Align aldehyde dehydrogenase (NAD+) (EC 1.2.1.3) (characterized)
to candidate Pf6N2E2_1370 Putative benzaldehyde dehydrogenase oxidoreductase protein (EC 1.2.1.28)
Query= BRENDA::P76217 (492 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_1370 Length = 490 Score = 208 bits (529), Expect = 4e-58 Identities = 157/489 (32%), Positives = 243/489 (49%), Gaps = 36/489 (7%) Query: 6 NGDWITGQGASRVKRNPVSGEVLWQGNDADAAQVEQACRAARAAFPRWARLSFAERHAVV 65 NGDW+ G + P +GE L + AD+A + +A R A A P WA L +R A+ Sbjct: 20 NGDWVPASGPLQSIIEPATGERLMRCATADSADIAKASRDAALAQPGWAALGPRQRAAIF 79 Query: 66 ERFAALLESNKAELTAIIARETGKPRWEAATEVTAMINKIAISIKAYHVRTGEQRSEMPD 125 + A + E + EL +ARETG ++ EV I + +A + + +P Sbjct: 80 RKAAEVAEHSFNELALYVARETGAALFKGQHEVR---EAIVLLHQAAGLLSQAHGVVLPS 136 Query: 126 GAASL---RHRPHGVLAVFGPYNFPGHLPNGHIVPALLAGNTIIFKPSELTPWSGE-AVM 181 A L R +PHGV+ V P+NFP L + PAL AGN ++ KP TP SG + Sbjct: 137 EAGRLSYARRQPHGVVGVISPFNFPLVLSMRSVAPALAAGNAVVLKPDPQTPVSGGFLIA 196 Query: 182 RLWQQAGLPPGVLNLVQGGRETGQALSALEDLDGLLFTGSANTGYQLHRQLSGQPEKILA 241 RL++ AGLP G+L ++ G + G+AL ++ + FTGS G ++ +++G+ K +A Sbjct: 197 RLFEVAGLPKGLLQVLPGAADAGEALCRDPNVRMIAFTGSTGAGRKV-AEVAGRNLKKVA 255 Query: 242 LEMGGNNPLIIDEVADIDAAVHLTIQSAFVTAGQRCTCARRLLLKSGAQGDAFLARLVAV 301 LE+GG NPLII E AD+D A A++ GQ C A L+L + + +LV Sbjct: 256 LELGGKNPLIILEDADLDLAARNAAWGAWLHQGQIC-MATGLILAHESIAEELTRKLVEK 314 Query: 302 SQRLTPGNWDDEPQPFIGGLISEQAAQQV-------VTAWQQLEAMGGRPLLAPRLLQAG 354 ++ LT GN + + +G LI+++ ++V V A +LEA G RL Sbjct: 315 ARALTVGN-AAQGEAALGPLINQRQLKRVHDIVSDSVRAGARLEAGGEH----DRLFYQA 369 Query: 355 TSL--LTPGIIEMTGVAGVPDEEVFGPLLRVWRYDTFDEAIRMANNTRFGLSCGLVSPER 412 T L + PG+ DEE+FGP+ V + T DEA+ +AN T +GL+ ++S Sbjct: 370 TVLSGVKPGMRAF-------DEEIFGPVATVVSFATDDEAVELANRTEYGLAAAIISSSV 422 Query: 413 EKFDQLLLEARAGIVNWNKPLTGAASTAPFGGIGASGN----HRPSAWYAADYCAWPMAS 468 + + + G+++ N PFGG GASGN P+ W +Y W + Sbjct: 423 GRAMAIGERLQCGMLHINDQTVADECINPFGGRGASGNGGSVGGPADW--DEYTQWQWVT 480 Query: 469 LESDSLTLP 477 ++ + P Sbjct: 481 VKDKAPVYP 489 Lambda K H 0.318 0.134 0.412 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: 629 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: 492 Length of database: 490 Length adjustment: 34 Effective length of query: 458 Effective length of database: 456 Effective search space: 208848 Effective search space used: 208848 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 (21.7 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