RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy6187
         (667 letters)



>d1aisb2 a.74.1.2 (B:1206-1300) Transcription factor IIB (TFIIB),
           core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}
          Length = 95

 Score = 28.2 bits (63), Expect = 0.99
 Identities = 10/79 (12%), Positives = 24/79 (30%)

Query: 283 CAVLKLSDGRKRSMSLWVEFITASGYLSARKIRSRFQTLVAQACDKCDYRESVKMIADTT 342
              L LS+  +R     ++     G  S +         +  A      + + + +A+  
Sbjct: 11  ADELGLSEKVRRRAIEILDEAYKRGLTSGKSPAGLVAAALYIASLLEGEKRTQREVAEVA 70

Query: 343 EVKLRILGKYVVQITPAFK 361
            V    +     ++    K
Sbjct: 71  RVTEVTVRNRYKELVEKLK 89


>d2fxua2 c.55.1.1 (A:147-371) Actin {Cow (Bos taurus) [TaxId: 9913]}
          Length = 225

 Score = 29.3 bits (65), Expect = 1.2
 Identities = 30/136 (22%), Positives = 46/136 (33%), Gaps = 17/136 (12%)

Query: 446 RHLDLPGNPITNYCMKSLLLYECEKHPSENDWEDHCVEFITASGYLSARKMRSRFQTLVA 505
             LDL G  +T+Y MK L         +    E   V  I         K +  +  L  
Sbjct: 30  MRLDLAGRDLTDYLMKILTERGYSFVTT---AEREIVRDI---------KEKLCYVALDF 77

Query: 506 QACDKLSKTRDAWVMSFT--DVESKLLIGGCRKKCLSILKTLRDRHLELPGNPKCL--SI 561
           +     + +  +   S+   D    + IG  R +C   L       +E  G  +    SI
Sbjct: 78  ENEMATAASSSSLEKSYELPD-GQVITIGNERFRCPETLFQPSFIGMESAGIHETTYNSI 136

Query: 562 LKTLRDRHLELPGNPV 577
           +K   D   +L  N V
Sbjct: 137 MKCDIDIRKDLYANNV 152


>d2gvka1 d.58.4.14 (A:8-316) Hypothetical protein BT1219
           {Bacteroides thetaiotaomicron [TaxId: 818]}
          Length = 309

 Score = 28.3 bits (63), Expect = 2.7
 Identities = 10/60 (16%), Positives = 20/60 (33%), Gaps = 7/60 (11%)

Query: 177 FKGKTPSSLENAAKQSKILYQLNKYYGERVQTRKASIAKTIREVCKVVQDVLREVEVQEP 236
           F G  P  +     ++ I    N        T        +++VC     ++R +  + P
Sbjct: 1   FGGHIPQDVAGKQGENVIFIVYN-------LTDSPDTVDKVKDVCANFSAMIRSMRNRFP 53


>d1u5tb1 a.4.5.54 (B:396-489) Vacuolar protein sorting-associated
           protein VPS36 {Baker's yeast (Saccharomyces cerevisiae)
           [TaxId: 4932]}
          Length = 94

 Score = 26.7 bits (59), Expect = 3.5
 Identities = 9/61 (14%), Positives = 20/61 (32%), Gaps = 7/61 (11%)

Query: 218 REVCKVVQDVLREVEVQEPRFISSLTECNGRF-----EGLDVITPTEFEVVLYLNQMGEL 272
           RE+ +      +++       I +L +    +      G  +I+P E        +   L
Sbjct: 18  REIYEFTLSEFKDLNSDTNYMIITLVDLYAMYNKSMRIGTGLISPMEMREA--CERFEHL 75

Query: 273 N 273
            
Sbjct: 76  G 76


>d1aisb1 a.74.1.2 (B:1108-1205) Transcription factor IIB (TFIIB),
           core domain {Archaeon Pyrococcus woesei [TaxId: 2262]}
          Length = 98

 Score = 26.0 bits (57), Expect = 5.6
 Identities = 16/70 (22%), Positives = 24/70 (34%)

Query: 283 CAVLKLSDGRKRSMSLWVEFITASGYLSARKIRSRFQTLVAQACDKCDYRESVKMIADTT 342
            A LKL    +   +         G +  R I S     V  AC       ++  IAD  
Sbjct: 13  TAQLKLPRHVEEEAARLYREAVRKGLIRGRSIESVMAACVYAACRLLKVPRTLDEIADIA 72

Query: 343 EVKLRILGKY 352
            V  + +G+ 
Sbjct: 73  RVDKKEIGRS 82


>d1vola1 a.74.1.2 (A:113-207) Transcription factor IIB (TFIIB), core
           domain {Human (Homo sapiens) [TaxId: 9606]}
          Length = 95

 Score = 25.7 bits (56), Expect = 6.6
 Identities = 8/70 (11%), Positives = 20/70 (28%)

Query: 283 CAVLKLSDGRKRSMSLWVEFITASGYLSARKIRSRFQTLVAQACDKCDYRESVKMIADTT 342
              + L   +    +           L  R   +     +  AC +     + K I   +
Sbjct: 13  ADRINLPRNKVDRTNNLFRQAYEQKSLKGRANDAIASACLYIACRQEGVPRTFKEICAVS 72

Query: 343 EVKLRILGKY 352
            +  + +G+ 
Sbjct: 73  RISKKEIGRC 82


>d1k8ka2 c.55.1.1 (A:161-418) Actin-related protein 3, Arp3 {Cow
           (Bos taurus) [TaxId: 9913]}
          Length = 258

 Score = 26.7 bits (58), Expect = 8.5
 Identities = 7/42 (16%), Positives = 16/42 (38%), Gaps = 6/42 (14%)

Query: 110 RHLDLPGNPITNYCMKSL------LLYECEKHPSENDWEDHC 145
           +H+ + G  IT +  + L      +  E     ++   E + 
Sbjct: 31  KHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYS 72



 Score = 26.7 bits (58), Expect = 8.5
 Identities = 7/42 (16%), Positives = 16/42 (38%), Gaps = 6/42 (14%)

Query: 446 RHLDLPGNPITNYCMKSL------LLYECEKHPSENDWEDHC 481
           +H+ + G  IT +  + L      +  E     ++   E + 
Sbjct: 31  KHIPIAGRDITYFIQQLLRDREVGIPPEQSLETAKAVKERYS 72


>d2zjrg1 c.21.1.1 (G:30-171) Ribosomal protein L13 {Deinococcus
           radiodurans [TaxId: 1299]}
          Length = 142

 Score = 26.1 bits (57), Expect = 9.9
 Identities = 7/25 (28%), Positives = 9/25 (36%)

Query: 572 LPGNPVTNYHMKTLLLYECEKHPNE 596
           LP           L +Y  E HP+ 
Sbjct: 106 LPKGRQGRAMHTRLKVYAGETHPHS 130


  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
   0.322    0.137    0.428 

Gapped
Lambda     K      H
   0.267   0.0556    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 2,535,641
Number of extensions: 121567
Number of successful extensions: 266
Number of sequences better than 10.0: 1
Number of HSP's gapped: 264
Number of HSP's successfully gapped: 18
Length of query: 667
Length of database: 2,407,596
Length adjustment: 91
Effective length of query: 576
Effective length of database: 1,158,166
Effective search space: 667103616
Effective search space used: 667103616
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 (21.9 bits)
S2: 56 (25.7 bits)