RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13237
         (84 letters)



>gnl|CDD|216401 pfam01267, F-actin_cap_A, F-actin capping protein alpha subunit. 
          Length = 269

 Score = 90.8 bits (226), Expect = 5e-24
 Identities = 38/73 (52%), Positives = 50/73 (68%)

Query: 4   RSLADFIEGNNVEVKGNLKVQVHYYEDGNVQLVSSKDIKETVVVTSEEQTAREIVKLIEE 63
           RS       +   +KG +KV VHYYEDGNVQL SSKD +ETV V++++ TA  IVK I E
Sbjct: 162 RSEWTLDSSSTGSLKGKIKVDVHYYEDGNVQLKSSKDFEETVSVSNDDATASSIVKAIRE 221

Query: 64  SETAYQQAISENY 76
           +E  YQ A++EN+
Sbjct: 222 AENEYQAALNENF 234


>gnl|CDD|119391 cd04508, TUDOR, Tudor domains are found in many eukaryotic
          organisms and have been implicated in protein-protein
          interactions in which methylated protein substrates
          bind to these domains. For example, the Tudor domain of
          Survival of Motor Neuron (SMN) binds to symmetrically
          dimethylated arginines of arginine-glycine (RG) rich
          sequences found in the C-terminal tails of Sm proteins.
          The SMN protein is linked to spinal muscular atrophy.
          Another example is the tandem tudor domains of 53BP1,
          which bind to histone H4 specifically dimethylated at
          Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA
          damage checkpoint signal.
          Length = 48

 Score = 28.7 bits (65), Expect = 0.058
 Identities = 7/29 (24%), Positives = 16/29 (55%)

Query: 15 VEVKGNLKVQVHYYEDGNVQLVSSKDIKE 43
            +  + KV+V + + GN ++V   D++ 
Sbjct: 20 TSILSDGKVEVFFVDYGNTEVVPLSDLRP 48


>gnl|CDD|227493 COG5164, SPT5, Transcription elongation factor [Transcription].
          Length = 607

 Score = 27.3 bits (60), Expect = 0.98
 Identities = 21/74 (28%), Positives = 32/74 (43%), Gaps = 2/74 (2%)

Query: 9   FIEGNNVEVKGNLKVQVHYYEDGNVQLVSSKDIKETVVVTSEEQTAREIVKLIEESETAY 68
           F  G  V +K N  V V    +GNV +V++KD  E++ V  ++      V L        
Sbjct: 286 FDFGETVSIKENNGVFV--KIEGNVCIVATKDFTESLKVDLDKMNPPVTVNLQNPKTNEL 343

Query: 69  QQAISENYMIIRKT 82
           ++ I      I KT
Sbjct: 344 ERKIVGRDPAIGKT 357


>gnl|CDD|222900 PHA02596, 5, baseplate hub subunit and tail lysozyme; Provisional.
          Length = 576

 Score = 27.0 bits (60), Expect = 1.3
 Identities = 15/27 (55%), Positives = 15/27 (55%), Gaps = 4/27 (14%)

Query: 12  GNNVEVKGNLKVQVH----YYEDGNVQ 34
             NV VKGNLKV V     YY  GNV 
Sbjct: 446 DRNVNVKGNLKVVVEGDAIYYNMGNVL 472


>gnl|CDD|197660 smart00333, TUDOR, Tudor domain.  Domain of unknown function
          present in several RNA-binding proteins. 10 copies in
          the Drosophila Tudor protein. Initial proposal that the
          survival motor neuron gene product contain a Tudor
          domain are corroborated by more recent database search
          techniques such as PSI-BLAST (unpublished).
          Length = 57

 Score = 25.3 bits (56), Expect = 1.5
 Identities = 8/28 (28%), Positives = 16/28 (57%)

Query: 15 VEVKGNLKVQVHYYEDGNVQLVSSKDIK 42
          V+V G    +V + + GN ++V   D++
Sbjct: 24 VKVDGEQLYEVFFIDYGNEEVVPPSDLR 51


