RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

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

Query= gi|254780295|ref|YP_003064708.1| tRNA pseudouridine synthase A
[Candidatus Liberibacter asiaticus str. psy62]
         (247 letters)



>1dj0_A Pseudouridine synthase I; alpha/beta fold, RNA-binding motif,
           RNA-modifying enzyme, lyase; 1.50A {Escherichia coli}
           SCOP: d.265.1.1 PDB: 2nqp_A 2nr0_A 2nre_A
          Length = 264

 Score =  271 bits (695), Expect = 9e-74
 Identities = 90/246 (36%), Positives = 130/246 (52%), Gaps = 2/246 (0%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQ 60
           + +  + IEY+GS Y+GWQRQ    S+Q  +EKA+  V  E + V  AGRTD+GVH   Q
Sbjct: 3   VYKIALGIEYDGSKYYGWQRQNEVRSVQEKLEKALSQVANEPITVFCAGRTDAGVHGTGQ 62

Query: 61  VAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQ 120
           V HF+             +NA L     I++  +  V   FHARFSA  R Y Y I   +
Sbjct: 63  VVHFETTALRKDAAWTLGVNANLP--GDIAVRWVKTVPDDFHARFSATARRYRYIIYNHR 120

Query: 121 APLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIRTIDHFDVNSF 180
              A+         + LD E M  AAQ L+G +DFT+FR++ CQ+ +P R + H +V   
Sbjct: 121 LRPAVLSKGVTHFYEPLDAERMHRAAQCLLGENDFTSFRAVQCQSRTPWRNVMHINVTRH 180

Query: 181 GNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPEGLY 240
           G  + + + A +F+H  +R+ VGSL  VG      + + + L A+DR      A  EGLY
Sbjct: 181 GPYVVVDIKANAFVHHMVRNIVGSLMEVGAHNQPESWIAELLAAKDRTLAAATAKAEGLY 240

Query: 241 FDSVEY 246
             +V+Y
Sbjct: 241 LVAVDY 246


>1vs3_A TRNA pseudouridine synthase A; TRUA, tRNA modification, structural
           genomics, NPPSFA; 2.25A {Thermus thermophilus HB8}
          Length = 249

 Score =  172 bits (437), Expect = 5e-44
 Identities = 84/249 (33%), Positives = 117/249 (46%), Gaps = 6/249 (2%)

Query: 1   MIRYCMIIEYNGSGYFGWQRQKNG-SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALR 59
           M R  ++ EY+G+ + G QRQ  G  ++QG +E+A+  +      V  AGRTD+GVHAL 
Sbjct: 1   MRRLLLLCEYDGTLFAGLQRQGRGLRTVQGELERALPGIGALPKAV-AAGRTDAGVHALA 59

Query: 60  QVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSAIRRSYLYRIITR 119
              H D+        + +ALN  L     +       V   FHAR  A+ R+Y YRI+ R
Sbjct: 60  MPFHVDVESAIPVEKVPEALNRLLPEDLKVVGAR--EVAPDFHARKDALWRAYRYRILVR 117

Query: 120 QAPLALEKGRAWLIPKSLDCENMRIAAQHLVGRHDFTTFRSIHCQASSPIR--TIDHFDV 177
             P  L + RA  + + LD E M  A   L+GRH+F  F     +               
Sbjct: 118 PHPSPLLRHRALWVRRPLDLEAMEEALSLLLGRHNFLGFAKEETRPGERELLEARLQVAE 177

Query: 178 NSFGNLIEIRVVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKECGPLAPPE 237
              G  + +    +SFL  Q+R  VG+L  VG GK     L+  L+  DR+  GP AP  
Sbjct: 178 GEAGLEVRLYFRGKSFLRGQVRGMVGTLLEVGLGKRPPESLKAILKTADRRLAGPTAPAH 237

Query: 238 GLYFDSVEY 246
           GLYF    Y
Sbjct: 238 GLYFVEAAY 246


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 34.9 bits (80), Expect = 0.018
 Identities = 42/231 (18%), Positives = 75/231 (32%), Gaps = 87/231 (37%)

Query: 25  SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLK 84
           S ++ S+E             +  G   S + ++      +L +E V   +    N++L 
Sbjct: 322 SILEDSLE-------------NNEG-VPSPMLSIS-----NLTQEQVQDYV-NKTNSHLP 361

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSY--------LYRIITR----QAPLALEKGRAWL 132
               + I   S+V+           ++         LY +       +AP  L++ R   
Sbjct: 362 AGKQVEI---SLVNG---------AKNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSR--- 406

