RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy397
         (202 letters)



>gnl|CDD|240256 PTZ00071, PTZ00071, 40S ribosomal protein S24; Provisional.
          Length = 132

 Score =  148 bits (376), Expect = 2e-46
 Identities = 54/94 (57%), Positives = 69/94 (73%), Gaps = 1/94 (1%)

Query: 7  ASTVTIKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSK-PENIFAFGF 65
           +  T++TRK++ N LL RKQ VV+VLHPGK +V K DI+EKL+K +K      I  FGF
Sbjct: 3  KAEFTVRTRKFLVNPLLNRKQFVVEVLHPGKGTVSKKDIKEKLAKQYKVADARTIVLFGF 62

Query: 66 QTNFGGGKSTGFALIYDSIDLAKKFEPKYRLQRV 99
          +T FGGGK+TGF LIYD++   KKFEPKYRL R+
Sbjct: 63 KTKFGGGKTTGFGLIYDNLAALKKFEPKYRLIRL 96


>gnl|CDD|224915 COG2004, RPS24A, Ribosomal protein S24E [Translation, ribosomal
          structure and biogenesis].
          Length = 107

 Score =  120 bits (302), Expect = 2e-35
 Identities = 37/90 (41%), Positives = 55/90 (61%)

Query: 10 VTIKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTNF 69
          + IK  +   N LL RK++V  V H G P+  + ++REKL+ M  +  E +     +T F
Sbjct: 2  MEIKILEKRDNPLLKRKEIVFVVYHEGSPTPSRKEVREKLAAMLGADKELVVVDYIKTEF 61

Query: 70 GGGKSTGFALIYDSIDLAKKFEPKYRLQRV 99
          G G+S G+A IYDS++ AKK EP+Y L+R 
Sbjct: 62 GKGRSKGYAKIYDSVERAKKIEPEYILERN 91


>gnl|CDD|216409 pfam01282, Ribosomal_S24e, Ribosomal protein S24e. 
          Length = 83

 Score =  118 bits (298), Expect = 4e-35
 Identities = 44/71 (61%), Positives = 57/71 (80%)

Query: 28 MVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFALIYDSIDLA 87
          MV +VLHPG+ +  + ++REKL+KM K   + +  FGF+T FGGGKSTGFALIYDS++ A
Sbjct: 1  MVFEVLHPGRATPSRKEVREKLAKMLKVDKDLVVVFGFKTEFGGGKSTGFALIYDSLEAA 60

Query: 88 KKFEPKYRLQR 98
          KKFEPKYRL+R
Sbjct: 61 KKFEPKYRLER 71


>gnl|CDD|179239 PRK01178, rps24e, 30S ribosomal protein S24e; Reviewed.
          Length = 99

 Score = 75.7 bits (187), Expect = 3e-18
 Identities = 31/79 (39%), Positives = 49/79 (62%)

Query: 20 NRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENIFAFGFQTNFGGGKSTGFAL 79
          N LLGR+++  +V H G  +  + D+R+KL+ M  +  E +     +T +G GKS G+A 
Sbjct: 11 NPLLGRREIKFEVYHEGSATPSRKDVRKKLAAMLNADKELVVVRKIKTEYGMGKSKGYAK 70

Query: 80 IYDSIDLAKKFEPKYRLQR 98
          +YD  + A+K EPKY L+R
Sbjct: 71 VYDDKERARKIEPKYILER 89


>gnl|CDD|218171 pfam04608, PgpA, Phosphatidylglycerophosphatase A.  This family
           represents a family of bacterial
           phosphatidylglycerophosphatases (EC:3.1.3.27), known as
           PgpA. It appears that bacteria possess several
           phosphatidylglycerophosphatases, and thus, PgpA is not
           essential in Escherichia coli.
          Length = 144

 Score = 29.8 bits (68), Expect = 0.52
 Identities = 13/40 (32%), Positives = 19/40 (47%), Gaps = 3/40 (7%)

Query: 96  LQRVSTKSLLVLIIATIGITSCQEAEHKI---DHSELVFD 132
           L+ +    L VL+   +GI  C  AE  +   D  E+V D
Sbjct: 36  LEGLELLVLEVLLAFLVGIWLCGLAEKLLGEHDPGEIVID 75


>gnl|CDD|222356 pfam13741, MRP-S25, Mitochondrial ribosomal protein S25.  This is
          the family of fungal 37S mitochondrial ribosomal S25
          proteins.
          Length = 229

 Score = 29.3 bits (66), Expect = 1.2
 Identities = 22/98 (22%), Positives = 36/98 (36%), Gaps = 7/98 (7%)

Query: 1  MKTVLSASTVTIKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENI 60
          MK   +A  V  +T  Y+   LL +K    DV+    P+   T  R+   +   +K    
Sbjct: 1  MKIQTNAVNVLQRTSAYLKAGLLKKKPAWYDVVADIPPTTLLT--RKPPPRHPSTKKRRK 58

