Align quinoprotein decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate 3607055 Dshi_0476 Pyrrolo-quinoline quinone (RefSeq)
Query= CharProtDB::CH_107432 (595 letters) >FitnessBrowser__Dino:3607055 Length = 600 Score = 343 bits (881), Expect = 9e-99 Identities = 205/567 (36%), Positives = 302/567 (53%), Gaps = 27/567 (4%) Query: 13 SLVLSAMLLAGAAHAAVSNEEILQDPKNPQQIVTNGLGVQGQRYSPLDLLNANNVKELRP 72 SL+ S + L A A +++ I Q + Q + G + RYS LD +NA NV +L+ Sbjct: 5 SLLTSGIALCAATVAYANDDLITQMDDSKQWAIQTG-DYKNHRYSELDEINAENVGDLQV 63 Query: 73 VWAFSFGGEKQRGQQAQPLIKDGVMYLTGSYSR-VFAVD-ARTGKKLWQYDARLPDDIRP 130 W FS G RG + PL+ MY+ + V+A+D + GK +W+Y+ + D+ P Sbjct: 64 AWTFSTG--VLRGHEGSPLVIGDTMYVHTPFPNIVYALDLSNEGKIIWKYEPKQDPDVIP 121 Query: 131 --CCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGYSISAAPMIVN 188 CCD +NRGVA +F D K+VAL+ +TG V+W + D G + +A + V Sbjct: 122 VMCCDTVNRGVAYADGKIFLHQADTKVVALDANTGDVLWEVQNGDPSIGETNTATVLPVK 181 Query: 189 GKLITGVAGGEFGVVGKIQAYNPENGELLWMRPTVEGHMGYVYKDGKAIENGISGGEAGK 248 K+I G++GGEFGV G + AY+ +GEL+W ++ + G GE Sbjct: 182 DKVIVGISGGEFGVRGHVTAYDINSGELVWRAYSLGPDDDMLVDPENTTHLGKPIGENSS 241 Query: 249 --TWPGDLWKTGGAAPWLGGYY--DPETNLILFGTGNPAPWNSHLRPGDNLYSSSRLALN 304 +W GD W GG W G+Y D E NL +GTGNP+ WN RPGDN ++ + +A + Sbjct: 242 LNSWEGDQWMIGGGTTW--GWYAADMEENLFYYGTGNPSTWNPAQRPGDNRWTMTVMARD 299 Query: 305 PDDGTIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEVKAAATADRNGFFYVLDRTNGKF 364 D G KW +Q TPHD WD+DGVNE I + G+ K DRNG Y +DR G+ Sbjct: 300 IDTGMAKWFYQMTPHDEWDYDGVNENILTEQEFDGEMRKLLTRFDRNGLAYTMDRVTGEL 359 Query: 365 IRGFPFVDKITWATGLDKD------GRPIYNDASRPGAPGSEAKGSSVFVAPAFLGAKNW 418 + F + W TG+D D GRP G + ++ + PA LG K+ Sbjct: 360 LVAEKFDPVVNWTTGVDMDPNSETYGRPQVVAQYSTAQNGEDV--NTTGICPAALGTKDQ 417 Query: 419 MPMAYNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDY--IGVLRAID 476 P AY+ T +FYVP+N MD ++Y G ++GA ++ P + + +G A D Sbjct: 418 QPAAYSPKTQVFYVPTNHVCMDYEPFRVSYTAGQPYVGATLSMYPAPDSHGGMGNFIAWD 477 Query: 477 PISGKEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGDKVWEFQTGSGVLGS 536 I+G+ +W +W G L T G++VF GT EG L+A +A TG++++ F+T SG++G+ Sbjct: 478 NINGEILWSIPEKFSVWSGALATAGDVVFYGTLEGHLKAVHADTGEELYRFKTPSGIIGN 537 Query: 537 PVTWEMDGEQYVSVVSGWGGAVPLWGG 563 +T+E DG QYV V+SG GG W G Sbjct: 538 VMTYEHDGRQYVGVLSGVGG----WAG 560 Lambda K H 0.317 0.137 0.438 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: 1370 Number of extensions: 123 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: 595 Length of database: 600 Length adjustment: 37 Effective length of query: 558 Effective length of database: 563 Effective search space: 314154 Effective search space used: 314154 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: 41 (21.6 bits) S2: 53 (25.0 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