RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17945
         (214 letters)



>gnl|CDD|240260 PTZ00084, PTZ00084, 40S ribosomal protein S3; Provisional.
          Length = 220

 Score =  169 bits (430), Expect = 4e-53
 Identities = 65/90 (72%), Positives = 76/90 (84%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           MESGAKGCEV+VSGKLR QRAKSMKF DG MI +G P  D+V++A RHVL+RQGV+G+KV
Sbjct: 127 MESGAKGCEVIVSGKLRAQRAKSMKFRDGYMISTGQPKKDFVDSAVRHVLMRQGVIGVKV 186

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEE 90
           KIMLP+D +GK GP  PLPD + VLEPKEE
Sbjct: 187 KIMLPYDPSGKNGPSAPLPDVITVLEPKEE 216



 Score = 67.0 bits (164), Expect = 1e-13
 Identities = 25/36 (69%), Positives = 30/36 (83%)

Query: 116 VLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEE 151
           V+G+KVKIMLP+D +GK GP  PLPD + VLEPKEE
Sbjct: 181 VIGVKVKIMLPYDPSGKNGPSAPLPDVITVLEPKEE 216


>gnl|CDD|130081 TIGR01008, rpsC_E_A, ribosomal protein S3, eukaryotic/archaeal
           type.  This model describes ribosomal protein S3 of the
           eukaryotic cytosol and of the archaea. TIGRFAMs model
           TIGR01009 describes the bacterial/organellar type,
           although the organellar types have a different
           architecture with long insertions and may score poorly
           [Protein synthesis, Ribosomal proteins: synthesis and
           modification].
          Length = 195

 Score =  111 bits (280), Expect = 7e-31
 Identities = 40/86 (46%), Positives = 52/86 (60%), Gaps = 9/86 (10%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           ME+GAKG EV +SGKL G+RA++ KF  G + HSG+P  + V+      LL+ GVLG+KV
Sbjct: 119 MEAGAKGVEVTISGKLTGERARTEKFAAGYLKHSGEPVEELVDKGFAIALLKLGVLGVKV 178

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLE 86
           KIM          P   LPD V + E
Sbjct: 179 KIM---------PPDVKLPDEVEIKE 195


>gnl|CDD|235247 PRK04191, rps3p, 30S ribosomal protein S3P; Reviewed.
          Length = 207

 Score = 94.2 bits (235), Expect = 5e-24
 Identities = 34/90 (37%), Positives = 55/90 (61%), Gaps = 9/90 (10%)

Query: 1   MESGAKGCEVVVSGKLRGQRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIKV 60
           ME+GA G E+++SGKL G+RA++ KF +G +  SG+P  + V+       L+ G++G++V
Sbjct: 121 MEAGALGVEIIISGKLTGERARTEKFTEGYIKKSGEPAEELVDRGFAIAKLKLGIIGVEV 180

Query: 61  KIMLPWDSTGKTGPKKPLPDNVNVLEPKEE 90
           +IM P D+         LPD + + EP E 
Sbjct: 181 RIMPP-DAK--------LPDEIEIKEPVEV 201


>gnl|CDD|223170 COG0092, RpsC, Ribosomal protein S3 [Translation, ribosomal
           structure and biogenesis].
          Length = 233

 Score = 93.9 bits (234), Expect = 1e-23
 Identities = 26/91 (28%), Positives = 42/91 (46%), Gaps = 7/91 (7%)

Query: 1   MESGAKGCEVVVSGKLRGQR-AKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIK 59
           M +GAKG ++ VSG+L G   A++ K+ +G +       +  ++  T       GV+G+K
Sbjct: 132 MRAGAKGIKIQVSGRLGGAEIARTEKYREGRVPLHTLRAD--IDYGTAEAHTTYGVIGVK 189

Query: 60  VKIMLPWDSTGKTGPKKPLPDNVNVLEPKEE 90
           V I            K  + +   V EP EE
Sbjct: 190 VWIYKG----EVLPDKVEIKEPAEVEEPAEE 216



 Score = 31.9 bits (73), Expect = 0.19
 Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 10/45 (22%)

