Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF657 Psest_0671 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__psRCH2:GFF657 Length = 506 Score = 345 bits (884), Expect = 3e-99 Identities = 198/483 (40%), Positives = 280/483 (57%), Gaps = 20/483 (4%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FIN E+ + V+ + F ++P G+ I + D D++KA+ AA AA W + Sbjct: 22 FINGEFVEPVNGQYFTNLSPVNGQPIAEFPRSDAADIEKALDAAHAA---ADAWGKTSVQ 78 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R +L ++AD IE++ LA ET DNGK + D+ + RY+AG G Sbjct: 79 ARSLILLQIADRIEQNLEMLAVTETWDNGKAVRETLNADIPLAADHFRYFAGCIRAQEGT 138 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 + ID +Y HEP+GV GQIIPWNFP+LM AWKL PALA GN VV+K AEQTPL Sbjct: 139 SAEIDEHTAAYHFHEPLGVVGQIIPWNFPILMAAWKLAPALAAGNCVVLKPAEQTPLGIT 198 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 + +I + PPGV+N+V G+G AG A+AS + + K+AFTGST +G I A + + Sbjct: 199 VLMEVIGDL-LPPGVLNVVQGYGREAGEALASSKRIAKIAFTGSTPVGSHIMKRAAEAII 257 Query: 280 KRVTLELGGKSPNIIMSDADM--DWAVEQAHFAL---FFNQGQCCCAGSRTFVQEDIYDE 334 T+ELGGKSPNI D +E+A L FFNQG+ C SR VQE IY Sbjct: 258 PS-TVELGGKSPNIYFEDIMQAEPTFIEKAAEGLVLGFFNQGEVCTCPSRALVQESIYAP 316 Query: 335 FVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADR 394 F+E + + G+P D++T G Q + QF KI+ Y+ K EGA++L GG AA++ Sbjct: 317 FMEAVMKKVAQIKRGDPLDTETMVGAQASQQQFDKIMSYLEIAKGEGAEVLTGG--AAEK 374 Query: 395 -------GYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAA 447 GY+IQPT+ M + +EEIFGPV+ + FK E + AN++ YGL A Sbjct: 375 LEGSLATGYYIQPTLLKGTNQ-MRVFQEEIFGPVIGVTTFKDEAEALAIANDTEYGLGAG 433 Query: 448 VFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKT 507 V+T+D+++A + +A++AG VW NCY ++ A + FGGYK SG GRE + L +Y + K Sbjct: 434 VWTRDINRAYRMGRAIKAGRVWTNCYHLYPAHAAFGGYKRSGVGRETHKMILDSYQQTKN 493 Query: 508 VTV 510 + + Sbjct: 494 LLI 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: 621 Number of extensions: 35 Number of successful extensions: 5 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