RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13665
         (105 letters)



>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 = 29.6 bits (66), Expect = 0.14
 Identities = 12/85 (14%), Positives = 23/85 (27%), Gaps = 42/85 (49%)

Query: 57  KDAKVIPEPD--------WPLVVLTSMAGY------------------------------ 78
           ++    P+ D         PL+ +  +A Y                              
Sbjct: 220 ENPSNTPDKDYLLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVT 279

Query: 79  --AMAPAPFEWSSFLICFSQ-LQLL 100
             A+A     W SF +   + + +L
Sbjct: 280 AVAIAETD-SWESFFVSVRKAITVL 303


>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 = 28.0 bits (61), Expect = 0.44
 Identities = 7/27 (25%), Positives = 10/27 (37%), Gaps = 10/27 (37%)

Query: 4  KNSVK----------ADPRPELKVTAT 20
          K ++K           D  P L + AT
Sbjct: 19 KQALKKLQASLKLYADDSAPALAIKAT 45


>3d5n_A Q97W15_sulso; NESG, SSR125, structural genomics, PSI-2, protein
          structure initiative, northeast structural genomics
          consortium; 2.80A {Sulfolobus solfataricus}
          Length = 197

 Score = 26.9 bits (60), Expect = 1.2
 Identities = 14/70 (20%), Positives = 29/70 (41%), Gaps = 5/70 (7%)

Query: 26 DKPLQRKHVKS-GALDPVLVPGGVAIETNKRRKDAKVIPEPDWPLVVLTSM-AGYAMAPA 83
          + P+  + ++  G L+ +++ G    E      D  VI  P W   + TS+  G      
Sbjct: 27 NTPIIMRTIRIYGDLEKIIIVGKYVNEMLPLLMDQIVIYNPFWNEGISTSLKLGLRFFK- 85

Query: 84 PFEWSSFLIC 93
            ++ + L+ 
Sbjct: 86 --DYDAVLVA 93


>3m62_A Ubiquitin conjugation factor E4; armadillo-like repeats, UBL
           conjugation pathway, DNA damage, nucleus,
           phosphoprotein; HET: 1PE; 2.40A {Saccharomyces
           cerevisiae} PDB: 3m63_A* 2qiz_A 2qj0_A
          Length = 968

 Score = 26.3 bits (57), Expect = 2.7
 Identities = 8/47 (17%), Positives = 14/47 (29%), Gaps = 9/47 (19%)

Query: 17  VTATTVHTYDKPLQRKHVKSGALDPVLVPGGVAIETNKRRKDAKVIP 63
           +   +    D+   + H+ S + DP               K   V P
Sbjct: 906 ILPASKMNIDRSTIKAHLLSDSTDPF---------NRMPLKLEDVTP 943


>1qw2_A Conserved hypothetical protein TA1206; structural genomics,
          beta/alpha, antiparallel beta sandwich, protein
          structure initiative; 1.50A {Thermoplasma acidophilum}
          SCOP: d.249.1.1
          Length = 102

 Score = 24.9 bits (54), Expect = 3.6
 Identities = 8/31 (25%), Positives = 12/31 (38%)

Query: 50 IETNKRRKDAKVIPEPDWPLVVLTSMAGYAM 80
          IE   +          + PL+ +    GYAM
Sbjct: 13 IEIGGKVYQFFKSDLGNAPLLFIKGSKGYAM 43


>2kr4_A Ubiquitin conjugation factor E4 B; U-BOX, UFD2, ring, E3 ligase,
          UBL conjugation pathway; NMR {Mus musculus}
          Length = 85

 Score = 24.6 bits (54), Expect = 4.1
 Identities = 5/26 (19%), Positives = 11/26 (42%)

Query: 17 VTATTVHTYDKPLQRKHVKSGALDPV 42
          V   +    D+ +  +H+ +   DP 
Sbjct: 28 VRLPSGTVMDRSIILRHLLNSPTDPF 53


>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin
          ligase, E4 polyubiquitin chain EL factor,
          phosphoprotein, UBL conjugation pathway; NMR {Homo
          sapiens} PDB: 3l1x_A 3l1z_B
          Length = 100

 Score = 24.3 bits (53), Expect = 5.5
 Identities = 6/47 (12%), Positives = 16/47 (34%), Gaps = 9/47 (19%)

Query: 17 VTATTVHTYDKPLQRKHVKSGALDPVLVPGGVAIETNKRRKDAKVIP 63
          V   +    D+ +  +H+ +   DP            +   ++ + P
Sbjct: 43 VRLPSGTIMDRSIILRHLLNSPTDPF---------NRQTLTESMLEP 80


>2c61_A A-type ATP synthase non-catalytic subunit B; hydrolase, H+ ATPase,
           A1AO, ATP synthesis, hydrogen ION transport, ION
           transport; 1.5A {Methanosarcina mazei GO1} PDB: 3dsr_A*
           3b2q_A* 2rkw_A* 3eiu_A*
          Length = 469

 Score = 24.6 bits (54), Expect = 7.1
 Identities = 7/13 (53%), Positives = 9/13 (69%)

Query: 69  LVVLTSMAGYAMA 81
           LV+LT +  YA A
Sbjct: 252 LVILTDITNYAEA 264


>1wgm_A Ubiquitin conjugation factor E4A; ubiquitinating enzyme,
          KIAA0126, structural genomics, riken structural
          genomics/proteomics initiative, RSGI; NMR {Homo
          sapiens} SCOP: g.44.1.2
          Length = 98

 Score = 24.0 bits (52), Expect = 7.8
 Identities = 8/47 (17%), Positives = 15/47 (31%), Gaps = 9/47 (19%)

Query: 17 VTATTVHTYDKPLQRKHVKSGALDPVLVPGGVAIETNKRRKDAKVIP 63
          V  ++  T D+    +H+ S   DP                  ++ P
Sbjct: 37 VLPSSRVTVDRSTIARHLLSDQTDPF---------NRSPLTMDQIRP 74


>3gqb_B V-type ATP synthase beta chain; A3B3, V-ATPase, ATP synthesis,
           ATP-binding, hydrogen ION TRA hydrolase, ION transport;
           2.80A {Thermus thermophilus HB8} PDB: 3a5c_D* 3a5d_D
           3j0j_D*
          Length = 464

 Score = 24.7 bits (54), Expect = 8.4
 Identities = 7/13 (53%), Positives = 9/13 (69%)

Query: 69  LVVLTSMAGYAMA 81
           LV+LT M  Y+ A
Sbjct: 254 LVILTDMTNYSEA 266


  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
   0.318    0.132    0.399 

Gapped
Lambda     K      H
   0.267   0.0833    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,526,596
Number of extensions: 78921
Number of successful extensions: 145
Number of sequences better than 10.0: 1
Number of HSP's gapped: 144
Number of HSP's successfully gapped: 12
Length of query: 105
Length of database: 6,701,793
Length adjustment: 70
Effective length of query: 35
Effective length of database: 4,747,323
Effective search space: 166156305
Effective search space used: 166156305
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 (21.7 bits)
S2: 51 (23.2 bits)