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 7024900 Shewana3_2074 ABC transporter related (RefSeq)
Query= TCDB::Q8DU37 (510 letters) >FitnessBrowser__ANA3:7024900 Length = 499 Score = 271 bits (692), Expect = 5e-77 Identities = 158/479 (32%), Positives = 270/479 (56%), Gaps = 13/479 (2%) Query: 5 VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64 ++E+++I+K + A + ++L L GE+HALLGENGAGKSTL+ ++ G G I Sbjct: 4 ILELKQISKHYPGVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILF 63 Query: 65 NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKA 124 G ++P + + GI V+Q LV TV +N+ LG E + G++ KK + +A Sbjct: 64 LGEPQHFNTPMDAQKAGISTVYQEVNLVPNLTVAQNLFLGYEPRRLGLIHFKKMYADARA 123 Query: 125 LSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIM 184 + ++ L +D +A ++D S+ QQ + I + + A +L+ DEPTA L E+Q L I+ Sbjct: 124 VLTQFKLDIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGIL 183 Query: 185 KSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSVSF 244 L +G +I+ ITH LD++ ++DR+TV+R G+ I + L E M+GRS+ Sbjct: 184 NQLKAKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQE 243 Query: 245 TI------EKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQS 298 + E+T T+ + +LS++D+ V +I+ ++L V G+ +G+AG+ G+G+S Sbjct: 244 QLVDKQEKERTVTRAEAVLLSLEDVSVK-----GSIQSMNLTVPKGQAVGLAGLLGSGRS 298 Query: 299 ELVQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLA 358 E+ A+ GL + SG + + GQ + + PEDR DG+I L++ EN+ Sbjct: 299 EVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIALCPEDRKIDGIIGPLSIRENII 358 Query: 359 LQTYYKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVD 418 L +A + L+ ++ E + + + + + P + SGGNQQK I+AR + Sbjct: 359 LA--LQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADKPIEQLSGGNQQKVILARWLA 416 Query: 419 RDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHD 477 +P LL++ +PTRG+D+GA I K + DEG ++L+ S ELDE++ S+++ V+ D Sbjct: 417 IEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVASSELDELVAFSNKVVVLRD 475 Score = 80.9 bits (198), Expect = 1e-19 Identities = 61/240 (25%), Positives = 120/240 (50%), Gaps = 8/240 (3%) Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329 G+ A++ +SL + AGE+ + G +G G+S LV+ +TG + G + G+ + Sbjct: 16 GVKALEDVSLRLFAGEVHALLGENGAGKSTLVKVMTGAQSKDMGDILFLGEPQHFNTPMD 75 Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLALQTYYKAPLSHNGVLNYSKINEHGRHLMQEF 389 + + V ++ + L+ LT+A+NL L Y L G++++ K+ R ++ +F Sbjct: 76 AQKAGISTVYQEVN---LVPNLTVAQNLFLG-YEPRRL---GLIHFKKMYADARAVLTQF 128 Query: 390 DVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAER 449 + + P +S QQ IAR V +L++ +PT LD ++ + L + Sbjct: 129 KL-DIDVSAPLSDYSIAVQQLIAIARGVAMSAKVLVLDEPTASLDAKEVQVLFGILNQLK 187 Query: 450 DEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGGSIEREEIN 509 +G A++ ++ LD++ +SDRI V+ +GQ G + +L M G S++ + ++ Sbjct: 188 AKGVAIVFITHFLDQVYQISDRITVLRNGQFIGEYLTAELPQPKLIEAMLGRSLQEQLVD 247 Score = 74.3 bits (181), Expect = 9e-18 Identities = 57/218 (26%), Positives = 109/218 (50%), Gaps = 6/218 (2%) Query: 24 INLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKINGSAVTIDSPSKSAQLGIG 83 +NL + KG+ L G G+G+S + N + GL SGSI + G + + P + GI Sbjct: 277 MNLTVPKGQAVGLAGLLGSGRSEVCNAVFGLDLVDSGSIHLAGQKLNLSQPVDAISAGIA 336 Query: 84 MVHQHFML---VEAFTVTENIILGNEVVKNGILDLKKAGQEIKA--LSEKYGLAV-DPNA 137 + + + + ++ ENIIL + L Q+ A +K +A D + Sbjct: 337 LCPEDRKIDGIIGPLSIRENIILALQARIGWWRYLSNTRQQEIAQFFIDKLQIATPDADK 396 Query: 138 KIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMKSLVKEGKSIILI 197 I +S G QQ+V + + L +L+ DEPT + E++ ++++L EG S+++ Sbjct: 397 PIEQLSGGNQQKVILARWLAIEPILLVLDEPTRGIDIGAHAEIVKLIRTLCDEGMSLLVA 456 Query: 198 THKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAE 235 + +LDE+ + +++V V+R ++ + + TSQ + + Sbjct: 457 SSELDELVAFSNKVVVLRDRYAVRELSGAELTSQHVMQ 494 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: 521 Number of extensions: 19 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 3 Length of query: 510 Length of database: 499 Length adjustment: 34 Effective length of query: 476 Effective length of database: 465 Effective search space: 221340 Effective search space used: 221340 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 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