Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate 7024901 Shewana3_2075 inner-membrane translocator (RefSeq)
Query= TCDB::Q9X050 (331 letters) >FitnessBrowser__ANA3:7024901 Length = 405 Score = 184 bits (468), Expect = 2e-51 Identities = 110/277 (39%), Positives = 161/277 (58%), Gaps = 11/277 (3%) Query: 48 ILRQTAVNLCIAVGMTFVILTGGIDLSVGSILGFSGAVTAKLLKYGLILSAFGVVLKFNP 107 IL ++A +++GM+ VI TGGIDLSVG+++ +GAV A LL +V + Sbjct: 100 ILNRSAPVALLSIGMSLVIATGGIDLSVGAVMAIAGAVCANLL----------LVPDISL 149 Query: 108 LGASIIGVLAGFAIGLFNGFIITRFNIPPFVATLGTMTAVRGFIMLLTKGHPITRLGDSF 167 + G++ G G NG +++ I P VATL M A RG L+ +G IT F Sbjct: 150 VTVIAAGLIVGLLAGCINGGLVSFLGIQPIVATLLLMVAGRGVAQLINQGQIITFQHPGF 209 Query: 168 DFIGSGWFLGIPMPVWIAAIATGVGIFILRKTQFGRYVYAVGGNEKAAVLSGVNSKLTKL 227 IG G FLG+PMPVWI +LRKT G ++ AVG N KA+ G+N K KL Sbjct: 210 AAIGVGQFLGLPMPVWIVIGMLTFSQLLLRKTALGLFIEAVGCNAKASRYLGINDKSIKL 269 Query: 228 WVYAISGILSAVAGLIVTARLDSAQP-NAGLMYELDAIAATVIGGASLSGGKGTLIGTVV 286 + Y I+G+ +A+AG+I TA + + NAGL ELDA+ A VIGGA+L+GG+ +LI +VV Sbjct: 270 FAYGIAGLCAALAGMISTADIQGSDANNAGLWLELDAVLAVVIGGAALTGGRFSLILSVV 329 Query: 287 GALIIGVLNDGLVLVGVSPFWQQVAKGFIIIAAVIAE 323 GALII L +++ G+ + + K +I+ ++ + Sbjct: 330 GALIIQTLATTIIVSGLPAKFNLLIKAIVILTVLLLQ 366 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: 360 Number of extensions: 22 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: 405 Length adjustment: 30 Effective length of query: 301 Effective length of database: 375 Effective search space: 112875 Effective search space used: 112875 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