RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780874|ref|YP_003065287.1| peptide chain release factor 1
[Candidatus Liberibacter asiaticus str. psy62]
         (357 letters)



>gnl|CDD|30565 COG0216, PrfA, Protein chain release factor A [Translation,
           ribosomal structure and biogenesis].
          Length = 363

 Score =  466 bits (1201), Expect = e-132
 Identities = 203/357 (56%), Positives = 274/357 (76%), Gaps = 7/357 (1%)

Query: 7   KQICDLKNRFAEIELRMSE---SPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQDLH 63
           +++  L  R+ E+E  +S+       D Y KL++EYA + PI+ K   Y + +++ +D  
Sbjct: 7   EKLESLLERYEELEALLSDPEVISDPDEYRKLSKEYAELEPIVEKYREYKKAQEDLEDAK 66

Query: 64  TVIGDHNSDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGS 123
            ++ +   D E+R++A+ E+  +E +I ELE E+  LLLPKD +DDK+ ILEIRAGTGG 
Sbjct: 67  EMLAE-EKDPEMREMAEEEIKELEAKIEELEEELKILLLPKDPNDDKNIILEIRAGTGGD 125

Query: 124 EAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFESGVH 183
           EAALF GDLFRMY RYA  + WKVE+LS+S+++ GGYKEI+A+ISG+GV+SR+KFESGVH
Sbjct: 126 EAALFAGDLFRMYSRYAESKGWKVEILSASESELGGYKEIIASISGKGVYSRLKFESGVH 185

Query: 184 RVQRVPATEASGRVHTSAATVAVLPEAAEI-DVDIPLEDIRIDTMRASGSGGQHVNTTDS 242
           RVQRVPATE+ GR+HTSAATVAVLPE  E+ +++I  +D+RIDT R+SG+GGQHVNTTDS
Sbjct: 186 RVQRVPATESQGRIHTSAATVAVLPEVEEVEEIEINPKDLRIDTFRSSGAGGQHVNTTDS 245

Query: 243 AVRITHIPTGIMVTSS-EKSQHQNRLRAMKVLRARLYDVERKRMANERSANRKLQIGSGD 301
           AVRITH+PTGI+V    E+SQH+N+ +AMKVLRARLYD ER++   E ++ RK Q+GSGD
Sbjct: 246 AVRITHLPTGIVVECQDERSQHKNKAKAMKVLRARLYDAERQKAQAEEASERKSQVGSGD 305

Query: 302 RSERIRTYNFSQGRITDHRINLTLYKLEYVLQGY-IDDIINPLLTAHQAKMIGSASE 357
           RSERIRTYNF Q R+TDHRINLTLYKL+ V++G  +D+II+ L+   QA+ +    E
Sbjct: 306 RSERIRTYNFPQNRVTDHRINLTLYKLDEVMEGGKLDEIIDALIAEDQAEQLAELGE 362


>gnl|CDD|37937 KOG2726, KOG2726, KOG2726, Mitochondrial polypeptide chain release
           factor [Translation, ribosomal structure and
           biogenesis].
          Length = 386

 Score =  302 bits (775), Expect = 8e-83
 Identities = 142/322 (44%), Positives = 200/322 (62%), Gaps = 5/322 (1%)

Query: 41  AISPIISKISIYDQKKQEEQDLHT--VIGDHNSDSEIRDLAQIEVLAIEKEIRELENEIN 98
             + +   ++    + +  ++L +   +     D ++ +LA+ E   I KEI    +E+ 
Sbjct: 65  DPAELDEVLNALSDRMKLVRELKSLKSLIKEGEDEDMDELAEEEAEEISKEIERSLHELE 124

Query: 99  YLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDG 158
             LLP D  D ++CI+E+RAG GG EA +F  +L  MY++YA    WK  VL  +  + G
Sbjct: 125 LSLLPSDPYDAEACIIEVRAGAGGQEAQIFTMELVDMYQKYAERLGWKARVLEKAPGESG 184

Query: 159 GYKEIVATISGRGVFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPE--AAEIDVD 216
           G K     I G   +  +KFE+GVHRVQRVP+TE SGR HTS A+VAV+P+    E+DV+
Sbjct: 185 GIKSATLEIEGESAYGYLKFEAGVHRVQRVPSTETSGRRHTSTASVAVIPQPGRDEVDVE 244

