Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_011951898.1 SWIT_RS05365 pyrroloquinoline quinone-dependent dehydrogenase
Query= BRENDA::D4P700 (796 letters) >NCBI__GCF_000016765.1:WP_011951898.1 Length = 669 Score = 477 bits (1228), Expect = e-139 Identities = 268/640 (41%), Positives = 361/640 (56%), Gaps = 29/640 (4%) Query: 166 ADGDWPAYARDQQGTRFSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEI--TDEVTPI 223 AD W + GTRF+P QI NV L+VAW++ TG++ R + ++ T+E TPI Sbjct: 45 ADTPWDQWGATAGGTRFTPAAQITPGNVAHLRVAWRYSTGELARRPEGMQVNSTNETTPI 104 Query: 224 KIRDTLYLCTPHQILFALDAATGKQKWKFDPGLKTNPTFQ---HVTCRGVSYHEFPAAKD 280 +L CTP + ALD ATG++KW +D K + +F+ CRGVS +D Sbjct: 105 LAAGSLITCTPFGRVIALDPATGREKWTYDA--KVDRSFKLPDQYICRGVSQW-----RD 157 Query: 281 ASNTQPA-LCSRRIYLPVNDGRLFALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPT 339 A PA +C+ RI L D R+ ALDA TG C FG G + + + + G + Sbjct: 158 ARAADPAGMCATRIILATVDMRVIALDARTGRPCAGFGEGGTVRVDPGK-LHHVGEVKLA 216 Query: 340 SPPVITDTTIVMAGAVTDNFSTREPSGAIRGFDVNTGKLLWVFDPGAKD--PNAIPADEH 397 +P I IV+ +V DN P G IR FD +G+ +W FDP + P+ + Sbjct: 217 APAAIVRDRIVIGTSVLDNVRANAPRGIIRAFDARSGREIWTFDPIPQQGGPDRDWMGDS 276 Query: 398 TFTMNSPNSWAPAVYDPKLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLV 457 T + N W+ DP+LD+VYLP +PD +GG R P R+A+SV+AL+A TG+LV Sbjct: 277 RRTTGAANVWSVISGDPELDMVYLPTSSASPDYYGGLR-PGDNRHANSVVALDAATGRLV 335 Query: 458 WSYQTVHHDLWDMDLPSQPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPE 517 W+ Q +HHD+WD D+P+QPTL DI D+ G +P + P K G +FV DRRTG + P E Sbjct: 336 WARQLIHHDIWDYDIPAQPTLVDI-DRGGRRIPALVQPTKQGYVFVFDRRTGAPLFPIDE 394 Query: 518 TPVPQGAAKGDHVSATQPYSELTFRP--KQNLTDKDMWGATMYDQLVCRVIFKRLRYEGP 575 PVPQG G+ +S TQP L RP Q +T WG T +D+ CR + R R EG Sbjct: 395 VPVPQGGVPGEWLSPTQPRPRLP-RPIVPQKITPDQAWGFTPWDKAKCRDLIARYRSEGL 453 Query: 576 FTPPSEQGTLVFPGNLGMFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKG 635 FTP +E+GT+ +P G WG ++DP RQ+ N + V +L R PG G Sbjct: 454 FTPITERGTITYPAASGGANWGAGAIDPARQVFFINSSRVASVIRLRKRKPGG-----SG 508 Query: 636 ATGGSGTETGIQPQYGVPYGVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGT 695 S TE + P G PY V+ LSPFG PC P WG ++A+DLKT +W +GT Sbjct: 509 TVQLSATED-VSPMAGTPYEVKREWLLSPFGAPCTPPPWGGLTAIDLKTGATLWDVPLGT 567 Query: 696 VRDSSPVPLPFK--MGMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQARLPAG 753 + D P+PLPF +G P +GGPVATAG V FI AT D +LRA TG+ LW+ RLP G Sbjct: 568 INDRLPIPLPFDVALGTPNIGGPVATAGGVLFIAATMDRHLRAIDMRTGKELWRDRLPGG 627 Query: 754 GQATPMTYEVNGKQYVVIAAGGHGSFGTKLGDYVIAYALP 793 Q TPM+Y G+QYVV+A+G H F T D ++AYALP Sbjct: 628 SQTTPMSYMAGGRQYVVVASGQHMWFQTPRSDEIVAYALP 667 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: 1991 Number of extensions: 141 Number of successful extensions: 17 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 796 Length of database: 669 Length adjustment: 40 Effective length of query: 756 Effective length of database: 629 Effective search space: 475524 Effective search space used: 475524 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 Apr 09 2024. 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