Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate Echvi_1280 Echvi_1280 Ribose/xylose/arabinose/galactoside ABC-type transport systems, permease components
Query= TCDB::Q9X050 (331 letters) >FitnessBrowser__Cola:Echvi_1280 Length = 318 Score = 385 bits (989), Expect = e-112 Identities = 189/314 (60%), Positives = 240/314 (76%) Query: 16 ISRYQSIFILLGLIVLFSFLSNRFLTLENFWIILRQTAVNLCIAVGMTFVILTGGIDLSV 75 I+++QS+ L+ L ++ S LS+RFLTL N W ++RQ +VN+CI+VGMT VILT GIDLSV Sbjct: 4 IAKFQSLIALIILCLVLSLLSDRFLTLANGWNVMRQVSVNICISVGMTLVILTAGIDLSV 63 Query: 76 GSILGFSGAVTAKLLKYGLILSAFGVVLKFNPLGASIIGVLAGFAIGLFNGFIITRFNIP 135 GSIL GAVTA L+K G+ + + + F PLGA I+GV GF +G FNG+ ITRF +P Sbjct: 64 GSILALCGAVTASLIKNGIAVEGLNLHIGFAPLGAVILGVGLGFGLGWFNGWTITRFKVP 123 Query: 136 PFVATLGTMTAVRGFIMLLTKGHPITRLGDSFDFIGSGWFLGIPMPVWIAAIATGVGIFI 195 PFVATL +T RG ML T G PI LG+ F F+G+GWFLGIPMPVWI A+ + + + Sbjct: 124 PFVATLAMLTIARGLTMLWTGGFPINGLGEDFAFLGTGWFLGIPMPVWITAVIVALAVLL 183 Query: 196 LRKTQFGRYVYAVGGNEKAAVLSGVNSKLTKLWVYAISGILSAVAGLIVTARLDSAQPNA 255 +KT+FGRYVYA+GGNE+AA LSG+N K+ VYAI+G L+AV G+IVT+RLDSAQPNA Sbjct: 184 TKKTKFGRYVYAIGGNERAARLSGINISRVKMTVYAIAGGLAAVGGMIVTSRLDSAQPNA 243 Query: 256 GLMYELDAIAATVIGGASLSGGKGTLIGTVVGALIIGVLNDGLVLVGVSPFWQQVAKGFI 315 G+ YELDAIAA VIGG SLSGGKGT++G V+G +IIGVLN+GLVL+ VSPFWQQV KG + Sbjct: 244 GISYELDAIAAVVIGGTSLSGGKGTIMGAVLGGIIIGVLNNGLVLLNVSPFWQQVVKGAV 303 Query: 316 IIAAVIAEKLGRGE 329 I+ AV+ +K E Sbjct: 304 ILLAVVIDKANSKE 317 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: 436 Number of extensions: 18 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: 331 Length of database: 318 Length adjustment: 28 Effective length of query: 303 Effective length of database: 290 Effective search space: 87870 Effective search space used: 87870 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: 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