Align Binding-protein-dependent transport systems inner membrane component (characterized, see rationale)
to candidate Synpcc7942_0949 Synpcc7942_0949 permease protein of sugar ABC transporter
Query= uniprot:A3DE72 (327 letters) >FitnessBrowser__SynE:Synpcc7942_0949 Length = 292 Score = 145 bits (367), Expect = 9e-40 Identities = 92/285 (32%), Positives = 141/285 (49%), Gaps = 15/285 (5%) Query: 34 MLIPTFVCMMCIHFIPMLQGIYLSLLDLNQLTMTKFLNAPFIGLKNYYEILFDEKSLIRR 93 + IP + + + P+L+ +LSL LN T L FIGL NY + D + Sbjct: 8 LTIPALLTITGVFAYPLLRAAWLSLQALNLNTQ---LQPVFIGLANYQRLWGDSR----- 59 Query: 94 GFWFALRNTAIYTVVVTFATFALGIILAMLVNREFKGRGIVRTALLMPWVVPSYVVGMTW 153 FW L NT ++TV LG+ +A+L+++ + RG +RT L+PWV+P+ V+ + W Sbjct: 60 -FWGDLFNTTVFTVTSVSLELVLGLAIALLLHQPSRWRGPLRTIALLPWVLPTAVMALGW 118 Query: 154 GFLWRQDSGLINIILCDILHILPEKPYWLVGSNQIWAIIIPT-IWRGLPLSMILMLAGLQ 212 +++ G+ N L L + WL W ++ +W+ P IL+LAG Q Sbjct: 119 AWIFNDPYGVWNDWLQQ-LGWIAAPINWLGNPRWAWLTLVAADVWKTTPFVAILLLAGRQ 177 Query: 213 SISPDYYEAADIDGANGWQKFWHITLPLLKPILAINVMFSLISNIYSFNIVSMMFGNGAG 272 +I D YEA ++GA WQ FW ITLPLL+P LAI ++F F++V +M G G Sbjct: 178 AIPEDLYEAHCLEGATAWQSFWQITLPLLRPQLAIALLFRSAQAFGLFDLVKVMTGGG-- 235 Query: 273 IPGEWGDLLMTYIQRNTFQMWRFGPGAA-ALMIVMFFVLGIVALW 316 P + L Y + FG GA A++ G+ +W Sbjct: 236 -PANSTETLALYAYTTALRYLDFGYGATLAIVTAAILAAGLGLIW 279 Lambda K H 0.330 0.145 0.468 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: 331 Number of extensions: 19 Number of successful extensions: 4 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: 327 Length of database: 292 Length adjustment: 27 Effective length of query: 300 Effective length of database: 265 Effective search space: 79500 Effective search space used: 79500 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