RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy12346
         (107 letters)



>gnl|CDD|234692 PRK00222, PRK00222, methionine sulfoxide reductase B;
          Provisional.
          Length = 142

 Score =  147 bits (374), Expect = 2e-47
 Identities = 52/82 (63%), Positives = 63/82 (76%)

Query: 13 NKEELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCG 72
          +KEE KK+LTP QY VTQE GTERPF+G+Y  N E G Y CIVC +PLFSS TKFDSGCG
Sbjct: 6  SKEEWKKQLTPEQYRVTQEHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSDTKFDSGCG 65

Query: 73 WPAFNDVLDQGKVKLTKDTSHG 94
          WP+F   +D+  ++  +DTSHG
Sbjct: 66 WPSFTKPIDEEAIRELRDTSHG 87


>gnl|CDD|223307 COG0229, COG0229, Conserved domain frequently associated with
          peptide methionine sulfoxide reductase
          [Posttranslational modification, protein turnover,
          chaperones].
          Length = 140

 Score =  139 bits (353), Expect = 3e-44
 Identities = 47/80 (58%), Positives = 57/80 (71%)

Query: 15 EELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGWP 74
          EELK++LTP QY VTQ  GTERPF+G+Y  N E G Y CIVC +PLFSS+ KFDSGCGWP
Sbjct: 7  EELKEKLTPEQYRVTQNHGTERPFTGEYLDNKEKGIYVCIVCGEPLFSSEDKFDSGCGWP 66

Query: 75 AFNDVLDQGKVKLTKDTSHG 94
          +F   +    +   +D SHG
Sbjct: 67 SFTKPISPDAITYKEDRSHG 86


>gnl|CDD|201899 pfam01641, SelR, SelR domain.  Methionine sulfoxide reduction is
          an important process, by which cells regulate
          biological processes and cope with oxidative stress.
          MsrA, a protein involved in the reduction of methionine
          sulfoxides in proteins, has been known for four decades
          and has been extensively characterized with respect to
          structure and function. However, recent studies
          revealed that MsrA is only specific for
          methionine-S-sulfoxides. Because oxidized methionines
          occur in a mixture of R and S isomers in vivo, it was
          unclear how stereo-specific MsrA could be responsible
          for the reduction of all protein methionine sulfoxides.
          It appears that a second methionine sulfoxide
          reductase, SelR, evolved that is specific for
          methionine-R-sulfoxides, the activity that is different
          but complementary to that of MsrA. Thus, these
          proteins, working together, could reduce both
          stereoisomers of methionine sulfoxide. This domain is
          found both in SelR proteins and fused with the peptide
          methionine sulfoxide reductase enzymatic domain
          pfam01625. The domain has two conserved cysteine and
          histidines. The domain binds both selenium and zinc.
          The final cysteine is found to be replaced by the rare
          amino acid selenocysteine in some members of the
          family. This family has methionine-R-sulfoxide
          reductase activity.
          Length = 124

 Score =  129 bits (327), Expect = 2e-40
 Identities = 44/81 (54%), Positives = 56/81 (69%)

Query: 14 KEELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGW 73
           EE K  L+P QY V + KGTE+PF+G+Y+ + E G Y CI C +PLFSS TKFDSGCGW
Sbjct: 1  DEEWKAVLSPEQYRVLRNKGTEKPFTGEYDDHFEEGIYVCIGCGEPLFSSTTKFDSGCGW 60

Query: 74 PAFNDVLDQGKVKLTKDTSHG 94
          P+F + +    +K T D SHG
Sbjct: 61 PSFFEPISGDAIKYTPDRSHG 81


>gnl|CDD|129454 TIGR00357, TIGR00357, methionine-R-sulfoxide reductase.  This
          model describes a domain found in PilB, a protein
          important for pilin expression, N-terminal to a domain
          coextensive to with the known peptide methionine
          sulfoxide reductase (MsrA), a protein repair enzyme, of
          E. coli. Among the early completed genomes, this module
          is found if and only if MsrA is also found, whether
          N-terminal to MsrA (as for Helicobacter pylori),
          C-terminal (as for Treponema pallidum), or in a
          separate polypeptide. Although the function of this
          region is not clear, an auxiliary function to MsrA is
          suggested [Protein fate, Protein modification and
          repair, Cellular processes, Adaptations to atypical
          conditions].
          Length = 134

 Score =  126 bits (318), Expect = 5e-39
 Identities = 46/84 (54%), Positives = 57/84 (67%)

Query: 11 KINKEELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSG 70
          K + EELKK+LTP+QY VTQ  GTE PF+ +Y  N E G Y  I C +PLFSS+ KFDSG
Sbjct: 1  KPSDEELKKKLTPLQYEVTQNAGTEPPFTNEYWDNKEEGIYVDITCGEPLFSSEDKFDSG 60

Query: 71 CGWPAFNDVLDQGKVKLTKDTSHG 94
          CGWP+F   + +  V   +D SHG
Sbjct: 61 CGWPSFYKPISEEVVAYERDESHG 84


>gnl|CDD|235499 PRK05550, PRK05550, bifunctional methionine sulfoxide reductase
          B/A protein; Provisional.
          Length = 283

 Score =  116 bits (293), Expect = 2e-33
 Identities = 39/76 (51%), Positives = 50/76 (65%), Gaps = 1/76 (1%)

Query: 15 EELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGWP 74
           +  K LTP +Y V ++KGTERPFSG+Y  + E G Y C  C  PLF S+ KF+SGCGWP
Sbjct: 1  MDKMKSLTPFEYRVIEDKGTERPFSGEYYDHDEKGVYLCRRCGAPLFRSEDKFNSGCGWP 60

