Align glycerol dehydrogenase (EC 1.1.1.6) (characterized)
to candidate AZOBR_RS07845 AZOBR_RS07845 glycerol dehydrogenase
Query= BRENDA::Q9WYQ4 (364 letters) >FitnessBrowser__azobra:AZOBR_RS07845 Length = 364 Score = 470 bits (1209), Expect = e-137 Identities = 243/364 (66%), Positives = 279/364 (76%), Gaps = 1/364 (0%) Query: 1 MITTTIFPGRYVQGAGAINILEEELSRFGERAFVVIDDFVDKNVLGENFFSSFTKVRVNK 60 MITT IFP RYVQG GA++ L E+L+R G+ V D FV K + G ++ +V +N Sbjct: 1 MITTAIFPARYVQGNGALDSLGEDLARLGKTVLAVTDSFVLKTLKGRLVEAAAGRVEMNI 60 Query: 61 QIFGGECSDEEIERLSGLVEEE-TDVVVGIGGGKTLDTAKAVAYKLKKPVVIVPTIASTD 119 Q F GECSDEEIERL+GL DVV GIGGGK LDTAKAVA+ L IVPT+ASTD Sbjct: 61 QEFRGECSDEEIERLTGLARAMGADVVAGIGGGKALDTAKAVAHALNARTAIVPTLASTD 120 Query: 120 APCSALSVIYTPNGEFKRYLFLPRNPDVVLVDTEIVAKAPARFLVAGMGDALATWFEAES 179 APCSALSVIYTP G FKRYL LPRNPD+VLVDT +VA AP RFLV+GMGDAL+TWFEAE Sbjct: 121 APCSALSVIYTPEGAFKRYLVLPRNPDLVLVDTGVVASAPVRFLVSGMGDALSTWFEAED 180 Query: 180 CKQKYAPNMTGRLGSMTAYALARLCYETLLEYGVLAKRSVEEKSVTPALEKIVEANTLLS 239 C+ K NMTGR+G MTA+ALARLCY+TLLEYGVLAK + E+ VTPALE+IVEANTLLS Sbjct: 181 CRIKRGGNMTGRVGPMTAFALARLCYDTLLEYGVLAKSACEQGVVTPALERIVEANTLLS 240 Query: 240 GLGFESGGLAAAHAIHNGLTVLENTHKYLHGEKVAIGVLASLFLTDKPRKMIEEVYSFCE 299 GLGFESGGLAAAHA+HNGLT LE TH HGEKVA G L L LTD+P +++EVY FC+ Sbjct: 241 GLGFESGGLAAAHAVHNGLTALEETHHCWHGEKVAFGTLTLLILTDRPPAVLDEVYGFCK 300 Query: 300 EVGLPTTLAEIGLDGVSDEDLMKVAEKACDKNETIHNEPQPVTSKDVFFALKAADRYGRM 359 VGLPTTLAEIGL GVSDE L+ AE+AC + ETIHNEP +T + V A+KAAD GR Sbjct: 301 AVGLPTTLAEIGLAGVSDERLLLAAERACAEGETIHNEPHEITPQRVLAAMKAADAEGRR 360 Query: 360 RKNL 363 RK L Sbjct: 361 RKGL 364 Lambda K H 0.318 0.135 0.384 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: 412 Number of extensions: 13 Number of successful extensions: 2 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: 364 Length of database: 364 Length adjustment: 29 Effective length of query: 335 Effective length of database: 335 Effective search space: 112225 Effective search space used: 112225 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 (21.7 bits) S2: 49 (23.5 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