Align quinoprotein decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate SM_b20173 SM_b20173 methanol dehydrogenase, large subunit
Query= CharProtDB::CH_107432 (595 letters) >FitnessBrowser__Smeli:SM_b20173 Length = 601 Score = 357 bits (917), Expect = e-103 Identities = 207/563 (36%), Positives = 308/563 (54%), Gaps = 22/563 (3%) Query: 15 VLSAMLLAGAAHAAVSNEEILQDPKNPQQIVTNGLGVQGQRYSPLDLLNANNVKELRPVW 74 +L+ M + G A A +N+E+ + +P Q RYS LD +N +NV +L+ W Sbjct: 7 MLAIMSIGGGAQVAFANDELQKLIDDPNQWAIQTGDYANLRYSKLDQINKDNVGKLQVAW 66 Query: 75 AFSFGGEKQRGQQAQPLIKDGVMYLTGSY-SRVFAVD-ARTGKKLWQYDARLPDDIRP-- 130 FS G RG + PL+ +MY+ + + V+A+D ++ G+ +W+Y+ + ++ P Sbjct: 67 TFSTG--VLRGHEGSPLVIGDLMYVHTPFPNTVYALDLSKDGQIVWKYEPKQDPNVIPVM 124 Query: 131 CCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSKKVADHKEGYSISAAPMIVNGK 190 CCD +NRGVA + +F D +VAL+ TGKV+WS K D +G + +A M V K Sbjct: 125 CCDTVNRGVAYADNKIFLHQADTTVVALDAKTGKVIWSVKNGDATKGETNTATVMPVKDK 184 Query: 191 LITGVAGGEFGVVGKIQAYNPENGELLWMRPTVEGHMGYVYKDGKAIENGISGGEAG--K 248 ++ G++GGEFGV G + AY+ +G++LW ++ + K G G+ Sbjct: 185 ILVGISGGEFGVRGHVTAYSMADGKVLWRGYSMGPDSDTLIDPEKTTHLGKPVGKDSGLT 244 Query: 249 TWPGDLWKTGGAAPWLGGYYDPETNLILFGTGNPAPWNSHLRPGDNLYSSSRLALNPDDG 308 TW GD WK GG W YDPE NL+ +GTGNP+ WN RPGDN +S + A + D G Sbjct: 245 TWEGDQWKIGGGTTWGWYSYDPEENLVYYGTGNPSTWNPTQRPGDNRWSMTIFARDVDTG 304 Query: 309 TIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEVKAAATADRNGFFYVLDRTNGKFIRGF 368 KW +Q TPHD WD+DGVNE+I + GK+ K DRNGF Y +DR G+ + Sbjct: 305 MAKWLYQMTPHDEWDYDGVNEMILTEQQIDGKDRKLLTHFDRNGFGYTMDRVTGELLVAE 364 Query: 369 PFVDKITWATGL------DKDGRPIYNDASRPGAPGSEAKGSSVFVAPAFLGAKNWMPMA 422 + + WAT + DK GRP G + ++ V PA LG K+ P A Sbjct: 365 KYDPTVNWATEVVMDPKSDKYGRPQVVAQYSTEQNGEDT--NTTGVCPAALGTKDQQPAA 422 Query: 423 YNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPLNEDY--IGVLRAIDPISG 480 Y+ T LFYVP+N MD ++Y G ++GA ++ P + + +G A D G Sbjct: 423 YSPKTELFYVPTNHVCMDYEPFRVSYTAGQPYVGATLSMYPPKDSHGGMGNFIAWDNKEG 482 Query: 481 KEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGDKVWEFQTGSGVLGSPVTW 540 K W +W G L T G++VF GT EG+L+A +A TG +++ F+T SGV+G+ +T+ Sbjct: 483 KIKWSLPEPFSVWSGALATAGDVVFYGTLEGYLKAVDAATGKELYRFKTPSGVIGNVMTY 542 Query: 541 EMDGEQYVSVVSGWGGAVPLWGG 563 +G+QYV+V+SG GG W G Sbjct: 543 AREGKQYVAVLSGVGG----WAG 561 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: 1440 Number of extensions: 125 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: 601 Length adjustment: 37 Effective length of query: 558 Effective length of database: 564 Effective search space: 314712 Effective search space used: 314712 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