Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate 16257 b2148 beta-methylgalactoside transporter inner membrane component (NCBI)
Query= TCDB::Q9X050 (331 letters) >FitnessBrowser__Keio:16257 Length = 336 Score = 204 bits (518), Expect = 3e-57 Identities = 127/316 (40%), Positives = 175/316 (55%), Gaps = 8/316 (2%) Query: 24 ILLGLIVLFSFLSNRFLTLENFWIILRQTAVNLCIAVGMTFVILTGGIDLSVGSILGFSG 83 +LL L+ + F FL+L N IL Q++V + IA+G+ +I+T G DLS G +G + Sbjct: 21 VLLVLLAIIIFQDPTFLSLLNLSNILTQSSVRIIIALGVAGLIVTQGTDLSAGRQVGLAA 80 Query: 84 AVTAKLLKYGLILSAFGVVLKFNPLGASIIGVLA-GFAIGLFNGFIITRFNIPPFVATLG 142 V A LL+ + + P+ I+ V A G IGL NG II N+ PF+ TLG Sbjct: 81 VVAATLLQSMDNANKVFPEMATMPIALVILIVCAIGAVIGLINGLIIAYLNVTPFITTLG 140 Query: 143 TMTAVRGFIML---LTKGHPITRLGDSFDFIGSGWF-LG---IPMPVWIAAIATGVGIFI 195 TM V G L PI+ F G+ LG + + A IA + Sbjct: 141 TMIIVYGINSLYYDFVGASPISGFDSGFSTFAQGFVALGSFRLSYITFYALIAVAFVWVL 200 Query: 196 LRKTQFGRYVYAVGGNEKAAVLSGVNSKLTKLWVYAISGILSAVAGLIVTARLDSAQPNA 255 KT+FG+ ++A+GGN +AA +SGVN L L +YA+SG+ A G++ R+ SA N Sbjct: 201 WNKTRFGKNIFAIGGNPEAAKVSGVNVGLNLLMIYALSGVFYAFGGMLEAGRIGSATNNL 260 Query: 256 GLMYELDAIAATVIGGASLSGGKGTLIGTVVGALIIGVLNDGLVLVGVSPFWQQVAKGFI 315 G MYELDAIAA V+GG S SGG GT+IG V G +I V+N GL +GV+P+WQ + KG I Sbjct: 261 GFMYELDAIAACVVGGVSFSGGVGTVIGVVTGVIIFTVINYGLTYIGVNPYWQYIIKGAI 320 Query: 316 IIAAVIAEKLGRGEKE 331 II AV + L K+ Sbjct: 321 IIFAVALDSLKYARKK 336 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: 405 Number of extensions: 36 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: 336 Length adjustment: 28 Effective length of query: 303 Effective length of database: 308 Effective search space: 93324 Effective search space used: 93324 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