Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate HSERO_RS09465 HSERO_RS09465 aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__HerbieS:HSERO_RS09465 Length = 506 Score = 382 bits (980), Expect = e-110 Identities = 217/488 (44%), Positives = 290/488 (59%), Gaps = 20/488 (4%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FI ++ V + F ++P G C+VA EDV+ A+ AA AA + W + + Sbjct: 22 FIGGKFVPPVKGEYFENISPVIGRAFCEVARSSAEDVELALDAAHAAKK---SWGKTSPT 78 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R +L ++AD +E + LA ETLDNGKP + D+ + + RY+A G Sbjct: 79 ERANMLLKIADRMEANLELLATAETLDNGKPIRETMAADIPLAIDHFRYFAAAVRTQEGS 138 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 PID D ++Y HEP+GV GQIIPWNFP+LM WKL PALA GN VV+K AEQTP + + Sbjct: 139 ICPIDNDTYAYHFHEPLGVVGQIIPWNFPILMAVWKLAPALAAGNCVVLKPAEQTPASIM 198 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 + LI + PPGVVNIV GFG AG +AS++ + K+AFTG T GR+I A S NL Sbjct: 199 VLIELIADL-IPPGVVNIVQGFGVEAGKPLASNKRIAKIAFTGETTTGRLIMQYA-SQNL 256 Query: 280 KRVTLELGGKSPNIIMSDA------DMDWAVEQAHFALF-FNQGQCCCAGSRTFVQEDIY 332 VTLELGGKSPNI +D D A+E FA+F NQG+ C SR VQE IY Sbjct: 257 IPVTLELGGKSPNIFFADVLDKDDDFFDKALE--GFAMFALNQGEVCTCPSRVLVQESIY 314 Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGG--- 389 + F+ER++ R + GNP D T G Q + Q +KIL YI+ GKQEGAK+L GGG Sbjct: 315 ERFIERALKRVAAIKQGNPLDKSTMIGAQASQEQLEKILSYIDIGKQEGAKVLAGGGREE 374 Query: 390 IAAD--RGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAA 447 + D GY+++PTVF + M I +EEIFGPV+ + FK EE + AN++ YGL A Sbjct: 375 LGGDLASGYYVKPTVF-QGNNKMRIFQEEIFGPVVSVTTFKDEEEALAIANDTLYGLGAG 433 Query: 448 VFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKT 507 ++T+D +A + + +QAG VW NCY ++ A + FGGYK SG GRE + L Y + K Sbjct: 434 LWTRDGTRAFRMGREIQAGRVWTNCYHLYPAHAAFGGYKQSGIGRENHKMMLDHYQQTKN 493 Query: 508 VTVKVPQK 515 + V K Sbjct: 494 LLVSYSPK 501 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: 630 Number of extensions: 31 Number of successful extensions: 8 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