RPS-BLAST 2.2.22 [Sep-27-2009]

Database: CddA 
           21,609 sequences; 6,263,737 total letters

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

Query= gi|254780342|ref|YP_003064755.1| substrate-binding region of
ABC-type glycine betaine transport system [Candidatus Liberibacter
asiaticus str. psy62]
         (309 letters)



>gnl|CDD|32296 COG2113, ProX, ABC-type proline/glycine betaine transport systems,
           periplasmic components [Amino acid transport and
           metabolism].
          Length = 302

 Score =  236 bits (604), Expect = 5e-63
 Identities = 96/295 (32%), Positives = 144/295 (48%), Gaps = 3/295 (1%)

Query: 4   ILAVCLFLTTFSISYARDADSCTPVRFADTGWTDIAATTAMTSVILEEILGYKTNIKLLA 63
                  L   + + A  A++   VR AD GWT   ATT +   IL+  LGY   +  L 
Sbjct: 9   AAVAAAALLAAAAAAAAAAEAGKTVRIADVGWTSGTATTNVAKKILKG-LGYTVELVTLD 67

Query: 64  VPVTFRSLKNKGIDIFMGYWYPSLEKFIAPYLEEGSIKLVAENLQGAKYMLAVNDVGFAL 123
             V ++SL    +D+F   W P+        +++  ++L   NL+GAK   AV       
Sbjct: 68  TAVMYQSLAKGDLDVFPEAWLPTTPDDYKKAVKDKKVELGGTNLEGAKQGWAVPKYVADA 127

Query: 124 GIKSYQDIAKYKKELGAKIYGIEPGNEGNQRILDMINNNKFSLKGFRLIEASELASFSQI 183
           GIKS  D+AK+K + G KIYGIEPG    + I D I      LKGF L+E+SE A  +  
Sbjct: 128 GIKSIADLAKFKDKFGGKIYGIEPGWGCMRVIEDAIKAYGLGLKGFELVESSEAAMLAAA 187

Query: 184 RRDQRNNIPAVFLSWEPHPINSDLNIHYLPGGEEISG--FGEASVYTVVRSDYLDKCPNI 241
            R  +   P VF  W PH +    ++ YL       G   G  +V+TVVR  + ++ PN+
Sbjct: 188 IRAAKRKEPIVFYGWSPHWMFGKYDLKYLEDPGPPKGANGGWETVHTVVRKGFAEEAPNV 247

Query: 242 SRLLKNIKFSVALENEMMKLILNNKQDRQFVGRTMLRTHPDLLKNWLIGVTTFDG 296
           ++LL N  F +A EN +M  + +     +   +  L+ +P++   W+ GV   DG
Sbjct: 248 AKLLANFSFPLAEENALMAAMDDGGATPEEAAKQWLKANPEIWDGWVSGVAAADG 302


>gnl|CDD|146609 pfam04069, OpuAC, Substrate binding domain of ABC-type glycine
           betaine transport system.  Part of a high affinity
           multicomponent binding-protein-dependent transport
           system involved in bacterial osmoregulation. This domain
           is often fused to the permease component of the
           transporter complex. Family members are often integral
           membrane proteins or predicted to be attached to the
           membrane by a lipid anchor. Glycine betaine is involved
           in protection from high osmolarity environments for
           example in Bacillus subtilis. The family member OpuBC is
           closely related, and involved in choline transport.
           Choline is necessary for the biosynthesis of glycine
           betaine. L-carnitine is important for osmoregulation in
           Listeria monocytogenes. Family also contains proteins
           binding l-proline (ProX), histidine (HisX) and taurine
           (TauA).
          Length = 256

 Score =  139 bits (352), Expect = 9e-34
 Identities = 54/248 (21%), Positives = 95/248 (38%), Gaps = 10/248 (4%)

Query: 27  PVRFADTGWTDIAATTAMTSVILEEILGYKTNI-KLLAVPVTFRSLKNKGIDIFMGYWYP 85
            +      WT+      + + +LE  LGY   +  L +  V F +L +  ID++   W  
Sbjct: 2   TIVIGSKNWTEQEILANIAAQLLEA-LGYVVELVGLGSTAVLFAALASGDIDLYPEEWTG 60

Query: 86  SLEKFIAPYLEEGSIKLVA-ENLQGAKYMLAVN-DVGFALGIKSYQDIAKYKKE---LGA 140
           +  +     +EE    LV      G  Y LAV   V    GIKS  D+AK   +      
Sbjct: 61  TTYEAYKKAVEEKLGLLVLGPLGAGNTYGLAVPKYVAEKPGIKSISDLAKPADDELGFKG 120

