RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy2089
         (216 letters)



>gnl|CDD|221996 pfam13232, Complex1_LYR_1, Complex1_LYR-like.  This is a family
          of proteins carrying the LYR motif of family
          Complex1_LYR, pfam05347, likely to be involved in Fe-S
          cluster biogenesis in mitochondria.
          Length = 61

 Score = 78.8 bits (195), Expect = 9e-20
 Identities = 29/59 (49%), Positives = 42/59 (71%)

Query: 41 ILKLYKALLRESSKFPAYNYRMYFLRRTREKFQSNKNVDNNEQISLLYNEGLKELEVLK 99
          +L LY+ LLR + KFP YN+R Y  RR R++F+ NK++ + E+I  L  EG K+LE+LK
Sbjct: 3  VLSLYRQLLRAARKFPDYNFREYIRRRIRDEFRKNKDLTDPEKIEKLLKEGKKQLELLK 61


>gnl|CDD|203236 pfam05347, Complex1_LYR, Complex 1 protein (LYR family).
          Proteins in this family have been identified as a
          component of the higher eukaryotic NADH complex. In
          Saccharomyces cerevisiae, the Isd11 protein has been
          shown to play a role in Fe/S cluster biogenesis in
          mitochondria. We have named this family LYR after a
          highly conserved tripeptide motif close to the
          N-terminus of these proteins.
          Length = 59

 Score = 75.3 bits (186), Expect = 2e-18
 Identities = 31/57 (54%), Positives = 41/57 (71%)

Query: 41 ILKLYKALLRESSKFPAYNYRMYFLRRTREKFQSNKNVDNNEQISLLYNEGLKELEV 97
          +L LY+ LLRE+ KFP YN R YF RR R++F+ NKN+ + E+I  L  EG K+LEV
Sbjct: 3  VLSLYRQLLREARKFPDYNAREYFRRRIRDEFRKNKNLTDPEKIEALLKEGKKQLEV 59


>gnl|CDD|221997 pfam13233, Complex1_LYR_2, Complex1_LYR-like.  This is a family of
           proteins carrying the LYR motif of family Complex1_LYR,
           pfam05347, likely to be involved in Fe-S cluster
           biogenesis in mitochondria.
          Length = 97

 Score = 31.3 bits (71), Expect = 0.10
 Identities = 17/73 (23%), Positives = 31/73 (42%), Gaps = 4/73 (5%)

Query: 41  ILKLYKALLRE----SSKFPAYNYRMYFLRRTREKFQSNKNVDNNEQISLLYNEGLKELE 96
           +L+LY+ LLRE      ++   +      R  R++F+ +    ++E       E    L 
Sbjct: 1   VLRLYRELLRELPKYPLRYNLLSSLSLGRRYVRKEFRRHAGATDDELAKEFLQEAENYLA 60

Query: 97  VLKRQVLISQLFK 109
            LK Q    +L +
Sbjct: 61  YLKAQRHYLELLE 73


>gnl|CDD|119192 pfam10672, Methyltrans_SAM, S-adenosylmethionine-dependent
           methyltransferase.  Members of this family are
           S-adenosylmethionine-dependent methyltransferases from
           gamma-proteobacterial species. The diversity in the
           roles of methylation is matched by the almost
           bewildering number of methyltransferase enzymes that
           catalyze the methylation reaction. Although several
           classes of methyltransferase enzymes are known, the
           great majority of methylation reactions are catalyzed by
           the S-adenosylmethionine-dependent methyltransferases.
          Length = 286

 Score = 30.2 bits (68), Expect = 0.75
 Identities = 9/33 (27%), Positives = 21/33 (63%)

Query: 178 FLTWFRLQFSTPSSIIIILPPESQRGAYVISAE 210
           F +W +++   P  ++II PP  Q+G++ ++ +
Sbjct: 184 FKSWGKIKKLGPYDLVIIDPPSFQKGSFALTKD 216


