RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddB 
           21,608 sequences; 5,994,473 total letters

Searching..................................................done

Query= gi|254780170|ref|YP_003064583.1| cationic amino acid ABC
transporter, periplasmic binding protein [Candidatus Liberibacter
asiaticus str. psy62]
         (342 letters)



>gnl|CDD|162200 TIGR01096, 3A0103s03R, lysine-arginine-ornithine-binding
           periplasmic protein. 
          Length = 250

 Score =  157 bits (400), Expect = 3e-39
 Identities = 58/284 (20%), Positives = 100/284 (35%), Gaps = 56/284 (19%)

Query: 32  KRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLA 91
           K G ++ G  TG   F    ANG   GFDVD  +AL   +    +K +++  N      +
Sbjct: 22  KEGSVRIGTETGYPPFESKDANGKLVGFDVDLAKALCKRMK---AKCKFVEQNFDGLIPS 78

Query: 92  LQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGI-SSVSQLSGASICV 150
           L++K++D +      ++  +    + F    Y  GQGF++ K   +  ++  L G ++ V
Sbjct: 79  LKAKKVDAIMAT--MSITPKRQKQIDFSDPYYATGQGFVVKKGSDLAKTLEDLDGKTVGV 136

Query: 151 QAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDR 210
           Q+GTT E  L DYFK        + ++  +  +   +A R DA   D S L    L    
Sbjct: 137 QSGTTHEQYLKDYFKP---GVDIVEYDSYDNANMDLKAGRIDAVFTDASVLAEGFLKPPN 193

Query: 211 PSEHVILPDIISKSPLAPAIIQGDTEWYNIVSWTHYAMVTAEELGITQKNINQVSKDTTN 270
             +   +   ++          GD                    GI  +  +        
Sbjct: 194 GKDFKFVGPSVTDEKY-----FGD------------------GYGIGLRKGDT------- 223

Query: 271 PDVQRFLGIDKSSNIGEALGLTKDWTYRIIRHMGNYGEMFDRNL 314
                             L    +     IR  G Y ++  +  
Sbjct: 224 -----------------ELKAAFNKALAAIRADGTYQKISKKWF 250


>gnl|CDD|128376 smart00062, PBPb, Bacterial periplasmic substrate-binding proteins.
            bacterial proteins, eukaryotic ones are in PBPe.
          Length = 219

 Score =  140 bits (356), Expect = 4e-34
 Identities = 56/227 (24%), Positives = 97/227 (42%), Gaps = 10/227 (4%)

Query: 36  LKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQSK 95
           L+ G N     F+    +G+  GFDVD  +A++  +     K++++ ++      AL+S 
Sbjct: 2   LRVGTNGDYPPFSFADEDGELTGFDVDLAKAIAKELG---LKVEFVEVSFDNLLTALKSG 58

Query: 96  QIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTT 155
           +ID+++     T  R   +   F    Y  GQ  ++ K   I S+  L G  + V AGTT
Sbjct: 59  KIDVVAAGMTITPERAKQV--DFSDPYYKSGQVILVRKDSPIKSLEDLKGKKVAVVAGTT 116

Query: 156 TELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEHV 215
            E  L         +   + ++   E  AA +A R DA   D  AL AL   +  P   +
Sbjct: 117 GEELLKKL----YPEAKIVSYDSQAEALAALKAGRADAAVADAPALAALVKQHGLPELKI 172

Query: 216 ILPDIISKSPLAPAIIQGDTEWYNIVSWTHYAMVTAEEL-GITQKNI 261
           +   + +    A A+ +GD E  + ++     +     L  I +K  
Sbjct: 173 VGDPLDTPEGYAFAVRKGDPELLDKINKALKELKADGTLKKIYEKWF 219


>gnl|CDD|183381 PRK11917, PRK11917, bifunctional adhesin/ABC transporter
           aspartate/glutamate-binding protein; Reviewed.
          Length = 259

 Score = 73.8 bits (181), Expect = 6e-14
 Identities = 61/216 (28%), Positives = 98/216 (45%), Gaps = 12/216 (5%)

