RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy3924
         (131 letters)



>gnl|CDD|201356 pfam00628, PHD, PHD-finger.  PHD folds into an interleaved type
          of Zn-finger chelating 2 Zn ions in a similar manner to
          that of the RING and FYVE domains. Several PHD fingers
          have been identified as binding modules of methylated
          histone H3.
          Length = 51

 Score = 42.5 bits (100), Expect = 1e-06
 Identities = 21/51 (41%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 38 VCEGCAQRHDEGRLILCDECDISYHIYCTDPPLDH--IPRGTWKCKWCAQC 86
           C  C +  D+G L+LCD CD  +H+ C  PPL+   IP G W C  C   
Sbjct: 1  YCAVCGKVDDDGELLLCDGCDRWFHLACLGPPLEPEEIPEGEWYCPECKPK 51


>gnl|CDD|214584 smart00249, PHD, PHD zinc finger.  The plant homeodomain (PHD)
          finger is a C4HC3 zinc-finger-like motif found in
          nuclear proteins thought to be involved in epigenetics
          and chromatin-mediated transcriptional regulation. The
          PHD finger binds two zinc ions using the so-called
          'cross-brace' motif and is thus structurally related to
          the RING finger and the FYVE finger. It is not yet
          known if PHD fingers have a common molecular function.
          Several reports suggest that it can function as a
          protein-protein interacton domain and it was recently
          demonstrated that the PHD finger of p300 can cooperate
          with the adjacent BROMO domain in nucleosome binding in
          vitro. Other reports suggesting that the PHD finger is
          a ubiquitin ligase have been refuted as these domains
          were RING fingers misidentified as PHD fingers.
          Length = 47

 Score = 42.2 bits (99), Expect = 1e-06
 Identities = 20/47 (42%), Positives = 23/47 (48%), Gaps = 1/47 (2%)

Query: 38 VCEGCAQRHDEGRLILCDECDISYHIYCTDPPL-DHIPRGTWKCKWC 83
           C  C +  D G L+ CD CD  YH  C  PPL +  P G W C  C
Sbjct: 1  YCSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47


>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
           function prediction only].
          Length = 669

 Score = 36.5 bits (84), Expect = 0.002
 Identities = 16/64 (25%), Positives = 22/64 (34%), Gaps = 10/64 (15%)

Query: 33  CLDCTVCEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWC-------AQ 85
              CT C       +   ++ CD C+I  H  C       +P G W C+ C         
Sbjct: 193 DDICTKCTS-THNENSNAIVFCDGCEICVHQSCYGIQF--LPEGFWLCRKCIYGEYQIRC 249

Query: 86  CLTC 89
           C  C
Sbjct: 250 CSFC 253


>gnl|CDD|240069 cd04718, BAH_plant_2, BAH, or Bromo Adjacent Homology domain,
          plant-specific sub-family with unknown function. BAH
          domains are found in a variety of proteins playing
          roles in transcriptional silencing and the remodeling
          of chromatin. It is assumed that in most or all of
          these instances the BAH domain mediates protein-protein
          interactions.
          Length = 148

 Score = 32.2 bits (73), Expect = 0.042
 Identities = 10/23 (43%), Positives = 14/23 (60%)

Query: 61 YHIYCTDPPLDHIPRGTWKCKWC 83
          +H+ C  PPL  +P G W C +C
Sbjct: 2  FHLCCLRPPLKEVPEGDWICPFC 24


>gnl|CDD|218505 pfam05216, UNC-50, UNC-50 family.  Gmh1p from S. cerevisiae is
           located in the Golgi membrane and interacts with ARF
           exchange factors.
          Length = 232

 Score = 29.1 bits (66), Expect = 0.46
 Identities = 8/30 (26%), Positives = 13/30 (43%)

Query: 70  LDHIPRGTWKCKWCAQCLTCGATGYHIYCT 99
           L  + R ++   +    L   A GY+ Y T
Sbjct: 156 LPLLIRDSFISLFVGNTLYLIALGYYFYIT 185


>gnl|CDD|233042 TIGR00598, rad14, DNA repair protein.  All proteins in this
          family for which functions are known are used for the
          recognition of DNA damage as part of nucleotide
          excision repair. This family is based on the
          phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
          Stanford University) [DNA metabolism, DNA replication,
          recombination, and repair].
          Length = 172

 Score = 28.6 bits (64), Expect = 0.77
 Identities = 13/44 (29%), Positives = 20/44 (45%), Gaps = 2/44 (4%)

Query: 28 SKGWRCLDCTVCEGCAQRHDEGRLILCDECDISYHIYCTDPPLD 71
          S  +   DC VC+ C  + D+ +L+   E    Y +   D  LD
Sbjct: 11 SYLFDHFDCAVCDNCRDKDDKYKLLTKTEAKEEYLL--KDCDLD 52


>gnl|CDD|234863 PRK00913, PRK00913, multifunctional aminopeptidase A; Provisional.
          Length = 483

 Score = 27.4 bits (62), Expect = 2.1
 Identities = 6/8 (75%), Positives = 7/8 (87%)

Query: 48  EGRLILCD 55
           EGRL+L D
Sbjct: 338 EGRLVLAD 345


>gnl|CDD|223338 COG0260, PepB, Leucyl aminopeptidase [Amino acid transport and
           metabolism].
          Length = 485

