Align monosaccharide-transporting ATPase (EC 3.6.3.17) (characterized)
to candidate GFF262 PGA1_c02740 sn-glycerol-3-phosphate import ATP-binding protein UgbC
Query= BRENDA::Q97UY8 (353 letters) >FitnessBrowser__Phaeo:GFF262 Length = 348 Score = 225 bits (574), Expect = 1e-63 Identities = 127/292 (43%), Positives = 191/292 (65%), Gaps = 19/292 (6%) Query: 1 MVRIIVKNVSKVFKKGKVVALDNVNINIENGERFGILGPSGAGKTTFMRIIAGLDVPSTG 60 M ++ + +V KV+ G V A+ + + IE+GE ++GPSG GK+T +R+IAGL+ + G Sbjct: 1 MAQVTLNSVRKVYPNG-VEAVTSSSFKIEDGEFVVLVGPSGCGKSTLLRMIAGLEDITEG 59 Query: 61 ELYFDDRLVASNGKLIVPPEDRKIGMVFQTWALYPNLTAFENIAFPLTNMKMSKEEIRKR 120 L DR+V + V P DR I MVFQ +ALYP++T +NIA+ L N K + EI+++ Sbjct: 60 TLEIGDRVVNN-----VDPADRDIAMVFQNYALYPHMTVRKNIAYGLKNRKTPEAEIKQK 114 Query: 121 VEEVAKILDIHHVLNHFPRELSGGQQQRVALARALVKDPSLLLLDEPFSNLDARMRDSAR 180 V E AK+L++ L+ P +LSGGQ+QRVA+ RA+V+DP+L L DEP SNLDA++R+ R Sbjct: 115 VAEAAKMLNLEEYLDRKPSQLSGGQRQRVAMGRAIVRDPALFLFDEPLSNLDAKLRNQMR 174 Query: 181 ALVKEVQSRLGVTLLVVSHDPADIFAIADRVGVLVKGKLVQVGKPEDLYDNPVSIQVASL 240 +K +Q RLGVT + V+HD + +ADR+ VL G++ Q+G P ++Y NP S+ VAS Sbjct: 175 IEIKALQRRLGVTSIYVTHDQVEAMTMADRIIVLNGGRIEQIGTPSEIYHNPASVFVASF 234 Query: 241 IG--EINELEGKVTN------EGVVIGSLRFPVSVSSDRAI-IGIRPEDVKL 283 +G +N L+ + N +GV +G+L S+ A+ +GIRPEDV+L Sbjct: 235 MGAPPMNLLDATIANGQVTLPDGVSMGAL----DTSAQGAVKLGIRPEDVQL 282 Lambda K H 0.319 0.139 0.390 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: 313 Number of extensions: 17 Number of successful extensions: 3 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: 353 Length of database: 348 Length adjustment: 29 Effective length of query: 324 Effective length of database: 319 Effective search space: 103356 Effective search space used: 103356 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 (21.7 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