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_085545416.1 B9Y55_RS11055 sugar ABC transporter ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >NCBI__GCF_900177735.1:WP_085545416.1 Length = 504 Score = 285 bits (728), Expect = 4e-81 Identities = 167/496 (33%), Positives = 276/496 (55%), Gaps = 12/496 (2%) Query: 5 VIEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKI 64 V+ M +++K F A ++L +R G +HAL+GENGAGKSTLM L G+ SG I++ Sbjct: 6 VLTMTKVSKAFPGVQALKDVSLSVRPGTVHALMGENGAGKSTLMKCLFGIYRMDSGKIEL 65 Query: 65 NGSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKN----GILDLKKAGQ 120 +G AV I +P + LGI M+HQ + V ENI LG VK LD K Sbjct: 66 DGKAVEIPNPKSALDLGISMIHQELHPIPHRPVMENIWLGRAPVKKLGPLSFLDCKAMEA 125 Query: 121 EIKALSEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQEL 180 + K L + + +DP +I +SV Q VEI K + A I++ DEP++ LT E+Q L Sbjct: 126 QTKELFKDLDMDIDPRQQIRHLSVSRIQSVEIAKAVSYSAKIIVMDEPSSSLTEDEVQHL 185 Query: 181 MTIMKSLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGR 240 I++ L G +II I+HK++EI ++D VT++R G + T S ++ D+ MVGR Sbjct: 186 FRIIRQLTARGIAIIYISHKIEEILQISDDVTIMRDGTLVGTWPSSELSTDDIISRMVGR 245 Query: 241 SVSFTIEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSEL 300 +++ +P E I+ + + + K +S E+K GEI+G+ G+ G ++EL Sbjct: 246 TMTNRFPPRQNQPGEVIMEVSGY---SSPYPKSFKDVSFELKKGEILGVGGLVGAQRTEL 302 Query: 301 VQAITGLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQ 360 ++A+ GLR SG L ++G+++ S + + E+R G+ L++ NL + Sbjct: 303 MEAVFGLRSTSSGTLKLRGEEIDLSSPIIAKRQKMALLTEERRATGIFPVLSVQSNLVVA 362 Query: 361 TY--YKAPLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVD 418 YK L G+LN +++ ++ V+ + + SGGNQQK ++AR + Sbjct: 363 NLAAYKGAL---GLLNSGAMSKDTDEGIKRLSVKTPSRGTLIRSLSGGNQQKVLLARWLL 419 Query: 419 RDPDLLIVSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDG 478 DPD+LI+ +PTRG+DVGA I+ + +GK+++++S EL E++ +SDRI V+ +G Sbjct: 420 IDPDILILDEPTRGIDVGAKYEIYTIMADLAKQGKSIIMISSELPELMGMSDRIMVMSEG 479 Query: 479 QIQGIVTPETTNKQEL 494 ++ GI+ ++++ Sbjct: 480 KLAGILNGAEATEEKI 495 Score = 96.7 bits (239), Expect = 2e-24 Identities = 66/223 (29%), Positives = 113/223 (50%), Gaps = 13/223 (5%) Query: 24 INLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKINGSAVTIDSPSKSAQLGIG 83 ++ +L+KGEI + G GA ++ LM + GL +SG++K+ G + + SP + + + Sbjct: 279 VSFELKKGEILGVGGLVGAQRTELMEAVFGLRSTSSGTLKLRGEEIDLSSPIIAKRQKMA 338 Query: 84 MVHQHFMLVEAF---TVTENIILGNEVVKNGILDLKKAG-------QEIKALSEKYGLAV 133 ++ + F +V N+++ N G L L +G + IK LS K Sbjct: 339 LLTEERRATGIFPVLSVQSNLVVANLAAYKGALGLLNSGAMSKDTDEGIKRLSVK---TP 395 Query: 134 DPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMKSLVKEGKS 193 I +S G QQ+V + + L DILI DEPT + E+ TIM L K+GKS Sbjct: 396 SRGTLIRSLSGGNQQKVLLARWLLIDPDILILDEPTRGIDVGAKYEIYTIMADLAKQGKS 455 Query: 194 IILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEM 236 II+I+ +L E+ ++DR+ V+ GK + + T + + ++ Sbjct: 456 IIMISSELPELMGMSDRIMVMSEGKLAGILNGAEATEEKIMKL 498 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: 551 Number of extensions: 24 Number of successful extensions: 7 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: 504 Length adjustment: 34 Effective length of query: 476 Effective length of database: 470 Effective search space: 223720 Effective search space used: 223720 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