RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy71
         (218 letters)



>gnl|CDD|177756 PLN00154, PLN00154, histone H2A; Provisional.
          Length = 136

 Score = 96.6 bits (240), Expect = 1e-25
 Identities = 43/54 (79%), Positives = 47/54 (87%), Gaps = 3/54 (5%)

Query: 1   VLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKATIAGGARFGLYPEVRR 54
           VLELAGNASKDLKVKRITPRHLQLAIRGDEELD+LIK TIAGG   G+ P + +
Sbjct: 77  VLELAGNASKDLKVKRITPRHLQLAIRGDEELDTLIKGTIAGG---GVIPHIHK 127


>gnl|CDD|185399 PTZ00017, PTZ00017, histone H2A; Provisional.
          Length = 134

 Score = 90.6 bits (225), Expect = 3e-23
 Identities = 34/53 (64%), Positives = 40/53 (75%), Gaps = 4/53 (7%)

Query: 1   VLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLI-KATIAGGARFGLYPEV 52
           VLELAGNA+KD K KRITPRH+QLAIR DEEL+ L+   TIA G   G+ P +
Sbjct: 65  VLELAGNAAKDNKKKRITPRHIQLAIRNDEELNKLLAGVTIASG---GVLPNI 114


>gnl|CDD|238029 cd00074, H2A, Histone 2A; H2A is a subunit of the nucleosome. The
           nucleosome is an octamer containing two H2A, H2B, H3,
           and H4 subunits. The H2A subunit performs essential
           roles in maintaining structural integrity of the
           nucleosome, chromatin condensation, and binding of
           specific chromatin-associated proteins.
          Length = 115

 Score = 80.8 bits (200), Expect = 6e-20
 Identities = 32/44 (72%), Positives = 37/44 (84%), Gaps = 1/44 (2%)

Query: 1   VLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIK-ATIAGG 43
           VLELAGNA++D K KRITPRHLQLA+R DEEL+ L+K  TIA G
Sbjct: 58  VLELAGNAARDNKKKRITPRHLQLAVRNDEELNKLLKGVTIASG 101


>gnl|CDD|227587 COG5262, HTA1, Histone H2A [Chromatin structure and dynamics].
          Length = 132

 Score = 76.8 bits (189), Expect = 5e-18
 Identities = 30/44 (68%), Positives = 35/44 (79%), Gaps = 1/44 (2%)

Query: 1   VLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIK-ATIAGG 43
           +LELAGNA++D K KRI PRHLQLAIR DEEL+ L+   TIA G
Sbjct: 64  ILELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLLGDVTIAQG 107


>gnl|CDD|197711 smart00414, H2A, Histone 2A. 
          Length = 106

 Score = 73.9 bits (182), Expect = 3e-17
 Identities = 32/44 (72%), Positives = 37/44 (84%), Gaps = 1/44 (2%)

Query: 1  VLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKA-TIAGG 43
          VLELAGNA++D K +RITPRHLQLAIR DEEL+ L+K  TIA G
Sbjct: 47 VLELAGNAARDNKKRRITPRHLQLAIRNDEELNKLLKGVTIAQG 90


>gnl|CDD|177758 PLN00157, PLN00157, histone H2A; Provisional.
          Length = 132

 Score = 63.3 bits (154), Expect = 4e-13
 Identities = 30/53 (56%), Positives = 37/53 (69%), Gaps = 4/53 (7%)

Query: 1   VLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIK-ATIAGGARFGLYPEV 52
           VLELAGNA++D K  RI PRH+QLA+R DEEL  L+   TIA G   G+ P +
Sbjct: 64  VLELAGNAARDNKKSRIVPRHIQLAVRNDEELSKLLGGVTIAAG---GVLPNI 113


>gnl|CDD|215080 PLN00156, PLN00156, histone H2AX; Provisional.
          Length = 139

 Score = 60.8 bits (147), Expect = 6e-12
 Identities = 30/53 (56%), Positives = 38/53 (71%), Gaps = 4/53 (7%)

Query: 1   VLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLIKA-TIAGGARFGLYPEV 52
           VLELAGNA++D K  RI PRH+QLA+R DEEL  L+ + TIA G   G+ P +
Sbjct: 67  VLELAGNAARDNKKNRIVPRHIQLAVRNDEELSKLLGSVTIAAG---GVLPNI 116


>gnl|CDD|165721 PLN00153, PLN00153, histone H2A; Provisional.
          Length = 129

 Score = 57.8 bits (139), Expect = 6e-11
 Identities = 31/53 (58%), Positives = 38/53 (71%), Gaps = 4/53 (7%)

