Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate WP_086510097.1 BZY95_RS11680 sn-glycerol-3-phosphate ABC transporter ATP-binding protein UgpC
Query= uniprot:D8IPI1 (406 letters) >NCBI__GCF_002151265.1:WP_086510097.1 Length = 368 Score = 304 bits (779), Expect = 2e-87 Identities = 176/376 (46%), Positives = 234/376 (62%), Gaps = 12/376 (3%) Query: 1 MADIHCQALAKHYAGGPPVLHPLDLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60 MA + + K + G ++ +DL IG+GEFVV +GPSGCGKST+LR+IAGLE I+ G Sbjct: 1 MASVTLDKINKVF-GSTHIIKDVDLAIGEGEFVVFVGPSGCGKSTLLRLIAGLESITDGE 59 Query: 61 LRIGGTVVNDLPARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRRVREVAA 120 L IG VVN+LP RER V MVFQ+YALYPHM+VY+N+AFGL+ K + RV A Sbjct: 60 LSIGDQVVNELPPRERGVGMVFQSYALYPHMTVYENMAFGLKLAKTAKETVHERVMATAR 119 Query: 121 LLNLEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQLRGDIKRL 180 +L LE LLERKP+A+SGGQ+QR A+ RA+ + P + LFDEPLSNLDA LR Q+R +I RL Sbjct: 120 ILQLEELLERKPKALSGGQRQRVAMGRAMAREPRILLFDEPLSNLDASLRVQMRNEIARL 179 Query: 181 HQRLRTTTVYVTHDQLEAMTLADRVILMQDGRIVQAGSPAELYRYPRNLFAAGFIGTPAM 240 H+RL +T VYVTHDQ+EAMTLAD+++++ GR+ Q GSP ELY+ P F AGFIG+P M Sbjct: 180 HKRLGSTMVYVTHDQVEAMTLADKIVVLDGGRVEQVGSPQELYQRPATKFVAGFIGSPTM 239 Query: 241 NFLSGTVQRQD--GQLFIETAHQRWALTGERFSRLRHAMAVKLAVRPDHVRIAGEREPAA 298 NFL + D G T AL + + A A+ L +RP+H+R++ A Sbjct: 240 NFLPARLLGADATGCRIGATGLTELALPQDASGHAQGA-ALTLGIRPEHLRLS-----EA 293 Query: 299 SLTCPVSVELVEILGAD--ALLTTRCGDQTLTALVPADRLPQPGATLTLALDQHELHVFD 356 + + VE LG + L + G+ L A + G +TLA D +H+FD Sbjct: 294 QGSEGFEIVNVEYLGNEVYVYLEPKEGETLLIQRGEAPTTWRVGQRVTLAPDPEHVHLFD 353 Query: 357 VESGENLSLPDAALTA 372 G LS+ A A Sbjct: 354 A-GGRALSVKAARAVA 368 Lambda K H 0.321 0.137 0.403 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: 379 Number of extensions: 13 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: 406 Length of database: 368 Length adjustment: 30 Effective length of query: 376 Effective length of database: 338 Effective search space: 127088 Effective search space used: 127088 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 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