Align Glycerol dehydrogenase; GDH; GLDH; GlyDH; EC 1.1.1.6 (characterized)
to candidate WP_089136115.1 CES79_RS01700 glycerol dehydrogenase
Query= SwissProt::P32816 (370 letters) >NCBI__GCF_002217945.1:WP_089136115.1 Length = 368 Score = 368 bits (945), Expect = e-106 Identities = 196/361 (54%), Positives = 250/361 (69%), Gaps = 2/361 (0%) Query: 5 RVFISPAKYVQGKNVITKIANYLEGIGNKTVVIADEIVWKIAGHTIVNELKKGNIAAEEV 64 ++F SP+ YVQG + A L +G+K +V+AD V+KI G ++ L + +V Sbjct: 3 KIFGSPSTYVQGSGALFDSAEALHKLGSKPIVMADTTVYKIVGKKFIDYLGQQKFDVRKV 62 Query: 65 VFSGEASRNEVERIANIARKAEAAIVIGVGGGKTLDTAKAVADELDAYIVIVPTAASTDA 124 F GEAS E++RI I + A ++IG+GGGKTLD+AKA+AD L + I+PT ASTDA Sbjct: 63 TFKGEASDKEIDRITGIGQDFGADLIIGLGGGKTLDSAKAIADNLKLPVAILPTLASTDA 122 Query: 125 PTSALSVIYSDDGVFESYRFYKKNPDLVLVDTKIIANAPPRLLASGIADALATWVEARSV 184 P S LSVIY+ DG FE YRFY KNPDLVLVDT+++ANAP RLLASGIADALAT VEA++V Sbjct: 123 PCSRLSVIYTPDGGFEKYRFYSKNPDLVLVDTQLVANAPTRLLASGIADALATNVEAQAV 182 Query: 185 IKSGGKTMAGGIPTIAAEAIAEKCEQTLFKYGKLAYESVKAKVVTPALEAVVEANTLLSG 244 K+ G+TM T+ AIAEKCE+TLF YG A ++ VTPALE +VEANTL+SG Sbjct: 183 AKANGQTMLNAKQTLVGNAIAEKCEETLFAYGLQAIDAAGVHAVTPALEKIVEANTLMSG 242 Query: 245 LGFESGGLAAAHAIHNGFTALEGE-IHHLTHGEKVAFGTLVQLALEEHSQQEIERYIELY 303 +GFESGGLAAAHAIHNG T+L E +H THGEKVAFGTL QL LE ++I Y+ Sbjct: 243 VGFESGGLAAAHAIHNGLTSLPNEALHAKTHGEKVAFGTLTQLFLEGRETEDIHTYLAFD 302 Query: 304 LSLDLPVTLEDIKLKDASREDILKVAKAATAEGETI-HNAFNVTADDVADAIFAADQYAK 362 L+L LP T +D+ + D S ED+LKV +AATA +T+ F VT DV A+ AD Y++ Sbjct: 303 LALGLPTTFDDLGIADISDEDLLKVGQAATAPADTMTEMPFEVTPADVVAAMKGADAYSR 362 Query: 363 A 363 A Sbjct: 363 A 363 Lambda K H 0.314 0.131 0.357 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: 331 Number of extensions: 7 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: 370 Length of database: 368 Length adjustment: 30 Effective length of query: 340 Effective length of database: 338 Effective search space: 114920 Effective search space used: 114920 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: 42 (22.0 bits) S2: 49 (23.5 bits)
This GapMind analysis is from Sep 24 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