Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate AO356_23205 AO356_23205 D-ribose transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_23205 Length = 517 Score = 363 bits (932), Expect = e-105 Identities = 202/499 (40%), Positives = 312/499 (62%), Gaps = 14/499 (2%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +LE+ N++K FPGV AL +V L+V+ G + AL+GENGAGKSTLMK+++G+Y GE+ Sbjct: 26 LLEVVNVSKGFPGVVALSDVQLRVRPGSVLALMGENGAGKSTLMKIIAGIYQPDA--GEL 83 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFNR 123 G F + GI +IHQEL L+P +SIAENI++G E + ++ + Sbjct: 84 RLRGKPVTFDTPLAALQAGIAMIHQELNLMPHMSIAENIWIGREQLNGLHMVDHGEMHRC 143 Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183 T LL+++ +K PE + ++ + ++Q+VEIAKA+S +LI+DEPT+++ E++ L Sbjct: 144 TARLLERLRIKLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITETEVAHLF 203 Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243 +++ + ++QG I ITHK+NEV +AD++ V RDG + + + D +I MVG Sbjct: 204 SIIADLKSQGKGIIYITHKMNEVFAIADEVAVFRDGAYIGLQ--RADSMDGDSLISMMVG 261 Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303 R+L +P R+ PIGE +L V++ + + ++ + GE++GIAGLMG+GR Sbjct: 262 RELSQLFPVREQPIGELVLSVRDLSL-------DGIFKGVSFDLHAGEILGIAGLMGSGR 314 Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363 T A ++FG + G++ +DG+PV +S AI+ G A +TEDRK GL ++L Sbjct: 315 TNVAEAIFGVTPS--TGGEIRLDGQPVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLE 372 Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423 N +A L I + D +LR+++ + Q LSGGNQQK +L++WL Sbjct: 373 NMEMAVLPHYVGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWL 432 Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483 +NP +LILDEPTRGIDVGAK EIY +I+ LA++G V+MISSE+PE+LG DR+ VM+E Sbjct: 433 MTNPRILILDEPTRGIDVGAKAEIYRLISYLASEGMAVIMISSELPEVLGMSDRVMVMHE 492 Query: 484 GRIVAELPKGEASQESIMR 502 G ++ L + EA+QE +M+ Sbjct: 493 GDLMGTLDRSEATQERVMQ 511 Lambda K H 0.316 0.135 0.374 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: 602 Number of extensions: 37 Number of successful extensions: 10 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: 512 Length of database: 517 Length adjustment: 35 Effective length of query: 477 Effective length of database: 482 Effective search space: 229914 Effective search space used: 229914 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 52 (24.6 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