RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy14719
         (160 letters)



>gnl|CDD|239088 cd02395, SF1_like-KH, Splicing factor 1 (SF1) K homology
           RNA-binding domain (KH). Splicing factor 1 (SF1)
           specifically recognizes the intron branch point sequence
           (BPS) UACUAAC in the pre-mRNA transcripts during
           spliceosome assembly. We show that the KH-QUA2 region of
           SF1 defines an enlarged KH (hnRNP K) fold which is
           necessary and sufficient for BPS binding. KH binds
           single-stranded RNA or DNA. It is found in a wide
           variety of proteins including ribosomal proteins,
           transcription factors and post-transcriptional modifiers
           of mRNA.
          Length = 120

 Score =  129 bits (326), Expect = 2e-39
 Identities = 57/99 (57%), Positives = 69/99 (69%), Gaps = 5/99 (5%)

Query: 1   MTAKQLELETGCKIMVRGKGSMRDKKKEEANRGKPNWEHLSEELHVLISVEDTENRAELK 60
            T KQLE ETG KI +RGKGSM+D KKEE  R  P + HL+E LHVLI+ E      E  
Sbjct: 26  NTLKQLEKETGAKISIRGKGSMKDGKKEEELR-GPKYAHLNEPLHVLITAETP---PEEA 81

Query: 61  LARAVEEVQKLLVPQAEG-EDELKKRQLMELAIINGTYR 98
           LA+AVE +++LL P  EG  DELK+ QL ELA++NGTYR
Sbjct: 82  LAKAVEAIEELLKPAIEGGNDELKREQLRELALLNGTYR 120



 Score = 46.9 bits (112), Expect = 2e-07
 Identities = 22/47 (46%), Positives = 29/47 (61%), Gaps = 4/47 (8%)

Query: 114 EEANRGKPNWEHLSEELHVLISVEDTENRAELKLARAVEEVQKLLVP 160
           EE  R  P + HL+E LHVLI+ E      E  LA+AVE +++LL P
Sbjct: 53  EEELR-GPKYAHLNEPLHVLITAETP---PEEALAKAVEAIEELLKP 95


>gnl|CDD|227503 COG5176, MSL5, Splicing factor (branch point binding protein) [RNA
           processing and modification].
          Length = 269

 Score = 50.7 bits (121), Expect = 3e-08
 Identities = 34/101 (33%), Positives = 52/101 (51%), Gaps = 8/101 (7%)

Query: 2   TAKQLELETGCKIMVRGKGSMRDKKKEEANRGKPNWEHLSEELHVLI--SVEDTENRAEL 59
           T KQLE  +  KI +RG GS   K+ + ++    + ++    LH LI    ED   R   
Sbjct: 175 TLKQLERISRAKIAIRGSGS--VKEGKISSDTPESLKNAEAVLHCLIEADSEDKICRLIK 232

Query: 60  KLARAVEEVQKLLVPQAEGEDELKKRQLMELAIINGTYRDN 100
               A+ E ++   P  EG+++LK+ QL  LA +NGT R +
Sbjct: 233 SQLNAIREARR--NP--EGQNDLKRFQLRWLAHLNGTLRAD 269


>gnl|CDD|173423 PTZ00133, PTZ00133, ADP-ribosylation factor; Provisional.
          Length = 182

 Score = 30.6 bits (69), Expect = 0.22
 Identities = 19/58 (32%), Positives = 31/58 (53%), Gaps = 7/58 (12%)

Query: 34  KPNWEHLSEELHVLISVEDTENRAELKLARAVEEVQKLLVPQAEGEDELKKRQLMELA 91
           +P W H  +  + LI V D+ +R  +  AR  EE++++L      EDEL+   L+  A
Sbjct: 75  RPLWRHYYQNTNGLIFVVDSNDRERIGDAR--EELERML-----SEDELRDAVLLVFA 125


>gnl|CDD|100796 PRK01156, PRK01156, chromosome segregation protein; Provisional.
          Length = 895

 Score = 27.9 bits (62), Expect = 2.5
 Identities = 22/82 (26%), Positives = 37/82 (45%), Gaps = 3/82 (3%)

Query: 79  EDELKKRQLMELAIINGTYRDNNAK--VLAAAVFVFSEEANRGKPNWEHLSEELHVLISV 136
           E++LK   L EL  I     D+     +    +   S E N    ++ +L   L+ L S+
Sbjct: 189 EEKLKSSNL-ELENIKKQIADDEKSHSITLKEIERLSIEYNNAMDDYNNLKSALNELSSL 247

Query: 137 EDTENRAELKLARAVEEVQKLL 158
           ED +NR E ++  A  ++   L
Sbjct: 248 EDMKNRYESEIKTAESDLSMEL 269


  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
   0.311    0.128    0.346 

Gapped
Lambda     K      H
   0.267   0.0737    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,113,384
Number of extensions: 765607
Number of successful extensions: 569
Number of sequences better than 10.0: 1
Number of HSP's gapped: 563
Number of HSP's successfully gapped: 42
Length of query: 160
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 71
Effective length of database: 6,990,096
Effective search space: 496296816
Effective search space used: 496296816
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 55 (24.9 bits)