RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|255764469|ref|YP_003064807.2| putative permease protein
[Candidatus Liberibacter asiaticus str. psy62]
         (361 letters)



>gnl|CDD|31138 COG0795, COG0795, Predicted permeases [General function prediction
           only].
          Length = 364

 Score =  138 bits (350), Expect = 1e-33
 Identities = 81/367 (22%), Positives = 163/367 (44%), Gaps = 10/367 (2%)

Query: 2   PGILWRYFFKYYLKTTLYFLLGAMILVFVIDLNEIQNQMGELPNYSISRGAVLAATRVPL 61
             +L RY  + YLKT L  LL  + ++ +IDL E+ N       Y      +L    +P 
Sbjct: 1   MMLLDRYLLREYLKTFLAILLVLLAILLIIDLLELLNGKAVDGRYPALDVLLLLLLSLPT 60

Query: 62  IIQQIIPFITLVVNIVVFFNLNRTSELVISRAIGISIWQLLNPFVVGSILLGIFTVLVIN 121
           ++  ++P   L+  ++    L+R SELV+ RA G+S+ +LL P ++ ++LL + + ++  
Sbjct: 61  LLPLVLPLALLIAALLTLGRLSRESELVVLRASGVSLKRLLRPVLILALLLSLLSFVLGL 120

Query: 122 PIATSGEKIGIDLIQQWKDNGDKQKSDIIPWMQISNPQQDIFIGAKKILPENHIWEDFTS 181
            +A   E+   +L+ Q K          +     +    D  I  + I  + +  +    
Sbjct: 121 WLAPWAEQKARELLAQAK--AGGPSLGSVEGGFWAKDGNDSLIFIESIDRDGNKLQGVFI 178

Query: 182 ITIDKKNKI--IHRKDADLAIIYNDKVKLKKVVEYQYGRIPIDKNSTTLNIPIKMDGFQK 239
              D   ++  ++  +  L  + +    L+ V   +Y   P + +S  ++          
Sbjct: 179 KRFDDNGRLSVVYAAEGALFELEDGSWILELVDGTRYEGTPKEGDSRIVDFDWYTLLLPD 238

Query: 240 FSEQFA-----SRSFYEIIKKMSFSNKSNIFHNYRAETQFYFLIVIPLMLVAMTLIAASV 294
              + A     + S  E+   +   NK N         + Y  + +PL+++AM L+A  +
Sbjct: 239 LLIREALLSPKALSLSELPTYILL-NKDNGQDRKTLLAELYRRLALPLLVLAMALLALPL 297

Query: 295 SLEFSRSNQPRIIVAYGIFSGFMLYTIITIMKSFGKSGILLPVAAALIPVILTISLSILI 354
           SL   RS +  + +  GI  G + Y ++ ++ +   +G L P  AA +P ++ ++L + +
Sbjct: 298 SLRNPRSGRLGLRLLGGILLGLLFYVLLFLLGALALAGKLPPFLAAWLPNLVFLALGLWL 357

Query: 355 LLQKEDG 361
           L +KE  
Sbjct: 358 LRRKERR 364


>gnl|CDD|146398 pfam03739, YjgP_YjgQ, Predicted permease YjgP/YjgQ family.  Members
           of this family are predicted integral membrane proteins
           of unknown function. They are about 350 amino acids long
           and contain about 6 transmembrane regions. They are
           predicted to be permeases although there is no
           verification of this.
          Length = 353

 Score =  127 bits (321), Expect = 5e-30
 Identities = 69/359 (19%), Positives = 153/359 (42%), Gaps = 16/359 (4%)

Query: 7   RYFFKYYLKTTLYFLLGAMILVFVIDLNEIQNQMGELPNYSISRGAVLAATRVPLIIQQI 66
           RY  + +LK  L  LL  ++L  ++DL  + + +       ++    L    +P I++ I
Sbjct: 1   RYILREFLKPFLLVLLVLLLLFLLVDLLRLLDLILG-GGLPLADILRLLLLLLPSILELI 59

Query: 67  IPFITLVVNIVVFFNLNRTSELVISRAIGISIWQLLNPFVVGSILLGIFTVLVINPIATS 126
           +P   L+  ++    L R SEL   RA GIS+ +LL P ++ ++LL + + L+   +   
Sbjct: 60  LPLALLLAVLLTLGRLARDSELTALRAAGISLKRLLRPVLILALLLSLLSFLLSEYLVPY 119

