Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate BPHYT_RS20740 BPHYT_RS20740 D-ribose transporter ATP binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__BFirm:BPHYT_RS20740 Length = 503 Score = 366 bits (940), Expect = e-106 Identities = 210/502 (41%), Positives = 317/502 (63%), Gaps = 17/502 (3%) Query: 5 ILEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEI 64 ++ ++ ++K FPGV+AL V ++ GE+HAL+GENGAGKSTLMK+L+GVY T GEI Sbjct: 4 LISVKRLSKRFPGVRALHEVQFELVAGEVHALMGENGAGKSTLMKILAGVYTRDT--GEI 61 Query: 65 HYEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASN-GVISWQQTFN- 122 YEG +F++ +++ +G+ IIHQEL L+ L+IA+N+F+G E G+ + N Sbjct: 62 LYEGQPVDFQSPREAQAVGVGIIHQELQLMNHLTIAQNMFIGREPRGRLGLFLDEDKLNA 121 Query: 123 RTRELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEAL 182 + ++L ++ + P L++ + V +QQ+VEIAKALS ++LI+DEPT++LN+++ L Sbjct: 122 QAHDILARMHVTLDPRALVSSLTVARQQMVEIAKALSFDSRVLIMDEPTSALNDAEIAEL 181 Query: 183 LNLLMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMV 242 ++ + + +G+ I I+HK++E++++AD++TVLRDG V T+ ++ + II MV Sbjct: 182 FRIIRDLKKRGVGIIYISHKMDELKQIADRVTVLRDGEYVATVAV--KDTTVQAIIGMMV 239 Query: 243 GRDLEDRYPPRDVPI-GETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGA 301 GR L D P + + GE LEV NA ++ D++ +RKGE++G AGLMGA Sbjct: 240 GRTLTDAAPSQHIANQGEVALEVTRLNA-------GPLVRDVSFALRKGEILGFAGLMGA 292 Query: 302 GRTEFAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNI 361 GRTE A +VFG +G++++ G + A+ G+ Y++EDRK GL ++ Sbjct: 293 GRTEVARAVFGADPIE--SGEIVVKGVKATIRNPSDAVARGIGYLSEDRKRFGLATGMSV 350 Query: 362 LHNTTLANLAG-VSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLS 420 N ++NL +S + + K A+ F L IR+ QE LSGGNQQK+V++ Sbjct: 351 ESNIVMSNLRKFLSLNFFLRRTQIRKTAAHFINLLAIRTPSATQEVRLLSGGNQQKIVIA 410 Query: 421 KWLFSNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYV 480 KWL + DVL DEPTRGIDVGAK EIY ++ LA GK ++MISSE+PE+L DRI V Sbjct: 411 KWLERDCDVLFFDEPTRGIDVGAKSEIYKLLRSLADQGKAIVMISSELPEILRMSDRIVV 470 Query: 481 MNEGRIVAELPKGEASQESIMR 502 M EGRI EL A+QE IM+ Sbjct: 471 MCEGRITGELAAAGATQERIMQ 492 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: 598 Number of extensions: 27 Number of successful extensions: 11 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: 503 Length adjustment: 34 Effective length of query: 478 Effective length of database: 469 Effective search space: 224182 Effective search space used: 224182 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