RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780520|ref|YP_003064933.1| flagellar basal body rod
modification protein [Candidatus Liberibacter asiaticus str. psy62]
         (131 letters)



>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 = 34.2 bits (77), Expect = 0.009
 Identities = 16/46 (34%), Positives = 20/46 (43%), Gaps = 17/46 (36%)

Query: 16 KSKSKKTLGQDAFLKLLITQIKHQDPTEPMKASEQVAQLAVFSQME 61
          K   KK L Q A LKL      + D + P       A LA+ + ME
Sbjct: 19 KQALKK-L-Q-ASLKL------YADDSAP-------A-LAIKATME 47


>2wyt_A Superoxide dismutase [CU-ZN]; oxidoreductase, disease mutation,
           amyotrophic lateral sclero antioxidant; HET: SO4; 1.00A
           {Homo sapiens} PDB: 2wyz_A* 1hl4_A 1spd_A 2c9v_A* 1hl5_A
           1pu0_A 2c9u_A 2c9s_A* 2v0a_A* 3ecu_A 3kh3_A 3kh4_A
           3gzp_A 2wko_A 3gzo_A 1uxl_A 3ecv_A 2yqx_A 2zky_A 1ozu_A
           ...
          Length = 153

 Score = 27.5 bits (61), Expect = 0.84
 Identities = 7/26 (26%), Positives = 11/26 (42%)

Query: 92  NADGSISGVVNAIQVSSTGLTAITVD 117
             DG + G++N  Q  S G   +   
Sbjct: 9   KGDGPVQGIINFEQKESNGPVKVWGS 34


>3dzy_A Retinoic acid receptor RXR-alpha; DNA-binding, HOST-virus
           interaction, metal-binding, nucleus, polymorphism,
           receptor, transcription, transcription regulation; HET:
           DNA REA BRL; 3.10A {Homo sapiens} PDB: 3dzu_A* 3e00_A*
          Length = 467

 Score = 26.4 bits (57), Expect = 1.9
 Identities = 9/66 (13%), Positives = 24/66 (36%), Gaps = 13/66 (19%)

Query: 25  QDAFLKLLITQIKHQDPTEPMK-------------ASEQVAQLAVFSQMEQSVQMNSTLQ 71
           ++     L    KH+ P +P +                +  +   F ++     +++ L 
Sbjct: 398 REKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLM 457

Query: 72  ELLKSN 77
           E+L++ 
Sbjct: 458 EMLEAP 463


>1xtm_B Hypothetical superoxide dismutase-like protein YOJM; SOD, Cu-Zn
           SOD, SOD-like, superoxide dismutase mutants, structural
           genomics; 1.60A {Bacillus subtilis} PDB: 1xtl_B 1s4i_B
           1u3n_A
          Length = 175

 Score = 25.7 bits (56), Expect = 3.4
 Identities = 6/29 (20%), Positives = 11/29 (37%), Gaps = 1/29 (3%)

Query: 89  NITNADGSISGVVNAIQVSSTGLTAITVD 117
            + N +G   G +   +    GL  I + 
Sbjct: 25  QLVNREGKAVGFIEIKESDDEGLD-IHIS 52


>3l9y_A Cu-znsod1, superoxide dismutase [CU-ZN]; greek-KEY-barrel,
           antioxidant, copper, cytoplasm, metal- binding,
           oxidoreductase; 1.80A {Bombyx mori} PDB: 3l9e_A
          Length = 154

 Score = 25.4 bits (55), Expect = 3.9
 Identities = 5/23 (21%), Positives = 9/23 (39%)

Query: 95  GSISGVVNAIQVSSTGLTAITVD 117
           G +SG V   Q        ++ +
Sbjct: 11  GDVSGTVFFDQQDEKSPVVVSGE 33


>3cc6_A Protein tyrosine kinase 2 beta; focal adhesion kinase, structural
           genomics, structural genomics consortium, SGC,
           alternative splicing; 1.60A {Homo sapiens} PDB: 3fzs_A*
           3et7_A 3fzo_A* 3fzr_A* 3fzp_A* 3fzt_A* 3h3c_A*
          Length = 281

 Score = 25.1 bits (54), Expect = 5.0
 Identities = 12/38 (31%), Positives = 21/38 (55%)

Query: 29  LKLLITQIKHQDPTEPMKASEQVAQLAVFSQMEQSVQM 66
           L  L+T+    DP++  + +E V  L+   QME+ + M
Sbjct: 243 LYTLMTRCWDYDPSDRPRFTELVCSLSDVYQMEKDIAM 280


