Align ABC-type transporter, integral membrane subunit, component of D-ribose porter (Nanavati et al., 2006). Induced by ribose (characterized)
to candidate 3609042 Dshi_2431 Monosaccharide-transporting ATPase (RefSeq)
Query= TCDB::Q9X050 (331 letters) >FitnessBrowser__Dino:3609042 Length = 328 Score = 164 bits (416), Expect = 2e-45 Identities = 96/316 (30%), Positives = 162/316 (51%), Gaps = 16/316 (5%) Query: 14 QRISRYQSIFIL--LGLIVLFSFLSNRFLTLENFWIILRQTAVNLCIAVGMTFVILTGGI 71 QR+ ++++ +L +G+ V SF S FL N IA M +I++G I Sbjct: 18 QRLKSWETLLLLVAIGIFVANSFASPYFLNAWNLSDATFNFTEKAMIAFAMALLIISGEI 77 Query: 72 DLSVGSILGFSGAVTAKLLKYGLILSAFGVVLKFNPLGASIIGVLAGFAIGLFNGFIITR 131 DLSV SI+ + ++ G+ G +IG+ G G FNG ++TR Sbjct: 78 DLSVASIIALASTAMGAAVQMGV-----------GTPGLVLIGLGVGLLCGAFNGVLVTR 126 Query: 132 FNIPPFVATLGTMTAVRGFIMLLTKGHPITRLGDSFDFIGSG--WFLGIPMPVWIAAIAT 189 +P V T+GTM+ RG ++ +SF + G G W++ I + + AI Sbjct: 127 MGLPSIVVTIGTMSLFRGISYIVLGDQAFRGYPESFSWFGQGYVWWV-ISFELVLFAIIA 185 Query: 190 GVGIFILRKTQFGRYVYAVGGNEKAAVLSGVNSKLTKLWVYAISGILSAVAGLIVTARLD 249 + +L KT FGR VYA+G N A+ SG+ + K ++ ++G++S VA + +TARL Sbjct: 186 VIYAMLLHKTNFGRAVYAIGNNATGAMFSGIRVQRVKFILFLLTGLMSGVAAICLTARLG 245 Query: 250 SAQPNAGLMYELDAIAATVIGGASLSGGKGTLIGTVVGALIIGVLNDGLVLVGVSPFWQQ 309 S +P+ + +EL+ + V+GG S+ GG GT++G V+ A ++G++ GL L+ V Sbjct: 246 STRPSIAMGWELEVVTMVVLGGVSILGGSGTILGVVIAAFVMGLVTFGLGLLNVPGIVMS 305 Query: 310 VAKGFIIIAAVIAEKL 325 + G ++I + +L Sbjct: 306 IVIGALLIGVIALPRL 321 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: 416 Number of extensions: 28 Number of successful extensions: 2 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