Align GguB aka ATU2346 aka AGR_C_4262, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate HSERO_RS05325 HSERO_RS05325 ribose ABC transporter permease
Query= TCDB::O05177 (398 letters) >FitnessBrowser__HerbieS:HSERO_RS05325 Length = 328 Score = 139 bits (349), Expect = 2e-37 Identities = 101/338 (29%), Positives = 163/338 (48%), Gaps = 71/338 (21%) Query: 53 NLTNLILQNSFIVIMALGMLLVIVAGHIDLSVGSIVAFVGAIAAILTVQWGMNPFLAALI 112 N N++ Q S + I+A+GM VI+ G IDLSVG+ Sbjct: 55 NWFNVLRQVSIVGILAVGMSFVILTGGIDLSVGA-------------------------- 88 Query: 113 CLVIGGIIGAAQGYWIAYHRIPSFIVTLAGMLVFRGLTLFVLGGKNIGPFPTDFQVISTG 172 + + G I A G++V GL P P + G Sbjct: 89 AMALAGTISA-------------------GLIVNSGL-----------PAPLAL-LCGVG 117 Query: 173 FLPDIGGIEG-LNTTSMILTVLITVALFYLAWRRRVVNVKHGIDVEPFGFFIVQNLLISG 231 IG + G L + +++T+A + V G+ + G + + L G Sbjct: 118 LATCIGLLNGALVAWGRMPAIIVTLA---------TMGVARGVGLIYSGGYPISGL--PG 166 Query: 232 AILFLGYQLSTYRGLPNVLIVMLVLIALYSFVTRRTTIGRRVYAMGGNEKATKLSGINTE 291 I + G + +P +I+ML++ AL + +RT GR VYA+GGNE A +LSG+ T Sbjct: 167 WISWFG--VGRIGMVPVPVILMLIVYALAWLLLQRTAFGRHVYAIGGNEMAARLSGVKTT 224 Query: 292 RLSFLTFVNMGVLAGLAGMIIATRLNSATPKAGVGFELDVIAACFIGGASASGGVGKITG 351 R+ + G +GLA +I+ RL S P AGVGFELD IAA +GG + +GG G + G Sbjct: 225 RIKLAVYAISGFTSGLAAIILTGRLMSGQPNAGVGFELDAIAAVVLGGTAIAGGRGLVVG 284 Query: 352 AVIGAFIMGVMNNGMSIVGLGIDFQQMVKGLVLLAAVF 389 +IGA ++G++NNG++++G+ Q +++G+++L A++ Sbjct: 285 TLIGAVLLGILNNGLNLMGINPYLQDIIRGVIILLAIY 322 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: 455 Number of extensions: 29 Number of successful extensions: 2 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: 328 Length adjustment: 29 Effective length of query: 369 Effective length of database: 299 Effective search space: 110331 Effective search space used: 110331 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