Query: 217 IPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMVTSS-EKSQHQNRLRAMKVLRA 275
           I  +D+RI+T RASG GGQHVN TDSAVR+THIPTGI+V    E+SQH+NR  A+K LRA
Sbjct: 245 IDEKDLRIETFRASGPGGQHVNKTDSAVRLTHIPTGIVVECQEERSQHKNRALALKRLRA 304

Query: 276 RLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHRINLTLYKLEYVLQGY 335
           +L  + R+  + E    RK Q+GS  RSE+IRTYNF Q R+TDHRI L  + LE  L G 
Sbjct: 305 KLAVIYREEKSEEEKKKRKAQVGSLKRSEKIRTYNFKQDRVTDHRIGLESHDLESFLDGN 364

Query: 336 IDDIINPLLTAHQAKMIGSASE 357
           +D++I  LL+  + + +    E
Sbjct: 365 LDELIEALLSLRREEDLAELLE 386


>gnl|CDD|31379 COG1186, PrfB, Protein chain release factor B [Translation,
           ribosomal structure and biogenesis].
          Length = 239

 Score =  191 bits (487), Expect = 2e-49
 Identities = 99/236 (41%), Positives = 143/236 (60%), Gaps = 4/236 (1%)

Query: 112 CILEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRG 171
             L I AG GG+EA  +   L RMY R+A  + +KVEVL +SD ++ G K     I G  
Sbjct: 1   AYLTIHAGAGGTEAQDWASMLLRMYTRWAERKGFKVEVLDTSDGEEAGIKSATLKIKGEN 60

Query: 172 VFSRMKFESGVHRVQRVPATEASGRVHTSAATVAVLPEAAE-IDVDIPLEDIRIDTMRAS 230
            +  +K E+GVHR+ R+   +++GR HTS A+V V PE    I+++IP +D+RIDT RAS
Sbjct: 61  AYGYLKTETGVHRLVRISPFDSNGRRHTSFASVEVFPELDISIEIEIPDDDLRIDTYRAS 120

Query: 231 GSGGQHVNTTDSAVRITHIPTGIMVTS-SEKSQHQNRLRAMKVLRARLYDVERKRMANER 289
           G+GGQHVN TDSAVR+TH+PTGI+V   +E+SQH N+  A K+L+ +LY + +++ + E+
Sbjct: 121 GAGGQHVNKTDSAVRLTHLPTGIVVLCQNERSQHLNKALARKMLKGKLYILAQEKRSQEK 180

Query: 290 SANRKLQIGSGDRSERIRTYNFSQGRIT-DHRINLTLYKLEYVLQGYIDDIINPLL 344
           +  R L+   G    +IR+Y     + T D R  +       VL G  D  I   L
Sbjct: 181 NRERALKKLIG-WGNQIRSYVLDPYQPTKDLRTGVERRNKSKVLDGDKDGFIKAYL 235


>gnl|CDD|144168 pfam00472, RF-1, RF-1 domain.  This domain is found in peptide
           chain release factors such as RF-1 and RF-2, and a
           number of smaller proteins of unknown function. This
           domain contains the peptidyl-tRNA hydrolase activity.
           The domain contains a highly conserved motif GGQ, where
           the glutamine is thought to coordinate the water that
           mediates the hydrolysis.
          Length = 114

 Score =  170 bits (433), Expect = 5e-43
 Identities = 61/114 (53%), Positives = 85/114 (74%), Gaps = 1/114 (0%)

Query: 208 PEAAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAVRITHIPTGIMVTSS-EKSQHQNR 266
           P   E++++IP  D+RIDT R+SG GGQ+VN T+SAVR+TH+PTGI+V    E+SQH+NR
Sbjct: 1   PLDEEVEIEIPPSDLRIDTFRSSGPGGQNVNKTESAVRLTHLPTGIVVKCQEERSQHKNR 60