Query: 116 VLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQKK 160
           V+G+KV I             + LPD V + EP E   PA   ++
Sbjct: 185 VIGVKVWIYKG----------EVLPDKVEIKEPAEVEEPAEESRE 219


>gnl|CDD|215779 pfam00189, Ribosomal_S3_C, Ribosomal protein S3, C-terminal
          domain.  This family contains a central domain
          pfam00013, hence the amino and carboxyl terminal
          domains are stored separately. This is a minimal
          carboxyl-terminal domain. Some are much longer.
          Length = 85

 Score = 75.6 bits (187), Expect = 3e-18
 Identities = 19/63 (30%), Positives = 35/63 (55%), Gaps = 3/63 (4%)

Query: 1  MESGAKGCEVVVSGKLRG-QRAKSMKFVDGLMIHSGDPCNDYVNTATRHVLLRQGVLGIK 59
           + GAKG ++ +SG+L G +RA++ K+ +G +          ++ A      + GV+G+K
Sbjct: 25 KKGGAKGIKIQISGRLNGAERARTEKYKEGRV--PLHTLRADIDYAFAEAKTKYGVIGVK 82

Query: 60 VKI 62
          V I
Sbjct: 83 VWI 85


>gnl|CDD|130082 TIGR01009, rpsC_bact, ribosomal protein S3, bacterial type.  This
           model describes the bacterial type of ribosomal protein
           S3. Chloroplast and mitochondrial forms have large,
           variable inserts between conserved N-terminal and
           C-terminal domains. This model recognizes all bacterial
           forms and many chloroplast forms above the trusted
           cutoff score. TIGRFAMs model TIGR01008 describes S3 of
           the eukaryotic cytosol and of the archaea [Protein
           synthesis, Ribosomal proteins: synthesis and
           modification].
          Length = 211

 Score = 30.4 bits (69), Expect = 0.50
 Identities = 23/64 (35%), Positives = 37/64 (57%), Gaps = 5/64 (7%)

Query: 1   MESGAKGCEVVVSGKLRGQR-AKSMKFVDGLM-IHSGDPCNDYVNTATRHVLLRQGVLGI 58
           M++GAKG +V VSG+L G   A++  + +G + +H+     DY   AT       G++G+
Sbjct: 142 MKAGAKGIKVQVSGRLGGAEIARTEWYKEGRVPLHTLRADIDY---ATAEAHTTYGIIGV 198

Query: 59  KVKI 62
           KV I
Sbjct: 199 KVWI 202


>gnl|CDD|223252 COG0174, GlnA, Glutamine synthetase [Amino acid transport and
           metabolism].
          Length = 443

 Score = 29.9 bits (68), Expect = 0.91
 Identities = 19/66 (28%), Positives = 30/66 (45%), Gaps = 14/66 (21%)

Query: 34  SGDP-CNDYVNTATRHVLLRQGVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVN 92
             DP  N Y+  A    +L  G+ GI+ K+             +P+  N+  L P+E   
Sbjct: 339 VPDPDANPYLAFA---AILAAGLDGIENKLEPG----------EPVDGNLYELSPEERKE 385

Query: 93  PTIPSS 98
           PT+P+S
Sbjct: 386 PTLPAS 391


>gnl|CDD|240517 cd13153, KOW_GPKOW_B, KOW motif of the "G-patch domain and KOW
          motifs-containing protein" (GPKOW) repeat B.  GPKOW
          contains one G-patch domain and two KOW motifs. GPKOW
          is a nuclear protein that regulated by catalytic (C)
          subunit of Protein Kinase A (PKA) and bind RNA in vivo.
          PKA may be involved in regulating multiple steps in
          post-transcriptional processing of pre-mRNAs. KOW
          domain is known as an RNA-binding motif that is shared
          so far among some families of ribosomal proteins, the
          essential bacterial transcriptional elongation factor
          NusG, the eukaryotic chromatin elongation factor Spt5,
          the higher eukaryotic KIN17 proteins and Mtr4. GPKOW is
          also known as the T54 protein or MOS2 homolog.
          Length = 51

 Score = 25.6 bits (57), Expect = 3.7
 Identities = 8/13 (61%), Positives = 9/13 (69%)

