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_078716498.1 B5D49_RS04560 ABC transporter ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >NCBI__GCF_900167125.1:WP_078716498.1 Length = 514 Score = 342 bits (877), Expect = 2e-98 Identities = 194/498 (38%), Positives = 305/498 (61%), Gaps = 13/498 (2%) Query: 5 VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64 ++ ++ +TK+F VAND I+L++ G + ALLGENGAGKSTLM+MLAG +P +G+I + Sbjct: 24 LVSIKGLTKRFGKVVANDDISLNIYPGRVKALLGENGAGKSTLMSMLAGRYQPDAGTIAL 83 Query: 65 NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKA 124 +G V S + + GIGMV+QHFMLVE+ TV EN++LG E + L+ K+ ++ Sbjct: 84 DGKPVRFSSARDAIEAGIGMVYQHFMLVESMTVAENVLLGQE--GSFFLNPKEMRNRVQE 141 Query: 125 LSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIM 184 LS +YGL +DP A+++D+S+G +QRVEILK LYR + +LIFDEPTAVLTP E L + Sbjct: 142 LSVRYGLDIDPAARVSDLSMGEKQRVEILKLLYRDSRVLIFDEPTAVLTPRETFHLFEAL 201 Query: 185 KSLVKEGKSIILITHKLDEIRSVADRVTVIRRGK-SIETVEVSGTTSQDLAEMMVGRSVS 243 + ++GKSI+ I+HKL+E+ +VAD + ++R+G+ E E T+ DLA MVG+ V Sbjct: 202 WKIAEQGKSIVFISHKLEEVLAVADEIAILRQGRIEGEFSESEVTSKADLACRMVGKEVL 261 Query: 244 FTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQA 303 +++ + +L +++L GI ++ ++ ++ GE++ + G+ GNGQ LV+A Sbjct: 262 LEVDREAMPHGDAVLQVRNLT-----GI-GLEDITFDLHQGEVVAVVGVAGNGQKALVEA 315 Query: 304 ITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYY 363 I GLRK + I G+ + + S+ ++PEDR L + +NL L T Sbjct: 316 ICGLRKPPVDTMFIMGKRWRDFYAKPSWKNSLAYIPEDRLGLATCRNLNLVDNLLLTT-- 373 Query: 364 KAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDL 423 + + L+ K L+++FD+R A SGGN QK+++ARE+ R P L Sbjct: 374 RQGFARGPWLDKKKAARDTTELIKKFDIRPGRIAALAWQLSGGNLQKSVLARELYRCPRL 433 Query: 424 LIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGI 483 ++ QPT+GLD+ A E + L+A R E +LLV+ +L+E L L+DR+AVI+ G+ + Sbjct: 434 IVAEQPTQGLDIAATEQVWNHLLAAR-EMAGILLVTGDLNEALQLADRVAVIYRGRFMDV 492 Query: 484 VTPETTNK-QELGILMAG 500 + K +G++MAG Sbjct: 493 FSVSDKQKVNRIGLMMAG 510 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: 554 Number of extensions: 28 Number of successful extensions: 8 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: 510 Length of database: 514 Length adjustment: 35 Effective length of query: 475 Effective length of database: 479 Effective search space: 227525 Effective search space used: 227525 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 Apr 09 2024. 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