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_085545006.1 B9Y55_RS08890 ABC transporter ATP-binding protein
Query= TCDB::Q8DU37 (510 letters) >NCBI__GCF_900177735.1:WP_085545006.1 Length = 512 Score = 452 bits (1163), Expect = e-131 Identities = 230/495 (46%), Positives = 325/495 (65%), Gaps = 1/495 (0%) Query: 6 IEMREITKKFDDFVANDHINLDLRKGEIHALLGENGAGKSTLMNMLAGLLEPTSGSIKIN 65 +E++ ITK F VAN+ +++ ++KGE+ ALLGENGAGK+TLM +L G+ G I ++ Sbjct: 12 VELKGITKYFPGTVANEDVHISVKKGEVLALLGENGAGKTTLMRILYGMYRQDQGKILVD 71 Query: 66 GSAVTIDSPSKSAQLGIGMVHQHFMLVEAFTVTENIILGNEVVKNGILDLKKAGQEIKAL 125 GS+V IDSP + LGIGM+HQHF LV +V EN++LG + LDL++ E++ L Sbjct: 72 GSSVRIDSPQDAMALGIGMIHQHFSLVPVHSVAENVVLGLGSSMDR-LDLERVSSELREL 130 Query: 126 SEKYGLAVDPNAKIADISVGAQQRVEILKTLYRGADILIFDEPTAVLTPSEIQELMTIMK 185 +YGL VDP K+ + VG QQRVEI+K LYR A ILI DEPTAVLTP E + L ++ Sbjct: 131 GSRYGLEVDPYGKVGQLPVGMQQRVEIVKALYRKARILIMDEPTAVLTPQETERLGEFVR 190 Query: 186 SLVKEGKSIILITHKLDEIRSVADRVTVIRRGKSIETVEVSGTTSQDLAEMMVGRSVSFT 245 +G S+ILITHKL E+ ++AD VTV+R GK + +V + ++ ++LA MMVGR + Sbjct: 191 EFTSQGNSVILITHKLGEVMAMADSVTVMRAGKVVGSVSTAESSERELARMMVGRDLELV 250 Query: 246 IEKTPTKPKETILSIKDLVVNENRGIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAIT 305 P E +LS+ DL V ++RG A+ GLSL V GEI GIAG+ GNGQ EL +AI Sbjct: 251 SGHREGLPGEPVLSVLDLTVKDDRGSIALNGLSLTVGRGEIFGIAGVSGNGQQELAEAIC 310 Query: 306 GLRKIKSGHLTIKGQDVTKLSTRKITELSVGHVPEDRHRDGLILELTMAENLALQTYYKA 365 GLR G +T+ G+D+T LS ++I VG++P DRH+DGL+L++++ EN L+ Sbjct: 311 GLRAPVDGSITLNGRDITGLSVKEIIASGVGYIPADRHKDGLVLDMSVEENFILKNSGDR 370 Query: 366 PLSHNGVLNYSKINEHGRHLMQEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLI 425 P +GV++ I EHG L+ F ++ + AK SGGNQQK +IARE+ LL+ Sbjct: 371 PYFRSGVMDGGSIGEHGAALVGRFSIKAPSPSTKAKALSGGNQQKVVIAREIGLGSSLLV 430 Query: 426 VSQPTRGLDVGAIEYIHKRLIAERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVT 485 QP RGLD+GA +Y+H L+ ER +GKA+LL+S EL E+L LSDR+ VI+ G+I ++ Sbjct: 431 AVQPIRGLDLGAADYVHSVLMEERSKGKAILLISTELSEVLTLSDRVGVIYGGRILDVLD 490 Query: 486 PETTNKQELGILMAG 500 + +G+LMAG Sbjct: 491 RSDMDVDRIGLLMAG 505 Score = 72.4 bits (176), Expect = 4e-17 Identities = 56/238 (23%), Positives = 115/238 (48%), Gaps = 15/238 (6%) Query: 270 GIPAIKGLSLEVKAGEIIGIAGIDGNGQSELVQAITGLRKIKSGHLTIKGQDVTKLSTRK 329 G A + + + VK GE++ + G +G G++ L++ + G+ + G + + G V S + Sbjct: 23 GTVANEDVHISVKKGEVLALLGENGAGKTTLMRILYGMYRQDQGKILVDGSSVRIDSPQD 82 Query: 330 ITELSVGHVPEDRHRDGLILELTMAENLAL---QTYYKAPLSHNGVLNYSKINEHGRHLM 386 L +G + + L+ ++AEN+ L + + L S++ E G Sbjct: 83 AMALGIGMIHQ---HFSLVPVHSVAENVVLGLGSSMDRLDLERVS----SELRELGSRYG 135 Query: 387 QEFDVRGANELIPAKGFSGGNQQKAIIAREVDRDPDLLIVSQPTRGLDVGAIEYIHKRLI 446 E D G +P G QQ+ I + + R +LI+ +PT L E + + + Sbjct: 136 LEVDPYGKVGQLPV-----GMQQRVEIVKALYRKARILIMDEPTAVLTPQETERLGEFVR 190 Query: 447 AERDEGKAVLLVSFELDEILNLSDRIAVIHDGQIQGIVTPETTNKQELGILMAGGSIE 504 +G +V+L++ +L E++ ++D + V+ G++ G V+ ++++EL +M G +E Sbjct: 191 EFTSQGNSVILITHKLGEVMAMADSVTVMRAGKVVGSVSTAESSERELARMMVGRDLE 248 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: 664 Number of extensions: 34 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: 512 Length adjustment: 35 Effective length of query: 475 Effective length of database: 477 Effective search space: 226575 Effective search space used: 226575 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