Align deoxynucleoside transporter, ATPase component (characterized)
to candidate BWI76_RS07240 BWI76_RS07240 D-ribose transporter ATP-binding protein
Query= reanno::Burk376:H281DRAFT_01113 (515 letters) >FitnessBrowser__Koxy:BWI76_RS07240 Length = 494 Score = 333 bits (854), Expect = 9e-96 Identities = 179/478 (37%), Positives = 289/478 (60%), Gaps = 8/478 (1%) Query: 16 LEVVGVHKRFTGVHALRGVSLSFQRGQIYHLLGENGCGKSTLIKIISGAQPPDEGQLVIE 75 LE G+ K F GV AL VSL + G ++ L+GENG GKSTL+K + G PD+G + ++ Sbjct: 6 LEAEGISKFFPGVKALDNVSLRVRPGTVHALMGENGAGKSTLMKCLIGIYRPDKGAIRVK 65 Query: 76 GVPHARLSALEALAAGIETVYQDLSLLPNMSVAENVALTSELATHEGRLARTFDRRVLAA 135 G P ++AL +GI ++Q+L+L+P+M+VAEN+ L E + D R LA Sbjct: 66 GEPVQFQDTMDALRSGISMIHQELNLVPHMTVAENIWLGREPMKYG-----FVDHRQLAR 120 Query: 136 TAARALEAVGLPGNSEFQSTLIEQLPLATRQLVAIARAIASEAKFVIMDEPTTSLTQKEV 195 L+ + + +++ L+ +L +A++Q+V IA+A++ A VIMDEPT++LT+ EV Sbjct: 121 QTQDLLDKLNIRLSAD---RLVGELSIASQQMVEIAKAVSWNADIVIMDEPTSALTESEV 177 Query: 196 DNLIAVLANLRAQGVTVLFVSHKLDECYAIGGEVIVLRDGQKMAQGPIAEFTKAQISELM 255 +L ++ +LR QG ++++SHK+DE +AI E+ V RDG + EFT+ + M Sbjct: 178 AHLFTIIRDLRQQGKAIIYISHKMDEIFAITDEISVFRDGTWVGSKQTTEFTRQSLITQM 237 Query: 256 TGRHLSNERYRESAHAQDIVLDVRGFTRAGQFSDVSFKLHGGEILGVTGLLDSGRNELAR 315 GR L+ + + + VL VR +R G F D++F + GEILGV GL+ +GR+E+ Sbjct: 238 VGRELTQLFPKFNNAIGEEVLTVRNLSRKGAFHDINFSVRRGEILGVAGLVGAGRSEVME 297 Query: 316 ALAGVAPAQSGDVLLDGQQIALRTPSDAKRHRIGYVPEDRLNEGLFLDKPIRDNVITAMI 375 +L G+ A SG+VL+DG + + +PS A + + EDR GLFL + +N+ + Sbjct: 298 SLFGMEKADSGEVLIDGMPVNIDSPSTAIEKGMALLTEDRKKSGLFLVLSVLENMSIVKM 357 Query: 376 SSLRDRFGQIDRTRAQALAEQTVKELQIATPGVDKPVQSLSGGNQQRVLIGRWLAIDPRV 435 + G + + + ++ L I TP +D+ + +LSGGNQQ+VLI RWL P++ Sbjct: 358 PEYIGKTGFVQHLKMAEDCMEQIRRLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQPKI 417 Query: 436 LILHGPTVGVDVGSKDIIYRIMQRLSQRGIGIILISDDLPELLQNCDRILMMKKGHVS 493 LIL PT G+DVG+K IY ++ L+ RG+ +I++S +LPE+L DR+++M +G ++ Sbjct: 418 LILDEPTRGIDVGAKAEIYHLISELANRGVAVIMVSSELPEILGMSDRVMVMHEGRIT 475 Lambda K H 0.319 0.135 0.376 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: 575 Number of extensions: 24 Number of successful extensions: 5 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: 515 Length of database: 494 Length adjustment: 34 Effective length of query: 481 Effective length of database: 460 Effective search space: 221260 Effective search space used: 221260 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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