Query: 61 FAFGFQTNFGGGKSTGFALIYDSIDLAKKFEPKYRLQR 98
             GF    G  K+       +  D  +K    +R  +
Sbjct: 59 TLSGFSKPQGVFKTR-----ANRRDKRQKPSRLFRPPK 91


>gnl|CDD|238482 cd00982, gltB_C, gltb_C. This domain is found at the C-terminus of
           the large subunit (gltB) of glutamate synthase (GltS).
           GltS encodes a complex iron-sulfur flavoprotein that
           catalyzes the synthesis of L-glutamate from L-glutamine
           and 2-oxoglutarate. It requires the transfer of ammonia
           and electrons among three distinct active centers that
           carry out L-Gln hydrolysis, conversion of 2-oxoglutarate
           into L-Glu, and electron uptake from a donor. These
           catalytic sites appear to occur in other domains within
           the protein, and not the domain in this CD. This
           particular domain has no known function, but it likely
           has a structural role as it interacts with the
           amidotransferase and FMN-binding domains of gltS.
          Length = 251

 Score = 29.0 bits (66), Expect = 1.3
 Identities = 12/37 (32%), Positives = 15/37 (40%), Gaps = 3/37 (8%)

Query: 68  NFGGGKSTGFALIYDSIDLAKKFEPKYRLQRVSTKSL 104
           NF  G S G A + D       FE K   + V  + L
Sbjct: 173 NFAAGMSGGVAYVLDE---DGDFEKKVNHEMVDLERL 206


>gnl|CDD|236141 PRK08032, fliD, flagellar capping protein; Reviewed.
          Length = 462

 Score = 29.3 bits (66), Expect = 1.6
 Identities = 11/32 (34%), Positives = 14/32 (43%), Gaps = 4/32 (12%)

Query: 47  EKLSKMFKSKPENIFAFGFQTNFGGGKSTGFA 78
           +KL+K  K  P  + A       G GK TG  
Sbjct: 360 DKLTKALKEDPAGVKAL----FVGDGKKTGIT 387


>gnl|CDD|215108 PLN00222, PLN00222, tubulin gamma chain; Provisional.
          Length = 454

 Score = 29.0 bits (65), Expect = 1.8
 Identities = 12/22 (54%), Positives = 16/22 (72%)

Query: 3   TVLSASTVTIKTRKYMTNRLLG 24
           TV+SAST T++   YM N L+G
Sbjct: 234 TVMSASTTTLRYPGYMNNDLVG 255


>gnl|CDD|220941 pfam11013, DUF2851, Protein of unknown function (DUF2851).  This
           bacterial family of proteins has no known function.
          Length = 377

 Score = 27.6 bits (62), Expect = 5.1
 Identities = 8/10 (80%), Positives = 8/10 (80%)

Query: 182 HCKGSDWYLH 191
           H K SDWYLH
Sbjct: 63  HLKSSDWYLH 72


>gnl|CDD|219226 pfam06911, Senescence, Senescence-associated protein.  This family
           contains a number of plant senescence-associated
           proteins of approximately 450 residues in length. In
           Hemerocallis, petals have a genetically based program
           that leads to senescence and cell death approximately 24
           hours after the flower opens, and it is believed that
           senescence proteins produced around that time have a
           role in this program. This family extends to the higher
           vertebrates where the full-length protein is often a
           Spartin, associated with mitochondrial membranes and
           transportation along microtubules.
          Length = 181

 Score = 26.9 bits (60), Expect = 6.0
 Identities = 14/89 (15%), Positives = 24/89 (26%), Gaps = 11/89 (12%)

Query: 1   MKTVLSASTVTIKTRKYMTNRLLGRKQMVVDVLHPGKPSVKKTDIREKLSKMFKSKPENI 60
           ++ V   S  T K  K + N +      V   L       KK    +       +     
Sbjct: 52  LRRVKKLSKATAKVSKSVLNGVGKVAGNVGSSLANSVAGKKKGKDGKGEPNFDGALG--- 108

Query: 61  FAFGFQTNFGGGKSTGFALIYDSIDLAKK 89
                           F+ + D ++ A K
Sbjct: 109 --------VALASLDAFSTVLDGLEEAAK 129


  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
   0.321    0.135    0.402 

Gapped
Lambda     K      H
   0.267   0.0626    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,900,571
Number of extensions: 907122
Number of successful extensions: 736
Number of sequences better than 10.0: 1
Number of HSP's gapped: 734
Number of HSP's successfully gapped: 19
Length of query: 202
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 110
Effective length of database: 6,857,034
Effective search space: 754273740
Effective search space used: 754273740
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 (21.9 bits)
S2: 56 (25.6 bits)