RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy4278
         (197 letters)



>gnl|CDD|218390 pfam05028, PARG_cat, Poly (ADP-ribose) glycohydrolase (PARG).
           Poly(ADP-ribose) glycohydrolase (PARG), is a
           ubiquitously expressed exo- and endoglycohydrolase which
           mediates oxidative and excitotoxic neuronal death.
          Length = 339

 Score =  181 bits (462), Expect = 1e-56
 Identities = 82/170 (48%), Positives = 111/170 (65%), Gaps = 10/170 (5%)

Query: 20  QELDQLETDIFFKQLLPKIISLALRLPNVLQCGIPLLKAHSNHSITLSQLQIASLLANAF 79
           +ELD+ E   FF++LLP +  LALRLP +L  GIPLLK     S+TL+Q QIA+LLAN+F
Sbjct: 3   EELDESEQKEFFEELLPAMARLALRLPELLPEGIPLLKQQDAGSVTLTQEQIAALLANSF 62

Query: 80  LCTYPRRNSNQPESQYANFPCINFSRLFQA----QSSCVSEKLKCLINYFVRVTTKDPTG 135
            C +PRR+S       ++FP INF RLFQ+    +S    EKLKCL++YF RV+   PTG
Sbjct: 63  FCLFPRRDSE-----ESSFPDINFDRLFQSLYPGRSESQEEKLKCLLHYFRRVSEDMPTG 117

Query: 136 LVTYSRRYLPHSQLPHWGDSRRKLPDLFISSEGMIENQ-RGLLQVDFANK 184
            V++ R+ L     P W  S   L  + + ++G+IE+Q +G LQVDFANK
Sbjct: 118 CVSFERKSLSPLDFPLWKKSTTNLCPVEVFTDGLIEDQGQGALQVDFANK 167


>gnl|CDD|226117 COG3589, COG3589, Uncharacterized conserved protein [Function
           unknown].
          Length = 360

 Score = 27.7 bits (62), Expect = 4.4
 Identities = 31/172 (18%), Positives = 52/172 (30%), Gaps = 12/172 (6%)

Query: 25  LETDIFFKQLLPKII-------SLALRLPNVLQCGIPLLKAHSNHSITLSQLQIASLLAN 77
              +  FK+   K         +   R P  L  G+P L+AH      +    +     +
Sbjct: 160 KRKNEIFKEYNIKTAAFISSDGAEGPRGP--LYEGLPTLEAHRYVEPFVQAKDLFKTGID 217

Query: 78  AFLC--TYPRRNSNQPESQYANFPCINFSRLFQAQSSCVSEKLKCLINYFVRVTTKDPTG 135
             L    +P     +  SQ  N        +     + V   +     +F R    +   
Sbjct: 218 DVLIGDQFPSEEELRAVSQAFNRNITEIKVVVIEDITEVELAILFEPEHFNRGDISEYVI 277

Query: 136 LVTYSRRYLPHSQLPHWGDSRRKLPDLFISSEGMIENQRGLLQVDFANKSHH 187
             T SR        P    + RK   + I + G     +G LQ+   N  + 
Sbjct: 278 RSTMSRVTYKQKIFPAHDTNERKKGSITIDNLG-YGRYKGELQIALKNLEND 328


>gnl|CDD|132723 cd02736, RNAP_III_Rpc1_C, Largest subunit (Rpc1) of Eukaryotic RNA
           polymerase III (RNAP III), C-terminal domain.
           Eukaryotic RNA polymerase III (RNAP III) is a large
           multi-subunit complex responsible for the synthesis of
           tRNAs, 5SrRNA, Alu-RNA, U6 snRNA, among others. Rpc1 is
           also known as C160 in yeast. Structure studies suggest
           that different RNA polymerase complexes share a similar
           crab-claw-shape structure. The C-terminal domain of
           Rpb1, the largest subunit of RNAP II, makes up part of
           the foot and jaw structures of RNAP II. The similarity
           between this domain and the C-terminal domain of Rpb1,
           its counterpart in RNAP II, suggests a similar
           functional and structural role.
          Length = 300

 Score = 27.6 bits (62), Expect = 4.5
 Identities = 14/50 (28%), Positives = 25/50 (50%), Gaps = 4/50 (8%)

