Align quinoprotein decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate AZOBR_RS24625 AZOBR_RS24625 methanol dehydrogenase
Query= CharProtDB::CH_107432 (595 letters) >FitnessBrowser__azobra:AZOBR_RS24625 Length = 627 Score = 380 bits (976), Expect = e-110 Identities = 219/570 (38%), Positives = 311/570 (54%), Gaps = 29/570 (5%) Query: 15 VLSAMLLAGAAHAAV----SNEEILQDPKNPQQIVTNGLGVQGQRYSPLDLLNANNVKEL 70 VLS LLA A A +N+ IL++ NP + GQRYSPLD + NNVK L Sbjct: 3 VLSRWLLASVAVVAAGSVSANDSILKNEANPNNWASQLGNYAGQRYSPLDQITTNNVKNL 62 Query: 71 RPVWAFSFGGEKQRGQQAQPLIKDGVMYLTGSY-SRVFAVDART-GKKLWQYDARLPDDI 128 + W+FS G RG + P++ VMY+ + ++VFA+D G+ +W+Y++ + Sbjct: 63 QVAWSFSTG--VLRGHEGGPIVVGDVMYIHTPFPNKVFALDLNNPGRVIWKYESVQDPTV 120 Query: 129 RP--CCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGYSISAAPMI 186 P CCD +NRGVA+ VF D LVAL+ TGK VW K DH +G +++AAP++ Sbjct: 121 IPVMCCDTVNRGVAVADGKVFLAQADNTLVALDAKTGKEVWKAKNGDHTKGETLTAAPLV 180 Query: 187 VNGKLITGVAGGEFGVVGKIQAYNPENGELLWMRPTVEGHMGYVYKDGKAIENGISGGEA 246 V K+ G++GGEFGV G + AY+ +G+++W + K + G G+ Sbjct: 181 VKDKVFVGISGGEFGVRGHLTAYDTNSGKMVWRAFSTGPDADVKIDPSKTMMMGKPIGQK 240 Query: 247 G---KTWPGDLWKTGGAAPWLGGYYDPETNLILFGTGNPAPWNSHLR-------PGDNLY 296 TWPG+ WK GG W YDP NLI +GTGNP WN R DN + Sbjct: 241 DLGVSTWPGEEWKRGGGTTWGWYTYDPALNLIYYGTGNPGTWNPTQRAVDKDRAKSDNKW 300 Query: 297 SSSRLALNPDDGTIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEVKAAATADRNGFFYV 356 S + A +PD G KW +Q TP D WDFDGVNE I + G++ K DRNGF Y Sbjct: 301 SMTIFARDPDTGEAKWVYQKTPFDEWDFDGVNENILADINMNGQQRKVLVNFDRNGFAYT 360 Query: 357 LDRTNGKFIRGFPFVDKITWATGLD-KDGRPIYNDASRPGAPGSEAKGSSVFVAPAFLGA 415 LDR G+ + F + WAT +D K GRP D A G + ++ V PA LG+ Sbjct: 361 LDRATGELLVAQKFDPTVNWATDVDMKTGRPNVVDKYSTFANGEDK--NTAAVCPAALGS 418 Query: 416 KNWMPMAYNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDY--IGVLR 473 K+ P +++ DTGLFYVP+N MD ++Y G A++G+ ++ P + +G Sbjct: 419 KDQQPASFSPDTGLFYVPTNHICMDYEPFSVSYTAGQAYVGSTVSMYPTPNSHGGMGNFI 478 Query: 474 AIDPISGKEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGDKVWEFQTGSGV 533 A D +GK VW +W G L+TKG + + GT EG+L A + K G ++W F+T SG+ Sbjct: 479 AWDAAAGKIVWSRPERFAVWSGALSTKGGVAYYGTLEGYLVAVDMKDGKELWRFKTPSGI 538 Query: 534 LGSPVTWEMDGEQYVSVVSGWGGAVPLWGG 563 +G+ T+ +G+QYV+V+SG GG W G Sbjct: 539 IGNINTYTHNGKQYVAVLSGVGG----WAG 564 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: 1524 Number of extensions: 132 Number of successful extensions: 15 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: 627 Length adjustment: 37 Effective length of query: 558 Effective length of database: 590 Effective search space: 329220 Effective search space used: 329220 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