RPS-BLAST 2.2.26 [Sep-21-2011]

Database: pdb70 
           27,921 sequences; 6,701,793 total letters

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

Query= psy12393
         (155 letters)



>2ysa_A Retinoblastoma-binding protein 6; zinc finger, CCHC, structural
          genomics, NPPSFA, national project on protein
          structural and functional analyses; NMR {Homo sapiens}
          Length = 55

 Score = 37.5 bits (87), Expect = 8e-05
 Identities = 11/36 (30%), Positives = 14/36 (38%)

Query: 17 KQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQL 52
              S Y C  C   GHYI +CP      F    ++
Sbjct: 2  SSGSSGYTCFRCGKPGHYIKNCPTNGDKNFESGPRI 37


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

 Score = 37.3 bits (86), Expect = 0.001
 Identities = 35/178 (19%), Positives = 53/178 (29%), Gaps = 44/178 (24%)

Query: 8   DLHLEKKSFKQPPSAYLCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKGEGLTPY 67
           D+H       Q     L     +  +YIT   +    PF K     LF+A  +G      
Sbjct: 100 DIHALAAKLLQENDTTLVKTKELIKNYITARIMAK-RPFDKKSNSALFRAVGEGNA-QLV 157

Query: 68  -----QG-KKRCFGE----YKCSK-CKRKWMSGNSWANMGQECIKCNIN---VYPHKQRP 113
                QG     F E    Y+         +     A    E I+  ++   V+      
Sbjct: 158 AIFGGQGNTDDYFEELRDLYQTYHVLVGDLIK--FSAETLSELIRTTLDAEKVFTQ---- 211

Query: 114 LEKPDGLDV----SDQSKVHPM-YLCE---KCK-----QLGYY---CRKY-CTPSSVR 154
                GL++     + S      YL      C      QL +Y    +    TP  +R
Sbjct: 212 -----GLNILEWLENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELR 264



 Score = 35.8 bits (82), Expect = 0.004
 Identities = 14/69 (20%), Positives = 21/69 (30%), Gaps = 20/69 (28%)

Query: 7   CDLH--LEKKSFKQPPSAYLCH----LCFVG----GHYITDCPLFNMSPFSKYRQLFLFQ 56
            ++   LE  S   P   YL         +G     HY+    L   +P          +
Sbjct: 213 LNILEWLENPS-NTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTP---------GE 262

Query: 57  ARPKGEGLT 65
            R   +G T
Sbjct: 263 LRSYLKGAT 271


>3ts2_A Protein LIN-28 homolog A; microrna biogenesis, protein-RNA complex,
           PRE-element, CCHC knuckle; HET: GMP; 2.01A {Mus
           musculus} PDB: 3trz_A* 3ts0_A*
          Length = 148

 Score = 28.8 bits (64), Expect = 0.53
 Identities = 10/24 (41%), Positives = 11/24 (45%)

Query: 17  KQPPSAYLCHLCFVGGHYITDCPL 40
           K PP    CH C    H +  CPL
Sbjct: 114 KLPPQPKKCHFCQSINHMVASCPL 137


>2cqf_A RNA-binding protein LIN-28; CCHC zinc-finger, structural
          genomics, NPPSFA, national project on protein
          structural and functional analyses; NMR {Homo sapiens}
          Length = 63

 Score = 25.7 bits (56), Expect = 2.3
 Identities = 10/24 (41%), Positives = 11/24 (45%)

Query: 17 KQPPSAYLCHLCFVGGHYITDCPL 40
          K PP    CH C    H +  CPL
Sbjct: 24 KLPPQPKKCHFCQSISHMVASCPL 47


>4ayb_B DNA-directed RNA polymerase; transferase, multi-subunit,
            transcription; 3.20A {Sulfolobus shibatae} PDB: 2wb1_B
            2y0s_B 2waq_B 4b1o_B 4b1p_R 2pmz_B 3hkz_B
          Length = 1131

 Score = 26.7 bits (59), Expect = 3.6
 Identities = 8/31 (25%), Positives = 18/31 (58%), Gaps = 3/31 (9%)

Query: 120  LDVSDQSKVHPMYLCEKCKQLGYYCRKYCTP 150
            LD SD++ ++   +C++C  +G+Y +     
Sbjct: 1053 LDNSDRTTIY---VCDQCGYIGWYDKNKNKY 1080


>2ljw_A ALR2454 protein; novel fold, structural genomics, northeast
          structural genomi consortium, NESG, PSI-biology,
          protein structure initiative function; NMR {Nostoc SP}
          Length = 110

 Score = 25.6 bits (56), Expect = 4.6
 Identities = 7/18 (38%), Positives = 10/18 (55%)

Query: 10 HLEKKSFKQPPSAYLCHL 27
          +LE+ SF    + Y  HL
Sbjct: 37 YLEQASFPMNETEYQEHL 54


>2wpn_A Periplasmic [nifese] hydrogenase, small subunit; metal-binding,
           oxidoreductase, oxygen tolerance; HET: FSX SBY PSW;
           2.04A {Desulfovibrio vulgaris}
          Length = 317

