Align GguA aka ATU2347 aka AGR_C_4264, component of Multiple sugar (arabinose, xylose, galactose, glucose, fucose) putative porter (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein
Query= TCDB::O05176 (512 letters) >FitnessBrowser__Koxy:BWI76_RS07240 Length = 494 Score = 396 bits (1018), Expect = e-115 Identities = 217/497 (43%), Positives = 323/497 (64%), Gaps = 14/497 (2%) Query: 6 LEMRNITKTFPGVKALENVNLKVKEGEIHALVGENGAGKSTLMKVLSGVYPAGTYEGEIH 65 LE I+K FPGVKAL+NV+L+V+ G +HAL+GENGAGKSTLMK L G+Y +G I Sbjct: 6 LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPD--KGAIR 63 Query: 66 YEGAVRNFRAINDSEDIGIIIIHQELALVPLLSIAENIFLGNEVASNGVISWQQTFNRTR 125 +G F+ D+ GI +IHQEL LVP +++AENI+LG E G + +Q +T+ Sbjct: 64 VKGEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYGFVDHRQLARQTQ 123 Query: 126 ELLKKVGLKESPETLITDIGVGKQQLVEIAKALSKSVKLLILDEPTASLNESDSEALLNL 185 +LL K+ ++ S + L+ ++ + QQ+VEIAKA+S + ++I+DEPT++L ES+ L + Sbjct: 124 DLLDKLNIRLSADRLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEVAHLFTI 183 Query: 186 LMEFRNQGMTSIIITHKLNEVRKVADQITVLRDGMTVKTLDCHQEEISEDVIIRNMVGRD 245 + + R QG I I+HK++E+ + D+I+V RDG V + E + +I MVGR+ Sbjct: 184 IRDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQT--TEFTRQSLITQMVGRE 241 Query: 246 LEDRYPPRDVPIGETILEVKNWNAYHQQHRDRQVLHDINVTVRKGEVVGIAGLMGAGRTE 305 L +P + IGE +L V+N + + HDIN +VR+GE++G+AGL+GAGR+E Sbjct: 242 LTQLFPKFNNAIGEEVLTVRNLSR-------KGAFHDINFSVRRGEILGVAGLVGAGRSE 294 Query: 306 FAMSVFGKSYGHRITGDVLIDGKPVDVSTVRKAIDAGLAYVTEDRKHLGLVLNDNILHNT 365 S+FG +G+VLIDG PV++ + AI+ G+A +TEDRK GL L ++L N Sbjct: 295 VMESLFGMEKAD--SGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENM 352 Query: 366 TLANLAG-VSKASIIDDIKEMKVASDFRTRLRIRSSGIFQETVNLSGGNQQKVVLSKWLF 424 ++ + + K + +K + + RL I++ + Q NLSGGNQQKV++++WL Sbjct: 353 SIVKMPEYIGKTGFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLL 412 Query: 425 SNPDVLILDEPTRGIDVGAKYEIYTIINQLAADGKGVLMISSEMPELLGNCDRIYVMNEG 484 + P +LILDEPTRGIDVGAK EIY +I++LA G V+M+SSE+PE+LG DR+ VM+EG Sbjct: 413 AQPKILILDEPTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEG 472 Query: 485 RIVAELPKGEASQESIM 501 RI L K +A QE+I+ Sbjct: 473 RITGILDKEDADQETIL 489 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: 667 Number of extensions: 38 Number of successful extensions: 10 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: 494 Length adjustment: 34 Effective length of query: 478 Effective length of database: 460 Effective search space: 219880 Effective search space used: 219880 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