Align Inositol transport system permease protein (characterized)
to candidate SM_b20714 SM_b20714 sugar uptake ABC transporter permease
Query= reanno::WCS417:GFF2333 (340 letters) >FitnessBrowser__Smeli:SM_b20714 Length = 341 Score = 457 bits (1175), Expect = e-133 Identities = 228/325 (70%), Positives = 280/325 (86%) Query: 15 KSRRRLPTELSIFLVLIGIGLVFELFGWIVRDQSFLMNSQRLVLMILQVSIIGLLAIGVT 74 +SRRR+P EL+IFLVLIGI LV+E+ GW+ QSFLMNSQRL +MILQVS+IG++A+GVT Sbjct: 16 RSRRRMPPELNIFLVLIGIALVYEVLGWLFVGQSFLMNSQRLTIMILQVSVIGIIAVGVT 75 Query: 75 QVIITTGIDLSSGSVLALSAMIAASLAQTSDFSRAVFPSLTDLPVWIPVAMGLGVGLLAG 134 QVIIT GIDLSSGSV+ ++AMI+AS+AQ S + RA++PSLTDLP +P+ +G+G+GLLAG Sbjct: 76 QVIITGGIDLSSGSVVGMTAMISASVAQASTWPRALYPSLTDLPAIVPIGLGVGIGLLAG 135 Query: 135 AINGSIIAVTGIPPFIATLGMMVSARGLARYYTEGQPVSMLSDSYTAIGHGAMPVIIFLV 194 ING +IA T IPPFIATLGMMVSARG++++YT+GQPVS L++ + IG G PVI+FLV Sbjct: 136 FINGQLIARTKIPPFIATLGMMVSARGVSKWYTKGQPVSGLTEQFNFIGTGIWPVIVFLV 195 Query: 195 VAVIFHIALRYTKYGKYTYAIGGNMQAARTSGINVKRHLIIVYSIAGLLAGLAGVVASAR 254 VA+IFHIALRYT+YGK+TYAIG N+QAAR SGINV+ HL+ VY+IAG+LAGLAGVV +AR Sbjct: 196 VALIFHIALRYTRYGKFTYAIGANVQAARVSGINVEAHLVKVYAIAGMLAGLAGVVTAAR 255 Query: 255 AATGQAGMGMSYELDAIAAAVIGGTSLAGGVGRITGTVIGALILGVMASGFTFVGVDAYI 314 A T QAGMG+ YELDAIAA VIGGTSL GGVGR+TGTVIG +ILGVM SGFTF+ VDAY Sbjct: 256 AQTAQAGMGVMYELDAIAATVIGGTSLTGGVGRVTGTVIGTVILGVMTSGFTFLRVDAYY 315 Query: 315 QDIIKGLIIVVAVVIDQYRNKRKLK 339 Q+I+KG+IIV AVV+D YR K + K Sbjct: 316 QEIVKGIIIVAAVVVDVYRQKGRKK 340 Lambda K H 0.325 0.140 0.394 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: 396 Number of extensions: 13 Number of successful extensions: 1 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: 340 Length of database: 341 Length adjustment: 28 Effective length of query: 312 Effective length of database: 313 Effective search space: 97656 Effective search space used: 97656 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 15 ( 7.0 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 40 (21.6 bits) S2: 49 (23.5 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