RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy14552
         (290 letters)



>gnl|CDD|220751 pfam10433, MMS1_N, Mono-functional DNA-alkylating methyl
           methanesulfonate N-term.  MMS1 is a protein that
           protects against replication-dependent DNA damage in
           Saccharomyces cerevisiae. MMS1 belongs to the DDB1
           family of cullin 4 adaptors and the two proteins are
           homologous. MMS1 bridges the interaction of MMS22 and
           Crt10 with Cul8/Rtt101. Cul8/Rtt101 is a cullin protein
           involved in the regulation of DNA replication subsequent
           to DNA damage. The N-terminal region of MMS1 and the
           C-terminal of MMS22 are required for the the MMS1-MMS22
           interaction. The human HIV-1 virion-associated protein
           Vpr assembles with DDB1 through interaction with DCAF1
           (chromatin assembly factor) to form an E3 ubiquitin
           ligase that targets cellular substrates for
           proteasome-mediated degradation and subsequent G2
           arrest.
          Length = 513

 Score = 66.6 bits (163), Expect = 2e-12
 Identities = 32/107 (29%), Positives = 50/107 (46%), Gaps = 9/107 (8%)

Query: 5   YIVVSFSNATLVLSI----GETVEEVSG-SGFYGTTPTLCCSAMGDNSIVQVYPDGIRHI 59
           Y++VSF   T VL +    GE VEEV   SG   +  TL      D  I+QV  + IR  
Sbjct: 385 YLLVSFPFETRVLQLPVDPGEEVEEVDEDSGLDLSVQTLAAGNTSDGVIIQVTENSIRLS 444

Query: 60  GAKNTTWKVSDKKESDKKKIVRCAVNQRQIVIALQGGRLIYFEMHPV 106
             +    K++D  E   + I   +VN   +++A+ G  L+   ++  
Sbjct: 445 DLELG--KITD--EWSDEIITAASVNGSLVLVAVAGRNLVSLRIYLG 487


>gnl|CDD|218251 pfam04762, IKI3, IKI3 family.  Members of this family are
           components of the elongator multi-subunit component of a
           novel RNA polymerase II holoenzyme for transcriptional
           elongation. This region contains WD40 like repeats.
          Length = 903

 Score = 30.7 bits (70), Expect = 1.1
 Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 9/67 (13%)

Query: 126 QIVIALQGGRLIYFEMHPETGILDECSETIQMESEVLCMALSNAPSGEQMSRFLAVGLAD 185
           Q+ +AL GG ++     P T ++ E   +I  +  +   A S  P  E     LA+   +
Sbjct: 87  QLCLALAGGDILLVTYDPGTTVV-EIVGSI--DVGISAAAWS--PDEE----LLALTTGE 137

Query: 186 NTVRLIS 192
           NTV L++
Sbjct: 138 NTVLLMT 144


>gnl|CDD|238121 cd00200, WD40, WD40 domain, found in a number of eukaryotic
           proteins that cover a wide variety of functions
           including adaptor/regulatory modules in signal
           transduction, pre-mRNA processing and cytoskeleton
           assembly; typically contains a GH dipeptide 11-24
           residues from its N-terminus and the WD dipeptide at its
           C-terminus and is 40 residues long, hence the name WD40;
           between GH and WD lies a conserved core; serves as a
           stable propeller-like platform to which proteins can
           bind either stably or reversibly; forms a propeller-like
           structure with several blades where each blade is
           composed of a four-stranded anti-parallel b-sheet;
           instances with few detectable copies are hypothesized to
           form larger structures by dimerization; each WD40
           sequence repeat forms the first three strands of one
           blade and the last strand in the next blade; the last
           C-terminal WD40 repeat completes the blade structure of
           the first WD40 repeat to create the closed ring
           propeller-structure; residues on the top and bottom
           surface of the propeller are proposed to coordinate
           interactions with other proteins and/or small ligands; 7
           copies of the repeat are present in this alignment.
          Length = 289

 Score = 30.0 bits (68), Expect = 1.3
 Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 6/44 (13%)

Query: 158 ESEVLCMALSNAPSGEQMSRFLAVGLADNTVRLISLAPQDCLKQ 201
              V C+A S         + LA G  D T+++  L   + L+ 
Sbjct: 9   TGGVTCVAFSPD------GKLLATGSGDGTIKVWDLETGELLRT 46



 Score = 29.2 bits (66), Expect = 2.3
 Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 7/42 (16%)

Query: 150 ECSETIQM-ESEVLCMALSNAPSGEQMSRFLAVGLADNTVRL 190
           EC +T+    + V  +A S  P G    + LA G AD T+R+
Sbjct: 252 ECVQTLSGHTNSVTSLAWS--PDG----KRLASGSADGTIRI 287