Query: 127 GEKIGIDLIQQWKDNGDKQKSDIIPWMQISNPQQDIFIGAKKILPENHIWEDFTSITIDK 186
             +    L+ +              +++  +    + I  KK+ P+  + E    I   +
Sbjct: 120 ANQKLEQLLAEILSKAPSLLLRPGLFLRDGD---GLIIYVKKVDPDGRLLEGVF-IYDFR 175

Query: 187 KNKIIHRKDADLAIIYNDKVK----LKKVVEYQYGRIPIDKN-----STTLNIPIKMDGF 237
              +     A  A + +D       L+    Y++ +   + +        +++ +     
Sbjct: 176 DGGLTSVITAKSATLDSDPNGGVWILENGTIYRFDKDGEELSILSFDRYEIDLSLTPKDL 235

Query: 238 QKFSEQFASRSFYEIIKKMSFSNKSNIFHNYRAETQFYFLIVIPLMLVAMTLIAASVSLE 297
              +      S  E+   +    K++     +   + +  + +PL  + + L+A  + L 
Sbjct: 236 SSLTADPEELSLSELYAYIKR-LKASGLDVRKYRAELHRRLALPLSCLVLALLALPLGLG 294

Query: 298 FSRSNQPRIIVAYGIFSGFMLYTIITIMKSFGKSGILLPVAAALIPVILTISLSILILL 356
             RS +    +   I  GF+ Y ++ + ++ G++G+L P+ AA +P +L + L + +LL
Sbjct: 295 SPRSGR-GAGLVLAILLGFLYYVLLFLGEALGENGVLPPLLAAWLPNLLFLLLGLYLLL 352


>gnl|CDD|173771 cd08529, STKc_FA2-like, Catalytic domain of the Protein
           Serine/Threonine Kinase, Chlamydomonas reinhardtii FA2
           and similar domains.  Serine/Threonine Kinases (STKs),
           Chlamydomonas reinhardtii FA2-like subfamily, catalytic
           (c) domain. STKs catalyze the transfer of the
           gamma-phosphoryl group from ATP to serine/threonine
           residues on protein substrates. The Chlamydomonas
           reinhardtii FA2-like subfamily belongs to the
           (NIMA)-related kinase (Nek) family. The Nek family
           includes seven different Chlamydomonas Neks (CNKs 1-6
           and Fa2). This subfamily includes FA2 and CNK4.  The Nek
           family is part of a larger superfamily that includes the
           catalytic domains of other protein STKs, protein
           tyrosine kinases, RIO kinases, aminoglycoside
           phosphotransferase, choline kinase, and phosphoinositide
           3-kinase.  Chlamydomonas reinhardtii FA2 was discovered
           in a genetic screen for deflagellation-defective
           mutants. It is essential for
           basal-body/centriole-associated microtubule severing,
           and plays a role in cell cycle progression. No cellular
           function has yet been ascribed to CNK4.
          Length = 256

 Score = 31.7 bits (72), Expect = 0.36
 Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 6/45 (13%)

Query: 170 LPENHIWEDFTSITID----KKNKIIHR--KDADLAIIYNDKVKL 208
           LPE+ +W  F  I +        KI+HR  K  +L +   D VK+
Sbjct: 98  LPEDQVWRFFIQILLGLAHLHSKKILHRDIKSLNLFLDAYDNVKI 142


>gnl|CDD|173757 cd08217, STKc_Nek2, Catalytic domain of the Protein
           Serine/Threonine Kinase, Never In Mitosis gene A-related
           kinase 2.  Serine/Threonine Kinases (STKs), Never In
           Mitosis gene A (NIMA)-related kinase 2 (Nek2) subfamily,
           catalytic (c) domain. STKs catalyze the transfer of the
           gamma-phosphoryl group from ATP to serine/threonine
           residues on protein substrates. The Nek2 subfamily is
           one of a family of 11 different Neks (Nek1-11) that are
           involved in cell cycle control. The Nek family is part
           of a larger superfamily that includes the catalytic
           domains of other protein STKs, protein tyrosine kinases,
           RIO kinases, aminoglycoside phosphotransferase, choline
           kinase, and phosphoinositide 3-kinase. The Nek2
           subfamily includes Aspergillus nidulans NIMA kinase, the
           founding member of the Nek family, which was identified
           in a screen for cell cycle mutants prevented from
           entering mitosis. NIMA is essential for mitotic entry
           and progression through mitosis, and its degradation is
           essential for mitotic exit. NIMA is involved in nuclear
           membrane fission. Vertebrate Nek2 is a cell
           cycle-regulated STK, localized in centrosomes and
           kinetochores, that regulates centrosome splitting at the
           G2/M phase. It also interacts with other mitotic kinases
           such as Polo-like kinase 1 and may play a role in
           spindle checkpoint. An increase in the expression of the
           human NEK2 gene is strongly associated with the
           progression of non-Hodgkin lymphoma.
          Length = 265

