RPS-BLAST 2.2.26 [Sep-21-2011]

Database: scop70_1_75 
           13,730 sequences; 2,407,596 total letters

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

Query= psy17123
         (105 letters)



>d1d3bb_ b.38.1.1 (B:) B core SNRNP protein {Human (Homo sapiens)
          [TaxId: 9606]}
          Length = 81

 Score = 54.4 bits (131), Expect = 7e-12
 Identities = 12/43 (27%), Positives = 22/43 (51%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRV 68
          + + +D  +R     GR   G  K FD  +NL+L +  E+ ++
Sbjct: 3  MLQHIDYRMRCILQDGRIFIGTFKAFDKHMNLILCDCDEFRKI 45


>d2fwka1 b.38.1.1 (A:24-115) U6 snRNA-associated sm-like protein
          LSM5 {Cryptosporidium parvum [TaxId: 5807]}
          Length = 92

 Score = 53.3 bits (128), Expect = 2e-11
 Identities = 17/43 (39%), Positives = 25/43 (58%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRV 68
          + K +   I V   G +E SG+L+GFD  +N+VLD+  EY   
Sbjct: 10 IDKCIGNRIYVVMKGDKEFSGVLRGFDEYVNMVLDDVQEYGFK 52


>d1th7a1 b.38.1.1 (A:3-78) Archaeal homoheptameric Sm protein
          {Sulfolobus solfataricus [TaxId: 2287]}
          Length = 76

 Score = 50.9 bits (122), Expect = 1e-10
 Identities = 14/42 (33%), Positives = 26/42 (61%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          L++ L+ ++ VK  G +E  G+L+ +D  +NLVL ++ E   
Sbjct: 12 LAESLNNLVLVKLKGNKEVRGMLRSYDQHMNLVLSDSEEIQS 53


>d1i4k1_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein
          {Archaeon Archaeoglobus fulgidus, AF-Sm1 [TaxId: 2234]}
          Length = 72

 Score = 50.9 bits (122), Expect = 1e-10
 Identities = 16/42 (38%), Positives = 23/42 (54%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          L++ L   + V+  GGRE  G L G+D  +NLVL +  E   
Sbjct: 8  LNRSLKSPVIVRLKGGREFRGTLDGYDIHMNLVLLDAEEIQN 49


>d1mgqa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein
          {Archaeon Methanobacterium thermoautotrophicum [TaxId:
          145262]}
          Length = 74

 Score = 50.1 bits (120), Expect = 2e-10
 Identities = 16/42 (38%), Positives = 23/42 (54%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          L   L+  + +K  G RE  G+LK FD  +NLVL++  E   
Sbjct: 11 LGNSLNSPVIIKLKGDREFRGVLKSFDLHMNLVLNDAEELED 52


>d1i8fa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein
          {Archaeon Pyrobaculum aerophilum [TaxId: 13773]}
          Length = 71

 Score = 48.6 bits (116), Expect = 8e-10
 Identities = 14/40 (35%), Positives = 21/40 (52%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEY 65
          L   + K + VK     E  GIL+ FD  +NL+L++  E 
Sbjct: 7  LQDSIGKQVLVKLRDSHEIRGILRSFDQHVNLLLEDAEEI 46


>d1h641_ b.38.1.1 (1:) Archaeal homoheptameric Sm protein
          {Archaeon Pyrococcus abyssi [TaxId: 29292]}
          Length = 71

 Score = 48.5 bits (116), Expect = 1e-09
 Identities = 14/42 (33%), Positives = 20/42 (47%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          + + LDK + V    G E  G L G+D  LN+VL +      
Sbjct: 7  IHRSLDKDVLVILKKGFEFRGRLIGYDIHLNVVLADAEMIQD 48


>d1m5q1_ b.38.1.1 (1:) Sm-Like archaeal protein Smap3 {Archaeon
          Pyrobaculum aerophilum [TaxId: 13773]}
          Length = 127

 Score = 49.7 bits (119), Expect = 1e-09
 Identities = 13/52 (25%), Positives = 24/52 (46%)

Query: 25 DLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVR 76
          +L+  L + ++V  + G    G+L   D  LN+VL N +      +  V + 
Sbjct: 4  ELNNLLGREVQVVLSNGEVYKGVLHAVDNQLNIVLANASNKAGEKFNRVFIM 55


>d1n9ra_ b.38.1.1 (A:) Small nuclear ribonucleoprotein F, Smf
          {Baker's yeast (Saccharomyces cerevisiae) [TaxId:
          4932]}
          Length = 68

 Score = 48.2 bits (115), Expect = 1e-09
 Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 1/43 (2%)

Query: 26 LSKFLDKVIRVKF-AGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          L   ++  + VK      E  G L   D   NL L+   E++ 
Sbjct: 1  LKGLVNHRVGVKLKFNSTEYRGTLVSTDNYFNLQLNEAEEFVA 43


>d1ljoa_ b.38.1.1 (A:) Archaeal homoheptameric Sm protein
          {Archaeon Archaeoglobus fulgidus, AF-Sm2 [TaxId: 2234]}
          Length = 75