>gnl|CDD|163458 TIGR03746, conj_TIGR03746, integrating conjugative element protein,
           PFL_4703 family.  Members of this protein family are
           found occasionally on plasmids such as the Pseudomonas
           putida TOL plasmid pWWO_p085. Usually, however, they are
           found on the bacterial main chromosome in regions
           flanked by markers of conjugative transfer and/or
           transposition. The function is unknown [Mobile and
           extrachromosomal element functions, Plasmid functions].
          Length = 202

 Score = 28.8 bits (65), Expect = 1.8
 Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)

Query: 170 IGLIKLIFFLTWFRLQFSTPSSIIIILPPESQRGA 204
           IGL+ LI    WF    + P  + I +PP+ + G+
Sbjct: 19  IGLLALILLALWFGW-RTAPKDLTIHVPPDLRSGS 52


>gnl|CDD|233994 TIGR02746, TraC-F-type, type-IV secretion system protein TraC.  The
           protein family described here is common among the F, P
           and I-like type IV secretion systems. Gene symbols
           include TraC (F-type), TrbE/VirB4 (P-type) and TraU
           (I-type). The protein conyains the Walker A and B motifs
           and so is a putative nucleotide triphosphatase.
          Length = 797

 Score = 28.8 bits (65), Expect = 2.8
 Identities = 12/51 (23%), Positives = 23/51 (45%), Gaps = 5/51 (9%)

Query: 72  FQSNKNVDNNEQISLLYNEGLKELEVLKRQVLISQLFKPDKLVIETQMQNS 122
           F    N+D + +  +L  E L++   L+  VL S + +     I  +M  +
Sbjct: 588 FNGPNNLDFSNRFVVLELEELEDRPDLQAVVLFSLMVR-----ITGEMYLT 633


>gnl|CDD|221876 pfam12969, DUF3857, Domain of Unknown Function with PDB structure
           (DUF3857).  This family is based on the first domain of
           the PDB structure PDB:3KD4(residues 1-228). It is
           structurally similar to domains in other hydrolases, eg.
           M1 family aminopeptidase (3ebi, Z=10, rmsd 3.6A for 152
           CA, seq id 12%), despite lack of any significant
           sequence similarity.
          Length = 177

 Score = 27.7 bits (62), Expect = 3.4
 Identities = 15/40 (37%), Positives = 22/40 (55%), Gaps = 5/40 (12%)

Query: 78  VDNNEQISLLYNEGLKELEVLKRQVLISQLFKPDKLVIET 117
           V+   QISL Y+   + LEV K +V+     +PD  +IE 
Sbjct: 24  VEEYSQISLSYDPDYETLEVHKARVI-----RPDGKIIEL 58


>gnl|CDD|111823 pfam02976, MutH, DNA mismatch repair enzyme MutH. 
          Length = 100

 Score = 26.3 bits (59), Expect = 5.8
 Identities = 5/32 (15%), Positives = 17/32 (53%)

Query: 81  NEQISLLYNEGLKELEVLKRQVLISQLFKPDK 112
            +++  +  EG +++ +  R++    L+ P +
Sbjct: 60  LKRVLWIPYEGERDIPLADRKIGSPFLWSPSE 91


>gnl|CDD|113403 pfam04631, Baculo_44, Baculovirus hypothetical protein.  This
           family includes several hypothetical baculoviral
           proteins, with predicted molecular weights of
           approximately 44 kD.
          Length = 372

 Score = 27.2 bits (61), Expect = 7.1
 Identities = 9/17 (52%), Positives = 12/17 (70%)

Query: 22  VECLALSTPVTHMSVSK 38
           VECL+L TP++  S  K
Sbjct: 306 VECLSLDTPISEYSPDK 322


  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    0.387 

Gapped
Lambda     K      H
   0.267   0.0783    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,738,201
Number of extensions: 981776
Number of successful extensions: 879
Number of sequences better than 10.0: 1
Number of HSP's gapped: 878
Number of HSP's successfully gapped: 24
Length of query: 216
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 123
Effective length of database: 6,812,680
Effective search space: 837959640
Effective search space used: 837959640
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: 57 (25.6 bits)