>1pzl_A Hepatocyte nuclear factor 4-alpha; transcription; HET: MYR; 2.10A
           {Homo sapiens} SCOP: a.123.1.1 PDB: 3fs1_A* 1m7w_A*
           1lv2_A*
          Length = 237

 Score = 25.0 bits (54), Expect = 6.0
 Identities = 8/67 (11%), Positives = 22/67 (32%), Gaps = 13/67 (19%)

Query: 25  QDAFLKLLITQIKHQDPTEPMK-------------ASEQVAQLAVFSQMEQSVQMNSTLQ 71
           +      L   I  +      +              + Q+ +   F ++    ++++ LQ
Sbjct: 171 RSQVQVSLEDYINDRQYDSRGRFGEXXXXXPTLQSITWQMIEQIQFIKLFGMAKIDNLLQ 230

Query: 72  ELLKSNN 78
           E+L   +
Sbjct: 231 EMLLGGS 237


>2p1t_A Retinoic acid receptor RXR-alpha; protein-ligand complex, hormone
           receptor; HET: 3TN; 1.80A {Homo sapiens} SCOP: a.123.1.1
           PDB: 1mvc_A* 1mzn_A* 1mv9_A* 2p1u_A* 2p1v_A* 2zxz_A*
           2zy0_A* 3fug_A* 3e94_A* 1fby_A* 3fc6_A* 1rdt_A* 3fal_A*
           1g5y_A* 1fm9_A* 1g1u_A 1fm6_A* 1k74_A* 2acl_A* 1xvp_A*
           ...
          Length = 240

 Score = 24.7 bits (53), Expect = 7.8
 Identities = 9/66 (13%), Positives = 24/66 (36%), Gaps = 13/66 (19%)

Query: 25  QDAFLKLLITQIKHQDPTEPMK-------------ASEQVAQLAVFSQMEQSVQMNSTLQ 71
           ++     L    KH+ P +P +                +  +   F ++     +++ L 
Sbjct: 171 REKVYASLEAYCKHKYPEQPGRFAKLLLRLPALRSIGLKCLEHLFFFKLIGDTPIDTFLM 230

Query: 72  ELLKSN 77
           E+L++ 
Sbjct: 231 EMLEAP 236


>1f1g_A Cuznsod, copper-zinc superoxide dismutase; nitric oxide,
           oxidoreductase; 1.35A {Saccharomyces cerevisiae} SCOP:
           b.1.8.1 PDB: 1f1a_A 1f18_A 1jcv_A 1b4l_A 1sdy_A 1yaz_A
           1yso_A 2jcw_A 1f1d_A 1jk9_A 1b4t_A
          Length = 154

 Score = 24.5 bits (53), Expect = 7.9
 Identities = 8/26 (30%), Positives = 13/26 (50%)

Query: 92  NADGSISGVVNAIQVSSTGLTAITVD 117
             D  +SGVV   Q S +  T ++ +
Sbjct: 9   KGDAGVSGVVKFEQASESEPTTVSYE 34


>3cjw_A COUP transcription factor 2; COUP-TFII, nuclear receptor, ligand
           binding domain, orphan receptor, three-layered helical
           sandwich, DNA-binding; 1.48A {Homo sapiens}
          Length = 244

 Score = 24.3 bits (52), Expect = 9.8
 Identities = 10/67 (14%), Positives = 25/67 (37%), Gaps = 13/67 (19%)

Query: 25  QDAFLKLLITQIKHQDPTEPMK-------------ASEQVAQLAVFSQMEQSVQMNSTLQ 71
           Q+     L   ++ Q P +P +              S  V +   F ++     + + ++
Sbjct: 168 QEKSQCALEEYVRSQYPNQPTRFGKLLLRLPSLRTVSSSVIEQLFFVRLVGKTPIETLIR 227

Query: 72  ELLKSNN 78
           ++L S +
Sbjct: 228 DMLLSGS 234


  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
   0.307    0.121    0.306 

Gapped
Lambda     K      H
   0.267   0.0561    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 855,570
Number of extensions: 30559
Number of successful extensions: 94
Number of sequences better than 10.0: 1
Number of HSP's gapped: 93
Number of HSP's successfully gapped: 25
Length of query: 131
Length of database: 5,693,230
Length adjustment: 82
Effective length of query: 49
Effective length of database: 3,705,222
Effective search space: 181555878
Effective search space used: 181555878
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 51 (23.8 bits)