 Score = 28.5 bits (64), Expect = 4.5
 Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 6/44 (13%)

Query: 158 ESEVLCMALSNAPSGEQMSRFLAVGLADNTVRLISLAPQDCLKQ 201
             EV  +A S  P GE+    L    +D T++L  L+   CL  
Sbjct: 177 TGEVNSVAFS--PDGEK----LLSSSSDGTIKLWDLSTGKCLGT 214


>gnl|CDD|217451 pfam03249, TSA, Type specific antigen.  There are several antigenic
           variants in Rickettsia tsutsugamushi, and a
           type-specific antigen (TSA) of 56-kilodaltons located on
           the rickettsial surface is responsible for the
           variation. TSA proteins are probably integral membrane
           proteins.
          Length = 502

 Score = 29.5 bits (66), Expect = 2.2
 Identities = 13/49 (26%), Positives = 23/49 (46%), Gaps = 3/49 (6%)

Query: 44  GDNSIVQVYPDGI---RHIGAKNTTWKVSDKKESDKKKIVRCAVNQRQI 89
           G+  I+Q+Y D +   RH G K    K++ ++E D          ++Q 
Sbjct: 339 GNEQIIQLYKDLVKLQRHAGIKKAMEKLAAQQEEDAGNQGGGDCKKKQG 387


>gnl|CDD|180119 PRK05500, PRK05500, bifunctional orotidine 5'-phosphate
           decarboxylase/orotate phosphoribosyltransferase protein;
           Validated.
          Length = 477

 Score = 29.3 bits (66), Expect = 2.5
 Identities = 15/50 (30%), Positives = 22/50 (44%)

Query: 156 QMESEVLCMALSNAPSGEQMSRFLAVGLADNTVRLISLAPQDCLKQKNLQ 205
           Q+  E L +  S       +++ L  GL  N   L+   PQD L   NL+
Sbjct: 199 QIAPERLILLRSIWAEKGNLNQILTAGLNSNGDGLLIPVPQDLLGAANLK 248


>gnl|CDD|235431 PRK05363, PRK05363, TMAO/DMSO reductase; Reviewed.
          Length = 280

 Score = 28.6 bits (65), Expect = 3.2
 Identities = 16/35 (45%), Positives = 19/35 (54%), Gaps = 11/35 (31%)

Query: 228 DEPAGPVTLGNLYLYVGL-------QNGALLRMVV 255
           DE   P+TL    L VGL       QNGA +R+VV
Sbjct: 158 DEAMHPLTL----LAVGLYGKTLPNQNGAPIRLVV 188


>gnl|CDD|235955 PRK07190, PRK07190, hypothetical protein; Provisional.
          Length = 487

 Score = 28.2 bits (63), Expect = 6.0
 Identities = 17/52 (32%), Positives = 26/52 (50%), Gaps = 7/52 (13%)

Query: 231 AGPVTLGNLYL--YVGLQNGALLRMVVDQTSGDLSDNRMRYLGSRPVKLFKI 280
           AGPV L   YL    GL       ++VD++ G L   R   L +R ++L ++
Sbjct: 13  AGPVGLMCAYLGQLCGLNT-----VIVDKSDGPLEVGRADALNARTLQLLEL 59


>gnl|CDD|234035 TIGR02860, spore_IV_B, stage IV sporulation protein B.  SpoIVB, the
           stage IV sporulation protein B of endospore-forming
           bacteria such as Bacillus subtilis, is a serine
           proteinase, expressed in the spore (rather than mother
           cell) compartment, that participates in a proteolytic
           activation cascade for Sigma-K. It appears to be
           universal among endospore-forming bacteria and occurs
           nowhere else [Cellular processes, Sporulation and
           germination].
          Length = 402

 Score = 27.7 bits (62), Expect = 8.0
 Identities = 11/45 (24%), Positives = 22/45 (48%)

Query: 71  KKESDKKKIVRCAVNQRQIVIALQGGRLIYFEMHPVSDKKESDKK 115
           K   D   ++  A  ++  +   +GG++I   + PV DK+E   +
Sbjct: 146 KNMDDLANLINKAGGEKLTLTIERGGKIIETVIKPVKDKEEGRYR 190


  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
   0.317    0.134    0.384 

Gapped
Lambda     K      H
   0.267   0.0716    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,222,809
Number of extensions: 1334197
Number of successful extensions: 926
Number of sequences better than 10.0: 1
Number of HSP's gapped: 925
Number of HSP's successfully gapped: 14
Length of query: 290
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 194
Effective length of database: 6,679,618
Effective search space: 1295845892
Effective search space used: 1295845892
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: 58 (26.1 bits)