Query: 133 IPKS---LDCENMR---IAA----QHLVG-----RHDFTTFRSIHCQASS---PI-RTID 173
           IP S   L   N R   +A+      LV        D     ++   A     P+  T D
Sbjct: 407 IPFSERKLKFSN-RFLPVASPFHSHLLVPASDLINKDL-VKNNVSFNAKDIQIPVYDTFD 464

Query: 174 HFDVNSF-GNLIE--IRVVARSFLH---------TQIRSF-------VGSL 205
             D+    G++ E  +  + R  +          T I  F       +G L
Sbjct: 465 GSDLRVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGASGLGVL 515



 Score = 28.0 bits (62), Expect = 2.0
 Identities = 6/53 (11%), Positives = 15/53 (28%), Gaps = 23/53 (43%)

Query: 55  VHALRQVAHFDLVREWVPVILCKALNAYLKISDTISILNLSIVDKQFHARFSA 107
           +  + Q+AH+        V+  K             +L  +    +  +    
Sbjct: 240 LIGVIQLAHY--------VVTAK-------------LLGFT--PGELRSYLKG 269



 Score = 27.2 bits (60), Expect = 3.8
 Identities = 15/129 (11%), Positives = 43/129 (33%), Gaps = 38/129 (29%)

Query: 90  SILNLSIVDKQFHARFSAIRRSYLYRIITR---QAPLALEKGRAWLIPKSLDCENMRI-- 144
            +LNL +   +F   +  +  + ++ +  +   +    L K +  +          +   
Sbjct: 82  QVLNLCL--TEFENCY--LEGNDIHALAAKLLQENDTTLVKTKELI----------KNYI 127

Query: 145 AAQHLVGR-----HDFTTFRSIHCQASSPIRTI--------DHFDVNSFGNLIEIRVVAR 191
            A+ +  R      +   FR+   + ++ +  I        D+F+      L ++     
Sbjct: 128 TARIMAKRPFDKKSNSALFRA-VGEGNAQLVAIFGGQGNTDDYFE-----ELRDLYQTYH 181

Query: 192 SFLHTQIRS 200
             +   I+ 
Sbjct: 182 VLVGDLIKF 190


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
           photosynthetic reaction center, peripheral antenna; HET:
           CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 28.4 bits (62), Expect = 1.6
 Identities = 9/27 (33%), Positives = 11/27 (40%), Gaps = 7/27 (25%)

Query: 197 Q-IRSFVGSLKLVGDGKWTSTDLEKAL 222
           Q ++    SLKL  D      D   AL
Sbjct: 20  QALKKLQASLKLYAD------DSAPAL 40


>3mfi_A DNA polymerase ETA; DNA damage, DNA repair, DNA replication, DNA
           synthesis, NUCL binding, magnesium; HET: DNA DOC TTD
           DTP; 1.76A {Saccharomyces cerevisiae} PDB: 3mfh_A*
           2r8j_A* 2r8k_A* 2wtf_A* 1jih_A*
          Length = 520

 Score = 27.5 bits (60), Expect = 3.1
 Identities = 7/27 (25%), Positives = 11/27 (40%)

Query: 154 DFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +     S      S +  I H D+N+F
Sbjct: 15  ELIQLGSPSKAYESSLACIAHIDMNAF 41


>1hks_A Heat-shock transcription factor; transcription regulation; NMR
           {Drosophila melanogaster} SCOP: a.4.5.22 PDB: 1hkt_A
          Length = 106

 Score = 27.1 bits (60), Expect = 3.6
 Identities = 11/42 (26%), Positives = 19/42 (45%)

Query: 188 VVARSFLHTQIRSFVGSLKLVGDGKWTSTDLEKALQAQDRKE 229
           ++  ++ H  + SF+  L + G  K TS D       +D  E
Sbjct: 45  LLPLNYKHNNMASFIRQLNMYGFHKITSIDNGGLRFDRDEIE 86


>3h9u_A Adenosylhomocysteinase; NAD CO-factor complex, structural genomics,
           SGC stockholm, structural genomics consortium, SGC,
           hydrolase, NAD; HET: NAD ADN PG4; 1.90A {Trypanosoma
           brucei} PDB: 3g1u_A* 1b3r_A* 1k0u_A* 1ky4_A* 2h5l_A*
           1xwf_A* 1d4f_A* 1ky5_A* 1li4_A* 1a7a_A*
          Length = 436

 Score = 26.8 bits (59), Expect = 4.4
 Identities = 22/125 (17%), Positives = 35/125 (28%), Gaps = 11/125 (8%)