>gnl|CDD|238110 cd00186, TOP1Ac, DNA Topoisomerase, subtype IA; DNA-binding,
           ATP-binding and catalytic domain of bacterial DNA
           topoisomerases I and III, and eukaryotic DNA
           topoisomerase III and eubacterial and archael reverse
           gyrases. Topoisomerases clevage single or double
           stranded DNA and then rejoin the broken phosphodiester
           backbone. Proposed catalytic mechanism of single
           stranded DNA cleavage is by phosphoryl transfer through
           a tyrosine nucleophile using acid/base catalysis. Tyr is
           activated by a nearby group (not yet identified) acting
           as a general base for nucleophilic attack on the 5'
           phosphate of the scissile bond. Arg and Lys stabilize
           the pentavalent transition state. Glu then acts as a
           proton donor for the leaving 3'-oxygen, upon cleavage of
           the scissile strand.
          Length = 381

 Score = 26.0 bits (58), Expect = 2.6
 Identities = 11/37 (29%), Positives = 18/37 (48%), Gaps = 2/37 (5%)

Query: 47  VTSEEQTAR--EIVKLIEESETAYQQAISENYMIIRK 81
           +   E TA+  E +  I E +  YQ+ + E Y   +K
Sbjct: 343 LVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKK 379


>gnl|CDD|149114 pfam07865, DUF1652, Protein of unknown function (DUF1652).  This
          is a family containing hypothetical bacterial proteins.
          Length = 69

 Score = 25.0 bits (55), Expect = 2.9
 Identities = 11/45 (24%), Positives = 21/45 (46%), Gaps = 6/45 (13%)

Query: 19 GNLKVQVHYYEDGNVQLVSSKDIKETVVVTSEEQTAREIVKLIEE 63
          G++ V++     G V L+       T +  S   + R++ +LI E
Sbjct: 25 GSMTVRLFDPASGRVDLLV------TGISLSALNSCRDVSRLIAE 63


>gnl|CDD|181997 PRK09620, PRK09620, hypothetical protein; Provisional.
          Length = 229

 Score = 25.6 bits (56), Expect = 2.9
 Identities = 15/40 (37%), Positives = 21/40 (52%), Gaps = 13/40 (32%)

Query: 25  VHYY--EDGNVQLVSSKDIKETVVVTSEEQTAREIVKLIE 62
           +HY   +DG  QL + KD           +TA+EIVK +E
Sbjct: 192 MHYVIGQDGKGQLCNGKD-----------ETAKEIVKRLE 220


>gnl|CDD|179631 PRK03692, PRK03692, putative UDP-N-acetyl-D-mannosaminuronic acid
          transferase; Provisional.
          Length = 243

 Score = 25.3 bits (56), Expect = 4.4
 Identities = 17/59 (28%), Positives = 29/59 (49%), Gaps = 8/59 (13%)

Query: 26 HYYEDGNVQ---LVSSKDIKETVVVTSEEQTAREIVKLIEESETAYQQAISENYMIIRK 81
          + + DG ++   LV+   I    V+T+E+    E+ +LI  +E  Y   IS    I +K
Sbjct: 26 YLFADGQLKTGTLVA---INAEKVLTAEDDA--ELRELINAAEYKYADGISVVRSIRKK 79


>gnl|CDD|236498 PRK09401, PRK09401, reverse gyrase; Reviewed.
          Length = 1176

 Score = 25.3 bits (56), Expect = 4.7
 Identities = 12/36 (33%), Positives = 21/36 (58%), Gaps = 2/36 (5%)

Query: 48   TSEEQTAR--EIVKLIEESETAYQQAISENYMIIRK 81
             SEE+T +  E +  +EE +  YQ+ + E Y  I++
Sbjct: 1136 VSEERTRKLEEKMDKVEEGKEDYQEVLKELYEEIKE 1171


>gnl|CDD|225357 COG2766, PrkA, Putative Ser protein kinase [Signal transduction
           mechanisms].
          Length = 649

 Score = 24.7 bits (54), Expect = 7.3
 Identities = 14/80 (17%), Positives = 28/80 (35%), Gaps = 8/80 (10%)

