Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate SM_b20714 SM_b20714 sugar uptake ABC transporter permease
Query= TCDB::Q9X050 (331 letters) >FitnessBrowser__Smeli:SM_b20714 Length = 341 Score = 218 bits (554), Expect = 2e-61 Identities = 122/307 (39%), Positives = 187/307 (60%), Gaps = 12/307 (3%) Query: 24 ILLGLIVLFSFLSNRF------LTLENFWIILRQTAVNLCIAVGMTFVILTGGIDLSVGS 77 +L+G+ +++ L F + + I++ Q +V IAVG+T VI+TGGIDLS GS Sbjct: 30 VLIGIALVYEVLGWLFVGQSFLMNSQRLTIMILQVSVIGIIAVGVTQVIITGGIDLSSGS 89 Query: 78 ILGFSGAVTAKLLKYGLILSAFGVVLKFNPLGASI-IGVLAGFAIGLFNGFIITRFNIPP 136 ++G + ++A + + A L P I +GV G G NG +I R IPP Sbjct: 90 VVGMTAMISASVAQASTWPRALYPSLTDLPAIVPIGLGVGIGLLAGFINGQLIARTKIPP 149 Query: 137 FVATLGTMTAVRGFIMLLTKGHPITRLGDSFDFIGSGWFLGIPMPVWIAAIATGVGIFIL 196 F+ATLG M + RG TKG P++ L + F+FIG+G + PV + + + L Sbjct: 150 FIATLGMMVSARGVSKWYTKGQPVSGLTEQFNFIGTGIW-----PVIVFLVVALIFHIAL 204 Query: 197 RKTQFGRYVYAVGGNEKAAVLSGVNSKLTKLWVYAISGILSAVAGLIVTARLDSAQPNAG 256 R T++G++ YA+G N +AA +SG+N + + VYAI+G+L+ +AG++ AR +AQ G Sbjct: 205 RYTRYGKFTYAIGANVQAARVSGINVEAHLVKVYAIAGMLAGLAGVVTAARAQTAQAGMG 264 Query: 257 LMYELDAIAATVIGGASLSGGKGTLIGTVVGALIIGVLNDGLVLVGVSPFWQQVAKGFII 316 +MYELDAIAATVIGG SL+GG G + GTV+G +I+GV+ G + V ++Q++ KG II Sbjct: 265 VMYELDAIAATVIGGTSLTGGVGRVTGTVIGTVILGVMTSGFTFLRVDAYYQEIVKGIII 324 Query: 317 IAAVIAE 323 +AAV+ + Sbjct: 325 VAAVVVD 331 Lambda K H 0.327 0.144 0.427 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: 445 Number of extensions: 24 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: 331 Length of database: 341 Length adjustment: 28 Effective length of query: 303 Effective length of database: 313 Effective search space: 94839 Effective search space used: 94839 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 (21.7 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