Query: 5   KSDLWFIDVKQLLQFQELDQLETDIFFKQLLPKIISLALRLPNVLQCGIP 54
             D  +I +K  L  + +++L   +    L   + SL  +LP+V+  GIP
Sbjct: 102 SPDDCYILIK--LDKKIIEKL--QLSKSNLYFLLQSLKRKLPDVVVSGIP 147


>gnl|CDD|220817 pfam10593, Z1, Z1 domain.  This uncharacterized domain was
           identified by Iyer and colleagues. It is found
           associated with a helicase domain of superfamily type
           II.
          Length = 231

 Score = 27.2 bits (61), Expect = 5.8
 Identities = 11/53 (20%), Positives = 20/53 (37%), Gaps = 3/53 (5%)

Query: 139 YSRRYLP--HSQLPHWGDSRRKLPDLFISSEGMIEN-QRGLLQVDFANKSHHL 188
           Y   + P      P W + +  LP +      ++ N       +D+AN  + L
Sbjct: 75  YEDDFEPGTDLDKPSWDEIQAALPKVIDDIRVVVVNSSTSKDSLDYANGENGL 127


>gnl|CDD|212464 cd01717, Sm_B, Sm protein B.  The eukaryotic Sm proteins (B/B', D1,
           D2, D3, E, F and G) assemble into a hetero-heptameric
           ring around the Sm site of the 2,2,7-trimethyl guanosine
           (m3G) capped U1, U2, U4 and U5 snRNAs (Sm snRNAs)
           forming the core of the snRNP particle. The snRNP
           particle, in turn, assembles with other components onto
           the pre-mRNA to form the spliceosome which is
           responsible for the excision of introns and the ligation
           of exons. Members of this family share a highly
           conserved Sm fold, containing an N-terminal helix
           followed by a strongly bent five-stranded antiparallel
           beta-sheet.
          Length = 80

 Score = 25.6 bits (57), Expect = 6.4
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 115 SEKLKCLINYFVRVTTKD 132
           S K+   INY +RVT +D
Sbjct: 2   SSKMLQYINYRMRVTLQD 19


>gnl|CDD|227403 COG5071, RPN5, 26S proteasome regulatory complex component
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 439

 Score = 26.8 bits (59), Expect = 7.6
 Identities = 11/65 (16%), Positives = 22/65 (33%), Gaps = 1/65 (1%)

Query: 92  ESQYANFPCINFSRLFQAQSSCVSEKLKCLIN-YFVRVTTKDPTGLVTYSRRYLPHSQLP 150
            + Y+   C     L     S   + +  L+N          P  ++++ +      QL 
Sbjct: 348 ANYYSRIHCSRLGVLLDMSPSETEQFISDLVNKGHFYAKINRPAQIISFEKSQNVQEQLN 407

Query: 151 HWGDS 155
            WG +
Sbjct: 408 EWGSN 412


>gnl|CDD|233750 TIGR02151, IPP_isom_2, isopentenyl-diphosphate delta-isomerase,
           type 2.  Isopentenyl-diphosphate delta-isomerase (IPP
           isomerase) interconverts isopentenyl diphosphate and
           dimethylallyl diphosphate. This model represents the
           type 2 enzyme. FMN, NADPH, and Mg2+ are required by this
           form, which lacks homology to the type 1 enzyme
           (TIGR02150). IPP is precursor to many compounds,
           including enzyme cofactors, sterols, and isoprenoids
           [Biosynthesis of cofactors, prosthetic groups, and
           carriers, Other].
          Length = 333

 Score = 26.8 bits (60), Expect = 8.1
 Identities = 12/27 (44%), Positives = 14/27 (51%)

Query: 20  QELDQLETDIFFKQLLPKIISLALRLP 46
           QEL Q E D  FK  L KI  +  +L 
Sbjct: 153 QELVQPEGDRNFKGWLEKIAEICSQLS 179


  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
   0.323    0.137    0.413 

Gapped
Lambda     K      H
   0.267   0.0762    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,758,459
Number of extensions: 866961
Number of successful extensions: 560
Number of sequences better than 10.0: 1
Number of HSP's gapped: 557
Number of HSP's successfully gapped: 14
Length of query: 197
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 105
Effective length of database: 6,857,034
Effective search space: 719988570
Effective search space used: 719988570
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 (22.0 bits)
S2: 56 (25.3 bits)