RPS-BLAST 2.2.26 [Sep-21-2011]

Database: CDD.v3.10 
           44,354 sequences; 10,937,602 total letters

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

Query= psy8505
         (118 letters)



>gnl|CDD|219933 pfam08612, Med20, TATA-binding related factor (TRF) of subunit 20
           of Mediator complex.  This family of proteins is related
           to TATA-binding protein (TBP). TBP is a highly conserved
           RNA polymerase II general transcription factor that
           binds to the core promoter and initiates assembly of the
           preinitiation complex. Human TRF has been shown to
           associate with an RNA polymerase II-SRB complex. This
           Med20 subunit of Mediator is found in the non-essential
           part of the head.
          Length = 197

 Score = 87.8 bits (218), Expect = 5e-23
 Identities = 36/96 (37%), Positives = 52/96 (54%), Gaps = 13/96 (13%)

Query: 18  KTVHVLHNSEQPASVFSILESGVPGGPGGPSGAVKNIPVVADSLFDLLMMKMTPVYTSKK 77
           K ++VL  SE P S FSI+ +                 +VADS F LLM K+   +T ++
Sbjct: 59  KLLYVLSLSEHPNSTFSIINNTAI------------TTLVADSFFQLLMEKLQSFWTQRQ 106

Query: 78  QTKVESKGPRFELGDFCVKLGSVSISQNFKAVLVEV 113
             K E  G  +ELGDF V++G+V  +  F+ +LVEV
Sbjct: 107 TVKGEGGGT-YELGDFRVRVGNVFQTTTFRGILVEV 141


>gnl|CDD|240322 PTZ00232, PTZ00232, variable surface protein Vir27; Provisional.
          Length = 363

 Score = 29.9 bits (67), Expect = 0.27
 Identities = 22/73 (30%), Positives = 32/73 (43%), Gaps = 7/73 (9%)

Query: 5   HAGTGRYAHLGSQKTVHVLHNSEQPASVFSILESGVPGGPGGPSGAVKNI-----PVVAD 59
           H  T R      +   ++ H SE P  + +I    +P       G+ KNI     PV+  
Sbjct: 248 HPATXRKPGRIXRSGAYLTHGSETPHELDTI--ETIPVDDTAEGGSSKNIAGSVVPVLGV 305

Query: 60  SLFDLLMMKMTPV 72
           S   LL+ K+TPV
Sbjct: 306 SSISLLLYKVTPV 318


>gnl|CDD|203376 pfam06016, Reovirus_L2, Reovirus core-spike protein lambda-2 (L2).
            This family consists of several Reovirus core-spike
            protein lambda-2 (L2) sequences. The reovirus L2 genome
            segment encodes the core spike protein lambda-2, which
            mediates enzymatic reactions in 5' capping of the viral
            plus-strand transcripts.
          Length = 1290

 Score = 29.8 bits (67), Expect = 0.36
 Identities = 21/104 (20%), Positives = 36/104 (34%), Gaps = 12/104 (11%)

Query: 14   LGSQKTVHVLHNSEQPASVFSILESGVPGGPGGPSGAVKNIPVVA---DSLFDLLMMKMT 70
            +G Q ++ +         VF++  +GV             I  V+   D+      + +T
Sbjct: 1037 VGQQCSIVIP--GFNAQDVFNVYFNGVLVFTTTDGNVASMIGQVSVQFDATNGEWTLTIT 1094

Query: 71   P----VYTSKKQTKVESKGPRFELGDFCVKLGSVSISQNFKAVL 110
            P    +   +    V S      LG F +    V+I   F A L
Sbjct: 1095 PSDPGILDVQL---VGSNANPVSLGSFVIDSPDVTIVLAFPAQL 1135


>gnl|CDD|215103 PLN00206, PLN00206, DEAD-box ATP-dependent RNA helicase;
           Provisional.
          Length = 518

 Score = 25.9 bits (57), Expect = 6.6
 Identities = 11/33 (33%), Positives = 17/33 (51%), Gaps = 6/33 (18%)

Query: 42  GGPGGPSGAVKNIPVVADS------LFDLLMMK 68
           G P  P+ AVK + +  ++      LFD+L  K
Sbjct: 331 GNPNRPNKAVKQLAIWVETKQKKQKLFDILKSK 363


>gnl|CDD|181092 PRK07721, fliI, flagellum-specific ATP synthase; Validated.
          Length = 438

 Score = 25.8 bits (57), Expect = 6.7
 Identities = 12/33 (36%), Positives = 15/33 (45%), Gaps = 3/33 (9%)

Query: 81  VESKGPRFELGDFCVKLGSVSISQNFKAVLVEV 113
           +ESKGP   +GD C            KA+  EV
Sbjct: 30  IESKGPESSIGDVCYIHTK---GGGDKAIKAEV 59


  Database: CDD.v3.10
    Posted date:  Mar 20, 2013  7:55 AM
  Number of letters in database: 10,937,602
  Number of sequences in database:  44,354
  
Lambda     K      H
   0.316    0.133    0.382 

Gapped
Lambda     K      H
   0.267   0.0724    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,614,170
Number of extensions: 462222
Number of successful extensions: 311
Number of sequences better than 10.0: 1
Number of HSP's gapped: 309
Number of HSP's successfully gapped: 12
Length of query: 118
Length of database: 10,937,602
Length adjustment: 81
Effective length of query: 37
Effective length of database: 7,344,928
Effective search space: 271762336
Effective search space used: 271762336
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 (21.6 bits)
S2: 53 (24.2 bits)