Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate PP_3569 PP_3569 quinate dehydrogenase (quinone)
Query= BRENDA::D4P700 (796 letters) >FitnessBrowser__Putida:PP_3569 Length = 805 Score = 597 bits (1540), Expect = e-175 Identities = 340/809 (42%), Positives = 458/809 (56%), Gaps = 50/809 (6%) Query: 14 LTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYALLLLA 73 L V+ A+L G + GG+ LA +GGSWY++IGG AM + L+ RR A +YA+ L+ Sbjct: 18 LGVIIALL-GLLLAAGGVKLAGLGGSWYFLIGGLAMAIAGVLIARRKKAGAWLYAVFLVG 76 Query: 74 TLAWGVWEVGTDFWALAPRTDVLVIFG-VWLVLPFVYRGLYQP-----GKGALGAMGVAL 127 T W + + G FW L R L +FG + +V+ VY L + G+GA G GV Sbjct: 77 TAIWALIDAGLVFWPLFSR---LFMFGAIGMVVALVYPLLARANGASAGRGAYGVAGVMA 133 Query: 128 VASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADG-DWPAYARDQQGTRFSPLK 186 V + P V A P P+ + DW Y + G+RF+ L Sbjct: 134 VVLVVAVGNMFVAHPSV------APTGKGPGMTPVETGKEQKDWAHYGNTEGGSRFAALD 187 Query: 187 QINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDAATG 246 QIN DNV +L+VAW +QTGD+ SD D++TP++I +++CTPH L ALDA TG Sbjct: 188 QINRDNVNKLKVAWTYQTGDVAI-SDGNGAEDQLTPLQIGSKVFICTPHNNLIALDADTG 246 Query: 247 KQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQP-------------ALCSRRI 293 K+ WK + ++ +Q CRG++Y + AA A TQP A C RR+ Sbjct: 247 KELWKNEINAQSK-VWQR--CRGMAYFDATAAI-AQPTQPNSSPITGVSVAAGANCQRRL 302 Query: 294 YLPVNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAG 353 DGRL A+DA+TGE C FGNNG++DL+ Y+ +S P++ TT+V+ G Sbjct: 303 LTNTIDGRLIAVDADTGEFCQGFGNNGQVDLKAGLGDVPDSYYQLSSAPLMAGTTVVVGG 362 Query: 354 AVTDNFSTREPSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYD 413 V DN T P G IRGFDV TG++ W FDPG + P + T+ ++PNSWAP YD Sbjct: 363 RVADNVQTDMPGGVIRGFDVITGEMRWAFDPGNPEDRQAPQGDKTYVRSTPNSWAPMSYD 422 Query: 414 PKLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLP 473 P ++ V+LPMG ++ DI+G R+ Y +SVLAL+ATTG W +QTVH+DLWD DLP Sbjct: 423 PAMNTVFLPMGSSSTDIYGVERSKLDHTYGASVLALDATTGNQKWVFQTVHNDLWDFDLP 482 Query: 474 SQPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSAT 533 QP+L D T DG +VP + K G I+VLDR TGK + E PV + S T Sbjct: 483 MQPSLIDFTKDDGQSVPAVVIGTKAGQIYVLDRATGKPLTQVDEVPVKPSNIPNEPYSPT 542 Query: 534 QPYS-ELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLG 592 QP S + Q LT+ DMWGAT YDQL+CR+ FK++RY+G +T P +L FPG+LG Sbjct: 543 QPKSVGMPQIGAQTLTESDMWGATPYDQLLCRIDFKKMRYDGLYTAPGTDLSLSFPGSLG 602 Query: 593 MFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGI--QPQY 650 WG IS DP N M L ++IP + A+GG TG+ P Sbjct: 603 GMNWGSISTDPVHGFIFVNDMRLGLWIQMIP-----SQNKGGAASGGEALNTGMGAVPLK 657 Query: 651 GVPYGVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSP----VPLPF 706 G PY V N FLS G+PC+ P +G ++A+D+KT +V W+ +GTV D+ P + LP Sbjct: 658 GTPYAVNKNRFLSVAGIPCQAPPFGTLTAIDMKTRQVAWQVPVGTVEDTGPLGIRMHLPI 717 Query: 707 KMGMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTY--EVN 764 K+G+P LGG ++T G + FI T D YLRA+ + G +W+ARLP G Q PMTY Sbjct: 718 KIGLPTLGGTLSTQGGLVFIAGTQDFYLRAYDSSNGNEIWKARLPVGSQGGPMTYVSPKT 777 Query: 765 GKQYVVIAAGGHGSFGTKLGDYVIAYALP 793 GKQYVVI AGG T GDYVI+YALP Sbjct: 778 GKQYVVITAGG-ARQSTDRGDYVISYALP 805 Lambda K H 0.319 0.137 0.433 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: 2229 Number of extensions: 155 Number of successful extensions: 14 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: 805 Length adjustment: 41 Effective length of query: 755 Effective length of database: 764 Effective search space: 576820 Effective search space used: 576820 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