Align quinoprotein decanol dehydrogenase; EC 1.1.-.- (characterized)
to candidate AZOBR_RS04835 AZOBR_RS04835 methanol dehydrogenase
Query= CharProtDB::CH_107432 (595 letters) >FitnessBrowser__azobra:AZOBR_RS04835 Length = 559 Score = 340 bits (871), Expect = 1e-97 Identities = 200/563 (35%), Positives = 299/563 (53%), Gaps = 45/563 (7%) Query: 55 RYSPLDLLNANNVKELRPVWAFSFGGEKQRGQQAQPLIKDGVMYLTGSY-SRVFAVDART 113 RYS LD ++ N V++L+ + FS G RG +A PL+ + MY+ Y ++++A+D Sbjct: 10 RYSELDEIDTNTVRDLQVSFTFSTG--VVRGHEAAPLVVNDTMYVVTPYPNKLYALDLTK 67 Query: 114 --GKKLWQYDARLPDDIR--PCCDVINRGVALYGDLVFFGTLDAKLVALNKDTGKVVWSK 169 W ++ R + CCD +NRG A +F TLDA+ VA++ +TG+ VW Sbjct: 68 PGAPAKWTFEPRPAASAQGVACCDYVNRGPAFADGRIFINTLDAQTVAVDAETGREVWRT 127 Query: 170 KVADHKEGYSISAAPMIVNGKLITGVAGGEFGVVGKIQAYNPENGELLWMR----PTVEG 225 K+ D +G +++ AP++V GK++ G AGGEFGV G I A + G+++W P + Sbjct: 128 KLGDINKGETMTMAPLVVKGKVLVGNAGGEFGVRGWITALDAGTGKIVWRAYNTGPDQDV 187 Query: 226 HMGYVYKDGKAIENGISGGEAGKTWPGDLWKTGGAAPWLGGYYDPETNLILFGTGNPAPW 285 +G YK E G G TWP + W+ GG W YDPE +LI GTGNP PW Sbjct: 188 LIGDDYKPFYDKEKGKDLGVG--TWPPNAWEIGGGTVWGWISYDPELDLIYHGTGNPGPW 245 Query: 286 NSHLRPGDNLYSSSRLALNPDDGTIKWHFQSTPHDGWDFDGVNELISFNYKDGGKEVKAA 345 N RPGDN ++ A NPD G +W +Q+ PHD +D+DG+NELI + G+ K Sbjct: 246 NPEQRPGDNKWTGGIFARNPDTGQARWFYQAVPHDLYDYDGINELILLDLPWQGQPRKVL 305 Query: 346 ATADRNGFFYVLDRTNGKFIRGFPFVDKITWATGLD-KDGRPIYNDASRPGAPGSEAKGS 404 +RNG+ YV+DR++G+ + P+ + G+D K G YN+ P G + Sbjct: 306 IRPERNGYLYVIDRSSGEVLAADPYFPANS-TKGVDLKTGLIEYNEEKHPRV-GKVVRD- 362 Query: 405 SVFVAPAFLGAKNWMPMAYNKDTGLFYVPSNEWGMDIWNEGIAYKKGAAFLGAGFTIKPL 464 + P GAK+W P A++ TG Y+P N MD + Y G ++GA + Sbjct: 363 ---ICPTAPGAKDWNPSAFSPKTGNVYIPHNNLCMDWESVEANYIAGTPYVGANVKMYAG 419 Query: 465 NEDYIGVLRAIDPISGKEVWRHKNYAPLWGGVLTTKGNLVFTGTPEGFLQAFNAKTGDKV 524 + G A DP ++VW K PLW G L T G LVF GT +G+ +A +A +G+ + Sbjct: 420 PGGHRGTFTAWDPAQRRKVWELKEDLPLWSGALATAGGLVFYGTMDGWFKAVDAGSGELL 479 Query: 525 WEFQTGSGVLGSPVTWE-MDGEQYVSVVSGWGGAVPLWGGEV---------AKRVKDF-- 572 W F+TGSG++G P+++ DG QY++++SG GG W G + A K F Sbjct: 480 WRFKTGSGIIGQPISYRGPDGRQYIAILSGVGG----WAGAIVAGDLDPHDASAAKGFVN 535 Query: 573 ---------NQGGMLWTFKLPKQ 586 +GGML+ F LP++ Sbjct: 536 AVSDLPQRTTKGGMLYVFALPQR 558 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: 1448 Number of extensions: 126 Number of successful extensions: 16 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: 559 Length adjustment: 36 Effective length of query: 559 Effective length of database: 523 Effective search space: 292357 Effective search space used: 292357 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