 Score = 46.7 bits (111), Expect = 5e-09
 Identities = 13/43 (30%), Positives = 20/43 (46%), Gaps = 1/43 (2%)

Query: 26 LSKFLDKVIRVKFA-GGRECSGILKGFDPLLNLVLDNTTEYLR 67
          +   + K+IRV+      +  G L+G D  +NL L N  E   
Sbjct: 10 VKSMVGKIIRVEMKGEENQLVGKLEGVDDYMNLYLTNAMECKG 52


>d1b34b_ b.38.1.1 (B:) D2 core SNRNP protein {Human (Homo sapiens)
          [TaxId: 9606]}
          Length = 93

 Score = 45.6 bits (108), Expect = 2e-08
 Identities = 12/48 (25%), Positives = 21/48 (43%)

Query: 22 SILDLSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVT 69
          S+L  S   +  + +     ++  G +K FD   N+VL+N  E     
Sbjct: 5  SVLTQSVKNNTQVLINCRNNKKLLGRVKAFDRHCNMVLENVKEMWTEV 52


>d1d3ba_ b.38.1.1 (A:) D3 core SNRNP protein {Human (Homo sapiens)
          [TaxId: 9606]}
          Length = 72

 Score = 40.5 bits (95), Expect = 1e-06
 Identities = 8/42 (19%), Positives = 15/42 (35%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR 67
          L +    ++  +   G    G L   +  +N  + N T   R
Sbjct: 7  LHEAEGHIVTCETNTGEVYRGKLIEAEDNMNCQMSNITVTYR 48


>d1b34a_ b.38.1.1 (A:) D1 core SNRNP protein {Human (Homo sapiens)
          [TaxId: 9606]}
          Length = 80

 Score = 39.7 bits (93), Expect = 3e-06
 Identities = 11/55 (20%), Positives = 23/55 (41%), Gaps = 4/55 (7%)

Query: 26 LSKFLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLR----VTYQSVQVR 76
          L K   + + ++   G +  G + G D  +N  L      L+    V  +++ +R
Sbjct: 6  LMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIR 60


>d1biaa2 b.34.1.1 (A:271-317) Biotin repressor/biotin holoenzyme
          synthetase, C-terminal domain {Escherichia coli [TaxId:
          562]}
          Length = 47

 Score = 24.6 bits (54), Expect = 0.79
 Identities = 10/48 (20%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 29 FLDKVIRVKFAGGRECSGILKGFDPLLNLVLDNTTEYLRVTYQSVQVR 76
          F+++ +++   G +E  GI +G D    L+L+            + +R
Sbjct: 1  FINRPVKLI-IGDKEIFGISRGIDKQGALLLEQDGIIKPWMGGEISLR 47


>d1neka3 d.168.1.1 (A:236-355) Succinate dehydogenase {Escherichia
           coli [TaxId: 562]}
          Length = 120

 Score = 24.6 bits (53), Expect = 2.2
 Identities = 9/53 (16%), Positives = 15/53 (28%)

Query: 1   MAAVNTTTDAGAETKDRKRKESILDLSKFLDKVIRVKFAGGRECSGILKGFDP 53
             ++      G          + L L     +V+  +  G  E S      DP
Sbjct: 55  ARSIMIEIREGRGCDGPWGPHAKLKLDHLGKEVLESRLPGILELSRTFAHVDP 107


>d1n0ua5 d.58.11.1 (A:726-842) Elongation factor 2 (eEF-2) {Baker's
           yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
          Length = 117

 Score = 24.2 bits (52), Expect = 2.5
 Identities = 6/21 (28%), Positives = 9/21 (42%), Gaps = 3/21 (14%)

Query: 15  KDRKRK---ESILDLSKFLDK 32
             RKR    E +    ++ DK
Sbjct: 96  AARKRHGMKEEVPGWQEYYDK 116


>d1cnza_ c.77.1.1 (A:) 3-isopropylmalate dehydrogenase, IPMDH
           {Salmonella typhimurium [TaxId: 90371]}
          Length = 363

 Score = 23.9 bits (51), Expect = 4.7
 Identities = 8/35 (22%), Positives = 14/35 (40%)

Query: 1   MAAVNTTTDAGAETKDRKRKESILDLSKFLDKVIR 35
             A+N   + G  T D  R  + +   +  D + R
Sbjct: 323 EQAINRALEEGVRTGDLARGAAAVSTDEMGDIIAR 357


  Database: scop70_1_75
    Posted date:  Mar 27, 2010  6:21 PM
  Number of letters in database: 2,407,596
  Number of sequences in database:  13,730
  
Lambda     K      H
   0.319    0.133    0.382 

Gapped
Lambda     K      H
   0.267   0.0615    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 355,847
Number of extensions: 14087
Number of successful extensions: 51
Number of sequences better than 10.0: 1
Number of HSP's gapped: 51
Number of HSP's successfully gapped: 19
Length of query: 105
Length of database: 2,407,596
Length adjustment: 65
Effective length of query: 40
Effective length of database: 1,515,146
Effective search space: 60605840
Effective search space used: 60605840
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 47 (22.1 bits)