Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate H281DRAFT_00993 H281DRAFT_00993 gamma-glutamyl-gamma-aminobutyraldehyde dehydrogenase
Query= BRENDA::P05091 (517 letters) >FitnessBrowser__Burk376:H281DRAFT_00993 Length = 497 Score = 379 bits (974), Expect = e-109 Identities = 201/477 (42%), Positives = 297/477 (62%), Gaps = 5/477 (1%) Query: 40 FINNEWHDAVSRKTFPTVNPSTGEVICQVAEGDKEDVDKAVKAARAAFQLGSPWRRMDAS 99 FI + +A S +TF T+NPSTG+V+ +A+ D +DVD+AV AAR AF+ G W + + Sbjct: 21 FIAGQRANAASNETFATLNPSTGKVLADIAKCDTKDVDRAVAAAREAFESGV-WSKAAPA 79 Query: 100 HRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLDMVLKCLRYYAGWADKYHGK 159 R +L RLA LI+ + LA LE L+ GKP +D+ C+R++A DK + Sbjct: 80 QRKAVLQRLAQLIDDNAEELALLEALEAGKPISECLGLDIPESAACIRWHAEVTDKRYDA 139 Query: 160 TIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKVAEQTPLTAL 219 P S EP+GV G ++PWNFP LM AWK+GPAL+ GN V++K AEQT L+ L Sbjct: 140 LSPSGASVVSMITREPIGVVGAVLPWNFPALMLAWKIGPALSVGNSVIVKPAEQTSLSTL 199 Query: 220 YVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNL 279 +A+L EAG P GV+N+V GFG +AG A+ H DVD VAFTGSTE G+ + +NL Sbjct: 200 RIADLALEAGLPAGVLNVVTGFGESAGQALGRHADVDLVAFTGSTETGKRFLRYSADTNL 259 Query: 280 KRVTLELGGKSPNIIMSD-ADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVER 338 KRV LE GGK+P +++ D A++D EQA A F+N G+ C AGSR V + +E+ Sbjct: 260 KRVVLECGGKNPQVVLPDVANLDAVAEQAVAAAFWNMGENCSAGSRILVPSSLKASLLEK 319 Query: 339 SVARAKSRVVGNPFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAA--DRGY 396 +A + G+P D + G ++E F+K+L +I + EGA+L+CGG G+ Sbjct: 320 VLAVLEVWKTGDPLDPDVKLGSLIEEMHFEKVLAHIEKARAEGARLVCGGKATRTDSGGW 379 Query: 397 FIQPTVFGDVQDGMTIAKEEIFGPVMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKA 456 F++PT+F +V M IA++E+FGPV+ +++ I+E V AN++ YGLAA+++T +++ A Sbjct: 380 FVEPTIFDNVTPQMRIARDEVFGPVVCFIEYADIDEAVHIANDTCYGLAASLWTDNVNHA 439 Query: 457 NYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSG-SGRELGEYGLQAYTEVKTVTVKV 512 + ++ ++AGTV VNC+ +PFGG+K SG GR+ Y Y E+KT +K+ Sbjct: 440 HKIAARIRAGTVTVNCFGEGDLSTPFGGFKQSGFGGRDKSVYAHDQYCELKTTWLKL 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: 627 Number of extensions: 28 Number of successful extensions: 5 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: 497 Length adjustment: 34 Effective length of query: 483 Effective length of database: 463 Effective search space: 223629 Effective search space used: 223629 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