Query: 141 KIYGIEPGNEGNQRILDMINNNKFSLKGFRLIEASELASFSQIRRDQRNNIPAVFLSWEP 200
           +  G   G    +    ++    + L  + L+E SE A  + +    +   P V  +W P
Sbjct: 121 EFIGRPDGWGCTRSTEGLLK--AYGLDKYELVEGSEAAMDALLYAAIKRGEPDVVYAWTP 178

Query: 201 HPINSDLNIHYLPGGEEISGFGEASVYTVVRSDYLDKCPNISRLLKNIKFSVALENEMMK 260
             +    ++  L   + +      +V  VVR  + +K P ++  L  +       NE+  
Sbjct: 179 DWMIKKYDLVVLEDPKGLFPPAY-NVVPVVRKGFAEKHPEVAAFLNKLSLDTEDLNELNA 237

Query: 261 LILNNKQD 268
            +    +D
Sbjct: 238 QVDVEGKD 245


>gnl|CDD|147350 pfam05128, DUF697, Domain of unknown function (DUF697).  Family of
           bacterial hypothetical proteins that is sometimes
           associated with GTPase domains.
          Length = 162

 Score = 27.1 bits (61), Expect = 5.6
 Identities = 10/20 (50%), Positives = 13/20 (65%)

Query: 140 AKIYGIEPGNEGNQRILDMI 159
           AK+YGIE G EG  R+   +
Sbjct: 62  AKLYGIELGYEGAIRLARSV 81


>gnl|CDD|144015 pfam00270, DEAD, DEAD/DEAH box helicase.  Members of this family
           include the DEAD and DEAH box helicases. Helicases are
           involved in unwinding nucleic acids. The DEAD box
           helicases are involved in various aspects of RNA
           metabolism, including nuclear transcription, pre mRNA
           splicing, ribosome biogenesis, nucleocytoplasmic
           transport, translation, RNA decay and organellar gene
           expression.
          Length = 167

 Score = 26.8 bits (60), Expect = 7.6
 Identities = 13/53 (24%), Positives = 20/53 (37%), Gaps = 9/53 (16%)

Query: 154 RILDMINNNKFSLKGFRLI---EASELAS------FSQIRRDQRNNIPAVFLS 197
           R+LD++      LK  +L+   EA  L          +I R        + LS
Sbjct: 105 RLLDLLERGGLLLKNLKLLVLDEAHRLLDQGFGDDLEEILRRLPPKRQILLLS 157


>gnl|CDD|33735 COG3954, PrkB, Phosphoribulokinase [Energy production and
           conversion].
          Length = 289

 Score = 26.5 bits (58), Expect = 9.1
 Identities = 7/19 (36%), Positives = 11/19 (57%)

Query: 189 NNIPAVFLSWEPHPINSDL 207
           N +P  F  W+P P  +D+
Sbjct: 108 NQVPGTFTPWQPLPEPTDV 126


>gnl|CDD|38590 KOG3380, KOG3380, KOG3380, Actin-related protein Arp2/3 complex,
           subunit ARPC5 [Cytoskeleton].
          Length = 152

 Score = 26.4 bits (58), Expect = 9.3
 Identities = 11/33 (33%), Positives = 16/33 (48%)

Query: 57  TNIKLLAVPVTFRSLKNKGIDIFMGYWYPSLEK 89
           T+IK   +    + L  + IDI M Y Y  +E 
Sbjct: 84  TSIKQADIEAAVKKLSTEEIDILMKYIYKGMEI 116


  Database: CddA
    Posted date:  Feb 4, 2011  9:38 PM
  Number of letters in database: 6,263,737
  Number of sequences in database:  21,609
  
Lambda     K      H
   0.321    0.138    0.405 

Gapped
Lambda     K      H
   0.267   0.0798    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 3,742,507
Number of extensions: 196299
Number of successful extensions: 412
Number of sequences better than 10.0: 1
Number of HSP's gapped: 406
Number of HSP's successfully gapped: 16
Length of query: 309
Length of database: 6,263,737
Length adjustment: 94
Effective length of query: 215
Effective length of database: 4,232,491
Effective search space: 909985565
Effective search space used: 909985565
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 (21.8 bits)
S2: 57 (25.6 bits)