Query: 10 VVVSGKLRGQRAK 22
          +VV GK RGQ  K
Sbjct: 5  MVVRGKHRGQVGK 17


>gnl|CDD|215637 PLN03223, PLN03223, Polycystin cation channel protein; Provisional.
          Length = 1634

 Score = 28.0 bits (62), Expect = 4.9
 Identities = 9/16 (56%), Positives = 10/16 (62%)

Query: 190  NPEDKPYLFRIKSTPG 205
            NP+  PY FR K  PG
Sbjct: 1070 NPQGLPYGFRFKPLPG 1085


>gnl|CDD|225817 COG3278, CcoN, Cbb3-type cytochrome oxidase, subunit 1
           [Posttranslational modification, protein turnover,
           chaperones].
          Length = 482

 Score = 27.4 bits (61), Expect = 7.4
 Identities = 8/33 (24%), Positives = 15/33 (45%)

Query: 168 LYLAGMLIAIWMSVQSLMGANKNPEDKPYLFRI 200
           LYL+GML+  +    ++ G      + P    +
Sbjct: 448 LYLSGMLLMAYNIWMTIRGGKPLEAEIPAAAPL 480


>gnl|CDD|236159 PRK08134, PRK08134, O-acetylhomoserine
           aminocarboxypropyltransferase; Validated.
          Length = 433

 Score = 27.0 bits (60), Expect = 8.3
 Identities = 11/29 (37%), Positives = 16/29 (55%)

Query: 6   KGCEVVVSGKLRGQRAKSMKFVDGLMIHS 34
           +G   V S  L+G RA   KF++ L + S
Sbjct: 339 RGAGSVFSFDLKGGRAAGRKFIESLKLFS 367


>gnl|CDD|131174 TIGR02119, panF, sodium/pantothenate symporter.  Pantothenate
           (vitamin B5) is a precursor of coenzyme A and is made
           from aspartate and 2-oxoisovalerate in most bacteria
           with completed genome sequences. However, some pathogens
           must import pantothenate. This model describes PanF, a
           sodium/pantothenate symporter, from a larger family of
           Sodium/substrate symporters (pfam00474). Several species
           that have this transporter appear to lack all enzymes of
           pantothenate biosynthesis, namely Haemophilus
           influenzae, Pasteurella multocida, Fusobacterium
           nucleatum, and Borrelia burgdorferi [Biosynthesis of
           cofactors, prosthetic groups, and carriers, Pantothenate
           and coenzyme A, Transport and binding proteins, Other].
          Length = 471

 Score = 27.0 bits (60), Expect = 8.3
 Identities = 24/71 (33%), Positives = 34/71 (47%), Gaps = 8/71 (11%)

Query: 115 SVLGIKVKIMLPWDSTGKTGPKKPLPDNVNVLEPKEEVNPAFPQKKLPFKTASLYLAGML 174
            V+GI   IML     G  G +  +PD    L   ++V P    K LP   A ++LA  +
Sbjct: 277 IVVGI---IMLGMHLAGVLG-RAVIPD----LTVPDKVIPLLAIKVLPPILAGIFLAAPM 328

Query: 175 IAIWMSVQSLM 185
            AI  +V SL+
Sbjct: 329 AAIMSTVNSLL 339


>gnl|CDD|234722 PRK00310, rpsC, 30S ribosomal protein S3; Reviewed.
          Length = 232

 Score = 26.7 bits (60), Expect = 8.7
 Identities = 11/18 (61%), Positives = 14/18 (77%)

Query: 1   MESGAKGCEVVVSGKLRG 18
           M +GAKG +V VSG+L G
Sbjct: 142 MRAGAKGIKVQVSGRLGG 159


  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
   0.314    0.135    0.402 

Gapped
Lambda     K      H
   0.267   0.0757    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,747,869
Number of extensions: 982377
Number of successful extensions: 558
Number of sequences better than 10.0: 1
Number of HSP's gapped: 552
Number of HSP's successfully gapped: 24
Length of query: 214
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 121
Effective length of database: 6,812,680
Effective search space: 824334280
Effective search space used: 824334280
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 57 (25.7 bits)