RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5290
         (536 letters)



>d1dzfa1 c.52.3.1 (A:5-143) Eukaryotic RPB5 N-terminal domain
           {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
          Length = 139

 Score =  163 bits (415), Expect = 5e-49
 Identities = 42/127 (33%), Positives = 68/127 (53%), Gaps = 9/127 (7%)

Query: 1   MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSELIVLVAHNDDP------TDQ 54
            ++  DRGY +TQ+E++  L+ FK ++ D  S  RP R  +       ++          
Sbjct: 16  KEMVKDRGYFITQEEVELPLEDFKAKYCD--SMGRPQRKMMSFQANPTEESISKFPDMGS 73

Query: 55  MFVFFPDEPKIGIKTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQSLVDMAPKYILEYFL 114
           ++V F DEP +G+KT+KT+   +QE+     I V Q  +TPSA + LV   P   +E F 
Sbjct: 74  LWVEFCDEPSVGVKTMKTFVIHIQEKNFQTGIFVYQNNITPSAMK-LVPSIPPATIETFN 132

Query: 115 ESELLIN 121
           E+ L++N
Sbjct: 133 EAALVVN 139


>d1eika_ d.78.1.1 (A:) RNA polymerase subunit RBP5 (RNA polymerase
           subunit H) {Archaeon Methanobacterium
           thermoautotrophicum [TaxId: 145262]}
          Length = 77

 Score = 49.7 bits (119), Expect = 1e-08
 Identities = 10/29 (34%), Positives = 17/29 (58%)

Query: 118 LLINITEHELVPEHIVLTPEEKQELLTRY 146
           +   I +H+LVPEH++L   E + +L   
Sbjct: 1   MKREILKHQLVPEHVILNESEAKRVLKEL 29


>d1dzfa2 d.78.1.1 (A:144-215) Eukaryotic RPB5 C-terminal domain
           {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}
          Length = 72

 Score = 48.5 bits (116), Expect = 3e-08
 Identities = 17/25 (68%), Positives = 21/25 (84%)

Query: 122 ITEHELVPEHIVLTPEEKQELLTRY 146
           IT HELVP+HI L+ +EK+ELL RY
Sbjct: 1   ITHHELVPKHIRLSSDEKRELLKRY 25


>gi|150401221|ref|YP_001324987.1|(10-76:78) DNA-directed RNA
           polymerase subunit H [Methanococcus aeolicus Nankai-3]  
           gi|166229324|sp|A6UV53.1|RPOH_META3 RecName:
           Full=DNA-directed RNA polymerase subunit H 
           gi|150013924|gb|ABR56375.1| RNA polymerase Rpb5
           [Methanococcus aeolicus Nankai-3]  E=2e-17 s/c=1.37
           id=62% cov=100%
          Length = 67

 Score = 34.2 bits (79), Expect = 0.003
 Identities = 9/18 (50%), Positives = 14/18 (77%)

Query: 129 PEHIVLTPEEKQELLTRY 146
           P+H V++ EE Q+LL +Y
Sbjct: 1   PKHEVISKEEVQKLLAKY 18


>d1jmxa1 a.3.1.7 (A:2-85) Quinohemoprotein amine dehydrogenase A
          chain, domains 1 and 2 {Pseudomonas putida [TaxId:
          303]}
          Length = 84

 Score = 26.8 bits (59), Expect = 1.8
 Identities = 10/41 (24%), Positives = 18/41 (43%), Gaps = 2/41 (4%)

Query: 1  MQLCHDRGYLVTQDELDQTLDQFKEQFGDKPSEKRPARSEL 41
          MQ+ H  G  ++ D+    +    ++ G  PSE    R  +
Sbjct: 43 MQVMH--GLQISDDDRRTLVKYLADKQGLAPSETDGVRYAM 81


>d1rmga_ b.80.1.3 (A:) Rhamnogalacturonase A {Aspergillus aculeatus
           [TaxId: 5053]}
          Length = 422

 Score = 28.1 bits (62), Expect = 3.2
 Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 3/60 (5%)

