Align glucose 1-dehydrogenase (PQQ, quinone) (EC 1.1.5.2) (characterized)
to candidate SMc01583 SMc01583 hypothetical protein
Query= BRENDA::I7A144 (352 letters) >FitnessBrowser__Smeli:SMc01583 Length = 396 Score = 179 bits (453), Expect = 1e-49 Identities = 123/340 (36%), Positives = 169/340 (49%), Gaps = 33/340 (9%) Query: 23 VEEVVGGLEVPWALAFLPDGGMLIAERPGRIRLFREGRLSTYAE-LPVYH-RGESGLLGL 80 VE + GLE PWA+ +PDG +++ ERPGR+R+ R+G+LS + +P G+ GLL + Sbjct: 54 VETLASGLEHPWAVEAMPDGALIVTERPGRLRILRDGKLSAAIKGVPTAAAHGQGGLLDV 113 Query: 81 ALHPRFPEAPYVYAYRTV-AEGGLRNQVVRLRHLGERGVLDRV--VLDGIPARPHGLHSG 137 AL +F +Y +V +GG +VR + L V + G H G Sbjct: 114 ALDRQFATNRTLYLTLSVRGDGGYGTVLVRAALSQDEQSLTEVKEIFRMNKFTRKGQHFG 173 Query: 138 GRIAFGPDGMLYVTTGEVYERELAQDLASLGGKILRLTPEGEPAPGNPFLGRRGARPEVY 197 RIA DG L+ G+ E E AQD G IL + +G NP+ G G E++ Sbjct: 174 SRIAIDKDGSLFFGIGDRGEGERAQDSRDHAGSILHINADGSIPASNPYRGGTGGLAEIW 233 Query: 198 SLGHRNPQGLAWHPKTGELFSSEHGPSGEQGYGHDEVNLIVPGGNYGWPRV--------- 248 S+GHRNPQG+ + P+ G+L + EHG G DEVN PG NYGWP + Sbjct: 234 SIGHRNPQGITFDPEGGKLLTVEHG-----ARGGDEVNNPQPGKNYGWPVITFGKDYSGV 288 Query: 249 -VGRGNDPR-YRDPLYFWPQGFPPGNLAFFR--------GDLYVAGLRGQALLRLVLEGE 298 +G G PL++W PG +A +R GDL +A L+ Q L RL + E Sbjct: 289 EIGEGTAKEGLEQPLFYWDPSIAPGAIAVYRGSMFPEWNGDLLIAALKYQLLARLDRD-E 347 Query: 299 RGRWRVLRVETALSG-FGRLREVQVGPDGALYVTTSNRDG 337 G V E G FGR+R+V V DGAL + T DG Sbjct: 348 TG--AVTNEERLFDGEFGRIRDVIVASDGALIMVTDEEDG 385 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: 504 Number of extensions: 27 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: 396 Length adjustment: 30 Effective length of query: 322 Effective length of database: 366 Effective search space: 117852 Effective search space used: 117852 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