Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 6938545 Sama_2648 aldehyde dehydrogenase (RefSeq)
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__SB2B:6938545 Length = 498 Score = 414 bits (1065), Expect = e-120 Identities = 219/474 (46%), Positives = 297/474 (62%), Gaps = 4/474 (0%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FIN + DAV ++TF ++P G ++ QVA + D D AV ARA F+ G W Sbjct: 24 FINGHYCDAVGKETFDCISPVDGRLLTQVASCQQADADIAVANARAVFESGV-WSLQSPV 82 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R +++ R A+L+E LA LETLD GKP S VD+ + +R+ DK + + Sbjct: 83 KRKKVMIRFAELLEAHADELALLETLDMGKPIAHSKAVDVAGAARAIRWSGEAIDKIYDE 142 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 P + EPVGV I+PWNFP+LM WKLGPALATGN VV+K +E++PLTA+ Sbjct: 143 LAPTPHNEIGMITREPVGVVAAIVPWNFPMLMACWKLGPALATGNSVVLKPSEKSPLTAI 202 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 +A L KEAG P GV+N++PGFG T G A+A H DVD + FTGST+I + + V AG SN+ Sbjct: 203 RMAQLAKEAGLPDGVLNVLPGFGHTVGQALALHMDVDTLVFTGSTKIAKQLMVYAGQSNM 262 Query: 280 KRVTLELGGKSPNIIMSDA-DMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338 KRV LE GGKSPNI+ +DA D+ A E A A+ FNQG+ C AGSR V+ + DE ++ Sbjct: 263 KRVWLEAGGKSPNIVFNDAPDLKAAAEAAASAIAFNQGEVCTAGSRLLVESGVKDELIKL 322 Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGG--IAADRGY 396 V ++ G+P D T G VD+ Q +LGYI G EGAKL+CGG +A G Sbjct: 323 IVKEMEAWQPGHPLDPATTCGAVVDKQQLDTVLGYIKAGHDEGAKLMCGGSQVLAETGGV 382 Query: 397 FIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKA 456 ++ PTVF V + M IA+EEIFGPVM ++ F ++E V AN++ YGLAA V+T D+ KA Sbjct: 383 YVAPTVFDGVTNQMKIAREEIFGPVMSVITFDGMDEAVAIANDTIYGLAAGVWTSDISKA 442 Query: 457 NYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTV 510 + ++AL++G VW+N YD +PFGGYK SG+GR+ + + YTEVK + Sbjct: 443 HKTAKALRSGMVWINHYDGGDMTAPFGGYKQSGNGRDKSLHAFEKYTEVKATWI 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: 25 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