Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate RR42_RS03365 RR42_RS03365 ribose ABC transporter permease
Query= TCDB::Q9X050 (331 letters) >FitnessBrowser__Cup4G11:RR42_RS03365 Length = 333 Score = 238 bits (608), Expect = 1e-67 Identities = 139/320 (43%), Positives = 193/320 (60%), Gaps = 12/320 (3%) Query: 9 KISWYQRISRYQSIFILLGLIVLFSFLSNRFLTLENFWIILRQTAVNLCIAVGMTFVILT 68 +++ +R+ + +L+ L + FS L+ F +N II +Q ++N+ +A GMTFVILT Sbjct: 19 RLTTQERLRALGMLPVLVLLCIGFSVLTENFAGWQNLSIIAQQASINMVLAAGMTFVILT 78 Query: 69 GGIDLSVGSILGFSGAVTAKLLKYGLILSAFGVVLKFNPLGASIIGVLAGFAIGLFNGFI 128 GGIDLSVGSIL S AV A L+ L V +L G G+ NG + Sbjct: 79 GGIDLSVGSILSIS-AVVAMLVSLMPQLGMLSVPA----------ALLCGLLFGIVNGAL 127 Query: 129 ITRFNIPPFVATLGTMTAVRGFIMLLTKGHPITRLGDSFDFIGSGWFLGIPMPVWIAAIA 188 + +PPF+ TLGT+TAVRG L+ I F FIG+G LG+P V IA Sbjct: 128 VAFMKLPPFIVTLGTLTAVRGLARLVGNDSTIYNPDIGFAFIGNGEVLGVPWLVIIAFAV 187 Query: 189 TGVGIFILRKTQFGRYVYAVGGNEKAAVLSGVNSKLTKLWVYAISGILSAVAGLIVTARL 248 V F+LR+T G +YAVGGN +AA LSG+ + L+VYA+SG+L+ + G++ +ARL Sbjct: 188 VAVSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARL 247 Query: 249 DSAQP-NAGLMYELDAIAATVIGGASLSGGKGTLIGTVVGALIIGVLNDGLVLVGVSPFW 307 +A G YELDAIAA ++GG S GG G+++GT+VGALII VL++GLVL+GVS W Sbjct: 248 YAANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIW 307 Query: 308 QQVAKGFIIIAAVIAEKLGR 327 Q + KG +II AV + R Sbjct: 308 QYIIKGLVIIGAVALDSYRR 327 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: 443 Number of extensions: 28 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: 331 Length of database: 333 Length adjustment: 28 Effective length of query: 303 Effective length of database: 305 Effective search space: 92415 Effective search space used: 92415 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