Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate CCNA_03695 CCNA_03695 aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Caulo:CCNA_03695 Length = 506 Score = 373 bits (958), Expect = e-108 Identities = 214/489 (43%), Positives = 286/489 (58%), Gaps = 22/489 (4%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FI +W + F +P G IC++A D+++A+ AA AA + W R A+ Sbjct: 22 FIGGQWVAPADGRYFDNSSPIHGRKICEIARSQAIDIERALDAAHAA---KAGWARTSAA 78 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R R+L R+AD +E + LA ET DNGKP + D+ + + RY+AG G Sbjct: 79 DRSRILLRIADRMEENLAALATAETWDNGKPIRETLAADIPLAIDHFRYFAGCLRSQEGS 138 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 ID D +Y HEP+GV GQIIPWNFPLLM WKL PALA GN VV+K AEQTP + + Sbjct: 139 ISEIDHDTIAYHFHEPLGVVGQIIPWNFPLLMACWKLAPALAAGNCVVLKPAEQTPASIM 198 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 A +I + P GV+NIV GFG AG +AS + K+AFTG T GR+I A + NL Sbjct: 199 VWAEMIGDL-LPAGVLNIVNGFGLEAGKPLASSPRIAKIAFTGETSTGRLIMQYA-AQNL 256 Query: 280 KRVTLELGGKSPNIIMSDAD------MDWAVEQAHFALF-FNQGQCCCAGSRTFVQEDIY 332 VTLELGGKSPNI D +D A+E F +F NQG+ C SR VQE IY Sbjct: 257 IPVTLELGGKSPNIFFDDVAREDDDYLDKALE--GFTMFALNQGEVCTCPSRALVQESIY 314 Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGG---- 388 ++F+ER++ R + V G+P D T G Q E Q KILGY++ G+ EGAKLL GG Sbjct: 315 EKFMERALKRVNAVVQGSPLDPATMIGAQASEEQLNKILGYMDIGRNEGAKLLAGGQRKI 374 Query: 389 --GIAADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAA 446 G AD GY+++PTVF + + M I +EEIFGPV+ + FKT EE + AN++ +GL A Sbjct: 375 LPGQLAD-GYYVEPTVF-EGHNKMRIFQEEIFGPVLAVTTFKTEEEALEIANDTAFGLGA 432 Query: 447 AVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVK 506 V+++D ++ + ++AG VW NCY + A + FGGYK SG GRE + L Y + K Sbjct: 433 GVWSRDANRCYRFGRGIEAGRVWTNCYHAYPAHAAFGGYKQSGVGRETHKMMLDHYQQTK 492 Query: 507 TVTVKVPQK 515 + V K Sbjct: 493 NMLVSYSPK 501 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: 630 Number of extensions: 25 Number of successful extensions: 7 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: 506 Length adjustment: 35 Effective length of query: 482 Effective length of database: 471 Effective search space: 227022 Effective search space used: 227022 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