Align quinoprotein decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate 3609287 Dshi_2673 Pyrrolo-quinoline quinone (RefSeq)
Query= CharProtDB::CH_107432 (595 letters) >FitnessBrowser__Dino:3609287 Length = 588 Score = 767 bits (1981), Expect = 0.0 Identities = 352/588 (59%), Positives = 452/588 (76%), Gaps = 21/588 (3%) Query: 12 VSLVLSAMLLAGAAHA-AVSNEEILQDPKNPQQIVTNGLGVQGQRYSPLDLLNANNVKEL 70 ++ V +A++ GAA+A ++ +++ D + +++TNG+G QRYSPL+ LN +NV+ L Sbjct: 5 IAAVTAAVVATGAAYAEGITEQDLANDQADTSRVLTNGMGRHLQRYSPLETLNKDNVENL 64 Query: 71 RPVWAFSFGGEKQRGQQAQPLIKDGVMYLTGSYSRVFAVDARTGKKLWQYDARLPDDIRP 130 P WAFS GGEKQRGQ+ QPLI DG+MY+TGSYSRV+A+D TGK++WQYDARLP+ I P Sbjct: 65 VPAWAFSLGGEKQRGQETQPLIYDGIMYITGSYSRVYAIDVETGKEIWQYDARLPEGILP 124 Query: 131 CCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGYSISAAPMIVNGK 190 CCDVINRG A+YGD +FGTLDA++VAL+ TG VVW KK+ D+K GYS +AAP+IVNG Sbjct: 125 CCDVINRGGAIYGDKFYFGTLDARIVALDLKTGDVVWRKKIDDYKAGYSYTAAPLIVNGL 184 Query: 191 LITGVAGGEFGVVGKIQAYNPENGELLWMRPTVEGHMGYVYKDGKAIENGISGGEAGKTW 250 ++TG +GGEFG+VG ++A + E GEL+W RP +EGHMG + + + G TW Sbjct: 185 VVTGNSGGEFGIVGAVEARDAETGELVWKRPVIEGHMGELNGEPSTMT-----GTLNATW 239 Query: 251 PGDLWKTGGAAPWLGGYYDPETNLILFGTGNPAPWNSHLRP---------GDNLYSSSRL 301 PGD+WKTGG A WLGG YD T+ ++FGTGNPAPWNSHLR GDNLY++SRL Sbjct: 240 PGDMWKTGGGATWLGGSYDARTDTLIFGTGNPAPWNSHLRGAGKPSEDGMGDNLYAASRL 299 Query: 302 ALNPDDGTIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEVKAAATADRNGFFYVLDRTN 361 ++P G IKWHFQ+TP +GWDFDGVNE+++++ ++G + ATADRNGFFYVLD + Sbjct: 300 GIDPATGEIKWHFQTTPREGWDFDGVNEVVAYDDREGNPRL---ATADRNGFFYVLDAAD 356 Query: 362 GKFIRGFPFVDKITWATGLDKDGRPIYNDASRPGAPGSEA---KGSSVFVAPAFLGAKNW 418 G F+ G PFV++I+WA+GLD++GRPI+ + +RPG P A KG +VF P FLG KNW Sbjct: 357 GSFVSGMPFVEQISWASGLDENGRPIFVEENRPGDPAEAADGKKGETVFAVPGFLGGKNW 416 Query: 419 MPMAYNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDYIGVLRAIDPI 478 MPMAY++ TG FYVP+NEWGMDIWNE I YKKGAA+LG+GFTIKPL ED+IG ++AIDP Sbjct: 417 MPMAYSQRTGNFYVPANEWGMDIWNEPITYKKGAAYLGSGFTIKPLFEDHIGAIKAIDPD 476 Query: 479 SGKEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGDKVWEFQTGSGVLGSPV 538 + + W +KN APLW GV+TT G LVF GTPEG A + +TG+K+W FQTGSG++G P+ Sbjct: 477 TMETKWVYKNDAPLWSGVMTTAGGLVFFGTPEGEFIALDDETGEKLWSFQTGSGIVGQPI 536 Query: 539 TWEMDGEQYVSVVSGWGGAVPLWGGEVAKRVKDFNQGGMLWTFKLPKQ 586 TWE DGEQYVSV+SGWGGAVPLWGGEVAK+V NQGGMLWTF+LPKQ Sbjct: 537 TWEQDGEQYVSVISGWGGAVPLWGGEVAKKVNYLNQGGMLWTFRLPKQ 584 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: 1732 Number of extensions: 135 Number of successful extensions: 16 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: 595 Length of database: 588 Length adjustment: 37 Effective length of query: 558 Effective length of database: 551 Effective search space: 307458 Effective search space used: 307458 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