Query: 447 VESPSGQKSYY--PGENSAPAGISSTESPGDIGVSGF-TSPGPQPYSLPSGLGGTEGVSP 503
           ++  S   SY       +AP+G S+T    D+  +   T+  P P    S   G    S 
Sbjct: 360 LKDSSSHTSYTTTSTVTAAPSGYSATTMAADLATAFGLTASIPIPTIPTSFYPGLTPYSA 419


>d1sd4a_ a.4.5.39 (A:) Penicillinase repressor BlaI {Staphylococcus
           aureus [TaxId: 1280]}
          Length = 122

 Score = 26.7 bits (59), Expect = 3.7
 Identities = 11/83 (13%), Positives = 28/83 (33%), Gaps = 17/83 (20%)

Query: 59  FPDEPKIGIKTIKTYCQRMQEET-----------IHRAII---VVQTGMTPSAKQSLVDM 104
                ++  KTI+T   R+ ++             + + I    ++     +    L   
Sbjct: 30  IQKYKEVSDKTIRTLITRLYKKEIIKRYKSENIYFYSSNIKEDDIKMKTAKTFLNKLYGG 89

Query: 105 APKYILEYFLESELLINITEHEL 127
             K ++  F ++E    +   E+
Sbjct: 90  DMKSLVLNFAKNE---ELNNKEI 109


>d1eswa_ c.1.8.1 (A:) Amylomaltase MalQ {Thermus aquaticus [TaxId:
           271]}
          Length = 500

 Score = 27.7 bits (61), Expect = 3.9
 Identities = 12/90 (13%), Positives = 30/90 (33%), Gaps = 1/90 (1%)

Query: 93  MTPSAKQSLVDMAPKYILEYFLESELLINITEHELVPEHIVLTPEEKQELLTRYWRSCVT 152
           +  S   ++     K   E   + ++     E  ++ E + +   E + L  R+    + 
Sbjct: 304 IPASCPTAVEGRWVKAPGEKLFQ-KIQEVFGEVPVLAEDLGVITPEVEALRDRFGLPGMK 362

Query: 153 IFWTQKRTGEEHFLKECSFESATVKSVYPS 182
           +       G E+     ++ +     VY  
Sbjct: 363 VLQFAFDDGMENPFLPHNYPAHGRVVVYTG 392


>d1h16a_ c.7.1.1 (A:) Pyruvate formate-lyase, PFL {Escherichia coli
           [TaxId: 562]}
          Length = 759

 Score = 27.5 bits (61), Expect = 4.8
 Identities = 6/44 (13%), Positives = 19/44 (43%)

Query: 133 VLTPEEKQELLTRYWRSCVTIFWTQKRTGEEHFLKECSFESATV 176
            +T +E QE++         + + +    +E F  +  + + ++
Sbjct: 295 KITEQEAQEMVDHLVMKLRMVRFLRTPEYDELFSGDPIWATESI 338


>d1vqo31 g.41.8.3 (3:1-92) Ribosomal protein L44e {Archaeon
          Haloarcula marismortui [TaxId: 2238]}
          Length = 92

 Score = 25.1 bits (55), Expect = 9.1
 Identities = 8/32 (25%), Positives = 12/32 (37%), Gaps = 1/32 (3%)

Query: 68 KTIKTYCQRMQEETIHRAIIVVQTGMTPSAKQ 99
          +   TYC    E   H  +  V++G     K 
Sbjct: 5  RRFNTYCPHCNEHQEHE-VEKVRSGRQTGMKW 35


  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
   0.315    0.134    0.401 

Gapped
Lambda     K      H
   0.267   0.0685    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,980,103
Number of extensions: 93811
Number of successful extensions: 182
Number of sequences better than 10.0: 1
Number of HSP's gapped: 180
Number of HSP's successfully gapped: 11
Length of query: 536
Length of database: 2,407,596
Length adjustment: 90
Effective length of query: 446
Effective length of database: 1,171,896
Effective search space: 522665616
Effective search space used: 522665616
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: 42 (22.0 bits)
S2: 55 (25.1 bits)