Align quinoprotein decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate GFF3407 PS417_17435 dehydrogenase
Query= CharProtDB::CH_107432 (595 letters) >FitnessBrowser__WCS417:GFF3407 Length = 591 Score = 1160 bits (3000), Expect = 0.0 Identities = 541/587 (92%), Positives = 574/587 (97%) Query: 1 MTRSPRRPMFAVSLVLSAMLLAGAAHAAVSNEEILQDPKNPQQIVTNGLGVQGQRYSPLD 60 MT+ RR FA+S++L A+LL+G A A+V++EEILQDPKNP QIVTNGLGVQGQRYSPLD Sbjct: 1 MTQPARRQPFALSVLLGAILLSGQAMASVTDEEILQDPKNPGQIVTNGLGVQGQRYSPLD 60 Query: 61 LLNANNVKELRPVWAFSFGGEKQRGQQAQPLIKDGVMYLTGSYSRVFAVDARTGKKLWQY 120 LN +NVKELRPVWAFSFGGEKQRGQQAQP+IKDGVMYLTGSYSRVFAVDARTGKKLWQY Sbjct: 61 TLNVDNVKELRPVWAFSFGGEKQRGQQAQPMIKDGVMYLTGSYSRVFAVDARTGKKLWQY 120 Query: 121 DARLPDDIRPCCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGYSI 180 DARLPDDIRPCCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGYSI Sbjct: 121 DARLPDDIRPCCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGYSI 180 Query: 181 SAAPMIVNGKLITGVAGGEFGVVGKIQAYNPENGELLWMRPTVEGHMGYVYKDGKAIENG 240 SAAP+++NGKLITGVAGGEFGVVGKI+AY+P+NGELLW RPTVEGHMGYVYKDGKA+ENG Sbjct: 181 SAAPLVINGKLITGVAGGEFGVVGKIEAYDPKNGELLWSRPTVEGHMGYVYKDGKAVENG 240 Query: 241 ISGGEAGKTWPGDLWKTGGAAPWLGGYYDPETNLILFGTGNPAPWNSHLRPGDNLYSSSR 300 ISGGEAGKTWPGDLWKTGGAAPWLGGYYDPETNL+LFGTGNPAPWNSHLRPGDNLYSSSR Sbjct: 241 ISGGEAGKTWPGDLWKTGGAAPWLGGYYDPETNLLLFGTGNPAPWNSHLRPGDNLYSSSR 300 Query: 301 LALNPDDGTIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEVKAAATADRNGFFYVLDRT 360 LALNPDDGTIKWHFQ+TPHDGWD+DGVNEL+SFNY +GGKE+KAAATADRNGFFYVLDRT Sbjct: 301 LALNPDDGTIKWHFQTTPHDGWDYDGVNELVSFNYTEGGKEIKAAATADRNGFFYVLDRT 360 Query: 361 NGKFIRGFPFVDKITWATGLDKDGRPIYNDASRPGAPGSEAKGSSVFVAPAFLGAKNWMP 420 NGKFIRGFPFVDKITWATGLDKDGRPIYNDASRPGAPGSEAKG+SVFVAPAFLGAKNWMP Sbjct: 361 NGKFIRGFPFVDKITWATGLDKDGRPIYNDASRPGAPGSEAKGTSVFVAPAFLGAKNWMP 420 Query: 421 MAYNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDYIGVLRAIDPISG 480 MAYN+DTGLFYVPSNEWGMD+WNEGIAYKKGAAFLGAGFTIKPLNEDYIGVLRAIDP +G Sbjct: 421 MAYNRDTGLFYVPSNEWGMDMWNEGIAYKKGAAFLGAGFTIKPLNEDYIGVLRAIDPKTG 480 Query: 481 KEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGDKVWEFQTGSGVLGSPVTW 540 KEVWRHKN+APLWGGVLTTKGNLVFTGTPEGFLQAFNAKTG+KVWEFQTGSGVLGSPVTW Sbjct: 481 KEVWRHKNFAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGEKVWEFQTGSGVLGSPVTW 540 Query: 541 EMDGEQYVSVVSGWGGAVPLWGGEVAKRVKDFNQGGMLWTFKLPKQL 587 EMDGEQYVSV+SGWGGAVPLWGGEVAKR+KDFNQGGMLWTFKLPK+L Sbjct: 541 EMDGEQYVSVLSGWGGAVPLWGGEVAKRIKDFNQGGMLWTFKLPKEL 587 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: 2006 Number of extensions: 137 Number of successful extensions: 13 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: 591 Length adjustment: 37 Effective length of query: 558 Effective length of database: 554 Effective search space: 309132 Effective search space used: 309132 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