Query: 267 LRAMKVLRARLYDVERKRMANERSANRKLQIGSGDRSERIRTYNFSQGRITDHR 320
            +A++ L+A+LY+ E ++   E    RK Q+  GDR E+IRTYNF QGR+ DHR
Sbjct: 61  EKALERLKAKLYEAELQKKREETKPTRKSQVRRGDRKEKIRTYNFPQGRVKDHR 114


>gnl|CDD|146218 pfam03462, PCRF, PCRF domain.  This domain is found in peptide
           chain release factors.
          Length = 115

 Score =  155 bits (395), Expect = 1e-38
 Identities = 59/109 (54%), Positives = 75/109 (68%)

Query: 71  SDSEIRDLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVG 130
            D E+R+LA+ E+  +EKE+ ELE E+  LLLP D  DDK+ ILEIRAG GG+EA LF  
Sbjct: 7   DDPELRELAEEELEELEKELEELEKELLNLLLPLDPYDDKNAILEIRAGAGGTEAQLFAE 66

Query: 131 DLFRMYERYAALRKWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMKFE 179
           DL RMY+RYA  + WKVEVL  S+ ++GG KE    I G G +  +KFE
Sbjct: 67  DLLRMYQRYAERKGWKVEVLDYSEGEEGGIKEATLEIEGEGAYGYLKFE 115


>gnl|CDD|38639 KOG3429, KOG3429, KOG3429, Predicted peptidyl-tRNA hydrolase
           [Translation, ribosomal structure and biogenesis].
          Length = 172

 Score = 35.4 bits (81), Expect = 0.022
 Identities = 26/126 (20%), Positives = 47/126 (37%), Gaps = 39/126 (30%)

Query: 210 AAEIDVDIPLEDIRIDTMRASGSGGQHVNTTDSAV------------------------- 244
           A      IPL+ + I   R+SG GGQ+VN  ++ V                         
Sbjct: 30  AIHFKGKIPLDQLEISYSRSSGPGGQNVNKVNTKVEVRFKVSNAEWIPEFLRNKLLTTEK 89

Query: 245 -RITHIPTGIMVTSSEKSQHQNRLRAMKVLRARLY-------------DVERKRMANERS 290
            RI      ++ +   +SQH+N    ++ LR  +               +++ R+  E++
Sbjct: 90  NRINKDGELVIYSDKTRSQHKNIADCLEKLRDIIRAAEQTPPVDPTEETIKKIRIRKEKA 149

Query: 291 ANRKLQ 296
              +LQ
Sbjct: 150 NRERLQ 155


>gnl|CDD|35429 KOG0208, KOG0208, KOG0208, Cation transport ATPase [Inorganic ion
           transport and metabolism].
          Length = 1140

 Score = 30.7 bits (69), Expect = 0.66
 Identities = 16/54 (29%), Positives = 23/54 (42%), Gaps = 5/54 (9%)

Query: 38  EYAAISPIISKISI----YDQKKQEEQDLHTVIGDHNSDSEIRDLAQIEVLAIE 87
            YA    IIS  SI    Y+ +KQ    L +++      + IRD     V + E
Sbjct: 215 YYAFCIVIISVYSIVLSVYETRKQS-IRLRSMVKFTCPVTVIRDGFWETVDSSE 267


>gnl|CDD|144201 pfam00521, DNA_topoisoIV, DNA gyrase/topoisomerase IV, subunit A. 
          Length = 428

 Score = 30.2 bits (69), Expect = 0.88
 Identities = 14/35 (40%), Positives = 20/35 (57%), Gaps = 2/35 (5%)

Query: 75  IRDLAQIEVLAIEKEIRELENEINYL--LLPKDTD 107
           +R L + E+  +EKEI ELE EI  L  +L  +  
Sbjct: 387 LRRLTKEEIEKLEKEIEELEKEIAELEKILASEKK 421


>gnl|CDD|38824 KOG3618, KOG3618, KOG3618, Adenylyl cyclase [General function
           prediction only].
          Length = 1318

 Score = 30.0 bits (67), Expect = 1.0
 Identities = 32/157 (20%), Positives = 55/157 (35%), Gaps = 32/157 (20%)

