Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate 203555 SO4480 aldehyde dehydrogenase (NCBI ptt file)
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__MR1:203555 Length = 506 Score = 379 bits (972), Expect = e-109 Identities = 209/483 (43%), Positives = 292/483 (60%), Gaps = 20/483 (4%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FI +W V+ K F +P G+ C++ D +D++ A+ AA AA W + + Sbjct: 22 FIGGKWVAPVNGKYFDNRSPVNGQNFCKIPRSDAQDIELALDAAHAA---KDAWGKTSVT 78 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R +L R+AD +E++ YLA ET +NGK + DL + + RY+AG G Sbjct: 79 ERSNILLRIADRVEQNLEYLAVAETWENGKAVRETLNADLPLFVDHFRYFAGCIRAQEGS 138 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 IDG+ SY EP+GV GQIIPWNFPLLM AWK+ PALA GN VV+K AEQTP++ L Sbjct: 139 AADIDGNTVSYHFPEPLGVVGQIIPWNFPLLMAAWKIAPALAAGNCVVLKPAEQTPVSIL 198 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIG-RVIQVAAGSSN 278 + LI++ PPGV+N+V GFG AG A+A+ + + K+AFTGSTE+G +++ AA S Sbjct: 199 VLLELIEDL-LPPGVLNVVNGFGAEAGQALATSKRIAKLAFTGSTEVGFHILKCAAES-- 255 Query: 279 LKRVTLELGGKSPNIIMSDA------DMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIY 332 L T+ELGGKSPN+ +D +D AVE A FFNQG+ C SR +QE IY Sbjct: 256 LIPSTVELGGKSPNLYFADVMDQEDEYLDKAVEGMLLA-FFNQGEVCTCPSRVLIQESIY 314 Query: 333 DEFVERSVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIA- 391 D F+E+ +ARA++ GNP D+ T+ G Q + QF KIL Y+ GK EGA++L GG + Sbjct: 315 DRFIEKVLARAQTIKQGNPLDTATQVGAQASQEQFDKILSYLAIGKDEGAQVLLGGSLCQ 374 Query: 392 ----ADRGYFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAA 447 +GY+I PT+ + M I +EEIFGPV+ + FK E + AN++ YGL A Sbjct: 375 LEGEQSKGYYISPTIMKG-HNKMRIFQEEIFGPVISVTTFKDEAEALAIANDTEYGLGAG 433 Query: 448 VFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGSGRELGEYGLQAYTEVKT 507 V+T+D+++A + + +QAG VW+NCY + A + FGGYK SG GRE + L Y K Sbjct: 434 VWTRDMNRAQRMGRGIQAGRVWINCYHAYPAHAAFGGYKKSGIGRETHKMMLNHYQNTKN 493 Query: 508 VTV 510 + V Sbjct: 494 LLV 496 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: 639 Number of extensions: 36 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: 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 Apr 09 2024. 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