Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate CA265_RS14635 CA265_RS14635 aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Pedo557:CA265_RS14635 Length = 501 Score = 365 bits (938), Expect = e-105 Identities = 209/483 (43%), Positives = 289/483 (59%), Gaps = 20/483 (4%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 +I ++ V F ++P G+V + A KED++ AV AA AF+ W + ++ Sbjct: 17 YIGGKFVAPVKGAYFDNISPIDGKVFTKAAHSTKEDLELAVDAAHEAFKT---WSKTSST 73 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R +LN++A +E + YLAA+ET+DNGK + DL + + RY+AG G Sbjct: 74 ERSIILNKIAQRMEDNLEYLAAVETIDNGKAVRETLAADLPLGVDHFRYFAGVIRAEEGS 133 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 +D + S HEP+GV QIIPWNFPLLM WKL PALA GN VV+K AE TP++ + Sbjct: 134 LSELDQNTVSLIVHEPIGVVAQIIPWNFPLLMGIWKLAPALAAGNCVVLKPAESTPVSIM 193 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 + LI + PPGVVN+V GFG G A+ ++ V K AFTGST GR++ A + N+ Sbjct: 194 VLMELIGDL-LPPGVVNVVNGFGSELGRALVTNPKVSKAAFTGSTPTGRLVMQYA-TENI 251 Query: 280 KRVTLELGGKSPNIIMS------DADMDWAVEQA-HFALFFNQGQCCCAGSRTFVQEDIY 332 VTLELGGKSPNI S DA +D AVE A FAL NQG+ C SR +QEDIY Sbjct: 252 IPVTLELGGKSPNIFFSSVMAEDDAFLDKAVEGAVMFAL--NQGEICTCPSRLLIQEDIY 309 Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGI-- 390 ++F+ + + R K+ +G+P D G Q + QF+KI YI GK+EGA++L GG I Sbjct: 310 EKFIAKVIERTKAIKIGSPLDRTVMMGAQASKIQFEKIAAYIKLGKEEGAEVLTGGEINE 369 Query: 391 ---AADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAA 447 GY+I+PT+F + M I +EEIFGPV+ + FKT+EE + AN++ YGL A Sbjct: 370 LPGELGGGYYIKPTIFKG-HNKMRIFQEEIFGPVLAVTTFKTVEEAIEIANDTLYGLGAG 428 Query: 448 VFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKT 507 V+T+D + + +A+QAG VWVN Y + A +PFGGYK SG GRE + L Y + K Sbjct: 429 VWTRDAHELYQVPRAIQAGRVWVNQYHAYPAGAPFGGYKQSGVGRENHKMMLGHYRQTKN 488 Query: 508 VTV 510 + + Sbjct: 489 MLI 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: 618 Number of extensions: 34 Number of successful extensions: 7 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: 501 Length adjustment: 34 Effective length of query: 483 Effective length of database: 467 Effective search space: 225561 Effective search space used: 225561 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