RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy5445
         (315 letters)



>gnl|CDD|183049 PRK11240, PRK11240, penicillin-binding protein 1C; Provisional.
          Length = 772

 Score = 30.8 bits (70), Expect = 0.97
 Identities = 9/24 (37%), Positives = 14/24 (58%)

Query: 21  FAMRGSSSELLLDPQQQLRKRKLL 44
           FA  G +++L L P   L +R L+
Sbjct: 453 FARHGKAAKLRLQPDDPLLERPLM 476


>gnl|CDD|203441 pfam06421, LepA_C, GTP-binding protein LepA C-terminus.  This
          family consists of the C-terminal region of several
          pro- and eukaryotic GTP-binding LepA proteins.
          Length = 108

 Score = 28.7 bits (65), Expect = 1.5
 Identities = 10/18 (55%), Positives = 14/18 (77%), Gaps = 1/18 (5%)

Query: 39 RKRKLLELAQNKNKKKVK 56
          RK+KLLE  Q + KK++K
Sbjct: 74 RKKKLLE-KQKEGKKRMK 90


>gnl|CDD|237115 PRK12489, PRK12489, anaerobic C4-dicarboxylate transporter;
           Reviewed.
          Length = 443

 Score = 29.9 bits (68), Expect = 1.9
 Identities = 9/21 (42%), Positives = 13/21 (61%)

Query: 216 YIIIHYFIIPFIICVVCSIVL 236
           ++I H FI+P +I V  S V 
Sbjct: 414 FVINHSFILPGLIGVSVSCVF 434


>gnl|CDD|111000 pfam02057, Glyco_hydro_59, Glycosyl hydrolase family 59. 
          Length = 669

 Score = 30.0 bits (67), Expect = 2.0
 Identities = 24/115 (20%), Positives = 47/115 (40%), Gaps = 22/115 (19%)

Query: 2   HQHRQSLRGL---YDTEQKSLVFAMRGSSSELLLDPQQQLRKRKLLELAQNKNKKKVKRT 58
           H+H   +R     ++   +   F ++GS SE+   P+ Q+   KL + ++    K++   
Sbjct: 373 HKHSMCIRPFLPYFNVSHQFATFVLKGSFSEI---PELQVWYTKLGKPSERLLFKQL--- 426

Query: 59  CKQKIWFYTTS-----------FFAMTAVSTGSSLLFLVPLYVDPAISTLTSDFN 102
               +W   +S            F +T ++TG    + +P    P  +    DFN
Sbjct: 427 --DSLWLLDSSGSFTLELEEDEIFTLTTLTTGRKGSYPLPPKSKPFPTNYKDDFN 479


>gnl|CDD|219547 pfam07741, BRF1, Brf1-like TBP-binding domain.  This region
          covers both the Brf homology II and III regions. This
          region is involved in binding TATA binding protein.
          Length = 95

 Score = 28.0 bits (63), Expect = 2.3
 Identities = 8/35 (22%), Positives = 19/35 (54%)

Query: 29 ELLLDPQQQLRKRKLLELAQNKNKKKVKRTCKQKI 63
          + L + +++  K+K  E   +  KKK ++  K++ 
Sbjct: 27 DYLEEQEEKELKQKADEGNNSGKKKKKRKAKKKRD 61


>gnl|CDD|235462 PRK05433, PRK05433, GTP-binding protein LepA; Provisional.
          Length = 600

 Score = 29.2 bits (67), Expect = 2.8
 Identities = 11/18 (61%), Positives = 14/18 (77%), Gaps = 1/18 (5%)

Query: 39  RKRKLLELAQNKNKKKVK 56
           RKRKLLE  Q + KK++K
Sbjct: 563 RKRKLLE-KQKEGKKRMK 579


>gnl|CDD|224802 COG1890, RPS1A, Ribosomal protein S3AE [Translation, ribosomal
           structure and biogenesis].
          Length = 214

