Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate HSERO_RS04810 HSERO_RS04810 aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__HerbieS:HSERO_RS04810 Length = 504 Score = 327 bits (838), Expect = 6e-94 Identities = 181/454 (39%), Positives = 254/454 (55%), Gaps = 5/454 (1%) Query: 58 NPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDRT 117 NP+TG +G V+ A AA+ A + W + + RGR L + +I + Sbjct: 43 NPATGRASLSYRDGGAAAVEAAAVAAQRAQR---QWWALSHAARGRALYAVGAVIRAEAE 99 Query: 118 YLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYTRHEPVG 177 LA LE + +GKP + ++ V + YYAGWADK++G+ IP+ +YTR EP G Sbjct: 100 PLARLEAISSGKP-IRDCRAEMQKVAEMFEYYAGWADKFYGEVIPVPSSHLNYTRREPYG 158 Query: 178 VCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALYVANLIKEAGFPPGVVNI 237 Q+ PWN P W+LGPALATGN V++K +E TP ++L +A L ++AG P G+VN+ Sbjct: 159 TVLQMTPWNAPAFTCGWQLGPALATGNAVLLKPSELTPFSSLAIARLGEQAGLPAGLVNV 218 Query: 238 VPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLKRVTLELGGKSPNIIMSD 297 + G G T + V KV F GS G +I AA + + V LELGGKS NII D Sbjct: 219 LAGLGQTMVPQAMATWTVKKVIFVGSPATGALIAKAAAARVMPCV-LELGGKSANIIFED 277 Query: 298 ADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGNPFDSKTE 357 AD+ A A A+F GQ C AGSR VQ +YD FVE A A+ +G P D TE Sbjct: 278 ADLRLAAFGAQAAIFSGAGQSCVAGSRLLVQRKVYDRFVETVAAGAEKIRLGAPLDDSTE 337 Query: 358 QGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQPTVFGDVQDGMTIAKEEI 417 GP + Q++ I + G + GA L G + GYF++PT+ + M +A+ EI Sbjct: 338 VGPINNRKQYEHIQRMVARGLEAGATLAAGHTRYGEEGYFVRPTLLAHASNAMEVARSEI 397 Query: 418 FGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDVFG 477 FGPV + F+ EE + AN+S +GLA AV+T+D+ +A+ ++ ++ AGT WVN Y Sbjct: 398 FGPVAVAIPFEDEEEAIAIANDSEFGLAGAVWTRDVARAHRVAASVNAGTFWVNSYKTIN 457 Query: 478 AQSPFGGYKMSGSGRELGEYGLQAYTEVKTVTVK 511 SPFGG+ SG GR G L YT+ K+V V+ Sbjct: 458 VASPFGGFNRSGYGRSSGMEALYDYTQTKSVWVE 491 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: 660 Number of extensions: 33 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: 504 Length adjustment: 35 Effective length of query: 482 Effective length of database: 469 Effective search space: 226058 Effective search space used: 226058 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