Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate SMa2213 SMa2213 aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Smeli:SMa2213 Length = 494 Score = 385 bits (988), Expect = e-111 Identities = 207/481 (43%), Positives = 290/481 (60%), Gaps = 7/481 (1%) Query: 39 IFINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDA 98 ++I+ +W S + TV+P T V G+ ED D+AV+AA AF G PW +M Sbjct: 9 MYIDGQWVAPASGEYIETVDPFTARPWALVPRGNAEDADRAVRAAHRAFSQG-PWGKMHP 67 Query: 99 SHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHG 158 + RGR++ R A LIE LA +E DNG+ + + + + YYAG+ADK G Sbjct: 68 TERGRIIQRFAALIEEHADALADIEVRDNGR-LLAEMTHQIRYIPRWYHYYAGFADKIEG 126 Query: 159 KTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTA 218 P D S++RHEP+GVC I+PWN PLL+ + K PALA GN +VMK AE T TA Sbjct: 127 TLHPCDKPALSFSRHEPLGVCVGIVPWNAPLLLFSLKAAPALAAGNTLVMKPAEFTSATA 186 Query: 219 LYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSN 278 L + L+++AGFP GV+N+V G+GP G + +H V FTGST+ G + A + + Sbjct: 187 LKLMELVEKAGFPTGVINVVTGYGPEVGEPLVTHPLTRHVGFTGSTKTGAHLYSLA-AKD 245 Query: 279 LKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338 +KRV+LELGGKSPNI+ DAD+D AV +F GQ C AGSR V I+DEF+E+ Sbjct: 246 VKRVSLELGGKSPNIVFGDADLDNAVRGVVGGIFGAVGQTCIAGSRLLVHRSIHDEFLEK 305 Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGG----IAADR 394 K+ +G+P +T+ GP + QF+K+LGYI+ ++EGA+L+ GGG Sbjct: 306 LAVFTKTARIGDPRKVETQIGPIANSMQFEKVLGYIDIARREGAELILGGGRPDLEECGT 365 Query: 395 GYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLD 454 GYFI+PT+F V + M IA+EE+FGPV+ + F EE + AN+S +GL A V+T D+ Sbjct: 366 GYFIEPTIFAGVSNDMRIAREEVFGPVLSAIVFDEPEEALAIANDSEFGLGAGVWTSDMR 425 Query: 455 KANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVKVPQ 514 A +S+ L+AG+VWVN Y +PFGGYK SG GRE G G+ Y + K V + + Sbjct: 426 LALKMSERLEAGSVWVNTYRDISYTTPFGGYKKSGIGRENGVAGIYEYLQTKAVWLSTAE 485 Query: 515 K 515 + Sbjct: 486 E 486 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: 642 Number of extensions: 27 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: 494 Length adjustment: 34 Effective length of query: 483 Effective length of database: 460 Effective search space: 222180 Effective search space used: 222180 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