Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate WP_057508775.1 ABB28_RS11575 PQQ-dependent sugar dehydrogenase
Query= BRENDA::I7A144 (352 letters) >NCBI__GCF_001431535.1:WP_057508775.1 Length = 540 Score = 202 bits (514), Expect = 2e-56 Identities = 130/346 (37%), Positives = 189/346 (54%), Gaps = 43/346 (12%) Query: 23 VEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFREGRLSTYAEL----PVYHRG-ESGL 77 + V GL PW+ AFLPDG +L+ E GR+ S+ L P++ +G +GL Sbjct: 197 IHTVATGLNRPWSAAFLPDGRVLVTEMGGRLLAIGPDGASSEISLDGLRPIFQQGGTTGL 256 Query: 78 LGLALHPRFPEAPYVY---AYRTVAEGGLRNQVVRLRHLGERGVLDRVVLDGIPARPHGL 134 + +AL PRF + ++Y Y + G+R ++R+R G++ RV+ + P G Sbjct: 257 MDIALDPRFAQNGWMYLTMGYGEASANGVR--LLRVRLAGDQIEDVRVLFNSTPKASAG- 313 Query: 135 HSGGRIAFGPDGMLYVTTGE-VYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGAR 193 ++GGRIAF PD L ++ G+ RE AQ+ A+ G ++R+ EG P NPF+GR G Sbjct: 314 NNGGRIAFLPDDSLVLSLGDGSRRREEAQNPANALGTVIRIDREGRPPADNPFVGRAGMA 373 Query: 194 PEVYSLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRVVGRGN 253 PE+YSLGHRNPQG+A P G+L +EHGP G DE+NLI+PGGNYGWP V G G Sbjct: 374 PEIYSLGHRNPQGIAVDPANGDLLLTEHGPR-----GGDEINLILPGGNYGWPIVTG-GM 427 Query: 254 D------------PRYRDPLYFWPQGFPPGNLAFF--------RGDLYVAGLRGQALLRL 293 D P Y+D L W P LA + RGDL V L+ +A+ R+ Sbjct: 428 DYPFARVSPFRSLPGYQDALLEWTPSIAPAGLAIYNGALFPQWRGDLLVPALKERAVRRV 487 Query: 294 VLEGERGRWRVLRVETALSGFG-RLREVQVGPDGALYVTTSNRDGR 338 + +G R++ + L R+R+V+V PDG++YV T + + Sbjct: 488 IRDGR----RIVGQQLLLGELNERIRDVKVAPDGSVYVLTDGTNAK 529 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: 657 Number of extensions: 44 Number of successful extensions: 6 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: 540 Length adjustment: 32 Effective length of query: 320 Effective length of database: 508 Effective search space: 162560 Effective search space used: 162560 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: 51 (24.3 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