Query: 9   ILCLIILFFTSFSTNA----SILGDIKKRGFLKCGINTGLVGFAEV-KANGDWKGFDVDF 63
            L +  L      +NA      L  IK +G L  G+   +  +A + +A G+ KGF++D 
Sbjct: 9   KLAVFALGACVAFSNANAAEGKLESIKSKGQLIVGVKNDVPHYALLDQATGEIKGFEIDV 68

Query: 64  CRALSSAIFDDPSKIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITY 123
            + L+ +I  D  KI+ + +NAK R   L +  +D +     +T+  E      F    Y
Sbjct: 69  AKLLAKSILGDDKKIKLVAVNAKTRGPLLDNGSVDAVI--ATFTITPERKRIYNFSEPYY 126

Query: 124 FDGQGFIMHKKKGISSVSQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEID 183
            D  G ++ K+K   S++ + GA+I V    TT+  + +  K   +      F     I 
Sbjct: 127 QDAIGLLVLKEKNYKSLADMKGANIGVAQAATTKKAIGEAAKKIGIDVKFSEFPDYPSIK 186

Query: 184 AAYRAHRCDAYTGDISALYALKLTNDRPSEHVILPD 219
           AA  A R DA++ D S L  L   +D+     ILPD
Sbjct: 187 AALDAKRVDAFSVDKSIL--LGYVDDKS---EILPD 217


>gnl|CDD|184969 PRK15007, PRK15007, putative ABC transporter arginine-biding
           protein; Provisional.
          Length = 243

 Score = 39.6 bits (92), Expect = 0.001
 Identities = 33/121 (27%), Positives = 54/121 (44%), Gaps = 16/121 (13%)

Query: 47  FAEVKANGDWKGFDVDFCRALSSAI-----FDDPSKIQYLPLNAKERFLALQSKQIDILS 101
           F  + AN    GFDVD  +AL   I     F + +    +P        +L+ ++++ + 
Sbjct: 34  FESIDANNQIVGFDVDLAQALCKEIDATCTFSNQAFDSLIP--------SLKFRRVEAVM 85

Query: 102 RNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTTTELTLA 161
              D T  RE  + L   P  Y+D     + ++   +SV QL G  + VQ GTT +  + 
Sbjct: 86  AGMDITPEREKQV-LFTTP--YYDNSALFVGQQGKYTSVDQLKGKKVGVQNGTTHQKFIM 142

Query: 162 D 162
           D
Sbjct: 143 D 143


>gnl|CDD|181908 PRK09495, glnH, glutamine ABC transporter periplasmic protein;
           Reviewed.
          Length = 247

 Score = 35.9 bits (83), Expect = 0.016
 Identities = 47/174 (27%), Positives = 65/174 (37%), Gaps = 47/174 (27%)

Query: 39  GINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYL--PLNAKERFLALQSKQ 96
             +T  V F E K    + GFD+D    L +AI  +  K+ Y   P++      ALQ+K 
Sbjct: 30  ATDTAFVPF-EFKQGDKYVGFDID----LWAAIAKEL-KLDYTLKPMDFSGIIPALQTKN 83

Query: 97  IDILSRNTDWTLLREISLGLAFRPIT------------YFDGQGFIMHKKKG--ISSVSQ 142
           +D               L LA   IT            Y+     +M K     I SV  
Sbjct: 84  VD---------------LALAGITITDERKKAIDFSDGYYKSGLLVMVKANNNDIKSVKD 128

Query: 143 LSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAY---RAHRCDA 193
           L G  + V++GT +     DY KA+          +   ID AY      R DA
Sbjct: 129 LDGKVVAVKSGTGS----VDYAKAN---IKTKDLRQFPNIDNAYLELGTGRADA 175


>gnl|CDD|182740 PRK10797, PRK10797, glutamate and aspartate transporter subunit;
           Provisional.
          Length = 302

 Score = 34.8 bits (80), Expect = 0.031
 Identities = 34/140 (24%), Positives = 59/140 (42%), Gaps = 6/140 (4%)

