RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= 020983
         (319 letters)



>d1twfc2 d.181.1.1 (C:42-172) RPB3 {Baker's yeast (Saccharomyces
           cerevisiae) [TaxId: 4932]}
          Length = 131

 Score =  158 bits (401), Expect = 3e-49
 Identities = 65/137 (47%), Positives = 86/137 (62%), Gaps = 6/137 (4%)

Query: 46  PTIAIDLVEIEVNSSVLNDEFIAHRLGLIPLTSERAMSMRFSRDCDACDGDGQCEFCSVE 105
           PT+AID VE+E N++VL DEFIAHRLGLIPL S     + +SRDC   D    C+ CSV 
Sbjct: 1   PTLAIDSVEVETNTTVLADEFIAHRLGLIPLQSMDIEQLEYSRDCFCEDH---CDKCSVV 57

Query: 106 FHLRAKCHSDQTLDVTSKDLYSSDHSVVPVDFVDPAGYDSTDQQRGIIIVKLRRGQELRL 165
             L+A   S+ T +V SKDL    + ++  +   P   D      G++I KLR+GQEL+L
Sbjct: 58  LTLQAFGESESTTNVYSKDLVIVSN-LMGRNIGHPIIQDKEG--NGVLICKLRKGQELKL 114

Query: 166 RAIARKGIGKDHAKWSP 182
             +A+KGI K+HAKW P
Sbjct: 115 TCVAKKGIAKEHAKWGP 131


>d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast
          (Saccharomyces cerevisiae) [TaxId: 4932]}
          Length = 135

 Score = 65.6 bits (160), Expect = 7e-14
 Identities = 21/51 (41%), Positives = 27/51 (52%)

Query: 10 PKVKIRELKDDYAKFELRDTDASMANALRRVMIAEVPTIAIDLVEIEVNSS 60
          P+VKIRE   D   F L + D +MAN+LRRVMIAE+        +      
Sbjct: 4  PQVKIREASKDNVDFILSNVDLAMANSLRRVMIAEIAAAIEFEYDPWNKLK 54



 Score = 56.7 bits (137), Expect = 8e-11
 Identities = 15/46 (32%), Positives = 29/46 (63%)

Query: 261 AKEDSFIFTVESTGAIKASQLVLNAIEVLKQKLDAVRLSEDTVEAD 306
           A+ D+F   VES G+I   Q+V+  I+ L++K+ ++ L+   ++ D
Sbjct: 90  AQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILLALTQMDQD 135


>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus
          thermophilus [TaxId: 274]}
          Length = 106

 Score = 29.5 bits (66), Expect = 0.19
 Identities = 11/46 (23%), Positives = 22/46 (47%), Gaps = 4/46 (8%)

Query: 9  FPKVKIRELKDDYAKFEL----RDTDASMANALRRVMIAEVPTIAI 50
           P   +R    +Y +F L    R    ++ N LRR++++ +P +  
Sbjct: 8  APVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPPVRR 53


>d1vjwa_ d.58.1.4 (A:) Ferredoxin A {Thermotoga maritima [TaxId:
           2336]}
          Length = 59

 Score = 27.2 bits (59), Expect = 0.57
 Identities = 14/54 (25%), Positives = 16/54 (29%), Gaps = 1/54 (1%)

Query: 84  MRFSRDCDACDGDGQCEF-CSVEFHLRAKCHSDQTLDVTSKDLYSSDHSVVPVD 136
           M+   D DAC G G CE  C   F L     +      T            P  
Sbjct: 1   MKVRVDADACIGCGVCENLCPDVFQLGDDGKAKVLQPETDLPCAKDAADSCPTG 54


>d1xppa_ d.74.3.2 (A:) DNA-directed RNA polymerase subunit L, RpoL
          {Thermoplasma acidophilum [TaxId: 2303]}
          Length = 99

 Score = 26.3 bits (58), Expect = 2.2
 Identities = 3/32 (9%), Positives = 14/32 (43%)

Query: 11 KVKIRELKDDYAKFELRDTDASMANALRRVMI 42
           +++   + +    E+ + D ++   L   ++
Sbjct: 4  SLRVISKEKNSITVEMINYDNTLLRTLVEEIL 35


>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha
          {Escherichia coli [TaxId: 562]}
          Length = 105

 Score = 26.0 bits (57), Expect = 3.2
 Identities = 11/44 (25%), Positives = 22/44 (50%), Gaps = 4/44 (9%)

Query: 11 KVKIRELKDDYAKFEL----RDTDASMANALRRVMIAEVPTIAI 50
           V I ++   +AK  L    R    ++ NALR ++++ +P +  
Sbjct: 12 LVDIEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPPVER 55


>d2d8va1 g.43.1.1 (A:8-61) Zinc finger FYVE domain-containing
           protein 19 {Mouse (Mus musculus) [TaxId: 10090]}
          Length = 54

 Score = 24.5 bits (53), Expect = 4.1
 Identities = 9/18 (50%), Positives = 9/18 (50%)

Query: 90  CDACDGDGQCEFCSVEFH 107
           C  CDGD  C  C  E H
Sbjct: 15  CAGCDGDLYCARCFREGH 32


>d2jnea1 g.41.18.1 (A:1-71) Hypothetical protein YfgJ {Escherichia
           coli [TaxId: 562]}
          Length = 71

 Score = 24.8 bits (54), Expect = 4.2
 Identities = 7/31 (22%), Positives = 11/31 (35%), Gaps = 7/31 (22%)

Query: 89  DCDAC-------DGDGQCEFCSVEFHLRAKC 112
            C  C       +G  +C  C     ++A C
Sbjct: 4   HCPQCQHVLDQDNGHARCRSCGEFIEMKALC 34


>d1l0ba2 c.15.1.3 (A:1705-1801) Breast cancer associated protein,
           BRCA1 {Rat (Rattus norvegicus) [TaxId: 10116]}
          Length = 97

 Score = 25.1 bits (55), Expect = 5.3
 Identities = 14/68 (20%), Positives = 27/68 (39%), Gaps = 3/68 (4%)

Query: 190 YEPEIHINEDLMESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIKKAE 249
            EP  ++ +D +E + L+   + V      +   D     + +V   A+T +D       
Sbjct: 10  CEPFTNMPKDELERM-LQLCGASVVKEL-PLLTRDTGAHPIVLVQPSAWT-EDNDCPDIG 66

Query: 250 AMGKPGLV 257
            + K  LV
Sbjct: 67  QLCKGRLV 74


>d1q47a_ b.69.12.1 (A:) Semaphorin 3a {Mouse (Mus musculus) [TaxId:
           10090]}
          Length = 495

 Score = 25.8 bits (56), Expect = 8.2
 Identities = 8/46 (17%), Positives = 17/46 (36%), Gaps = 6/46 (13%)

Query: 201 MESLSLEEKQSWVESSPTKVFDIDPNTGQVYVVDAEAYTYDDEVIK 246
           +E + LEE   + E +     ++     Q+Y+           V +
Sbjct: 447 LEEVLLEEMTVFREPTTISAMELSTKQQQLYI------GSTAGVAQ 486


  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
   0.317    0.134    0.379 

Gapped
Lambda     K      H
   0.267   0.0628    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,197,258
Number of extensions: 56562
Number of successful extensions: 167
Number of sequences better than 10.0: 1
Number of HSP's gapped: 165
Number of HSP's successfully gapped: 16
Length of query: 319
Length of database: 2,407,596
Length adjustment: 85
Effective length of query: 234
Effective length of database: 1,240,546
Effective search space: 290287764
Effective search space used: 290287764
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: 53 (24.4 bits)