 Score = 29.9 bits (68), Expect = 1.2
 Identities = 25/112 (22%), Positives = 43/112 (38%), Gaps = 31/112 (27%)

Query: 167 KKILPENHIWEDFTSIT---------IDKKNKIIHR--KDADLAIIYNDKVKLKKVVEYQ 215
           +K + E  IW   T +           D  N ++HR  K A++ +  N+ VKL       
Sbjct: 99  RKYIEEEFIWRILTQLLLALYECHNRSDPGNTVLHRDLKPANIFLDANNNVKL------- 151

Query: 216 YGRIPIDKNSTTLNIPIKMDGFQKFSEQFASRSFY---EIIKKMSFSNKSNI 264
            G   + K          +     F++ +    +Y   E +  MS+  KS+I
Sbjct: 152 -GDFGLAKI---------LGHDSSFAKTYVGTPYYMSPEQLNHMSYDEKSDI 193


>gnl|CDD|33991 COG4269, COG4269, Predicted membrane protein [Function unknown].
          Length = 364

 Score = 29.4 bits (66), Expect = 1.3
 Identities = 16/69 (23%), Positives = 25/69 (36%)

Query: 257 SFSNKSNIFHNYRAETQFYFLIVIPLMLVAMTLIAASVSLEFSRSNQPRIIVAYGIFSGF 316
            FS    +   YR       L V+P MLVA  LI A+ +  +  +      +     +  
Sbjct: 183 RFSFDLKLGAFYRIYAILAGLAVLPFMLVAGYLIFAAFAAAYLSALGGNAQLETLALTLQ 242

Query: 317 MLYTIITIM 325
           M   I+   
Sbjct: 243 MQGQIVLAY 251


>gnl|CDD|38896 KOG3692, KOG3692, KOG3692, Uncharacterized conserved protein
           [Function unknown].
          Length = 881

 Score = 29.7 bits (66), Expect = 1.5
 Identities = 10/41 (24%), Positives = 18/41 (43%)

Query: 234 MDGFQKFSEQFASRSFYEIIKKMSFSNKSNIFHNYRAETQF 274
           +DGF    ++F+     + +     + KSN+ HNY      
Sbjct: 369 LDGFLDIEKKFSENRCEKALPMAHSAYKSNLPHNYTMTVHK 409


>gnl|CDD|30697 COG0349, Rnd, Ribonuclease D [Translation, ribosomal structure and
           biogenesis].
          Length = 361

 Score = 28.7 bits (64), Expect = 2.2
 Identities = 12/53 (22%), Positives = 19/53 (35%), Gaps = 4/53 (7%)

Query: 153 MQISNPQQDIFIGAKKILPENHIWEDFTSITIDKK-NKIIHRKDADLAIIYND 204
           +QIS+ +    I     L          ++  D    KI H    DL ++ N 
Sbjct: 39  IQISDGEGASLI---DPLAGILDLPPLVALLADPNVVKIFHAARFDLEVLLNL 88


>gnl|CDD|35161 COG5602, SIN3, Histone deacetylase complex, SIN3 component
           [Chromatin structure and dynamics].
          Length = 1163

 Score = 28.1 bits (62), Expect = 3.8
 Identities = 12/45 (26%), Positives = 22/45 (48%)

Query: 151 PWMQISNPQQDIFIGAKKILPENHIWEDFTSITIDKKNKIIHRKD 195
           P   +SN  +D F   K+ L + +++ +F  +      KII + D
Sbjct: 407 PISHLSNESEDFFERIKQYLKDKNLYHEFLKLLNLYSQKIIDKND 451


>gnl|CDD|173772 cd08530, STKc_CNK2-like, Catalytic domain of the Protein
           Serine/Threonine Kinase, Chlamydomonas reinhardtii CNK2,
            and similar domains.  Serine/Threonine Kinases (STKs),
           Chlamydomonas reinhardtii Never In Mitosis gene A
           (NIMA)-related kinase 1 (CNK2)-like subfamily, catalytic
           (c) domain. STKs catalyze the transfer of the
           gamma-phosphoryl group from ATP to serine/threonine
           residues on protein substrates. The Chlamydomonas
           reinhardtii CNK2-like subfamily belongs to the
           (NIMA)-related kinase (Nek) family. The Nek family
           includes seven different Chlamydomonas Neks (CNKs 1-6
           and Fa2). This subfamily includes CNK1, and -2.  The Nek
           family is part of a larger superfamily that includes the
           catalytic domains of other protein STKs, protein
           tyrosine kinases, RIO kinases, aminoglycoside
           phosphotransferase, choline kinase, and phosphoinositide
           3-kinase.  Chlamydomonas reinhardtii CNK2 has both
           cilliary and cell cycle functions. It influences
           flagellar length through promoting flagellar
           disassembly, and it regulates cell size, through
           influencing the size threshold at which cells commit to
           mitosis.
          Length = 256

