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_078427103.1 BK574_RS00955 ABC transporter ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >NCBI__GCF_002019605.1:WP_078427103.1 Length = 509 Score = 630 bits (1625), Expect = 0.0 Identities = 315/503 (62%), Positives = 398/503 (79%) Query: 4 HVIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIK 63 +VIEM++I K+F VAND++ L +++GEIHALLGENGAGKSTLMN+L GL +P G I Sbjct: 3 YVIEMKDIRKEFPGIVANDNVTLQVKQGEIHALLGENGAGKSTLMNVLFGLYQPEKGEIL 62 Query: 64 INGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIK 123 + G V I P+ + +LGIGMVHQHFMLVE FTVTENIILG E G +++KKA + ++ Sbjct: 63 VKGKPVKITDPNVANRLGIGMVHQHFMLVEKFTVTENIILGKEPTAGGKINIKKAAKAVE 122 Query: 124 ALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTI 183 +S++YGLAVDP AKI DISVG QQRVEILKTLYRGA+ILIFDEPTA LTP EI EL+ I Sbjct: 123 TISKQYGLAVDPYAKIQDISVGMQQRVEILKTLYRGAEILIFDEPTAALTPQEITELIQI 182 Query: 184 MKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSVS 243 MK LV EGKSIILITHKL EI V DR TVIRRG+ I TV++S +T LA MMVGR V+ Sbjct: 183 MKKLVSEGKSIILITHKLKEIMEVCDRCTVIRRGRGIGTVDISESTPDSLAAMMVGREVN 242 Query: 244 FTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQA 303 F++EK P +PK+ +L IKDLVV ++R I A+ L LEV AGEI+G+AG+DGNGQ+EL++A Sbjct: 243 FSVEKDPAQPKDAVLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEA 302 Query: 304 ITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYY 363 ITGLRK G++ + GQD+T L+ RKIT VGH+P+DRH+ GL+L+ T+ EN+ LQTYY Sbjct: 303 ITGLRKPTGGNIQLNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLDFTVGENIVLQTYY 362 Query: 364 KAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDL 423 + P S +GVLN+++I + L++++DVR +E A+ SGGNQQKAIIAREVDR PDL Sbjct: 363 QKPYSTSGVLNFNEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDL 422 Query: 424 LIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGI 483 LI +QPTRGLDVGAIE IH RL+ ERD+GKAVLL+S ELDE+LN+SDRIAVI++G+I I Sbjct: 423 LIAAQPTRGLDVGAIESIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAI 482 Query: 484 VTPETTNKQELGILMAGGSIERE 506 V + TN+ ELG+LMAGGS ++E Sbjct: 483 VDADKTNENELGLLMAGGSAKKE 505 Score = 115 bits (289), Expect = 3e-30 Identities = 81/258 (31%), Positives = 141/258 (54%), Gaps = 17/258 (6%) Query: 5 VIEMRE-ITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIK 63 V+++++ + K D A + ++L++ GEI + G +G G++ L+ + GL +PT G+I+ Sbjct: 256 VLQIKDLVVKDSRDITAVNDLHLEVHAGEILGVAGVDGNGQTELIEAITGLRKPTGGNIQ 315 Query: 64 INGSAVTIDSPSKSAQLGIGMV----HQHFMLVEAFTVTENIILGNEVVK----NGILDL 115 +NG +T +P K G+G + H+H ++++ FTV ENI+L K +G+L+ Sbjct: 316 LNGQDITGLTPRKITGAGVGHIPQDRHKHGLVLD-FTVGENIVLQTYYQKPYSTSGVLNF 374 Query: 116 KKAGQEIKALSEKYGLAVDPNAKIAD-ISVGAQQRVEILKTLYRGADILIFDEPTAVLTP 174 + ++ L E Y + +A +S G QQ+ I + + R D+LI +PT L Sbjct: 375 NEIYKKANELIEDYDVRTPSEHTLARALSGGNQQKAIIAREVDRSPDLLIAAQPTRGLDV 434 Query: 175 SEIQELMTIMKSLVKE---GKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQ 231 I+ +I LVKE GK+++LI+ +LDE+ +V+DR+ VI GK + V+ T Sbjct: 435 GAIE---SIHHRLVKERDKGKAVLLISLELDEVLNVSDRIAVIYEGKIVAIVDADKTNEN 491 Query: 232 DLAEMMVGRSVSFTIEKT 249 +L +M G S E T Sbjct: 492 ELGLLMAGGSAKKEGETT 509 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: 774 Number of extensions: 30 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: 509 Length adjustment: 34 Effective length of query: 476 Effective length of database: 475 Effective search space: 226100 Effective search space used: 226100 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