Query: 25  SILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAI---FDDPS-KIQY 80
           S L  I K G +  G     V F+         G+  D+  A+  A+    + P  +++ 
Sbjct: 31  STLDKIAKNGVIVVGHRESSVPFSYYDNQQKVVGYSQDYSNAIVEAVKKKLNKPDLQVKL 90

Query: 81  LPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSV 140
           +P+ ++ R   LQ+   D    +T   L R+     AF    +  G   +  K   I   
Sbjct: 91  IPITSQNRIPLLQNGTFDFECGSTTNNLERQKQA--AFSDTIFVVGTRLLTKKGGDIKDF 148

Query: 141 SQLSGASICVQAGTTTELTL 160
           + L G ++ V +GTT+E+ L
Sbjct: 149 ADLKGKAVVVTSGTTSEVLL 168


>gnl|CDD|183061 PRK11260, PRK11260, cystine transporter subunit; Provisional.
          Length = 266

 Score = 34.3 bits (79), Expect = 0.045
 Identities = 33/135 (24%), Positives = 55/135 (40%), Gaps = 5/135 (3%)

Query: 24  ASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPL 83
             +L  +K+RG L  G+      F+    +G   GF+V+F  AL+  +     K    P 
Sbjct: 31  EGLLNKVKERGTLLVGLEGTYPPFSFQGEDGKLTGFEVEFAEALAKHL---GVKASLKPT 87

Query: 84  NAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKG-ISSVSQ 142
                  +L SK+ID++      +  R+     +  P T    Q  +    +G I + + 
Sbjct: 88  KWDGMLASLDSKRIDVVINQVTISDERKKKYDFS-TPYTVSGIQALVKKGNEGTIKTAAD 146

Query: 143 LSGASICVQAGTTTE 157
           L G  + V  GT  E
Sbjct: 147 LKGKKVGVGLGTNYE 161


>gnl|CDD|150404 pfam09724, DUF2036, Uncharacterized conserved protein (DUF2036).
           This family of proteins includes members ranging in size
           from approximately 300 to 460 residues. There are a
           number of well-conserved domains along the length.
          Length = 325

 Score = 28.8 bits (65), Expect = 2.0
 Identities = 16/42 (38%), Positives = 20/42 (47%), Gaps = 7/42 (16%)

Query: 58  GFDVDFCRALSSAIFDDP--SKIQY-----LPLNAKERFLAL 92
           G D+D  +    A+ D P    IQY     LP + KERF  L
Sbjct: 267 GMDLDLDQLRGYALLDRPAEETIQYLSEEDLPTDPKERFKEL 308


>gnl|CDD|184972 PRK15010, PRK15010, ABC transporter lysine/arginine/ornithine
           binding periplasmic protein; Provisional.
          Length = 260

 Score = 27.7 bits (61), Expect = 4.6
 Identities = 37/151 (24%), Positives = 62/151 (41%), Gaps = 10/151 (6%)

Query: 8   SILCLIILFFTSFSTNASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKGFDVDFCRAL 67
           SIL L +L     S  AS    + +    + G +T    F+   A GD+ GFD+D    +
Sbjct: 4   SILALSLL--VGLSAAASSYAALPETV--RIGTDTTYAPFSSKDAKGDFVGFDIDLGNEM 59

Query: 68  SSAIFDDPSKIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYFDGQ 127
              +     K  ++  +      +L++K+ID +  +   T  R+    +AF    Y    
Sbjct: 60  CKRM---QVKCTWVASDFDALIPSLKAKKIDAIISSLSITDKRQQE--IAFSDKLYAADS 114

Query: 128 GFIMHKKKGIS-SVSQLSGASICVQAGTTTE 157
             I  K   I  ++  L G  + V  G+T E
Sbjct: 115 RLIAAKGSPIQPTLDSLKGKHVGVLQGSTQE 145


>gnl|CDD|180730 PRK06851, PRK06851, hypothetical protein; Provisional.
          Length = 367

 Score = 27.6 bits (62), Expect = 5.3
 Identities = 25/105 (23%), Positives = 40/105 (38%), Gaps = 21/105 (20%)