 Score = 26.8 bits (60), Expect = 3.4
 Identities = 6/8 (75%), Positives = 7/8 (87%)

Query: 48  EGRLILCD 55
           EGRL+L D
Sbjct: 337 EGRLVLAD 344


>gnl|CDD|238247 cd00433, Peptidase_M17, Cytosol aminopeptidase family, N-terminal
           and catalytic domains.  Family M17 contains zinc- and
           manganese-dependent exopeptidases ( EC  3.4.11.1),
           including leucine aminopeptidase. They catalyze removal
           of amino acids from the N-terminus of a protein and play
           a key role in protein degradation and in the metabolism
           of biologically active peptides. They do not contain
           HEXXH motif (which is used as one of the signature
           patterns to group the peptidase families) in the
           metal-binding site. The two associated zinc ions and the
           active site are entirely enclosed within the C-terminal
           catalytic domain in leucine aminopeptidase. The enzyme
           is a hexamer, with the catalytic domains clustered
           around the three-fold axis, and the two trimers related
           to one another by a two-fold rotation. The N-terminal
           domain is structurally similar to the ADP-ribose binding
           Macro domain. This family includes proteins from
           bacteria, archaea, animals and plants.
          Length = 468

 Score = 26.7 bits (60), Expect = 3.9
 Identities = 6/8 (75%), Positives = 7/8 (87%)

Query: 48  EGRLILCD 55
           EGRL+L D
Sbjct: 324 EGRLVLAD 331


>gnl|CDD|224627 COG1713, COG1713, Predicted HD superfamily hydrolase involved in
           NAD metabolism [Coenzyme metabolism].
          Length = 187

 Score = 26.5 bits (59), Expect = 4.2
 Identities = 9/15 (60%), Positives = 11/15 (73%)

Query: 103 LDHIIFVQDKIRPKR 117
           LD I++V DKI P R
Sbjct: 119 LDKILYVADKIEPGR 133


>gnl|CDD|144538 pfam00981, Rota_NS53, Rotavirus RNA-binding Protein 53 (NS53).
          This protein is also known as NSP1. NS53 is encoded by
          gene 5. It is made in low levels in the infected cells
          and is a component of early replication. The protein is
          known to accumulate on the cytoskeleton of the infected
          cell. NS53 is an RNA binding protein that contains a
          characteristic cysteine rich region.
          Length = 488

 Score = 26.5 bits (59), Expect = 4.6
 Identities = 21/82 (25%), Positives = 27/82 (32%), Gaps = 47/82 (57%)

Query: 10 SVCRDVKLHDLPISKVILSKGWRCLDC------TVCEGCAQRHDEGRLILCDECDISYHI 63
           V R       P +K+   KGW CLDC      T C GC+                 YH+
Sbjct: 28 DVWRPA-----PPTKI---KGW-CLDCCQHTDLTYCRGCSL----------------YHV 62

Query: 64 YCTDPPLDHIPRGTWKCKWCAQ 85
                          C+WC+Q
Sbjct: 63 ----------------CQWCSQ 68


>gnl|CDD|240379 PTZ00360, PTZ00360, sexual stage antigen; Provisional.
          Length = 543

 Score = 26.6 bits (59), Expect = 5.3
 Identities = 11/29 (37%), Positives = 17/29 (58%)

Query: 2   NCDVIAYGSVCRDVKLHDLPISKVILSKG 30
           N  V AYG +  D  L ++ ++ +I SKG
Sbjct: 374 NFQVYAYGQLLDDSHLREIRLNDIIGSKG 402


>gnl|CDD|188119 TIGR01206, lysW, lysine biosynthesis protein LysW.  This very
          small, poorly characterized protein has been shown
          essential in Thermus thermophilus for an unusual
          pathway of Lys biosynthesis from aspartate by way of
          alpha-aminoadipate (AAA) rather than diaminopimelate.
          It is found also in Deinococcus radiodurans and
          Pyrococcus horikoshii, which appear to share the AAA
          pathway [Amino acid biosynthesis, Aspartate family].
          Length = 54

 Score = 24.9 bits (54), Expect = 5.5
 Identities = 10/27 (37%), Positives = 14/27 (51%), Gaps = 1/27 (3%)

Query: 49 GRLILCDECDISYHIYCTDPP-LDHIP 74
          G L++CDEC     +   DP  L+  P
Sbjct: 20 GELVICDECGAELEVVSLDPLRLEQAP 46


>gnl|CDD|182933 PRK11057, PRK11057, ATP-dependent DNA helicase RecQ; Provisional.
          Length = 607

 Score = 26.2 bits (58), Expect = 5.7
 Identities = 11/22 (50%), Positives = 11/22 (50%), Gaps = 5/22 (22%)

Query: 48  EGRLILCDECDISYHIYCTDPP 69
           EGR   C  CDI     C DPP
Sbjct: 391 EGRQEPCGNCDI-----CLDPP 407


  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
   0.327    0.142    0.511 

Gapped
Lambda     K      H
   0.267   0.0722    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,389,291
Number of extensions: 513242
Number of successful extensions: 638
Number of sequences better than 10.0: 1
Number of HSP's gapped: 634
Number of HSP's successfully gapped: 41
Length of query: 131
Length of database: 10,937,602
Length adjustment: 86
Effective length of query: 45
Effective length of database: 7,123,158
Effective search space: 320542110
Effective search space used: 320542110
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 53 (24.2 bits)