Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate H281DRAFT_02714 H281DRAFT_02714 monosaccharide ABC transporter membrane protein, CUT2 family
Query= TCDB::Q9X050 (331 letters) >FitnessBrowser__Burk376:H281DRAFT_02714 Length = 331 Score = 246 bits (629), Expect = 4e-70 Identities = 132/301 (43%), Positives = 193/301 (64%), Gaps = 14/301 (4%) Query: 21 SIFILLGLIVLFSFLSNRFLTLENFWIILRQTAVNLCIAVGMTFVILTGGIDLSVGSILG 80 S+ +L+GL++ S S FLT N + R ++ +++GM VI+TGGIDLSVGS++G Sbjct: 32 SVLLLVGLLI--SVFSPYFLTTNNLMGVFRSFSLIALMSIGMMLVIITGGIDLSVGSVMG 89 Query: 81 FSGAVTAKLLKYGLILSAFGVVLKFNPLGASIIGVLAGFAIGLFNGFIITRFNIPPFVAT 140 S VTA + ++G +N A G+ G A+G FNGF+IT +PPF+AT Sbjct: 90 LSSLVTALVFQHG-----------YNAPAAIGAGLAVGIAVGAFNGFMITWIQLPPFIAT 138 Query: 141 LGTMTAVRGFIMLLTKGHPITR-LGDSFDFIGSGWFLGIPMPVWIAAIATGVGIFILRKT 199 LGT++ RG + ++TKG P+T + DSF FIG G+ +P PV I T V ++R+T Sbjct: 139 LGTLSIGRGLMYIITKGVPVTPDVPDSFTFIGQGYIGFVPFPVVILLAMTAVFSVVMRQT 198 Query: 200 QFGRYVYAVGGNEKAAVLSGVNSKLTKLWVYAISGILSAVAGLIVTARLDSAQPNAGLMY 259 +FGRYVYA GGNE AA LSGV + K VY +SG+++++AG+I +R SA+P +G Sbjct: 199 RFGRYVYATGGNEVAARLSGVRTARVKFTVYVLSGLIASMAGVIAFSRFVSAEPASGFGA 258 Query: 260 ELDAIAATVIGGASLSGGKGTLIGTVVGALIIGVLNDGLVLVGVSPFWQQVAKGFIIIAA 319 ELD IAA IGGASLSGG G++ G ++GA + G++ +G+VL+ + + QQ G +I+ A Sbjct: 259 ELDVIAAAAIGGASLSGGAGSVEGAIIGAALAGIITNGVVLLNIDTYAQQAITGCVILIA 318 Query: 320 V 320 V Sbjct: 319 V 319 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: 429 Number of extensions: 29 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 331 Length of database: 331 Length adjustment: 28 Effective length of query: 303 Effective length of database: 303 Effective search space: 91809 Effective search space used: 91809 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