Query: 1   VLELAGNASKDLKVKRITPRHLQLAIRGDEELDSLI-KATIAGGARFGLYPEV 52
           VLELAGNA++D K  RI PRH+QLAIR DEEL  L+ + TIA G   G+ P +
Sbjct: 62  VLELAGNAARDNKKNRIVPRHIQLAIRNDEELGKLLGEVTIASG---GVLPNI 111


>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4. 
          Length = 75

 Score = 40.6 bits (96), Expect = 3e-05
 Identities = 15/29 (51%), Positives = 20/29 (68%)

Query: 1  VLELAGNASKDLKVKRITPRHLQLAIRGD 29
          +LE AG  ++  K K ITPR +QLA+R D
Sbjct: 47 ILEDAGLLARHAKRKTITPRDIQLAVRLD 75


>gnl|CDD|240330 PTZ00252, PTZ00252, histone H2A; Provisional.
          Length = 134

 Score = 31.1 bits (70), Expect = 0.17
 Identities = 17/42 (40%), Positives = 27/42 (64%), Gaps = 2/42 (4%)

Query: 13  KVKRITPRHLQLAIRGDEELDSLIKATIAGGARFGLYPEVRR 54
           K KR+TPR + LA+R D++L SL+K      +R G+ P + +
Sbjct: 77  KPKRLTPRTVTLAVRHDDDLGSLLKNVTL--SRGGVMPSLNK 116


>gnl|CDD|107224 cd06467, p23_NUDC_like, p23_like domain of NUD (nuclear
          distribution) C and similar proteins. Aspergillus
          nidulas (An) NUDC is needed for nuclear movement.
          AnNUDC is localized at the hyphal cortex, and binds
          NUDF at spindle pole bodies (SPBs) and in the cytoplasm
          at different stages in the cell cycle. At the SPBs it
          is part of the dynein molecular motor/NUDF complex that
          regulates microtubule dynamics.  Mammalian(m) NUDC
          associates both with the dynein complex and also with
          an anti-inflammatory enzyme, platelet activating factor
          acetylhydrolase I, PAF-AH(I) complex, through binding
          mNUDF, the regulatory beta subunit of PAF-AH(I).  mNUDC
          is important for cell proliferation both in normal and
          tumor tissues.  Its expression is elevated in various
          cell types undergoing mitosis or stimulated to
          proliferate, with high expression levels observed in
          leukemic cells and tumors.  For a leukemic cell line,
          human NUDC was shown to activate the thrombopoietin
          (TPO) receptor (Mpl) by binding to its extracellular
          domain, and promoting cell proliferation and
          differentiation.  This group also includes the human
          broadly immunogenic tumor associated antigen, CML66,
          which is highly expressed in a variety of solid tumors
          and in leukemias. In normal tissues high expression of
          CML66 is limited to testis and heart.
          Length = 85

 Score = 27.9 bits (63), Expect = 1.3
 Identities = 14/27 (51%), Positives = 21/27 (77%), Gaps = 1/27 (3%)

Query: 6  GNASKDLKVKRITPRHLQLAIRGDEEL 32
          G  SKD+KV+ ITP+HL++ ++G E L
Sbjct: 19 GTKSKDVKVE-ITPKHLKVGVKGGEPL 44


>gnl|CDD|237053 PRK12315, PRK12315, 1-deoxy-D-xylulose-5-phosphate synthase;
           Provisional.
          Length = 581

 Score = 28.0 bits (63), Expect = 4.0
 Identities = 11/34 (32%), Positives = 19/34 (55%)

Query: 133 AKCDQLTSLGLDLRYLLDGALRSPLTKTLKETRD 166
           ++ +   ++GLD RY+ DG     L +  KE +D
Sbjct: 198 SENNLFKAMGLDYRYVEDGNDIESLIEAFKEVKD 231


