Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate CCNA_01575 CCNA_01575 glucose / sorbosone dehydrogenase
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__Caulo:CCNA_01575 Length = 408 Score = 173 bits (438), Expect = 8e-48 Identities = 123/356 (34%), Positives = 180/356 (50%), Gaps = 41/356 (11%) Query: 14 GLARGQGLRVEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLF-REGRLS-TYAELP-VY 70 GL G + + + GLE PW +AFLP G +L+ ER GR+R+ ++G+LS LP +Y Sbjct: 55 GLVSGVSGQYQTLASGLEHPWGMAFLPSGEILVTERAGRLRVVGKDGKLSPAVTGLPAIY 114 Query: 71 HRGESGLLGLALHPRFPEAPYVY-AYRTVAEGGLRNQVVRLR-HLGERGVLD--RVVLDG 126 G+ GLLG+ L P + + VY AY + V R + LG ++ +V+ Sbjct: 115 AEGQGGLLGVTLDPDYAKNGLVYWAYAEEIDSVNGTAVARGKLTLGAAPKVENVQVIWRQ 174 Query: 127 IPARPHGLHSGGRIAFGPDGMLYVTTGE-VYE--RELAQDLASLGGKILRLTPEGEPAPG 183 P LH GGR+ F G L++TTGE Y R +Q+L GK++R+ +G Sbjct: 175 TPKMASPLHFGGRVVFDRAGKLFITTGERAYPAGRVQSQNLDGTLGKVVRINADGSIPSD 234 Query: 184 NPFLGRRGARPEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNY 243 NPF+ GA+P+++SLGHRN Q A G L++ EHG G DE+N PG NY Sbjct: 235 NPFVNTAGAKPDIWSLGHRNIQS-ATLDAQGRLWTVEHG-----ARGGDELNRPEPGKNY 288 Query: 244 GWPRVV------------GRGNDPRYRDPLYFWPQGFPPGNLAFF--------RGDLYVA 283 GWP + G P+Y+W P +A + +G L + Sbjct: 289 GWPLITYGEEYSGKAISDGATQKEGLEQPVYYWDPVIAPSGMALYDGALFPALKGSLLIG 348 Query: 284 GLRGQALLRLVLEGERGRWRVLRVETALSGF-GRLREVQVGPDGALYVTTSNRDGR 338 +R Q + RLVL+ + +V+ E + GR+R+V VGPDGA+YV T DG+ Sbjct: 349 SMREQHVARLVLKDD----KVVGEERLFTDIGGRVRDVAVGPDGAIYVLTDEGDGK 400 Lambda K H 0.322 0.146 0.460 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: 542 Number of extensions: 37 Number of successful extensions: 7 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: 352 Length of database: 408 Length adjustment: 30 Effective length of query: 322 Effective length of database: 378 Effective search space: 121716 Effective search space used: 121716 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 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