Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate PP_2761 PP_2761 putative Ribose ABC transporter, permease protein
Query= TCDB::Q9X050 (331 letters) >FitnessBrowser__Putida:PP_2761 Length = 328 Score = 143 bits (361), Expect = 5e-39 Identities = 99/311 (31%), Positives = 160/311 (51%), Gaps = 17/311 (5%) Query: 24 ILLGLIVLFSFLSNRFLTLENFWIILRQTAVNLCI-AVGMTFVILTGGIDLSVGSILGFS 82 + +++ F+ + FLT+ N +L V L I A+GMT+ I GGIDLSVG+ L FS Sbjct: 29 LFAAVLLFFALKAPGFLTVGNLSSLLLNNFVLLAIVAIGMTYAIAAGGIDLSVGTALDFS 88 Query: 83 GAVTAKLLKYGLILSAFGVVLKFNPLGASIIGVLAGFAIGLFNGFIITRFNIPPFVATLG 142 LL G FG+ + G+LAG GLFN +I I PF+ATLG Sbjct: 89 ALTFVLLLNAG-----FGLYVAIPG------GLLAGSLAGLFNAGLIAGLRISPFLATLG 137 Query: 143 TMTAVRGFIMLLTKG-HPITRLGDSFDFIGSGWFLGIPMPVWIAAIATGVGIFILRKTQF 201 T+ LL++G PI + + LG+P+P+ + A+ V +L + + Sbjct: 138 TLFIGSSVQKLLSEGGQPIYLEAQVRSGLATERMLGVPLPLLLVALLALVYGVVLARGRL 197 Query: 202 GRYVYAVGGNEKAAVLSGVNSKLTKLWVYAISGILSAVAGLIVTARLDSAQPNAGLMYEL 261 GR + +G A SG+ + V+ S SA+AG+++ A +++ P +G + + Sbjct: 198 GREIIVLGSQPLVARYSGLAQRRIAALVFIASAFASALAGILLPATVNAYAPMSGNAFLM 257 Query: 262 DAIAATVIGGASLSGGKGTLIGTVVGALIIGVLNDGLVLVGVSPFWQQVAKGFIIIAAVI 321 +AI A IG + + GT++G L + V +GL+L+G + FWQQVA G +I++ ++ Sbjct: 258 NAIGAVFIGATLSLHNRVNVPGTLLGVLFLNVTANGLLLIGWNFFWQQVATGVLILSVLL 317 Query: 322 ----AEKLGRG 328 + +LG G Sbjct: 318 FSFASRRLGAG 328 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: 374 Number of extensions: 29 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: 328 Length adjustment: 28 Effective length of query: 303 Effective length of database: 300 Effective search space: 90900 Effective search space used: 90900 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