 Score = 26.2 bits (57), Expect = 5.8
 Identities = 20/116 (17%), Positives = 35/116 (30%), Gaps = 22/116 (18%)

Query: 5   SLCDLHLEKKSFKQPPSAY---LCHLCFVGGHYITDCPLFNMSPFSKYRQLFLFQARPKG 61
            L ++     S  +P   +   +   C     Y  D  + + +   K    +        
Sbjct: 219 GLAEVVKVLDSDGRPTPFFGRNIHENCPYLDKY--DEGVMSATFTDKVGCRY-------- 268

Query: 62  EGLTPYQGKKRCFGEYKCSKC-KRKWMSGNSWANMGQECIKCNINVYPHKQRPLEK 116
                      C G    + C +RKW  G +W      CI C    +P  + P  +
Sbjct: 269 --------DLGCKGPMTMADCFERKWNGGVNWCVQNAVCIGCVEPDFPDGKSPFYQ 316


>1wza_A Alpha-amylase A; hydrolase, halophilic, thermophilic; 1.60A
           {Halothermothrix orenii} SCOP: b.71.1.1 c.1.8.1
          Length = 488

 Score = 26.0 bits (58), Expect = 5.8
 Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 8/32 (25%)

Query: 118 DGLDVSDQSKVHPMY--------LCEKCKQLG 141
            G DV+D  K++P Y        L E   Q G
Sbjct: 64  HGYDVTDYYKINPDYGTLEDFHKLVEAAHQRG 95


>3h0g_B DNA-directed RNA polymerase II subunit RPB2; transcription,
            multi-protein complex, DNA- binding, magnesium; 3.65A
            {Schizosaccharomyces pombe}
          Length = 1210

 Score = 26.4 bits (58), Expect = 5.9
 Identities = 6/30 (20%), Positives = 11/30 (36%), Gaps = 4/30 (13%)

Query: 124  DQSKVHPMYLCEKCKQLGYYCRK----YCT 149
            D S  + + +C+ C  +     K     C 
Sbjct: 1142 DCSDAYRVIVCDICGLIAIASYKKDSYECR 1171


>2li8_A Protein LIN-28 homolog A; zinc finger, micro RNA,
          transcription-RNA complex; NMR {Homo sapiens}
          Length = 74

 Score = 24.6 bits (53), Expect = 6.5
 Identities = 10/24 (41%), Positives = 11/24 (45%)

Query: 17 KQPPSAYLCHLCFVGGHYITDCPL 40
          K PP    CH C    H +  CPL
Sbjct: 41 KLPPQPKKCHFCQSISHMVASCPL 64


>2e4u_A Metabotropic glutamate receptor 3; G-protein-coupled receptor,
           neuron, central nerve system, SI protein; HET: NAG GLU;
           2.35A {Rattus norvegicus} PDB: 2e4v_A* 2e4w_A* 2e4x_A*
           2e4y_A*
          Length = 555

 Score = 25.5 bits (56), Expect = 9.2
 Identities = 8/54 (14%), Positives = 12/54 (22%), Gaps = 8/54 (14%)

Query: 59  PKGEGLTPYQGKKRCFGEYKCSKCKRKWMSGNSWANMGQECIKCNINVYPHKQR 112
              E      G   C+    C  C         +      C+ C    +P    
Sbjct: 490 APNEMKNMQPGDVCCW---ICIPC-----EPYEYLVDEFTCMDCGPGQWPTADL 535


>1twf_B DNA-directed RNA polymerase II 140 kDa polypeptid; transcription,
            mRNA, multiprotein complex; HET: UTP; 2.30A
            {Saccharomyces cerevisiae} SCOP: e.29.1.1 PDB: 1i3q_B
            1i6h_B 1k83_B* 1nik_B 1nt9_B 1pqv_B 1r5u_B 1r9s_B*
            1r9t_B* 1sfo_B* 1twa_B* 1twc_B* 1i50_B* 1twg_B* 1twh_B*
            1wcm_B 1y1v_B 1y1w_B 1y1y_B 1y77_B* ...
          Length = 1224

 Score = 25.6 bits (56), Expect = 9.5
 Identities = 3/20 (15%), Positives = 8/20 (40%)

Query: 124  DQSKVHPMYLCEKCKQLGYY 143
            + S    +++C  C  +   
Sbjct: 1153 EASDAFRVHICGICGLMTVI 1172


  Database: pdb70
    Posted date:  Sep 4, 2012  3:40 AM
  Number of letters in database: 6,701,793
  Number of sequences in database:  27,921
  
Lambda     K      H
   0.324    0.140    0.479 

Gapped
Lambda     K      H
   0.267   0.0620    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 2,379,839
Number of extensions: 125046
Number of successful extensions: 306
Number of sequences better than 10.0: 1
Number of HSP's gapped: 303
Number of HSP's successfully gapped: 42
Length of query: 155
Length of database: 6,701,793
Length adjustment: 86
Effective length of query: 69
Effective length of database: 4,300,587
Effective search space: 296740503
Effective search space used: 296740503
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: 41 (22.0 bits)
S2: 53 (24.4 bits)