Align gluconate 5-dehydrogenase (EC 1.1.1.69); D-sorbitol dehydrogenase (acceptor) (subunit 1/2) (EC 1.1.99.21) (characterized)
to candidate PP_1444 PP_1444 quinoprotein glucose dehydrogenase
Query= BRENDA::Q70JN9 (743 letters) >FitnessBrowser__Putida:PP_1444 Length = 803 Score = 469 bits (1207), Expect = e-136 Identities = 262/671 (39%), Positives = 365/671 (54%), Gaps = 43/671 (6%) Query: 91 DVPQMAPQQSASPASGDWAAYGHDDSQMRYSPLSEITPQNADQLKVAFVYHTGSYPRPGQ 150 D +MA A P G+W AYG + RYSPL +ITPQNA +L+ A+ TG P Sbjct: 155 DSSEMASAAPAMP-DGEWQAYGRTEHGDRYSPLRQITPQNAYRLEEAWRIRTGDLPTEND 213 Query: 151 TNKWAAETTPIKVGDGLYMCSAQNDIMKIDPATGKEIWRHNINEKYEAIPYTA----ACK 206 + + TP+KV LY C+A + ++ +DP TG EIWR++ K + C+ Sbjct: 214 PVELTNQNTPLKVNGMLYACTAHSRLLALDPDTGAEIWRYDPQVKSPTGTFKGFAHMTCR 273 Query: 207 GVTYFTS--------SQVPE--------GQPCHNRILEGTLDMRLIAVDAATGNLCEGFG 250 GV+Y+ S P+ Q C R+ T D RLIA++A G +CEGF Sbjct: 274 GVSYYDENRYVSRDGSPAPKITDAGQAVAQACPRRLYLPTADARLIAINADNGKVCEGFA 333 Query: 251 NGGQVNLMQGLGESVPGFVSMTTPPPVVNGVVVVNHEVLDGQRRWAPSGVIRGYDAESGK 310 N G ++L G+G G T+P + +V++ V D + PSGVIR YD G Sbjct: 334 NQGVIDLTTGIGPFTAGGYYSTSPAAITRDLVIIGGHVTDNESTNEPSGVIRAYDVHDGH 393 Query: 311 FLWAWDVNRPNDHSQPTGNNHYSRGTPNSWAAMTGDNALGLVYVPTGNSASDYYSALRSP 370 +W WD N P+D YSR + N W+ + D LG++Y+P GN D + A R+P Sbjct: 394 LVWNWDSNNPDDTKPLAAGKMYSRNSANMWSIASVDEDLGMIYLPLGNQTPDQWGADRTP 453 Query: 371 EENKVSSAVVALDVKTGSPRWVFQTVHKDVWDYDIGSQATLMDMPGQDGQPVPALIMPTK 430 K S+ VVALD+ TG RW +Q H D+WD D+GSQ TL+ + DG PA+I+PTK Sbjct: 454 GAEKYSAGVVALDLATGKARWNYQFTHHDLWDMDVGSQPTLVHLKTDDGVK-PAIIVPTK 512 Query: 431 RGQTFVLDRRDGKPILPVEERPAPSPGVIPGDPRSPTQPWSTGMPALRVPDLKETDMWGM 490 +G +VLDRRDG PI+P+ E P P G + GD SPTQ S L P+L E MWG Sbjct: 513 QGSLYVLDRRDGTPIVPIREIPTPQ-GAVEGDHTSPTQARSD--LNLLGPELTEQAMWGA 569 Query: 491 SPIDQLFCRIKFRRANYTGEFTPPSVDKPWIEYPGYNGGSDWGSVSYDPQSGILIANWNI 550 +P DQ+ CRI+FR Y G++TPPS ++ + YPG G +WGSVS DP +L + N Sbjct: 570 TPFDQMLCRIQFRELRYEGQYTPPS-EQGSLVYPGNVGVFNWGSVSVDPVRQLLFTSPNY 628 Query: 551 TPMYDQLVTRKKADELGLMPIDDPNYKPGGGGAEGNGAMDGTPYGIVVTPFWDQYTGMMC 610 ++V R++ E + +P G PY +++ PF G+ C Sbjct: 629 MAFVSKMVPREQVAEGSKRESETSGVQPN----------TGAPYAVIMHPFMSP-LGVPC 677 Query: 611 NRPPYGMITAIDMKHGQKVLWQHPLGTARANGPWGLPTGLPWEIGTPNNGGSVVTAGGVV 670 P +G + AID+ KV+W+H GT R + P LP GLP +G P+ GGS+VTAGGV Sbjct: 678 QAPAWGYVAAIDL-FTNKVVWKHKNGTTRDSTP--LPIGLP--VGVPSMGGSIVTAGGVG 732 Query: 671 FIAAATDNQIRAIDEHTGKVVWSAVLPGGGQANPMTYEA-NGHQYVAIMAGGHHFMMTPV 729 F++ D +RA D + GK +W A LP GGQA PM+Y +G QYV + AGGH + T + Sbjct: 733 FLSGTLDQYLRAYDVNNGKELWKARLPAGGQATPMSYTGKDGKQYVLVTAGGHGSLGTKM 792 Query: 730 SDQLVVYALPD 740 D ++ Y L + Sbjct: 793 GDYIIAYKLAE 803 Lambda K H 0.315 0.134 0.428 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: 2010 Number of extensions: 135 Number of successful extensions: 10 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: 743 Length of database: 803 Length adjustment: 41 Effective length of query: 702 Effective length of database: 762 Effective search space: 534924 Effective search space used: 534924 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: 42 (22.0 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