Align ABC transporter for D-Sorbitol, permease component 2 (characterized)
to candidate Synpcc7942_0949 Synpcc7942_0949 permease protein of sugar ABC transporter
Query= reanno::acidovorax_3H11:Ac3H11_2943 (316 letters) >FitnessBrowser__SynE:Synpcc7942_0949 Length = 292 Score = 108 bits (270), Expect = 2e-28 Identities = 82/279 (29%), Positives = 137/279 (49%), Gaps = 16/279 (5%) Query: 36 PRLLLTPAMATLFLWMIVPLVMTIYFSLIRYNLMQPDQTGFAGLENFEFFVTDPSFGTAV 95 PR L PA+ T+ PL+ + SL NL Q F GL N++ D F + Sbjct: 5 PRWLTIPALLTITGVFAYPLLRAAWLSLQALNLNTQLQPVFIGLANYQRLWGDSRFWGDL 64 Query: 96 VNTILLLGSVILITVVLGVAIALLINEPFPGRGIVRVLLISPFFVMPTVNALMWKNMMMN 155 NT + + + + +VLG+AIALL+++P RG +R + + P+ + V AL W + + Sbjct: 65 FNTTVFTVTSVSLELVLGLAIALLLHQPSRWRGPLRTIALLPWVLPTAVMALGWAWIFND 124 Query: 156 PIYGV----LAQV-WIFFGAAPVDWLTDHPLFSVIVMVS---WQWLPFATLIFMTALQSM 207 P YGV L Q+ WI AAP++WL +P ++ + +V+ W+ PF ++ + Q++ Sbjct: 125 P-YGVWNDWLQQLGWI---AAPINWL-GNPRWAWLTLVAADVWKTTPFVAILLLAGRQAI 179 Query: 208 NHEQLEASRMDGANYLQQLRYLYVPHLGRSVAVVVMIELIFLLSIFAEIYTTTAGGPGDA 267 + EA ++GA Q + +P L +A+ ++ +F + T GGP ++ Sbjct: 180 PEDLYEAHCLEGATAWQSFWQITLPLLRPQLAIALLFRSAQAFGLFDLVKVMTGGGPANS 239 Query: 268 STNVTFLIFKQALLNFDAGVASAGALFAVVLANIAAVFL 306 + + + AL D G GA A+V A I A L Sbjct: 240 TETLALYAYTTALRYLDFGY---GATLAIVTAAILAAGL 275 Lambda K H 0.331 0.142 0.436 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: 288 Number of extensions: 18 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: 316 Length of database: 292 Length adjustment: 27 Effective length of query: 289 Effective length of database: 265 Effective search space: 76585 Effective search space used: 76585 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.9 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