RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2244
         (73 letters)



>gnl|CDD|202700 pfam03604, DNA_RNApol_7kD, DNA directed RNA polymerase, 7 kDa
          subunit. 
          Length = 32

 Score = 49.2 bits (118), Expect = 3e-10
 Identities = 19/28 (67%), Positives = 24/28 (85%)

Query: 22 ECHFENEIRPRDPIRCRECGYRIMYKKR 49
          EC  E E++P DPIRC+ECG+RI+YKKR
Sbjct: 5  ECGAEVELKPGDPIRCKECGHRILYKKR 32


>gnl|CDD|128906 smart00659, RPOLCX, RNA polymerase subunit CX.  present in RNA
          polymerase I, II and III.
          Length = 44

 Score = 49.3 bits (118), Expect = 4e-10
 Identities = 23/31 (74%), Positives = 27/31 (87%)

Query: 22 ECHFENEIRPRDPIRCRECGYRIMYKKRTKR 52
          EC  ENEI+ +D +RCRECGYRI+YKKRTKR
Sbjct: 7  ECGRENEIKSKDVVRCRECGYRILYKKRTKR 37


>gnl|CDD|224907 COG1996, RPC10, DNA-directed RNA polymerase, subunit RPC10
          (contains C4-type Zn-finger) [Transcription].
          Length = 49

 Score = 29.6 bits (67), Expect = 0.024
 Identities = 10/20 (50%), Positives = 12/20 (60%)

Query: 33 DPIRCRECGYRIMYKKRTKR 52
            IRC  CG RI+ K+R K 
Sbjct: 23 RGIRCPYCGSRILVKERPKV 42


>gnl|CDD|221660 pfam12600, DUF3769, Protein of unknown function (DUF3769).  This
           family of proteins is found in bacteria and eukaryotes.
           Proteins in this family are typically between 560 and
           931 amino acids in length.
          Length = 403

 Score = 26.9 bits (60), Expect = 0.92
 Identities = 7/25 (28%), Positives = 11/25 (44%), Gaps = 2/25 (8%)

Query: 42  YRIMYKKRTKRCILYFKP--QTGGF 64
             + + +RT    L + P  Q GG 
Sbjct: 371 IELEWSRRTYGVGLRYNPVLQIGGI 395


>gnl|CDD|234747 PRK00398, rpoP, DNA-directed RNA polymerase subunit P;
          Provisional.
          Length = 46

 Score = 24.9 bits (55), Expect = 1.3
 Identities = 9/17 (52%), Positives = 13/17 (76%)

Query: 35 IRCRECGYRIMYKKRTK 51
          +RC  CGYRI++K+R  
Sbjct: 22 VRCPYCGYRILFKERPP 38


>gnl|CDD|235242 PRK04179, rpl37e, 50S ribosomal protein L37e; Reviewed.
          Length = 62

 Score = 25.4 bits (56), Expect = 1.4
 Identities = 11/19 (57%), Positives = 11/19 (57%), Gaps = 1/19 (5%)

Query: 35 IRCRECGYRIMYKKRTKRC 53
          IRCR CG R  Y  R K C
Sbjct: 18 IRCRRCG-RHSYNVRKKYC 35


>gnl|CDD|223840 COG0769, MurE, UDP-N-acetylmuramyl tripeptide synthase [Cell
           envelope biogenesis, outer membrane].
          Length = 475

 Score = 25.4 bits (56), Expect = 2.8
 Identities = 10/42 (23%), Positives = 18/42 (42%), Gaps = 2/42 (4%)

Query: 13  PGDIEKYYLEC--HFENEIRPRDPIRCRECGYRIMYKKRTKR 52
            G +E Y       FE+     + +   + G+ + YK+R K 
Sbjct: 198 HGTMEYYGAAKAVLFESLPHSGEAVINPDDGHGLDYKERLKN 239


>gnl|CDD|185076 PRK15121, PRK15121, right oriC-binding transcriptional activator;
           Provisional.
          Length = 289

 Score = 25.0 bits (55), Expect = 3.4
 Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 10/40 (25%)

Query: 7   LVGKCLPG---------DIEKYYLECHFENEIRPRDPIRC 37
           + G C+P          DIE+YY     +   RP + +RC
Sbjct: 243 VYGTCMPMLNLTRRKGQDIERYYPAEDAKAGDRPIN-LRC 281


>gnl|CDD|215083 PLN00162, PLN00162, transport protein sec23; Provisional.
          Length = 761

 Score = 25.3 bits (56), Expect = 3.6
 Identities = 7/11 (63%), Positives = 8/11 (72%)

Query: 31 PRDPIRCRECG 41
          P DP+RCR C 
Sbjct: 50 PYDPLRCRTCR 60


>gnl|CDD|145202 pfam01907, Ribosomal_L37e, Ribosomal protein L37e.  This family
          includes ribosomal protein L37 from eukaryotes and
          archaebacteria. The family contains many conserved
          cysteines and histidines suggesting that this protein
          may bind to zinc.
          Length = 54

 Score = 23.7 bits (52), Expect = 4.8
 Identities = 9/19 (47%), Positives = 10/19 (52%), Gaps = 1/19 (5%)

Query: 35 IRCRECGYRIMYKKRTKRC 53
            CR CG R  Y  + KRC
Sbjct: 16 TLCRRCG-RRSYHVQKKRC 33


>gnl|CDD|236983 PRK11788, PRK11788, tetratricopeptide repeat protein; Provisional.
          Length = 389

 Score = 24.4 bits (54), Expect = 5.6
 Identities = 5/15 (33%), Positives = 9/15 (60%)

Query: 29  IRPRDPIRCRECGYR 43
           ++ +   RCR CG+ 
Sbjct: 349 LKRKPRYRCRNCGFT 363


>gnl|CDD|205629 pfam13451, zf-trcl, Probable zinc-binding domain.  This is a
          probably zinc-binding domain with two CxxC sequence
          motifs found in various families of bacteria.
          Length = 49

 Score = 23.3 bits (51), Expect = 5.6
 Identities = 9/23 (39%), Positives = 12/23 (52%), Gaps = 5/23 (21%)

Query: 18 KYYLECHFENEIRPRDPIRCREC 40
          ++Y E  F NE     P+RC  C
Sbjct: 22 EFYAEKGFTNE-----PVRCPAC 39


>gnl|CDD|235514 PRK05580, PRK05580, primosome assembly protein PriA; Validated.
          Length = 679

 Score = 24.0 bits (53), Expect = 9.3
 Identities = 4/8 (50%), Positives = 6/8 (75%)

Query: 37  CRECGYRI 44
           CR+CG+  
Sbjct: 384 CRDCGWVA 391


  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
   0.327    0.146    0.479 

Gapped
Lambda     K      H
   0.267   0.0722    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,658,928
Number of extensions: 263777
Number of successful extensions: 363
Number of sequences better than 10.0: 1
Number of HSP's gapped: 363
Number of HSP's successfully gapped: 25
Length of query: 73
Length of database: 10,937,602
Length adjustment: 43
Effective length of query: 30
Effective length of database: 9,030,380
Effective search space: 270911400
Effective search space used: 270911400
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.2 bits)