Query: 175 RMKFESGVHRVQRVPATEASG---RVHTSAATVAVLPEAAEI----DVDIPLEDIRIDTM 227
           R KF+   + V      E+SG   +VH S AT   L +  E+     ++   + +    +
Sbjct: 452 RFKFDVWSNDVNLANLMESSGVAGKVHISEATAKYLDDRYEMEEGKVIEGLGQSVVAGQL 511

Query: 228 RASGSG--------GQHVNTTDSAVRITHIPTGIMVTSSEKSQHQNRLRAMKVLRARLYD 279
           R +  G        GQ   +   +             S  +    N ++  K    R  D
Sbjct: 512 RRTNPGTLKTYLISGQRGASAKES-----------RCSVAEVLSLNSMKMRKKSSGRDRD 560

Query: 280 VERKRMANERSANRKLQI--GSG----DRSERIRTYN 310
            E    +   S   + Q    SG      +ER+RT++
Sbjct: 561 FEVIDGSQVSSIPPRGQGRESSGSLKIKLAERVRTFD 597


>gnl|CDD|32549 COG2414, COG2414, Aldehyde:ferredoxin oxidoreductase [Energy
           production and conversion].
          Length = 614

 Score = 29.1 bits (65), Expect = 1.8
 Identities = 19/70 (27%), Positives = 25/70 (35%), Gaps = 1/70 (1%)

Query: 77  DLAQIEVLAIEKEIRELENEINYLLLPKDTDDDKSCILEIRAGTGGSEAALFVGDLFRMY 136
           ++   ++L   + I  LE   N     K  DD     +      GG  A     DL  M 
Sbjct: 526 EMTPEDLLKAGERIYNLERAYNVKAGVKPEDDTLPKRVFEEPLPGGP-AKGDRNDLEEML 584

Query: 137 ERYAALRKWK 146
           E Y  LR W 
Sbjct: 585 EEYYKLRGWD 594


>gnl|CDD|31718 COG1529, CoxL, Aerobic-type carbon monoxide dehydrogenase, large
           subunit CoxL/CutL homologs [Energy production and
           conversion].
          Length = 731

 Score = 28.8 bits (64), Expect = 2.6
 Identities = 22/122 (18%), Positives = 42/122 (34%), Gaps = 5/122 (4%)

Query: 119 GTGGSEAALFVGDLFRMYERYAALR-KWKVEVLSSSDNDDGGYKEIVATISGRGVFSRMK 177
           G+ GS      G          A +       +  +D +D   ++    + G    S + 
Sbjct: 503 GSVGSRGTAVAGSAVIDAAAKLAEKDPVAAARMLGADAEDVVLEDGAFKVGGGDRRSAVS 562

Query: 178 FESGVHR-VQRVPATEASGRVHTSAATVAVLPEAAEIDVDIPLEDIRIDTMRASGSGGQH 236
            +    + +    A  AS     +    A     AE++VD    ++R+  + A    G+ 
Sbjct: 563 LKEVAGKGLAPGLAVAASFGSDNTYPYGAH---IAEVEVDPETGEVRVLRVVAVDDCGRV 619

Query: 237 VN 238
           VN
Sbjct: 620 VN 621


>gnl|CDD|37877 KOG2666, KOG2666, KOG2666, UDP-glucose/GDP-mannose dehydrogenase
           [Carbohydrate transport and metabolism, Signal
           transduction mechanisms].
          Length = 481

 Score = 28.4 bits (63), Expect = 3.3
 Identities = 18/57 (31%), Positives = 28/57 (49%), Gaps = 7/57 (12%)

Query: 4   LSHKQICDLKNRFAEIELRMSESPSVDAYIKLTEEYAAISPIISKISIYDQKKQEEQ 60
           +S K+I  L   F +      E+P++D    L E+ A       ++SIYD +  EEQ
Sbjct: 322 VSDKKIAILGFAFKKDTGDTRETPAIDVCKGLLEDKA-------RLSIYDPQVTEEQ 371


>gnl|CDD|147274 pfam05009, EBV-NA3, Epstein-Barr virus nuclear antigen 3 (EBNA-3). 
           This family contains EBNA-3A, -3B, and -3C which are
           latent infection nuclear proteins important for
           Epstein-Barr virus (EBV)-induced B-cell immortalisation
           and the immune response to EBV infection.
          Length = 254

