Align aminobutyraldehyde dehydrogenase (EC 1.2.1.19) (characterized)
to candidate Ga0059261_0516 Ga0059261_0516 vanillin dehydrogenase (EC 1.2.1.67)
Query= BRENDA::G5DDC2 (506 letters) >FitnessBrowser__Korea:Ga0059261_0516 Length = 478 Score = 219 bits (558), Expect = 2e-61 Identities = 165/484 (34%), Positives = 240/484 (49%), Gaps = 24/484 (4%) Query: 21 PPAQGRRLPVVNPTTEAHIGEIPAGTAEDVDAAVAAARAALKRNRGRDWARAPGAVRAKY 80 PPA G+ +NP T E A T + + AV AA AA W+ R Sbjct: 6 PPAPGKTFARLNPVTGEVATEAQAFTVDQANEAVEAAAAAFPA-----WSTLGPNARRAA 60 Query: 81 LRAIAAKVIERKQELAKLEALDCGKPYDEAAWDMDDVAGCFEYFADQAEALDKRQNSPVS 140 L A + + ++ + + G A +++ +A AL + V Sbjct: 61 LNKAAEALAAKAEDFVEAMNGEIGATEGWARFNLMLAVSMVR----EAAALTTQIGGEV- 115 Query: 141 LPMETFKCHLR--REPIGVVGLITPWNYPLLMATWKVAPALAAGCAAVLKPSELASVTCL 198 +P + C REP+GV+ I PWN P+++ VA LA G VLK SE T Sbjct: 116 IPSDKPGCIAMAIREPVGVMLGIAPWNAPIILGVRAVAAPLACGNTVVLKASEQCPRTHS 175 Query: 199 ELADICKEVGLPPGVLNIVTGLGPDAGAPLSA---HPDVDKVAFTGSFETGKKIMAAAAP 255 +A+ E LP G ++IVT DA + A +P + ++ FTGS G+ I AA Sbjct: 176 LIAEAFDEA-LPKGAVSIVTNAPEDAPEIVGALIDNPHIRRINFTGSTAVGRIIAKRAAE 234 Query: 256 MVKPVTLELGGKSPIVVFDDVDIDKAVEWTLFGCFWTNGQICSATSRLLVHTKIAKEFNE 315 +KPV LELGGK+P++V +D D+D+AV+ FG F GQIC +T R++V +A F E Sbjct: 235 HLKPVLLELGGKAPMLVLEDADLDEAVKAAAFGAFMNQGQICMSTERIIVVDAVADAFVE 294 Query: 316 KMVAWAKNIKVSDPLEEGCRLGPVVSEGQYEKIKKFILNAKSEGATILTGGVRPAHLE-- 373 K A + V DP E LG VV + +K I +A + GA + GG LE Sbjct: 295 KFAAKVGTMPVGDPREGKTPLGAVVDQKTVAHVKALIGDALAAGAVQVNGG---GVLEGT 351 Query: 374 KGFFIEPTIITDITTSMEIWREEVFGPVLCVKEFSTEDEAIELANDTQYGLAGAVISGDR 433 G + +I +T M+++R+E FGPV+ V E AI LANDT+YGL+ +V + D Sbjct: 352 GGVLMPAHVIDHVTPDMKLFRDESFGPVVGVIRARDEAHAILLANDTEYGLSASVFTRDT 411 Query: 434 ERCQRLSEEIDAGIIWVN-CSQPCFCQAPWGGNKRSGFGRELGEGGIDNYLSVKQVTEYI 492 R R++ +I +GI VN + Q P+GG K SG+GR G+ GID + ++ +T I Sbjct: 412 ARGLRVARQIKSGICHVNGPTVHDEAQMPFGGVKASGYGRFGGKAGIDAFTELRWIT--I 469 Query: 493 SDEP 496 EP Sbjct: 470 ETEP 473 Lambda K H 0.318 0.135 0.421 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: 569 Number of extensions: 27 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: 506 Length of database: 478 Length adjustment: 34 Effective length of query: 472 Effective length of database: 444 Effective search space: 209568 Effective search space used: 209568 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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