 Score = 27.4 bits (61), Expect = 5.7
 Identities = 16/48 (33%), Positives = 27/48 (56%), Gaps = 6/48 (12%)

Query: 167 KKILPENHIWEDFTSITIDKK----NKIIHR--KDADLAIIYNDKVKL 208
           +K++PE  IW  F  +    +     KI+HR  K A++ ++ ND VK+
Sbjct: 97  RKLIPEQEIWRIFIQLLRGLQALHEQKILHRDLKSANILLVANDLVKI 144


>gnl|CDD|32883 COG3069, DcuC, C4-dicarboxylate transporter [Energy production and
           conversion].
          Length = 451

 Score = 27.6 bits (61), Expect = 5.9
 Identities = 14/48 (29%), Positives = 23/48 (47%), Gaps = 5/48 (10%)

Query: 306 IIVAYGIFSGFMLYT-----IITIMKSFGKSGILLPVAAALIPVILTI 348
           +IVA G+F+  +        +I+   SFG  GI L +   L+  +  I
Sbjct: 315 LIVAAGVFAQGLKTIGAIDALISGATSFGSGGIGLMLILVLLTFLAAI 362


>gnl|CDD|39823 KOG4623, KOG4623, KOG4623, Uncharacterized conserved protein
           [Function unknown].
          Length = 611

 Score = 27.4 bits (60), Expect = 6.3
 Identities = 30/155 (19%), Positives = 49/155 (31%), Gaps = 24/155 (15%)

Query: 203 NDKVKLKKVVEYQYGRIPIDKNSTTLNIP--IKMDGFQK-FSEQFASRSFYEIIKKMSFS 259
           N      KV+ Y        K      +P              QF  R FY         
Sbjct: 161 NKYEAKNKVLGY------WLKEQLNYKVPHHNPKALRVLWLLRQFGRRFFYL-------- 206

Query: 260 NKSNIFHNYRAETQFYFLI---VIPLMLVAMTLIAASVSLEFSRSNQPRIIV---AYGIF 313
            +S ++H Y +   F       ++ L  +    + AS S  FS +    I+V    Y   
Sbjct: 207 -QSIVWHLYHSMIIFLLPDGIRILFLKAIDYFHLDASSSKIFSPNWLQFILVFWLPYWYK 265

Query: 314 SGFMLYTIITIMKSFGKSGILLPVAAALIPVILTI 348
             F+L T +     + +     P+A      +L+ 
Sbjct: 266 MMFLLSTELFGAAQYIQCQATYPIALLPCLYLLSC 300


>gnl|CDD|147682 pfam05656, DUF805, Protein of unknown function (DUF805).  This
           family consists of several bacterial proteins of unknown
           function.
          Length = 112

 Score = 26.9 bits (60), Expect = 8.2
 Identities = 23/96 (23%), Positives = 41/96 (42%), Gaps = 7/96 (7%)

Query: 269 RAETQFYFLIVIPLMLVAMTLIAASVSLEFSRSNQPRIIVAYGIFSGFMLYTIITIMKSF 328
           R+E  ++ L  I + LV + L A         S    ++    +     + ++   ++  
Sbjct: 11  RSEYWWFVLFNILITLVLLILDALLGISSSLLSGGGLLLGLISLA--IFIPSLAVTVRRL 68

Query: 329 ---GKSGILLPVAAALIPVILTISLSILILLQKEDG 361
              G+SG  L +   LIP+I  I L +L+LL    G
Sbjct: 69  HDTGRSGWWLLL--LLIPLIGFIVLLVLLLLPGTPG 102


  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
   0.326    0.142    0.411 

Gapped
Lambda     K      H
   0.267   0.0713    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,451,750
Number of extensions: 249955
Number of successful extensions: 1127
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1118
Number of HSP's successfully gapped: 101
Length of query: 361
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 266
Effective length of database: 4,210,882
Effective search space: 1120094612
Effective search space used: 1120094612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 58 (26.2 bits)