Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate H281DRAFT_00328 H281DRAFT_00328 alcohol dehydrogenase (cytochrome c)
Query= BRENDA::D4P700 (796 letters) >FitnessBrowser__Burk376:H281DRAFT_00328 Length = 575 Score = 182 bits (462), Expect = 4e-50 Identities = 188/671 (28%), Positives = 269/671 (40%), Gaps = 153/671 (22%) Query: 122 AMGVALVASAAVLTYSVFNDPQVVNGALPATADNAPQAQPLSNIADGDWPAYARDQQGTR 181 A VA V S + T + +D V T D AQ +D W Y R G Sbjct: 15 ATSVAAVVSLSCATAAFADDYPAV------TYDRLSAAQ-----SDPGWLTYYRTYNGQA 63 Query: 182 FSPLKQINHDNVKELQVAWQFQTGDMKRPSDPGEITDEVTPIKIRDTLYLCTPHQILFAL 241 SPLKQI+ NVK+L+ W + K P+D + E TPI L++ TP ++A Sbjct: 64 HSPLKQIDTSNVKQLKQVWSY-----KFPADLQQ-GFEATPIVNGHYLFVTTPKDNVYAF 117 Query: 242 DAATGKQKWKFDPGLKTNPTFQHVTCRGVSYHEFPAAKDASNTQPALCSRRIYLPVNDGR 301 DAA+GKQ WKF+P L +F+ C D N AL + +Y+ + +G Sbjct: 118 DAASGKQLWKFEPKLGAE-SFKTACC------------DVINRGVALYGKNVYVAMLNGE 164 Query: 302 LFALDAETGERCPAFGNNGELDLQHKQPVTTPGM-YEPTSPPVITDTTIVMAGAVTDNFS 360 + ALDA+TG L ++ + PG+ Y + P+ D +V+ G+ + Sbjct: 165 VVALDAQTGS------------LAWRKTMFEPGVGYAFSLAPLAIDGALVV-GSAGGEYG 211 Query: 361 TREPSGAIRGFDVNTGKLLW----VFDPGAKDPNAIP--ADEHTFTMNSPNSWAPAVYDP 414 R G I + + G +LW V G K N P EH +W YD Sbjct: 212 AR---GFIAALNPDNGNVLWKRFTVPAAGEKGANTWPDGMQEH----GGAPAWLTGTYDA 264 Query: 415 KLDIVYLPMGVTTPDIWGGNRTPEQERYASSVLALNATTGKLVWSYQTVHHDLWDMDLPS 474 +Y GV P W + P Y+ S+LAL+ TG L W YQ HD WD D + Sbjct: 265 ASRTLY--WGVGNPGPWLADLRPGDNLYSDSLLALDPKTGDLKWHYQYTKHDTWDYDGVN 322 Query: 475 QPTLADITDKDGNTVPVIYAPAKTGNIFVLDRRTGKTVVPAP---ETPVPQGAAKGDHVS 531 P LA+I +D N +I+A + G +DR TGK + P T V A G V Sbjct: 323 TPVLANIKYQDKNYDAIIHAD-RNGYFHAIDRGTGKLIYAKPFVKATSVTGYTADGVPVQ 381 Query: 532 ATQPYSELTFRPKQNLTDKDMWGATMYDQLVCRVIFKRLRYEGPFTPPSEQGTLVFPGNL 591 Y PK T + P L Sbjct: 382 DPSKY------PKTGTTIE-----------------------------------TCPSFL 400 Query: 592 GMFEWGGISVDPHRQIAIANPMALPFVSKLIPRGPGNPEEPPKGATGGSGTETGIQPQYG 651 G W +S DP RQ+AI P S + + G Sbjct: 401 GGKNWWSVSYDPDRQVAIV----------------------PALHACMSLSGKSVTYMEG 438 Query: 652 VPY---GVELNPFLSPFGLPCKQPAWGYVSAVDLKTNEVVWKQRIGTVRDSSPVPLPFKM 708 +PY G E+ P G +G + A+D+ T + +W + Sbjct: 439 LPYLGEGFEIKPEPGSKG-------YGELQAIDVTTGKKMWS---------------YWS 476 Query: 709 GMPMLGGPVATAGKVFFIGATADNYLRAFSTDTGELLWQA-RLPAGGQATPMTYEVNGKQ 767 +P GG TA + F G + D +L AF + TG++LW++ +L +G A P +EV+GK+ Sbjct: 477 KLPWNGGVATTASGLAFSG-SLDGHLYAFDSSTGKVLWKSPKLASGIVAQPSVFEVDGKE 535 Query: 768 YVVIAAGGHGS 778 YV I AG G+ Sbjct: 536 YVAILAGYGGA 546 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: 1559 Number of extensions: 120 Number of successful extensions: 16 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 9 Number of HSP's successfully gapped: 4 Length of query: 796 Length of database: 575 Length adjustment: 39 Effective length of query: 757 Effective length of database: 536 Effective search space: 405752 Effective search space used: 405752 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: 54 (25.4 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