Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate AO356_25765 AO356_25765 carnitine dehydratase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_25765 Length = 493 Score = 386 bits (992), Expect = e-112 Identities = 210/478 (43%), Positives = 300/478 (62%), Gaps = 8/478 (1%) Query: 41 INNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSP-WRRMDAS 99 I EW DA+S KTF ++NP+ + ++ + D+ DV++AV+AA++AF SP WR + A+ Sbjct: 10 IGGEWVDALSGKTFESLNPALAQPWAELPDADEADVERAVQAAQSAFD--SPAWRGLTAT 67 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 RG+LL RL DLI ++ LA LE+ DNGK + + + + Y AG ADK G Sbjct: 68 ARGKLLRRLGDLIAENKEQLAQLESRDNGK-LIRETRGQVGYLPEFFHYTAGLADKLEGG 126 Query: 160 TIPIDG-DFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTA 218 T+P+D D F+YT HE +GV IIPWN PL + A KL PALA GN +V+K +E T Sbjct: 127 TLPLDKPDLFAYTVHEAMGVVAAIIPWNSPLYLTAIKLAPALAAGNTIVIKPSEHASATV 186 Query: 219 LYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSN 278 L +A L EAG PPGVVN+V G+GP+ GAA+ H V K+AFTG R + V + + N Sbjct: 187 LELARLALEAGIPPGVVNVVTGYGPSTGAALTRHPLVRKIAFTGGAATARHV-VRSSAEN 245 Query: 279 LKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338 +++LELGGKSPNII +DAD+D A+ A ++ GQ C +GSR VQ++IYDEFV R Sbjct: 246 FAKLSLELGGKSPNIIFADADLDSAINGAIAGIYAASGQSCVSGSRLLVQDEIYDEFVSR 305 Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAAD--RGY 396 V RA+ +GNP + +E GP Q + G + EGA+L GG + G+ Sbjct: 306 LVERAQRIRIGNPQEDASEMGPMATAQQLAVVEGLVADAIAEGARLRLGGKRPQNLGDGW 365 Query: 397 FIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKA 456 F +PT+F ++ M I +EE+FGPV +++FK E + AN+S +GLAA ++T+DL +A Sbjct: 366 FYEPTLFECDRNSMKIMQEEVFGPVASVIRFKDEAEALAIANDSQFGLAAGIWTRDLGRA 425 Query: 457 NYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKVPQ 514 + L++ +++G +WVN Y A +P GG+K SG GRE G + AYTE+KTV + + Q Sbjct: 426 HRLARDVRSGIIWVNTYRAVSAMAPIGGFKNSGYGRESGIDSVLAYTELKTVWINLSQ 483 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: 614 Number of extensions: 35 Number of successful extensions: 6 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: 493 Length adjustment: 34 Effective length of query: 483 Effective length of database: 459 Effective search space: 221697 Effective search space used: 221697 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