Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate GFF3161 PGA1_c32120 aldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Phaeo:GFF3161 Length = 485 Score = 340 bits (872), Expect = 7e-98 Identities = 198/474 (41%), Positives = 276/474 (58%), Gaps = 15/474 (3%) Query: 41 INNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDASH 100 I+ W T P NPS G +CQ+A GD D+D AV AARAA L PW M A+ Sbjct: 16 IDGSWQAPAGGGTLPLTNPSDGSPLCQIARGDARDIDAAVAAARAA--LDGPWGGMTATE 73 Query: 101 RGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGKT 160 RGRLL R+ ++ LA LE +D GKP + D + + L +Y G ADK HG+T Sbjct: 74 RGRLLTRMGQMVLERVDTLAQLEAMDVGKP-LTQARADAVALARYLEFYGGAADKLHGET 132 Query: 161 IPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTALY 220 IP + YT EP GV G I+PWN+P+ + +G ALA GN V+K AE+ LTAL Sbjct: 133 IPYQAGYTVYTLREPHGVTGHIVPWNYPMQIIGRSVGAALAMGNACVLKPAEEACLTALA 192 Query: 221 VANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLK 280 A++ EAG P G +N+VPG G AGAA+A H VD ++FTGS G ++Q AAG +N+ Sbjct: 193 FAHIAVEAGLPAGALNVVPGIGAEAGAALAGHPGVDHISFTGSVRTGALVQQAAG-ANVV 251 Query: 281 RVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSV 340 VTLELGGKSP ++ DAD++ A+ A N GQ C A SR VQ +YD+ V ++ Sbjct: 252 PVTLELGGKSPQLVFDDADLEAALPFLVNAGIQNAGQTCSAASRILVQRGVYDQ-VRAAM 310 Query: 341 ARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKL-LCGGGI----AADRG 395 A A S++ P S GP + Q + + GY+ +GA L + G+ A+D+G Sbjct: 311 AAAYSQLTVGPALSDLRLGPLISTRQKEIVEGYL----AKGADLAIAAQGVLSEEASDKG 366 Query: 396 YFIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDK 455 +++PT+F DV +A+EEIFGPV ++ F+ E V AN++ YGL A ++T+D + Sbjct: 367 AYVRPTLFADVGADHPLAQEEIFGPVQVLIPFEDEAEAVRIANSTDYGLVAGIWTRDGAR 426 Query: 456 ANYLSQALQAGTVWVNCYDV-FGAQSPFGGYKMSGSGRELGEYGLQAYTEVKTV 508 L++ L+AG V++N Y G + PFGG SG GRE G L ++++KTV Sbjct: 427 QMRLAKRLRAGQVFLNNYGAGGGVELPFGGVGKSGHGREKGFEALYGFSQLKTV 480 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: 640 Number of extensions: 31 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: 485 Length adjustment: 34 Effective length of query: 483 Effective length of database: 451 Effective search space: 217833 Effective search space used: 217833 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