Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate HSERO_RS05250 HSERO_RS05250 D-ribose transporter ATP binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__HerbieS:HSERO_RS05250 Length = 520 Score = 370 bits (951), Expect = e-107 Identities = 207/502 (41%), Positives = 316/502 (62%), Gaps = 18/502 (3%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 ++ +RN+ K FPGV AL+N ++ GE+HAL+GENGAGKSTLMK+LSGVY + G+I Sbjct: 22 VIALRNVCKRFPGVLALDNCQFELAAGEVHALMGENGAGKSTLMKILSGVYQRDS--GDI 79 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVA-SNGVISWQQTFNR 123 +G ++ +GI IIHQEL L+ LS A+NIF+G E + G+ + NR Sbjct: 80 LLDGKPVEITEPRQAQALGIGIIHQELNLMNHLSAAQNIFIGREPRKAMGLFIDEDELNR 139 Query: 124 -TRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEAL 182 + ++ L P T + ++ V +QQ+VEIAKALS ++LI+DEPTA+LN ++ L Sbjct: 140 QAAAIFARMRLDMDPSTPVGELTVARQQMVEIAKALSFDSRVLIMDEPTAALNNAEIAEL 199 Query: 183 LNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMV 242 ++ + + QG+ + I+HK++E+R++AD+++V+RDG + T+ +E S D II MV Sbjct: 200 FRIIRDLQAQGVGIVYISHKMDELRQIADRVSVMRDGKYIATVP--MQETSMDTIISMMV 257 Query: 243 GRDL--EDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMG 300 GR L E R PP D + +LEV+ N + + D++ T+RKGE++G AGLMG Sbjct: 258 GRALDGEQRIPP-DTSRNDVVLEVRGLNR-------GRAIRDVSFTLRKGEILGFAGLMG 309 Query: 301 AGRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDN 360 AGRTE A ++FG G+++I G + + A+ G+ Y++EDRKH GL + + Sbjct: 310 AGRTEVARAIFGADPLE--AGEIIIHGGKAVIKSPADAVAHGIGYLSEDRKHFGLAVGMD 367 Query: 361 ILHNTTLANLAGVSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 + N L+++ ++ +D + A + +L I++ + Q+ LSGGNQQK+V++ Sbjct: 368 VQANIALSSMGRFTRVGFMDQRAIREAAQMYVRQLAIKTPSVEQQARLLSGGNQQKIVIA 427 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 KWL + D+L DEPTRGIDVGAK EIY +++ LA GK ++MISSE+PE+L R+ V Sbjct: 428 KWLLRDCDILFFDEPTRGIDVGAKSEIYKLLDALAEQGKAIVMISSELPEVLRMSHRVLV 487 Query: 481 MNEGRIVAELPKGEASQESIMR 502 M EGRI EL + +A+QE IM+ Sbjct: 488 MCEGRITGELARADATQEKIMQ 509 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: 618 Number of extensions: 30 Number of successful extensions: 9 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: 520 Length adjustment: 35 Effective length of query: 477 Effective length of database: 485 Effective search space: 231345 Effective search space used: 231345 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