Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate SMc00110 SMc00110 glucose dehydrogenase
Query= BRENDA::D4P700 (796 letters) >FitnessBrowser__Smeli:SMc00110 Length = 777 Score = 791 bits (2042), Expect = 0.0 Identities = 396/790 (50%), Positives = 512/790 (64%), Gaps = 20/790 (2%) Query: 10 VVRFLTVLFAVLTGAFMLIGGIWLATIGGSWYYIIGGAAMLLTAFLLWRRNSAALVVYAL 69 V+ V+FAV+ G + GG L +GGS YY+I G LLTAFLL+RR +AAL VYAL Sbjct: 2 VIVLTAVVFAVI-GLALCGGGTRLLLLGGSPYYLIAGLGFLLTAFLLFRRRAAALWVYAL 60 Query: 70 LLLATLAWGVWEVGTDFWALAPRTDVLVIFGVWLVLPFVYR--GLYQPGKGALGAMG--V 125 ++L +LAW +WEVG D+W L PR V+++ G+WL+ P++ R G P GA + Sbjct: 61 VVLGSLAWAIWEVGFDWWQLGPRGGVIILLGLWLLTPWIRRPLGFVSPTGEQYGASAWPL 120 Query: 126 ALVA--SAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTRFS 183 ALV+ S V YS+ DP + G LP A A N+ G+W Y R G R+S Sbjct: 121 ALVSLLSVGVALYSMTQDPHDIRGDLPGEV--AANANLGGNVPPGEWHQYGRTPFGQRYS 178 Query: 184 PLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFALDA 243 PL QI +NV LQVAWQ+QTGD+K P D E T +VTP+K++DTLY+CTPH ALDA Sbjct: 179 PLDQIRPENVANLQVAWQYQTGDVKLPEDVSETTYQVTPLKVKDTLYVCTPHNWAIALDA 238 Query: 244 ATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVNDGRLF 303 ATG++KWK+D NP QH TCRGV+Y PAA S C+ R+YLP +D RL Sbjct: 239 ATGQEKWKYDSNSGMNPDRQHQTCRGVTYWADPAAAPGSP-----CAERVYLPTSDARLI 293 Query: 304 ALDAETGERCPAFGNNGELDLQHKQPVTTPGMYEPTSPPVITDTTIVMAGAVTDNFSTRE 363 ALDA GE C +F +NG L L+ G Y TSPPV +++ GAV DN+ST E Sbjct: 294 ALDATNGEVCTSFADNGVLHLEQGMKHNPAGYYYSTSPPVAVGDRLIIGGAVNDNYSTTE 353 Query: 364 PSGAIRGFDVNTGKLLWVFDPGAKDPNAIPADEHTFTMNSPNSWAPAVYDPKLDIVYLPM 423 SG IR F++NTG L+W +D G D A T+T NSPNSW+ YD L +VY+PM Sbjct: 354 QSGVIRAFNINTGALIWNWDSGNPDVTAPLPPGQTYTTNSPNSWSVFSYDEGLGLVYIPM 413 Query: 424 GVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPSQPTLADITD 483 G PD G R+ E+Y+SS++AL+ TG + W QTVHHDLWDMD+P+QP L DIT Sbjct: 414 GNQVPDQLGMGRSEHVEKYSSSIVALDINTGAVRWVRQTVHHDLWDMDVPAQPALLDITR 473 Query: 484 KDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAPETPVPQGAAKGDHVSATQPYSELTFRP 543 +DG VP + P K G+I+VLDRR+G+ ++P E P P GA D + TQP S LTF P Sbjct: 474 EDGTVVPALVGPTKQGDIYVLDRRSGEPIIPIEEVPAPGGAIPEDFTAPTQPVSGLTFMP 533 Query: 544 KQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNLGMFEWGGISVDP 603 L ++DMWG +M+DQL CR+ F+ L+YEG +TPPS +GT+V+PGN G F WG ++VDP Sbjct: 534 PP-LMERDMWGISMFDQLACRIEFRTLKYEGRYTPPSLEGTIVYPGNFGTFNWGSVAVDP 592 Query: 604 HRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYGVPYGVELNPFLS 663 RQ+ P L F S+L+PR + PKG G G+E G+ G PYGV + PFL Sbjct: 593 ERQVMFGMPTYLAFTSRLVPR----DQIAPKG-EGEKGSEQGLNRNEGAPYGVFMGPFLG 647 Query: 664 PFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLPFKMGMPMLGGPVATAGKV 723 P G+PC+ P WGYV+ DL+T ++ +K + GTV D +P+PLPFK+G+P +GGP+ T G + Sbjct: 648 PLGIPCQAPPWGYVAGADLRTGKIAYKHKNGTVYDMTPLPLPFKLGVPGIGGPMITKGGL 707 Query: 724 FFIGATADNYLRAFSTDTGELLWQARLPAGGQATPMTYEVNGKQYVVIAAGGHGSFGTKL 783 F+GA D+Y RA+ TGE LW+ARLPAGGQ+TPMTY V KQYV+I AGGHGS GTK Sbjct: 708 AFLGAAVDDYFRAYDLTTGEQLWEARLPAGGQSTPMTYTVGEKQYVLIVAGGHGSVGTKP 767 Query: 784 GDYVIAYALP 793 GDYVIAY LP Sbjct: 768 GDYVIAYTLP 777 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: 2303 Number of extensions: 166 Number of successful extensions: 12 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: 777 Length adjustment: 41 Effective length of query: 755 Effective length of database: 736 Effective search space: 555680 Effective search space used: 555680 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