSNLKRVTLELGGKSPNIIMSDA-DMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIY 332 AG SN+KRV LE GGKSPNI+ +DA ++ A A A+ FNQG+ C AGSR V+ + Sbjct: 257 AGESNMKRVWLEAGGKSPNIVFNDAPNLKEAAIAAASAIAFNQGEVCTAGSRLLVESGVK 316 Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGG--I 390 +E + A ++ G+P D T G VD+ Q + +L YI G EGA+L GG + Sbjct: 317 EELINLIEAEMQAWQPGHPLDPATTCGAVVDQQQLENVLRYIRAGVAEGAQLRQGGQQVL 376 Query: 391 AADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFT 450 A G ++ PT+F +V++ MTIAKEEIFGPV+ ++ F +EE + N++ YGLAA V+T Sbjct: 377 AETGGVYVAPTIFANVKNEMTIAKEEIFGPVLSVITFDGMEEAIRIGNDTIYGLAAGVWT 436 Query: 451 KDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTV 510 D+ KA+ ++AL++G VW+N YD +PFGGYK SG+GR+ + YTE+K + Sbjct: 437 SDISKAHKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFDKYTEIKATWI 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: 601 Number of extensions: 26 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 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