 Score = 27.4 bits (61), Expect = 5.9
 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 5/56 (8%)

Query: 274 RARLYDVERKRMANERSANRKLQIGS-----GDRSERIRTYNFSQGRITDHRINLT 324
           R R  D+ R  +      + KL   S     G R+  +  Y++   R+   RI LT
Sbjct: 4   RQRCRDIRRGPLPIRGQRHWKLTSPSRTWPMGYRTASLWMYSYEDDRVGADRIMLT 59


>gnl|CDD|145318 pfam02092, tRNA_synt_2f, Glycyl-tRNA synthetase beta subunit. 
          Length = 549

 Score = 27.4 bits (62), Expect = 6.1
 Identities = 17/52 (32%), Positives = 23/52 (44%), Gaps = 18/52 (34%)

Query: 271 KVLRARLYDVE-------RKRMANERSANRKL-------QIGS-GDRSERIR 307
           +VLRARL D E       +  +    S   KL       ++GS  D+ ERI 
Sbjct: 315 RVLRARLADAEFFYEEDLKTPLE---SRVEKLKKVVFQEKLGSLYDKVERIE 363


>gnl|CDD|29149 cd00187, TOP4c, DNA Topoisomerase, subtype IIA; domain A';
           bacterial DNA topoisomerase IV (C subunit, ParC),
           bacterial DNA gyrases (A subunit, GyrA),mammalian DNA
           toposiomerases II. DNA topoisomerases are essential
           enzymes that regulate the conformational changes in DNA
           topology by catalysing the concerted breakage and
           rejoining of DNA strands during normal cellular growth..
          Length = 445

 Score = 27.1 bits (60), Expect = 8.2
 Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 6/67 (8%)

Query: 41  AISPIISKISIYDQKKQ------EEQDLHTVIGDHNSDSEIRDLAQIEVLAIEKEIRELE 94
            I  +I+ I   D+ K+      E+     +  D   D  +R L ++E   + KE++ELE
Sbjct: 359 NIDEVINLIRSSDEAKKALIEELEKLGFSEIQADAILDMRLRRLTKLEREKLLKELKELE 418

Query: 95  NEINYLL 101
            EI  L 
Sbjct: 419 AEIEDLE 425


>gnl|CDD|36703 KOG1490, KOG1490, KOG1490, GTP-binding protein CRFG/NOG1 (ODN
           superfamily) [General function prediction only].
          Length = 620

 Score = 26.9 bits (59), Expect = 9.9
 Identities = 28/160 (17%), Positives = 53/160 (33%), Gaps = 25/160 (15%)

Query: 18  EIELRMSESPSVD-----AYIKLTEEYAAISPIISKISIYD----------QKKQEEQDL 62
           +IE     + +V+          + +Y  +  I+   ++ D              EE++ 
Sbjct: 394 DIEAENGGAYNVELRDKYILQDPSWKYDIMPEILDGKNVADFVDPEIEAKLLALDEEEER 453

Query: 63  HTVIGDHNSDSEIRDLAQIEVLAIEKEIRE---------LENEINYLLLPKDTDDDKSCI 113
               G ++SD EI D  + EVL     IRE          + + N  +LP+        +
Sbjct: 454 LEREGYYDSDQEIEDEDEEEVLEKASRIREKNKLTMLAARQKKKNRPVLPRTAGRTLDEL 513

Query: 114 LEIRAGTGGSEAALFVGDLFRMYERYAALRKWKVEVLSSS 153
                 + G ++        R     A      +E + S 
Sbjct: 514 QS-SLQSLGLDSDSIEERARRAANEMADGSGVDLEEIRSK 552


  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
   0.316    0.132    0.362 

Gapped
Lambda     K      H
   0.267   0.0671    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,076,939
Number of extensions: 212062
Number of successful extensions: 575
Number of sequences better than 10.0: 1
Number of HSP's gapped: 564
Number of HSP's successfully gapped: 24
Length of query: 357
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 262
Effective length of database: 4,210,882
Effective search space: 1103251084
Effective search space used: 1103251084
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: 41 (21.6 bits)
S2: 58 (26.2 bits)