Query: 25  SSIQGSIEKAIFLVTGEIVVVHGAGRTDSGVHALRQVAHFDLVREWVPVILCKALNAYLK 84
           S + G       ++ G+   V G G    G  A         V     V     +NA   
Sbjct: 196 SLVDGIKRATDVMIAGKTACVCGYGDVGKGC-AAALRGFGARVV----VTEVDPINALQA 250

Query: 85  ISDTISILNLSIVDKQFHARFSAIRRSYLYRIITRQAPLALEKGRAWLIPKSLDCENMRI 144
             +   +L +  V ++ H   +         IIT +    +            D E   I
Sbjct: 251 AMEGYQVLLVEDVVEEAHIFVTTTG---NDDIITSEHFPRMRDDAIVCNIGHFDTE---I 304

Query: 145 AAQHL 149
               L
Sbjct: 305 QVAWL 309


>3p3y_A Neurofascin; IG domains, cell adhesion; HET: NAG; 2.60A {Homo
           sapiens} PDB: 3p40_A*
          Length = 404

 Score = 26.6 bits (57), Expect = 5.2
 Identities = 6/34 (17%), Positives = 12/34 (35%)

Query: 22  KNGSSIQGSIEKAIFLVTGEIVVVHGAGRTDSGV 55
            NG  +Q +       V G+ ++      +   V
Sbjct: 348 VNGEPLQSAPPNPNREVAGDTIIFRDTQISSRAV 381


>2o8l_A V8 protease, taphylococcal serine; serine protease, enzyme,
           hydrolase; 1.50A {Staphylococcus aureus} SCOP: b.47.1.1
           PDB: 1qy6_A
          Length = 274

 Score = 26.0 bits (56), Expect = 7.8
 Identities = 11/63 (17%), Positives = 22/63 (34%), Gaps = 3/63 (4%)

Query: 5   CMIIEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTGEIVVVHGAGRTD---SGVHALRQV 61
               +   +   G   Q + S+  G+    +F    E++ +H  G  +     V     V
Sbjct: 143 MWESKGKITYLKGEAMQYDLSTTGGNSGSPVFNEKNEVIGIHWGGVPNEFNGAVFINENV 202

Query: 62  AHF 64
            +F
Sbjct: 203 RNF 205


>1moe_A Anti-CEA MAB T84.66; anti carcinoembryonic antigen, diabody,
          dimer, SCFV, variable domain, immune system; 2.60A {Mus
          musculus} SCOP: b.1.1.1 b.1.1.1
          Length = 240

 Score = 26.0 bits (57), Expect = 7.8
 Identities = 10/33 (30%), Positives = 17/33 (51%)

Query: 8  IEYNGSGYFGWQRQKNGSSIQGSIEKAIFLVTG 40
          ++  G G+  W +QK G   +  I +A  L +G
Sbjct: 29 VDIFGVGFLHWYQQKPGQPPKLLIYRASNLESG 61


>2wam_A RV2714, conserved hypothetical alanine and leucine rich protein;
           unknown function; 2.60A {Mycobacterium tuberculosis}
          Length = 351

 Score = 25.7 bits (56), Expect = 9.1
 Identities = 9/38 (23%), Positives = 13/38 (34%), Gaps = 6/38 (15%)

Query: 143 RIAAQHLVGRHDFTTFRSIHC------QASSPIRTIDH 174
           R+AA HL    D     S         ++  P+ T   
Sbjct: 83  RLAAAHLKAALDTELVASFAIDELLDYRSRRPLMTFKT 120


>1jih_A DNA polymerase ETA; translesion, yeast, translation; HET: DNA;
           2.25A {Saccharomyces cerevisiae} SCOP: d.240.1.1 e.8.1.7
           PDB: 2r8j_A* 2r8k_A*
          Length = 513

 Score = 25.7 bits (55), Expect = 9.5
 Identities = 7/27 (25%), Positives = 11/27 (40%)

Query: 154 DFTTFRSIHCQASSPIRTIDHFDVNSF 180
           +     S      S +  I H D+N+F
Sbjct: 8   ELIQLGSPSKAYESSLACIAHIDMNAF 34


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.325    0.138    0.421 

Gapped
Lambda     K      H
   0.267   0.0400    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,212,469
Number of extensions: 99465
Number of successful extensions: 365
Number of sequences better than 10.0: 1
Number of HSP's gapped: 361
Number of HSP's successfully gapped: 19
Length of query: 247
Length of database: 5,693,230
Length adjustment: 90
Effective length of query: 157
Effective length of database: 3,511,270
Effective search space: 551269390
Effective search space used: 551269390
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 55 (25.8 bits)