Align ABC transporter for D-Glucose-6-Phosphate, ATPase component (characterized)
to candidate Synpcc7942_1406 Synpcc7942_1406 ATPase
Query= reanno::WCS417:GFF4321 (386 letters) >FitnessBrowser__SynE:Synpcc7942_1406 Length = 368 Score = 189 bits (481), Expect = 8e-53 Identities = 107/256 (41%), Positives = 160/256 (62%), Gaps = 12/256 (4%) Query: 6 LRNVNKTYGAGLPDTLKNIELSIKEGEFLILVGPSGCGKSTLMNCIAGLETITGGAIMIG 65 L V K + + + ++ GE L LVGPSGCGK+TL+ IAG E++ G+I + Sbjct: 9 LDRVCKQFSGSSLAAVDQVSFELEAGEILGLVGPSGCGKTTLLRMIAGFESLQSGSIQLA 68 Query: 66 DQDVS----GMSPKDRDIAMVFQSYALYPTMSVRENIEFGLKIRKMPQADIDAEVARVA- 120 + V+ + P+ R + MVFQ YAL+P ++V +N+ FGL+ RK A VAR A Sbjct: 69 GETVATAQRSLPPETRSVGMVFQDYALFPHLTVLDNVCFGLRDRKG-----SAAVARQAL 123 Query: 121 KLLQIEHLLNRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180 L+ +E L R P +LSGGQQQRVA+ RALA +P + L DEPLSNLD ++R+ +R E++ Sbjct: 124 ALVGLEGLERRYPHELSGGQQQRVALARALAPQPPLILLDEPLSNLDVQVRLRLRQELRD 183 Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKEIYNNPANQFVASFIGSPP 240 + ++ + T + VTHDQ EA+++ D+VAVM+ G +Q G P+E++ +PA++FVA F+ Sbjct: 184 ILRQAQATAILVTHDQEEALSICDRVAVMRLGRFEQIGQPEELFQHPASRFVAEFLSQ-- 241 Query: 241 MNFVPLRLQRKDGRLV 256 NF+ Q R V Sbjct: 242 ANFLATEYQGDAWRTV 257 Lambda K H 0.318 0.135 0.382 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: 320 Number of extensions: 14 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: 386 Length of database: 368 Length adjustment: 30 Effective length of query: 356 Effective length of database: 338 Effective search space: 120328 Effective search space used: 120328 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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