Align RnsB, component of The (deoxy)ribonucleoside permease; probably takes up all deoxy- and ribonucleosides (cytidine, uridine, adenosine and toxic analogues, fluorocytidine and fluorouridine tested), but not ribose or nucleobases (characterized)
to candidate WP_084935209.1 HA51_RS14055 sugar ABC transporter ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >NCBI__GCF_002095475.1:WP_084935209.1 Length = 494 Score = 304 bits (779), Expect = 4e-87 Identities = 170/494 (34%), Positives = 282/494 (57%), Gaps = 6/494 (1%) Query: 1 MAQHVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSG 60 M +E I+K F A D+++L ++ G +HAL+GENGAGKSTLM L G+ P G Sbjct: 1 MTAFALEAEGISKFFPGVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKG 60 Query: 61 SIKINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQ 120 +I+I G V + + GI M+HQ LV TV ENI LG E +K G +D K + Sbjct: 61 TIRIKGEPVQFQDTMDALRSGISMIHQELNLVPYMTVAENIWLGREPMKYGFVDHGKLNK 120 Query: 121 EIKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQEL 180 + + L + + + + + ++S+ AQQ VEI K + +DI+I DEPT+ LT +E+ L Sbjct: 121 QTQELLNRLNIRLKADRMVGELSIAAQQMVEIAKAVSWNSDIVIMDEPTSALTETEVAHL 180 Query: 181 MTIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGR 240 TI++ L ++GK+II I+HK+DEI ++ D +++ R G + + S T Q L MVGR Sbjct: 181 FTIIRDLREQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSEFTRQSLITQMVGR 240 Query: 241 SVSFTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSEL 300 ++ K + +L++++L + ++ V+ GEI+G+AG+ G G+SE+ Sbjct: 241 ELTQLFPKFNGEIGADVLTVRNLTCKDR-----FTDINFTVRKGEILGVAGLVGAGRSEV 295 Query: 301 VQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQ 360 ++++ G+ SG + I G V S E + + EDR + GL L L++ EN+++ Sbjct: 296 MESLFGMESFDSGEVLIDGVPVKIDSPSTAIEKGMAFLTEDRKKSGLFLVLSVMENMSI- 354 Query: 361 TYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRD 420 +S G +++ K+ + +++ +++ SGGNQQK +IAR + Sbjct: 355 VNMPDYVSKAGFVSHMKMAQDCMEQIRKLNIKTPTMDQIINNLSGGNQQKVLIARWLLAQ 414 Query: 421 PDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQI 480 P +LI+ +PTRG+DVGA I++ + + G A+++VS EL EIL +SDR+ V+H G+I Sbjct: 415 PKILILDEPTRGIDVGAKAEIYRLISELANRGVAIIMVSSELPEILGMSDRVMVMHGGRI 474 Query: 481 QGIVTPETTNKQEL 494 GI+ E N++ + Sbjct: 475 TGILDKEEANQETI 488 Score = 91.3 bits (225), Expect = 7e-23 Identities = 58/231 (25%), Positives = 119/231 (51%), Gaps = 8/231 (3%) Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329 G+ A+ +SL +K G + + G +G G+S L++ + G+ + G + IKG+ V T Sbjct: 17 GVKALDNVSLRIKPGSVHALMGENGAGKSTLMKCLIGMYRPDKGTIRIKGEPVQFQDTMD 76 Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEF 389 + + ++ + L+ +T+AEN+ L + P+ + G +++ K+N+ + L+ Sbjct: 77 ALRSGISMIHQELN---LVPYMTVAENIWLG---REPMKY-GFVDHGKLNKQTQELLNRL 129 Query: 390 DVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAER 449 ++R + + + S QQ IA+ V + D++I+ +PT L + ++ + R Sbjct: 130 NIRLKADRMVGE-LSIAAQQMVEIAKAVSWNSDIVIMDEPTSALTETEVAHLFTIIRDLR 188 Query: 450 DEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAG 500 ++GKA++ +S ++DEI ++D I++ DG G +Q L M G Sbjct: 189 EQGKAIIYISHKMDEIFTITDEISIFRDGTWVGSNNTSEFTRQSLITQMVG 239 Lambda K H 0.315 0.135 0.363 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: 573 Number of extensions: 32 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 510 Length of database: 494 Length adjustment: 34 Effective length of query: 476 Effective length of database: 460 Effective search space: 218960 Effective search space used: 218960 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: 42 (22.0 bits) S2: 52 (24.6 bits)
This GapMind analysis is from Sep 24 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