Query: 15  LFFTSFSTNA------SILGDIKKRGFLKCGINTGLVGFAEVKAN-GDWKGFDVDF--C- 64
           LF  + +         S+   +K R FLK    TG     +  A   + +GFDV+   C 
Sbjct: 192 LFLGAITPKGAVDFVPSLTEGVKNRYFLKGRPGTGKSTMLKKIAKAAEERGFDVEVYHCG 251

Query: 65  -----------RALSSAIFDDPSKIQYLPLNAKERFLALQSKQID 98
                        L+ AIFD  +  +Y P    +  + +  + ID
Sbjct: 252 FDPDSLDMVIIPELNFAIFDSTAPHEYFPSREGDEIIDMYDELID 296


>gnl|CDD|184492 PRK14081, PRK14081, triple tyrosine motif-containing protein;
           Provisional.
          Length = 667

 Score = 27.3 bits (61), Expect = 6.0
 Identities = 12/38 (31%), Positives = 23/38 (60%)

Query: 75  PSKIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREI 112
           P++I Y+ L  KE +L     +I+++ +NT   L++ I
Sbjct: 480 PAEIDYILLPVKEYYLVGDDIEIEVIIQNTKDVLIKYI 517


>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein TraB;
           Provisional.
          Length = 475

 Score = 27.1 bits (60), Expect = 6.7
 Identities = 17/69 (24%), Positives = 31/69 (44%), Gaps = 14/69 (20%)

Query: 121 ITYFDGQGFIMHKKKGISSVSQLS---GASICVQAGTTTEL-----------TLADYFKA 166
           + +  G GF+    +G+   SQ +   GA+    AG   ++           TL+DY+  
Sbjct: 323 LGWAWGAGFVDGIGQGMERASQPAVGLGATAAYGAGDVLKMGIGGGASKAAQTLSDYYIK 382

Query: 167 HNMKYHPIV 175
              +YHP++
Sbjct: 383 RAEQYHPVI 391


>gnl|CDD|130712 TIGR01651, CobT, cobaltochelatase, CobT subunit.  This model
           describes the aerobic cobalamin pathway Pseudomonas
           denitrificans CobT gene product, which is a cobalt
           chelatase subunit, with a MW ~70 kDa. The aerobic
           pathway cobalt chelatase is a heterotrimeric,
           ATP-dependent enzyme that catalyzes cobalt insertion
           during cobalamin biosynthesis. The other two subunits
           are the P. denitrificans CobS (TIGR01650) and CobN
           (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid
           potential confusion with the nonhomologous Salmonella
           typhimurium/E.coli cobT gene product, the P.
           denitrificans gene symbol is not used in the name of
           this model.
          Length = 600

 Score = 27.2 bits (60), Expect = 6.9
 Identities = 13/37 (35%), Positives = 19/37 (51%), Gaps = 4/37 (10%)

Query: 22  TNASILGDIKKRGFLKCGINTGLVGFAEVKANGDWKG 58
           T A+   DI  R   +CG+   ++GF   +A   WKG
Sbjct: 411 TVAATCADILARTLERCGVKVEILGFT-TRA---WKG 443


>gnl|CDD|179119 PRK00772, PRK00772, 3-isopropylmalate dehydrogenase; Provisional.
          Length = 358

 Score = 27.0 bits (61), Expect = 6.9
 Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 6/33 (18%)

Query: 201 LYALKLTNDRPSEHVILPDIISKSPLAPAIIQG 233
           L+A    N RP    + P +   SPL P I+ G
Sbjct: 101 LFA----NLRP--AKLYPGLADASPLKPEIVAG 127


  Database: CddB
    Posted date:  Feb 4, 2011  9:54 PM
  Number of letters in database: 5,994,473
  Number of sequences in database:  21,608
  
Lambda     K      H
   0.322    0.138    0.418 

Gapped
Lambda     K      H
   0.267   0.0590    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 5,668,018
Number of extensions: 361042
Number of successful extensions: 696
Number of sequences better than 10.0: 1
Number of HSP's gapped: 688
Number of HSP's successfully gapped: 23
Length of query: 342
Length of database: 5,994,473
Length adjustment: 94
Effective length of query: 248
Effective length of database: 3,963,321
Effective search space: 982903608
Effective search space used: 982903608
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 57 (26.0 bits)