Query: 75 AFNDVLDQGKVKLTKD 90
          +F+D +  G VK   D
Sbjct: 61 SFDDEIP-GAVKRLPD 75


>gnl|CDD|184456 PRK14018, PRK14018, trifunctional thioredoxin/methionine sulfoxide
           reductase A/B protein; Provisional.
          Length = 521

 Score = 93.8 bits (233), Expect = 8e-24
 Identities = 37/84 (44%), Positives = 49/84 (58%)

Query: 11  KINKEELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSG 70
           K +  ELK+ LT  QY +TQ   TER FS +Y+   + G Y  +V  +PLFSS  K+DSG
Sbjct: 379 KPSDAELKRTLTEEQYQITQNAATERAFSHEYDHLFKPGIYVDVVSGEPLFSSADKYDSG 438

Query: 71  CGWPAFNDVLDQGKVKLTKDTSHG 94
           CGWP+F   +D   V    D S+ 
Sbjct: 439 CGWPSFTRPIDAKVVTEHDDFSYN 462


>gnl|CDD|180121 PRK05508, PRK05508, methionine sulfoxide reductase B;
          Provisional.
          Length = 119

 Score = 85.9 bits (213), Expect = 3e-23
 Identities = 37/73 (50%), Positives = 45/73 (61%), Gaps = 1/73 (1%)

Query: 18 KKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYTCIVCAQPLFSSQTKFDSGCGWPAFN 77
             LTP +  V   KGTE PFSG+YN   E GTY C  C  PL+ S+ KF SGCGWP+F+
Sbjct: 1  YNELTPEEEAVILRKGTEPPFSGEYNDFFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFD 60

Query: 78 DVLDQGKVKLTKD 90
          D + +G VK   D
Sbjct: 61 DEI-KGAVKRIPD 72


>gnl|CDD|107135 PHA02119, PHA02119, hypothetical protein.
          Length = 87

 Score = 27.4 bits (60), Expect = 0.85
 Identities = 10/38 (26%), Positives = 16/38 (42%)

Query: 15 EELKKRLTPMQYHVTQEKGTERPFSGKYNKNTESGTYT 52
          EELK++L P+   V  E   +R F   ++         
Sbjct: 19 EELKRKLAPVGKFVADEMIRQRSFKISFDVAKFPAIMP 56


>gnl|CDD|163484 TIGR03772, anch_rpt_subst, anchored repeat ABC transporter,
           substrate-binding protein.  Members of this protein
           family are ABC transporter permease subunits as
           identified by pfam00950, but additionally contain the
           Actinobacterial insert domain described by TIGR03769.
           Some homologs (lacking the insert) have been described
           as transporters of manganese or of chelated iron.
           Members of this family typically are found along with an
           ATP-binding cassette protein, a permease, and an
           LPXTG-anchored protein with two or three copies of the
           TIGR03769 insert that occurs just once in this protein
           family [Transport and binding proteins, Unknown
           substrate].
          Length = 479

 Score = 25.6 bits (56), Expect = 6.1
 Identities = 7/21 (33%), Positives = 9/21 (42%)

Query: 77  NDVLDQGKVKLTKDTSHGKLY 97
             VLD G   L  D    ++Y
Sbjct: 224 ATVLDAGHADLAVDLDQQRIY 244


>gnl|CDD|111311 pfam02404, SCF, Stem cell factor.  Stem cell factor (SCF) is a
          homodimer involved in hematopoiesis. SCF binds to and
          activates the SCF receptor (SCFR), a receptor tyrosine
          kinase. The crystal structure of human SCF has been
          resolved and a potential receptor-binding site
          identified.
          Length = 273

 Score = 25.3 bits (55), Expect = 8.0
 Identities = 17/49 (34%), Positives = 22/49 (44%), Gaps = 2/49 (4%)

Query: 44 KNTESGTYTCIVCAQPLFSSQTKFDSGCGWPAFNDVLDQGKV--KLTKD 90
          K T++   TCI     LF+   K  S C  P  +DV D  K+   L  D
Sbjct: 2  KKTQTWIITCIYLQLLLFNPLVKTQSICRNPVTDDVKDITKLVANLPND 50


>gnl|CDD|147759 pfam05782, ECM1, Extracellular matrix protein 1 (ECM1).  This
           family consists of several eukaryotic extracellular
           matrix protein 1 (ECM1) sequences. ECM1 has been shown
           to regulate endochondral bone formation, stimulate the
           proliferation of endothelial cells and induce
           angiogenesis. Mutations in the ECM1 gene can cause
           lipoid proteinosis, a disorder which causes generalised
           thickening of skin, mucosae and certain viscera.
           Classical features include beaded eyelid papules and
           laryngeal infiltration leading to hoarseness.
          Length = 419

 Score = 25.0 bits (54), Expect = 9.8
 Identities = 9/32 (28%), Positives = 15/32 (46%)

Query: 17  LKKRLTPMQYHVTQEKGTERPFSGKYNKNTES 48
           L+K L P Q  + Q++    P + +     ES
Sbjct: 117 LQKELPPPQVPIEQKEVKPAPLADQSPPEPES 148


  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    0.132    0.409 

Gapped
Lambda     K      H
   0.267   0.0704    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,981,977
Number of extensions: 374725
Number of successful extensions: 206
Number of sequences better than 10.0: 1
Number of HSP's gapped: 206
Number of HSP's successfully gapped: 14
Length of query: 107
Length of database: 10,937,602
Length adjustment: 72
Effective length of query: 35
Effective length of database: 7,744,114
Effective search space: 271043990
Effective search space used: 271043990
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.2 bits)