 Score = 28.1 bits (63), Expect = 4.8
 Identities = 18/89 (20%), Positives = 32/89 (35%), Gaps = 16/89 (17%)

Query: 46  LAQNKNKKKVKRTCKQKIWF--YTTSFFAMTAVST--GSSLLFLVPLYVDPAISTLTSDF 101
           +A  K +KKV+   K+K W+      +F    V     +    L+   V+  ++ LT DF
Sbjct: 1   MAGKKGQKKVRDKWKEKKWYTIKAPPYFGGVEVGKTPANDPDKLIGRVVEVTLADLTGDF 60

Query: 102 NPNPV------------TCVTILNRTETG 118
           + +                +T     E  
Sbjct: 61  SKSHRKLKFRIDDVEGDKALTRFKGHELT 89


>gnl|CDD|225419 COG2864, FdnI, Cytochrome b subunit of formate dehydrogenase
           [Energy production and conversion].
          Length = 218

 Score = 28.1 bits (63), Expect = 5.7
 Identities = 10/58 (17%), Positives = 20/58 (34%), Gaps = 4/58 (6%)

Query: 61  QKIWFYTTSFFAMTAVSTGSSLLFLVPLYVDP----AISTLTSDFNPNPVTCVTILNR 114
           QK+ F+T     +  + TG  +               +S L   F    +  + I++ 
Sbjct: 114 QKLLFWTAILAIVLLLITGIVIWRPYFAPYFSIPLLRLSLLLHAFAAVILIFIIIVHI 171


>gnl|CDD|182213 PRK10054, PRK10054, putative transporter; Provisional.
          Length = 395

 Score = 28.2 bits (63), Expect = 7.0
 Identities = 13/37 (35%), Positives = 22/37 (59%), Gaps = 1/37 (2%)

Query: 204 IVMDKYDEEEQMYIIIHYFIIPFI-ICVVCSIVLCVM 239
           I+ DK+D++  M + I  F   FI I +V ++ L V+
Sbjct: 65  ILADKFDKKRYMLLAITAFASGFIAIPLVNNVTLVVL 101


>gnl|CDD|236226 PRK08299, PRK08299, isocitrate dehydrogenase; Validated.
          Length = 402

 Score = 27.9 bits (63), Expect = 7.3
 Identities = 14/33 (42%), Positives = 19/33 (57%), Gaps = 6/33 (18%)

Query: 181 NFASS---YGMQDKSYPCYYSRKNTTIVMDKYD 210
           +FA +   YG+  K YP Y S KNT  ++  YD
Sbjct: 189 DFARASFNYGLDRK-YPVYLSTKNT--ILKAYD 218


>gnl|CDD|233167 TIGR00881, 2A0104, phosphoglycerate transporter family protein.
           [Transport and binding proteins, Carbohydrates, organic
           alcohols, and acids].
          Length = 379

 Score = 27.7 bits (62), Expect = 7.6
 Identities = 15/82 (18%), Positives = 37/82 (45%), Gaps = 9/82 (10%)

Query: 222 FIIPFIICVVCSIVLC-VMHCECQCNDNIATSLPPSKQRPDDEQNYVKDVGGTDLGPQNY 280
           FI+P II ++ S++   ++      +   +  LPP+++ P++E +   +    +L  +  
Sbjct: 153 FIVPGIIAIIVSLICFLLLR-----DSPQSCGLPPAEEMPNEEPDGDAEKKEEELTKKQI 207

Query: 281 KNEELLPT---ILCAISYRLTY 299
             + +L        ++ Y   Y
Sbjct: 208 FLQYVLLNKVLWYISLGYVFVY 229


  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
   0.322    0.136    0.424 

Gapped
Lambda     K      H
   0.267   0.0665    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,440,937
Number of extensions: 1408285
Number of successful extensions: 1309
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1307
Number of HSP's successfully gapped: 22
Length of query: 315
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 218
Effective length of database: 6,635,264
Effective search space: 1446487552
Effective search space used: 1446487552
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: 59 (26.6 bits)