RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13111
         (127 letters)



>1twf_A B220, DNA-directed RNA polymerase II largest subunit; transcription,
            mRNA, multiprotein complex; HET: UTP; 2.30A
            {Saccharomyces cerevisiae} SCOP: e.29.1.2 PDB: 1i3q_A
            1i6h_A 1k83_A* 1nik_A 1nt9_A 1pqv_A 1r5u_A 1r9s_A*
            1r9t_A* 1sfo_A* 1twa_A* 1twc_A* 1i50_A* 1twg_A* 1twh_A*
            1wcm_A 1y1v_A 1y1w_A 1y1y_A 1y77_A* ...
          Length = 1733

 Score = 30.1 bits (67), Expect = 0.21
 Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 1/60 (1%)

Query: 31   TAIGQNHSAAGPMPIPKVNNYHQTYSPWAFSVPGSSPHSPLKYMKLSYASAPGKLPSSPT 90
            +    ++S   P   P   +Y  T   ++ + P  SP SP  Y   S + +P     SPT
Sbjct: 1578 SPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPTSPSYSPTSPSYSPT 1636



 Score = 28.5 bits (63), Expect = 0.59
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 4/58 (6%)

Query: 36   NHSAAGPMPIPKVNNYHQTYSPWAFSVPGSSPHSPLKYMKLSYA---SAPGKLPSSPT 90
            ++S   P   P    Y  T   ++ + P  SP SP  Y   S +   ++P   P+SP+
Sbjct: 1646 SYSPTSPSYSPTSPAYSPTSPSYSPTSPSYSPTSP-SYSPTSPSYSPTSPNYSPTSPS 1702


>3iyl_X VP3; non-enveloped virus, membrane penetration protein, autocleav
           myristol group, icosahedral virus; HET: MYR; 3.30A
           {Grass carp reovirus} PDB: 3k1q_C 3k1q_B
          Length = 1214

 Score = 26.7 bits (58), Expect = 2.4
 Identities = 16/44 (36%), Positives = 18/44 (40%), Gaps = 1/44 (2%)

Query: 40  AGPMPIP-KVNNYHQTYSPWAFSVPGSSPHSPLKYMKLSYASAP 82
           A P PI   V   HQT     FS PG  P   L    ++   AP
Sbjct: 594 AQPEPIAIGVPGMHQTTPASQFSHPGVWPPGFLNPQLINPQQAP 637


>1ej6_B Lambda1; icosahedral, non-equivalence, dsRNA virus, methylase,
           methyltransferase, guanylyltransferase, zinc finger,
           icosahedral virus; 3.60A {Reovirus SP} SCOP: i.7.1.1
           PDB: 2cse_V
          Length = 1275

 Score = 26.0 bits (56), Expect = 4.4
 Identities = 13/44 (29%), Positives = 17/44 (38%), Gaps = 1/44 (2%)

Query: 40  AGPMPIP-KVNNYHQTYSPWAFSVPGSSPHSPLKYMKLSYASAP 82
            G   IP     Y Q+    AFS P + P   +    +S   AP
Sbjct: 657 VGFETIPMDNQIYTQSRRASAFSTPHTWPRCFMNIQLISPIDAP 700


>1agx_A Glutaminase-asparaginase; bacterial amidohydrolase; 2.90A
           {Acinetobacter glutaminasificans} SCOP: c.88.1.1
          Length = 331

 Score = 25.7 bits (57), Expect = 4.5
 Identities = 7/30 (23%), Positives = 11/30 (36%), Gaps = 5/30 (16%)

Query: 1   MSSYAHSDQCQNGRVDPEYQKNLSKPGLVA 30
            SS     +   G V    ++   K G +A
Sbjct: 274 RSS-----RVAQGFVLRNAEQPDDKYGWIA 298


>3rlf_G Maltose transport system permease protein MALG; integral membrane
           protein, ATPase, ABC transporter, membrane
           transmembrane; HET: UMQ MAL PGV ANP; 2.20A {Escherichia
           coli} PDB: 3fh6_G 2r6g_G* 3puv_G* 3pux_G* 3puy_G*
           3puz_G* 3pv0_G* 3puw_G*
          Length = 296

 Score = 25.8 bits (57), Expect = 4.9
 Identities = 5/11 (45%), Positives = 5/11 (45%)

Query: 23  LSKPGLVATAI 33
           LS P L    I
Sbjct: 210 LSVPILAVVFI 220


>1wsa_A Asparaginase, asparagine amidohydrolase; periplasmic; 2.20A
           {Wolinella succinogenes} SCOP: c.88.1.1
          Length = 330

 Score = 25.6 bits (57), Expect = 5.8
 Identities = 6/22 (27%), Positives = 10/22 (45%)

Query: 9   QCQNGRVDPEYQKNLSKPGLVA 30
           +  +G    E + +  K G VA
Sbjct: 276 RVGSGSTTQEAEVDDKKLGFVA 297


>3nco_A Endoglucanase fncel5A; fncel5A, F. nodosum RT17-B1, hydrolase;
           1.50A {Fervidobacterium nodosum} PDB: 3rjx_A 3rjy_A*
          Length = 320

 Score = 25.2 bits (55), Expect = 7.1
 Identities = 10/55 (18%), Positives = 22/55 (40%), Gaps = 5/55 (9%)

Query: 28  LVATAIGQNHSAAGPMPIPKVNN----YHQTYSPWAFSVPGSSPHSPLKYMKLSY 78
           ++      N+S    + +    N    +H  Y P+ F+  G+   SP   + + +
Sbjct: 175 IIDVPNWSNYSYVRELKLVDDKNIIVSFHY-YEPFNFTHQGAEWVSPTLPIGVKW 228


>1nns_A L-asparaginase II; amidrohydrolase, crystallographic comparison
           hydrolase; 1.95A {Escherichia coli} SCOP: c.88.1.1 PDB:
           3eca_A 1ho3_A 1jaz_A 1ihd_A 1jja_A 4eca_A*
          Length = 326

 Score = 25.2 bits (56), Expect = 7.6
 Identities = 5/22 (22%), Positives = 10/22 (45%)

Query: 9   QCQNGRVDPEYQKNLSKPGLVA 30
           +   G    + + + +K G VA
Sbjct: 272 RVPTGATTQDAEVDDAKYGFVA 293


>3h0g_A DNA-directed RNA polymerase II subunit RPB1; transcription,
            multi-protein complex, DNA- binding, magnesium; 3.65A
            {Schizosaccharomyces pombe}
          Length = 1752

 Score = 25.0 bits (54), Expect = 9.9
 Identities = 17/60 (28%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 31   TAIGQNHSAAGPMPIPKVNNYHQTYSPWAFSVPGSSPHSPLKYMKLSYASAPGKLPSSPT 90
            +A   ++S   P   P   +Y  T   ++ + P  SP SP  Y   S + +P     SPT
Sbjct: 1607 SATSPSYSPTSPSYSPTSPSYSPTSPSYSPTSPSYSPTSP-SYSPTSPSYSPTSPSYSPT 1665


  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
   0.315    0.129    0.422 

Gapped
Lambda     K      H
   0.267   0.0675    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,910,521
Number of extensions: 92106
Number of successful extensions: 227
Number of sequences better than 10.0: 1
Number of HSP's gapped: 224
Number of HSP's successfully gapped: 21
Length of query: 127
Length of database: 6,701,793
Length adjustment: 83
Effective length of query: 44
Effective length of database: 4,384,350
Effective search space: 192911400
Effective search space used: 192911400
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: 51 (23.5 bits)