Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate GFF2332 PS417_11890 D-ribose transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__WCS417:GFF2332 Length = 517 Score = 366 bits (939), Expect = e-105 Identities = 205/499 (41%), Positives = 314/499 (62%), Gaps = 14/499 (2%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 +LE+ NI+K FPGV AL +V L+V+ G + AL+GENGAGKSTLMK+++G+Y GEI Sbjct: 23 LLEIVNISKGFPGVVALADVQLRVRPGTVLALMGENGAGKSTLMKIIAGIYQPDA--GEI 80 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNE-VASNGVISWQQTFNR 123 G F ++ GI +IHQEL L+P +SIAENI++G E + S +++ ++ Sbjct: 81 RLRGKPIVFETPLAAQKAGIAMIHQELNLMPHMSIAENIWIGREQLNSLHMVNHREMHRC 140 Query: 124 TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALL 183 T ELL ++ + PE + ++ + ++Q+VEIAKA+S +LI+DEPT+++ E + L Sbjct: 141 TAELLARLRINLDPEEQVGNLSIAERQMVEIAKAVSYDSDILIMDEPTSAITEKEVAHLF 200 Query: 184 NLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVG 243 +++ + ++QG + ITHK+NEV +AD++ V RDG + + ++ D +I MVG Sbjct: 201 SIIADLKSQGKGIVYITHKMNEVFAIADEVAVFRDGHYIGLQ--RADSMNSDSLISMMVG 258 Query: 244 RDLEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGR 303 R+L +P R+ PIG+ +L V++ V D++ + GE++GIAGLMG+GR Sbjct: 259 RELSQLFPLRETPIGDLLLTVRDLTL-------DGVFKDVSFDLHAGEILGIAGLMGSGR 311 Query: 304 TEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILH 363 T A ++FG + +G + +DGK V +S AI+ G A +TEDRK GL ++L Sbjct: 312 TNVAETIFGITPSS--SGQITLDGKAVRISDPHMAIEKGFALLTEDRKLSGLFPCLSVLE 369 Query: 364 NTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWL 423 N +A L + I + D +LR+++ + Q LSGGNQQK +L++WL Sbjct: 370 NMEMAVLPHYTGNGFIQQKALRALCEDMCKKLRVKTPSLEQCIDTLSGGNQQKALLARWL 429 Query: 424 FSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNE 483 +NP +LILDEPTRGIDVGAK EIY +I LA++G V+MISSE+PE+LG DR+ VM+E Sbjct: 430 MTNPRLLILDEPTRGIDVGAKAEIYRLIAFLASEGMAVIMISSELPEVLGMSDRVMVMHE 489 Query: 484 GRIVAELPKGEASQESIMR 502 G ++ L + EA+QE +M+ Sbjct: 490 GELMGTLDRSEATQEKVMQ 508 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: 619 Number of extensions: 47 Number of successful extensions: 11 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: 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 Apr 09 2024. 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