RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy9417
         (161 letters)



>gnl|CDD|239621 cd03562, CID, CID (CTD-Interacting Domain) domain family; CID is
           present in several RNA-processing factors such as Pcf11
           and Nrd1. Pcf11 is a conserved and essential subunit of
           the yeast cleavage factor IA, which is required for
           polyadenylation-dependent 3'-RNA processing and
           transcription termination. Nrd1 is implicated in
           polyadenylation-independent 3'-RNA processing. CID binds
           tightly to the carboxy-terminal domain (CTD) of  RNA
           polymerase (Pol) II. During transcription, Pol II
           synthesizes eukaryotic messenger RNA. Transcription is
           coupled to RNA processing through the CTD, which
           consists of up to 52 repeats of the sequence Tyr 1-Ser
           2-Pro 3-Thr 4-Ser 5-Pro 6-Ser 7. CID contains eight
           alpha-helices in a right-handed superhelical
           arrangement, which closely resembles that of the VHS
           domains and ARM (Armadillo) repeat proteins, except for
           its two amino-terminal helices.
          Length = 114

 Score = 66.1 bits (162), Expect = 8e-15
 Identities = 26/89 (29%), Positives = 46/89 (51%), Gaps = 7/89 (7%)

Query: 74  ISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFKYK 133
            S+  I  + KLA++   + K +V+ +EK I KC  + KLP LY++D+I+     ++K  
Sbjct: 16  NSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLLDSIVKNVGRKYKEF 75

Query: 134 DVYAPRFARNLYRTFGYVFQ-CPDEDRKK 161
                 F+  L   F   ++   ++ RKK
Sbjct: 76  ------FSEFLVPLFLDAYEKVDEKTRKK 98



 Score = 54.5 bits (132), Expect = 3e-10
 Identities = 17/46 (36%), Positives = 28/46 (60%)

Query: 12 ISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 57
           S+  I  + KLA++   + K +V+ +EK I KC  + KLP LY++
Sbjct: 16 NSQPSIQTLTKLAIENRKHAKEIVEIIEKHIKKCPPEQKLPLLYLL 61


>gnl|CDD|214731 smart00582, RPR, domain present in proteins, which are involved in
           regulation of nuclear pre-mRNA. 
          Length = 124

 Score = 64.6 bits (158), Expect = 4e-14
 Identities = 27/90 (30%), Positives = 46/90 (51%), Gaps = 5/90 (5%)

Query: 74  ISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQFK-- 131
            S+  I  + K A++   + K +V+  EK+I K     KLP LY++D+I+  ++ ++   
Sbjct: 11  NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLLDSIVQNSKRKYGSE 70

Query: 132 YKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           + D   P F   L R  G     P+E +KK
Sbjct: 71  FGDELGPVFQDALRRVLGA---APEELKKK 97



 Score = 46.1 bits (110), Expect = 4e-07
 Identities = 15/46 (32%), Positives = 25/46 (54%)

Query: 12 ISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 57
           S+  I  + K A++   + K +V+  EK+I K     KLP LY++
Sbjct: 11 NSQESIQTLTKWAIEHASHAKEIVELWEKYIKKAPVPRKLPLLYLL 56


>gnl|CDD|218279 pfam04818, CTD_bind, RNA polymerase II-binding domain.  This domain
           binds to the phosphorylated C-terminal domain (CTD) of
           RNA polymerase II.
          Length = 64

 Score = 38.3 bits (90), Expect = 9e-05
 Identities = 16/50 (32%), Positives = 28/50 (56%), Gaps = 2/50 (4%)

Query: 112 KLPGLYVIDAIIHQARLQFKYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
           KLP LY+ + ++  ++   K KD +   F+  L   F +V++  DE+ KK
Sbjct: 1   KLPLLYLANDVVQNSKH--KNKDEFVKAFSPVLPDAFAHVYKEGDEEVKK 48


>gnl|CDD|227041 COG4697, COG4697, Uncharacterized protein conserved in archaea
           [Function unknown].
          Length = 319

 Score = 28.7 bits (64), Expect = 1.4
 Identities = 11/63 (17%), Positives = 23/63 (36%), Gaps = 7/63 (11%)

Query: 20  IVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAKI 79
           IV    K +H+++  + +  + +WK K   +L           E+   N     +   + 
Sbjct: 99  IVDFQNKYSHFHEGDLITRVRLLWKEKDVDRLY-------PFGEVRLYNPYSDRLLLIRE 151

Query: 80  TGI 82
            G 
Sbjct: 152 DGF 154


>gnl|CDD|236009 PRK07392, PRK07392, threonine-phosphate decarboxylase; Validated.
          Length = 360

 Score = 26.9 bits (60), Expect = 4.6
 Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 7/34 (20%)

Query: 96  VVQSVEKFIWKCKSQYKLPGLYVIDAIIHQARLQ 129
           +++S+ KF       Y LPGL +  AI H  RLQ
Sbjct: 210 ILRSLTKF-------YSLPGLRLGYAIAHPDRLQ 236


>gnl|CDD|219445 pfam07517, SecA_DEAD, SecA DEAD-like domain.  SecA protein binds to
           the plasma membrane where it interacts with proOmpA to
           support translocation of proOmpA through the membrane.
           SecA protein achieves this translocation, in association
           with SecY protein, in an ATP dependent manner. This
           domain represents the N-terminal ATP-dependent helicase
           domain, which is related to the pfam00270.
          Length = 381

 Score = 26.3 bits (59), Expect = 7.1
 Identities = 12/67 (17%), Positives = 23/67 (34%), Gaps = 4/67 (5%)

Query: 36  QSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYK- 94
           +  E      K +  L       +  + LL            ++   +  ALKA H ++ 
Sbjct: 242 KKEEDEEDDEKRRNVLLTEEGAKKEEELLLIDLLYDEWAENLELLHHINQALKAHHLFER 301

Query: 95  ---YVVQ 98
              Y+V+
Sbjct: 302 DVDYIVR 308


  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
   0.322    0.137    0.416 

Gapped
Lambda     K      H
   0.267   0.0709    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,938,592
Number of extensions: 685341
Number of successful extensions: 498
Number of sequences better than 10.0: 1
Number of HSP's gapped: 496
Number of HSP's successfully gapped: 14
Length of query: 161
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 72
Effective length of database: 6,990,096
Effective search space: 503286912
Effective search space used: 503286912
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: 55 (25.0 bits)