Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Echvi_0481 Echvi_0481 NAD-dependent aldehyde dehydrogenases
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Cola:Echvi_0481 Length = 509 Score = 370 bits (949), Expect = e-107 Identities = 204/481 (42%), Positives = 288/481 (59%), Gaps = 16/481 (3%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FI ++ V + F ++P G+V +VA G D++ A+ AA AF W R A+ Sbjct: 25 FIGGKFVPPVDGEYFDVISPVDGQVFTKVARGKAADIELALDAAHKAFPA---WSRTSAT 81 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R +L ++AD IE YLAA+ET+DNGKP + DL +V+ RY+AG G Sbjct: 82 ERSNILLKIADRIENKLEYLAAVETIDNGKPVRETINADLALVVDHFRYFAGVIRAEEGS 141 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 +D S EP+G+ GQIIPWNFP+LM WK+ PALA G ++K AEQTP + + Sbjct: 142 IAELDQHTVSVNVKEPIGIVGQIIPWNFPMLMATWKMAPALAAGCCTIVKPAEQTPASIM 201 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 + +I + P GV+N+V GFGP AG +A +DKVAFTG T GR+I A S NL Sbjct: 202 ILMEVIGDL-LPAGVLNVVNGFGPEAGKPLAQSPRLDKVAFTGETTTGRLIMQYA-SENL 259 Query: 280 KRVTLELGGKSPNII---MSDADMDWAVEQAHFALFF--NQGQCCCAGSRTFVQEDIYDE 334 VT+ELGGKSPN+ + DAD ++ + A+ F NQG+ C SR V E IYD Sbjct: 260 NPVTMELGGKSPNVFFPSVMDADDEFLDKCLEGAVMFALNQGEVCTCPSRILVHEKIYDA 319 Query: 335 FVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIA--- 391 F+E+ +ARA++ +G+P D T G Q + QF+KIL YI+ GKQEGA++L GG +A Sbjct: 320 FMEKVIARAEAIQMGHPLDKTTMMGAQASKDQFEKILSYIDIGKQEGAEVLTGGEVAKLN 379 Query: 392 --ADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVF 449 + GY+++PT+ + M + +EEIFGPV + FK +EE + +N++ YGL A V+ Sbjct: 380 SGLENGYYVKPTLLKG-HNKMRVFQEEIFGPVCSVATFKDVEEAISISNDTLYGLGAGVW 438 Query: 450 TKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTVT 509 T+D +A + +A++AG VWVNCY + A +PFGGYK SG GRE L Y + K + Sbjct: 439 TRDAHEAYQVPRAIKAGRVWVNCYHAYPAHAPFGGYKKSGFGRETHLMMLNHYRQNKNML 498 Query: 510 V 510 + Sbjct: 499 I 499 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: 659 Number of extensions: 40 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: 509 Length adjustment: 35 Effective length of query: 482 Effective length of database: 474 Effective search space: 228468 Effective search space used: 228468 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