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 BWI76_RS27035 BWI76_RS27035 xylose ABC transporter ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >FitnessBrowser__Koxy:BWI76_RS27035 Length = 513 Score = 287 bits (735), Expect = 6e-82 Identities = 173/489 (35%), Positives = 280/489 (57%), Gaps = 20/489 (4%) Query: 5 VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTS--GSI 62 ++EM+ ITK F A D+++L L GE+ +L GENG+GKSTLM +L G+ S G I Sbjct: 4 LLEMKNITKTFGAVKAIDNVSLRLNAGEVVSLCGENGSGKSTLMKVLCGIYPHGSYEGEI 63 Query: 63 KINGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEI 122 +G + + + GI ++HQ LV+ TV ENI LG E+ ++G+LD + Sbjct: 64 IFSGETLQPGHIRDTERKGIAIIHQELALVKHLTVLENIFLGAEISRHGLLDYETMTLRC 123 Query: 123 KALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMT 182 + L + LA+ P+ ++ D+ +G QQ VEI K L + +LI DEPTA LT E L+ Sbjct: 124 EKLLAQVNLAISPDTRVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETAILLN 183 Query: 183 IMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSV 242 I++ L G + I I+HKL+E+++++D + VIR G+ I T G + D+ MMVGR + Sbjct: 184 IIRDLQNHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRNADGMSEDDIITMMVGREL 243 Query: 243 SFTIEKTPTKPKETILSIKDLVV--NENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSEL 300 + + IL +++L NR I + +S ++ GEI+GIAG+ G G++E Sbjct: 244 TALYPSEAHSCGDEILRVENLTAWHPVNRHIKRVNDVSFSLRRGEILGIAGLVGAGRTEA 303 Query: 301 VQAITGLRKIK-SGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAEN--L 357 VQ + G+ + G + I GQ VT + ++ + VPEDR +DG++ + + +N L Sbjct: 304 VQCLFGVWPGRWQGKIFIDGQPVTIHTCQQAIAQGIAMVPEDRKKDGIVPVMAVGKNITL 363 Query: 358 ALQTYYKAPLSHNGVLNYSKINEHGRHL-----MQEFDVRGANELIPAKGFSGGNQQKAI 412 A + PL S +++ G L +Q ++ ++ + SGGNQQKAI Sbjct: 364 AALNQFTGPL--------SSLDDAGEQLCIQQSIQRLKIKTSSPELAIGRLSGGNQQKAI 415 Query: 413 IAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRI 472 +AR + +P +LI+ +PTRG+D+GA I+K + +G AV+++S EL E+L LSDR+ Sbjct: 416 LARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVIVISSELPEVLGLSDRV 475 Query: 473 AVIHDGQIQ 481 V+H+G+++ Sbjct: 476 LVMHEGKLK 484 Score = 78.6 bits (192), Expect = 5e-19 Identities = 64/220 (29%), Positives = 105/220 (47%), Gaps = 8/220 (3%) Query: 24 INLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPT-SGSIKINGSAVTIDSPSKSAQLGI 82 ++ LR+GEI + G GAG++ + L G+ G I I+G VTI + ++ GI Sbjct: 280 VSFSLRRGEILGIAGLVGAGRTEAVQCLFGVWPGRWQGKIFIDGQPVTIHTCQQAIAQGI 339 Query: 83 GMVHQHFM---LVEAFTVTENIILGNEVVKNGILD-LKKAGQEIKALSEKYGLAV---DP 135 MV + +V V +NI L G L L AG+++ L + P Sbjct: 340 AMVPEDRKKDGIVPVMAVGKNITLAALNQFTGPLSSLDDAGEQLCIQQSIQRLKIKTSSP 399 Query: 136 NAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMKSLVKEGKSII 195 I +S G QQ+ + + L ILI DEPT + E+ ++ LV++G ++I Sbjct: 400 ELAIGRLSGGNQQKAILARCLLLNPRILILDEPTRGIDIGAKYEIYKLINQLVQQGIAVI 459 Query: 196 LITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAE 235 +I+ +L E+ ++DRV V+ GK + G T + + E Sbjct: 460 VISSELPEVLGLSDRVLVMHEGKLKANLINQGLTQEQVME 499 Score = 73.6 bits (179), Expect = 2e-17 Identities = 60/236 (25%), Positives = 118/236 (50%), Gaps = 18/236 (7%) Query: 271 IPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRKI 330 + AI +SL + AGE++ + G +G+G+S L++ + G+ H + +G+ + T Sbjct: 17 VKAIDNVSLRLNAGEVVSLCGENGSGKSTLMKVLCGIYP----HGSYEGEIIFSGET--- 69 Query: 331 TELSVGHVPEDRHRDGLIL---ELTMAENLAL--QTYYKAPLSHNGVLNYSKINEHGRHL 385 L GH+ D R G+ + EL + ++L + + A +S +G+L+Y + L Sbjct: 70 --LQPGHI-RDTERKGIAIIHQELALVKHLTVLENIFLGAEISRHGLLDYETMTLRCEKL 126 Query: 386 MQEFDVRGANELIPAKGFSG-GNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKR 444 + + ++ + + G G G QQ IA+ +++ LLI+ +PT L + Sbjct: 127 LAQVNLAISPDT--RVGDLGLGQQQLVEIAKALNKQVRLLILDEPTASLTEQETAILLNI 184 Query: 445 LIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAG 500 + ++ G A + +S +L+E+ +SD I VI DGQ G + ++ ++ +M G Sbjct: 185 IRDLQNHGIACIYISHKLNEVKAISDTICVIRDGQHIGTRNADGMSEDDIITMMVG 240 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: 567 Number of extensions: 29 Number of successful extensions: 9 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: 513 Length adjustment: 35 Effective length of query: 475 Effective length of database: 478 Effective search space: 227050 Effective search space used: 227050 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