Align quinoprotein glucose dehydrogenase; EC 1.1.5.2 (characterized)
to candidate PP_1444 PP_1444 quinoprotein glucose dehydrogenase
Query= CharProtDB::CH_002195 (796 letters) >FitnessBrowser__Putida:PP_1444 Length = 803 Score = 749 bits (1933), Expect = 0.0 Identities = 383/808 (47%), Positives = 524/808 (64%), Gaps = 30/808 (3%) Query: 5 NTGSRRLLVTLTALFAALCGLYLLIGGGWLVAIGGSWYYPIAGLVMLGVAWMLWRSKRAA 64 N GSR L + AL L GL LL GG L +GGS YY IAG+ +L ++ A Sbjct: 7 NQGSRWLPRLIGALLL-LMGLALLAGGIKLSQLGGSLYYLIAGIGFALSGVLLLAQRQIA 65 Query: 65 LWLYAALLLGTMIWGVWEVGFDFWALTPRSDILVFFGIWLILPFVWRRLVIPASGAVAAL 124 L LY +LLG+ +W ++EVG D+W L PR I G+ L+LP+ R L+ PAS A AL Sbjct: 66 LGLYGLVLLGSTVWALFEVGLDWWQLVPRLAIWFAIGVVLLLPWARRPLIGPASKANTAL 125 Query: 125 V-VALLISGGILTWAGFNDPQEINGTLSADATPAEAISP-VADQDWPAYGRNQEGQRFSP 182 + VA++ SG + F P E+ G L D++ + +P + D +W AYGR + G R+SP Sbjct: 126 LGVAVVASGACALASQFTHPGEVFGELGRDSSEMASAAPAMPDGEWQAYGRTEHGDRYSP 185 Query: 183 LKQINADNVHNLKEAWVFRTGDVKQPNDPGEITNEVTPIKVGDTLYLCTAHQRLFALDAA 242 L+QI N + L+EAW RTGD+ NDP E+TN+ TP+KV LY CTAH RL ALD Sbjct: 186 LRQITPQNAYRLEEAWRIRTGDLPTENDPVELTNQNTPLKVNGMLYACTAHSRLLALDPD 245 Query: 243 SGKEKWHYDPELK----TNESFQHVTCRGVSYHEA------------KAETASPEVMADC 286 +G E W YDP++K T + F H+TCRGVSY++ K A V C Sbjct: 246 TGAEIWRYDPQVKSPTGTFKGFAHMTCRGVSYYDENRYVSRDGSPAPKITDAGQAVAQAC 305 Query: 287 PRRIILPVNDGRLIAINAENGKLCETFANKGVLNLQSNMPDTKPGLYEPTSPPIITDKTI 346 PRR+ LP D RLIAINA+NGK+CE FAN+GV++L + + G Y TSP IT + Sbjct: 306 PRRLYLPTADARLIAINADNGKVCEGFANQGVIDLTTGIGPFTAGGYYSTSPAAITRDLV 365 Query: 347 VMAGSVTDNFSTRETSGVIRGFDVNTGELLWAFDPGAKDPNAIPSDEHTFTFNSPNSWAP 406 ++ G VTDN ST E SGVIR +DV+ G L+W +D D + ++ NS N W+ Sbjct: 366 IIGGHVTDNESTNEPSGVIRAYDVHDGHLVWNWDSNNPDDTKPLAAGKMYSRNSANMWSI 425 Query: 407 AAYDAKLDLVYLPMGVTTPDIWGGNRTPEQERYASSILALNATTGKLAWSYQTVHHDLWD 466 A+ D L ++YLP+G TPD WG +RTP E+Y++ ++AL+ TGK W+YQ HHDLWD Sbjct: 426 ASVDEDLGMIYLPLGNQTPDQWGADRTPGAEKYSAGVVALDLATGKARWNYQFTHHDLWD 485 Query: 467 MDLPAQPTLADITVNGQKVPVIYAPAKTGNIFVLDRRNGELVVPAPEKPVPQGAAKGDYV 526 MD+ +QPTL + + P I P K G+++VLDRR+G +VP E P PQGA +GD+ Sbjct: 486 MDVGSQPTLVHLKTDDGVKPAIIVPTKQGSLYVLDRRDGTPIVPIREIPTPQGAVEGDHT 545 Query: 527 TPTQPFSELSFRPTKDLSGADMWGATMFDQLVCRVMFHQMRYEGIFTPPSEQGTLVFPGN 586 +PTQ S+L+ +L+ MWGAT FDQ++CR+ F ++RYEG +TPPSEQG+LV+PGN Sbjct: 546 SPTQARSDLNLL-GPELTEQAMWGATPFDQMLCRIQFRELRYEGQYTPPSEQGSLVYPGN 604 Query: 587 LGMFEWGGISVDPNREVAIANPMALPFVSKLIPRGPGNPMEQPKDAKGTGTESGIQPQYG 646 +G+F WG +SVDP R++ +P + FVSK++PR + + +K SG+QP G Sbjct: 605 VGVFNWGSVSVDPVRQLLFTSPNYMAFVSKMVPR-----EQVAEGSKRESETSGVQPNTG 659 Query: 647 VPYGVTLNPFLSPFGLPCKQPAWGYISALDLKTNEVVWKKRIGTPQDSMPFPMPVPVPFN 706 PY V ++PF+SP G+PC+ PAWGY++A+DL TN+VVWK + GT +DS P P+ +PV Sbjct: 660 APYAVIMHPFMSPLGVPCQAPAWGYVAAIDLFTNKVVWKHKNGTTRDSTPLPIGLPV--- 716 Query: 707 MGMPMLGGPISTAGNVLFIAATADNYLRAYNMSNGEKLWQGRLPAGGQATPMTYE-VNGK 765 G+P +GG I TAG V F++ T D YLRAY+++NG++LW+ RLPAGGQATPM+Y +GK Sbjct: 717 -GVPSMGGSIVTAGGVGFLSGTLDQYLRAYDVNNGKELWKARLPAGGQATPMSYTGKDGK 775 Query: 766 QYVVISAGGHGSFGTKMGDYIVAYALPD 793 QYV+++AGGHGS GTKMGDYI+AY L + Sbjct: 776 QYVLVTAGGHGSLGTKMGDYIIAYKLAE 803 Lambda K H 0.319 0.137 0.436 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: 2194 Number of extensions: 124 Number of successful extensions: 13 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: 796 Length of database: 803 Length adjustment: 41 Effective length of query: 755 Effective length of database: 762 Effective search space: 575310 Effective search space used: 575310 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: 55 (25.8 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