Query: 6   LADFIEGNNVEVKGNLKVQVHYYEDGNVQLVSSKD--------IKETVVVTSEEQTAREI 57
           L+     ++ EV        +  E    +   S +        +K  +     E   +E+
Sbjct: 431 LSRAFNFDHEEVIAPPVHLFYIVEGLIEREQFSDEERERYLDFVKGYLRPEYAEFIGKEV 490

Query: 58  VKLIEESETAYQQAISENYM 77
            K   ES + Y Q + + Y+
Sbjct: 491 QKAYLESYSEYGQNLFDRYV 510


>gnl|CDD|185710 cd07900, Adenylation_DNA_ligase_I_Euk, Adenylation domain of
          eukaryotic DNA Ligase I.  ATP-dependent polynucleotide
          ligases catalyze phosphodiester bond formation using
          nicked nucleic acid substrates with the high energy
          nucleotide of ATP as a cofactor in a three step
          reaction mechanism. DNA ligases play a vital role in
          the diverse processes of DNA replication, recombination
          and repair. ATP-dependent ligases are present in many
          organisms such as viruses, bacteriophages, eukarya,
          archaea and bacteria. Some organisms express a variety
          of different ligases which appear to be targeted to
          specific functions. There are three classes of
          ATP-dependent DNA ligases in eukaryotic cells (I, III
          and IV). DNA ligase I is required for the ligation of
          Okazaki fragments during lagging-strand DNA synthesis
          and for base excision repair (BER). DNA ligases have a
          highly modular architecture consisting of a unique
          arrangement of two or more discrete domains. The
          adenylation and C-terminal
          oligonucleotide/oligosaccharide binding (OB)-fold
          domains comprise a catalytic core unit that is common
          to most members of the ATP-dependent DNA ligase family.
          The adenylation domain binds ATP and contains many of
          the active-site residues. DNA ligase I is the main
          replicative ligase in eukaryotes. The common catalytic
          core unit comprises six conserved sequence motifs (I,
          III, IIIa, IV, V and VI) that define this family of
          related nucleotidyltransferases.
          Length = 219

 Score = 24.4 bits (54), Expect = 7.5
 Identities = 7/15 (46%), Positives = 10/15 (66%)

Query: 23 VQVHYYEDGNVQLVS 37
           Q+H  EDG V++ S
Sbjct: 44 AQIHLLEDGKVKIFS 58


>gnl|CDD|182123 PRK09866, PRK09866, hypothetical protein; Provisional.
          Length = 741

 Score = 24.4 bits (53), Expect = 9.0
 Identities = 9/58 (15%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 18  KGNLKVQ-VHYYEDGNVQLVSSKDIKETVVVTSEEQTAREIVKLIEESETAYQQAISE 74
           +  +  Q    ++D +  L   +   ET++ T++   +R+      E E+   + +++
Sbjct: 495 QDAVNAQLAALFQDDSEPLSEIRTRCETLLQTAQNTISRDFTLRFAELESTLCRVLTD 552


>gnl|CDD|225768 COG3227, LasB, Zinc metalloprotease (elastase) [Amino acid
           transport and metabolism].
          Length = 507

 Score = 24.3 bits (53), Expect = 9.5
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 7/72 (9%)

Query: 13  NNVEVKGNLKVQVHYYEDGNVQLVS-----SKDIKETVVVTSEEQTAREIVKLIEESETA 67
           N V VKG+ +V VH  ++G V+ V+      KD+       S EQ A  I +     E  
Sbjct: 91  NGVPVKGS-EVIVHLDKNGVVKAVNGFVNKKKDLPTNTPKISAEQ-AIAIARKQFGYERL 148

Query: 68  YQQAISENYMII 79
            +   +E  + +
Sbjct: 149 TESPKAELMVRV 160


  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    0.335 

Gapped
Lambda     K      H
   0.267   0.0748    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,968,175
Number of extensions: 304232
Number of successful extensions: 368
Number of sequences better than 10.0: 1
Number of HSP's gapped: 367
Number of HSP's successfully gapped: 44
Length of query: 84
Length of database: 10,937,602
Length adjustment: 52
Effective length of query: 32
Effective length of database: 8,631,194
Effective search space: 276198208
Effective search space used: 276198208
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: 53 (24.2 bits)