Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate RR42_RS03365 RR42_RS03365 ribose ABC transporter permease
Query= TCDB::O05177 (398 letters) >FitnessBrowser__Cup4G11:RR42_RS03365 Length = 333 Score = 147 bits (371), Expect = 4e-40 Identities = 112/378 (29%), Positives = 183/378 (48%), Gaps = 76/378 (20%) Query: 21 RSNIREYGMLIALVAIMVFFQFYTGGILFRPVNLTNLILQNSFIVIMALGMLLVIVAGHI 80 + +R GML LV + + F T NL+ + Q S +++A GM VI+ G I Sbjct: 23 QERLRALGMLPVLVLLCIGFSVLTENFAGWQ-NLSIIAQQASINMVLAAGMTFVILTGGI 81 Query: 81 DLSVGSIVAFVGAIAAILTV--QWGMNPFLAALICLVIGGIIGAAQGYWIAYHRIPSFIV 138 DLSVGSI++ +A ++++ Q GM AAL+C ++ GI+ A +A+ ++P Sbjct: 82 DLSVGSILSISAVVAMLVSLMPQLGMLSVPAALLCGLLFGIVNGAL---VAFMKLP---- 134 Query: 139 TLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTGFLPDIGGIEGLNTTSMILTVLITVAL 198 PF +++ G L + G+ Sbjct: 135 ----------------------PF-----IVTLGTLTAVRGLA----------------- 150 Query: 199 FYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISGAILFLGYQLSTYRGLPNVLIVMLVLIA 258 R+V I GF + N G +L G+P ++I+ ++A Sbjct: 151 -------RLVGNDSTIYNPDIGFAFIGN----GEVL----------GVPWLVIIAFAVVA 189 Query: 259 LYSFVTRRTTIGRRVYAMGGNEKATKLSGINTERLSFLTFVNMGVLAGLAGMIIATRLNS 318 + FV RRT +G ++YA+GGN +A +LSGI + + G+LAGL G++ + RL + Sbjct: 190 VSWFVLRRTVLGLQIYAVGGNAEAARLSGIKVWVVLLFVYAVSGLLAGLGGVMSSARLYA 249 Query: 319 ATP-KAGVGFELDVIAACFIGGASASGGVGKITGAVIGAFIMGVMNNGMSIVGLGIDFQQ 377 A + G +ELD IAA +GG S GG G I G ++GA I+ V++NG+ ++G+ +Q Sbjct: 250 ANGLQLGQSYELDAIAAVILGGTSFVGGTGSIVGTLVGALIIAVLSNGLVLLGVSDIWQY 309 Query: 378 MVKGLVLLAAVFFDVYNK 395 ++KGLV++ AV D Y + Sbjct: 310 IIKGLVIIGAVALDSYRR 327 Lambda K H 0.329 0.145 0.422 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: 476 Number of extensions: 29 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 398 Length of database: 333 Length adjustment: 29 Effective length of query: 369 Effective length of database: 304 Effective search space: 112176 Effective search space used: 112176 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 (21.8 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