Align ABC transporter for D-Glucose-6-Phosphate, permease component 2 (characterized)
to candidate Synpcc7942_0949 Synpcc7942_0949 permease protein of sugar ABC transporter
Query= reanno::WCS417:GFF4323 (302 letters) >FitnessBrowser__SynE:Synpcc7942_0949 Length = 292 Score = 132 bits (331), Expect = 1e-35 Identities = 84/271 (30%), Positives = 136/271 (50%), Gaps = 8/271 (2%) Query: 21 PKLVLAPSMFIVLVGFYGYIL----WTFVLSFTNSTFLPTYKWAGLAQYARLFDNDRWWV 76 P+ + P++ + + G + Y L W + + +T L + GLA Y RL+ + R+W Sbjct: 5 PRWLTIPAL-LTITGVFAYPLLRAAWLSLQALNLNTQLQPV-FIGLANYQRLWGDSRFWG 62 Query: 77 ASKNLAVFGGMFIGITLVIGVTLAIFLDQKIRREGFIRTIYLYPMALSMIVTGTAWKWLL 136 N VF + + LV+G+ +A+ L Q R G +RTI L P L V W W+ Sbjct: 63 DLFNTTVFTVTSVSLELVLGLAIALLLHQPSRWRGPLRTIALLPWVLPTAVMALGWAWIF 122 Query: 137 NPGMGL-DKLLRDWGWEGFRLDWLIDPDRVVYCLVIAAVWQASGFIMAMFLAGLRGVDQS 195 N G+ + L+ GW ++WL +P LV A VW+ + F+ + LAG + + + Sbjct: 123 NDPYGVWNDWLQQLGWIAAPINWLGNPRWAWLTLVAADVWKTTPFVAILLLAGRQAIPED 182 Query: 196 IVRAAQIDGASMPRIYWSVVLPSLRPVFFSAVMILAHIAIKSFDLVAAMTAGGPGYSSDL 255 + A ++GA+ + +W + LP LRP A++ + A FDLV MT GGP S++ Sbjct: 183 LYEAHCLEGATAWQSFWQITLPLLRPQLAIALLFRSAQAFGLFDLVKVMTGGGPANSTET 242 Query: 256 PAMFMYSFTFSRGQMGMGSASAILMLGAILA 286 A++ Y+ G G+ AI + AILA Sbjct: 243 LALYAYTTALRYLDFGYGATLAI-VTAAILA 272 Lambda K H 0.330 0.141 0.455 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: 16 Number of successful extensions: 2 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: 302 Length of database: 292 Length adjustment: 26 Effective length of query: 276 Effective length of database: 266 Effective search space: 73416 Effective search space used: 73416 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.1 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.8 bits) S2: 48 (23.1 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