>gnl|CDD|187565 cd05255, SQD1_like_SDR_e, UDP_sulfoquinovose_synthase (Arabidopsis
           thaliana SQD1 and related proteins), extended (e) SDRs. 
           Arabidopsis thaliana UDP-sulfoquinovose-synthase (
           SQD1), an extended SDR,  catalyzes the transfer of
           SO(3)(-) to UDP-glucose in the biosynthesis of plant
           sulfolipids. Members of this subgroup share the
           conserved SDR catalytic residues, and a partial match to
           the characteristic extended-SDR NAD-binding motif.
           Extended SDRs are distinct from classical SDRs. In
           addition to the Rossmann fold (alpha/beta folding
           pattern with a central beta-sheet) core region typical
           of all SDRs, extended SDRs have a less conserved
           C-terminal extension of approximately 100 amino acids.
           Extended SDRs are a diverse collection of proteins, and
           include isomerases, epimerases, oxidoreductases, and
           lyases; they typically have a TGXXGXXG cofactor binding
           motif. SDRs are a functionally diverse family of
           oxidoreductases that have a single domain with a
           structurally conserved Rossmann fold, an
           NAD(P)(H)-binding region, and a structurally diverse
           C-terminal region. Sequence identity between different
           SDR enzymes is typically in the 15-30% range; they
           catalyze a wide range of activities including the
           metabolism of steroids, cofactors, carbohydrates,
           lipids, aromatic compounds, and amino acids, and act in
           redox sensing. Classical SDRs have an TGXXX[AG]XG
           cofactor binding motif and a YXXXK active site motif,
           with the Tyr residue of the active site motif serving as
           a critical catalytic residue (Tyr-151, human
           15-hydroxyprostaglandin dehydrogenase numbering). In
           addition to the Tyr and Lys, there is often an upstream
           Ser and/or an Asn, contributing to the active site;
           while substrate binding is in the C-terminal region,
           which determines specificity. The standard reaction
           mechanism is a 4-pro-S hydride transfer and proton relay
           involving the conserved Tyr and Lys, a water molecule
           stabilized by Asn, and nicotinamide. Atypical SDRs
           generally lack the catalytic residues characteristic of
           the SDRs, and their glycine-rich NAD(P)-binding motif is
           often different from the forms normally seen in
           classical or extended SDRs. Complex (multidomain) SDRs
           such as ketoreductase domains of fatty acid synthase
           have a GGXGXXG NAD(P)-binding motif and an altered
           active site motif (YXXXN). Fungal type ketoacyl
           reductases have a TGXXXGX(1-2)G NAD(P)-binding motif.
          Length = 382

 Score = 28.1 bits (63), Expect = 4.3
 Identities = 15/51 (29%), Positives = 20/51 (39%), Gaps = 9/51 (17%)

Query: 133 AKCDQLTSLGLDLRYLLDGALRSPLTKTLKETRDKLSDTIKLRCAEDRWKP 183
           AK  +L  LGL+  YL +  L S +     +  D        R  E R  P
Sbjct: 336 AKNTKLLDLGLEPHYLSESLLDS-ILNFAVKYAD--------RVDEKRILP 377


>gnl|CDD|223952 COG1021, EntE, Peptide arylation enzymes [Secondary metabolites
           biosynthesis, transport, and catabolism].
          Length = 542

 Score = 27.4 bits (61), Expect = 6.4
 Identities = 11/52 (21%), Positives = 18/52 (34%), Gaps = 2/52 (3%)

Query: 156 PLTKTLKETRDKLSDTIKLRCAEDRWKPYNLNNRQQRDKFLTEFTDAGLTSM 207
            LT  L +   +  D I +   E R     L+  Q+ D+        G+   
Sbjct: 29  TLTDILTDHAARYPDRIAVIDGERRLSYAELD--QRADRLAAGLRRLGIKPG 78


>gnl|CDD|233807 TIGR02275, DHB_AMP_lig, 2,3-dihydroxybenzoate-AMP ligase.  Proteins
           in this family belong to the AMP-binding enzyme family
           (pfam00501). Members activate 2,3-dihydroxybenzoate
           (DHB) by ligation of AMP from ATP with the release of
           pyrophosphate; many are involved in synthesis of
           siderophores such as enterobactin, vibriobactin,
           vulnibactin, etc. The most closely related proteine
           believed to differ in function activates salicylate
           rather than DHB [Transport and binding proteins, Cations
           and iron carrying compounds].
          Length = 526

 Score = 27.1 bits (60), Expect = 9.1
 Identities = 13/52 (25%), Positives = 21/52 (40%), Gaps = 2/52 (3%)

Query: 156 PLTKTLKETRDKLSDTIKLRCAEDRWKPYNLNNRQQRDKFLTEFTDAGLTSM 207
           PLT  L++   +  D I + C   +W    L+  Q+ D      T  G+   
Sbjct: 24  PLTDILRDQAARYPDAIAIICGNRQWSYRELD--QRADNLAAGLTKLGIKQG 73


  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
   0.320    0.134    0.384 

Gapped
Lambda     K      H
   0.267   0.0718    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,705,878
Number of extensions: 974918
Number of successful extensions: 797
Number of sequences better than 10.0: 1
Number of HSP's gapped: 796
Number of HSP's successfully gapped: 25
Length of query: 218
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 125
Effective length of database: 6,812,680
Effective search space: 851585000
Effective search space used: 851585000
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 (21.8 bits)
S2: 57 (25.8 bits)