RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16837
         (204 letters)



>gnl|CDD|233185 TIGR00918, 2A060602, The Eukaryotic (Putative) Sterol Transporter
           (EST) Family. 
          Length = 1145

 Score =  138 bits (348), Expect = 1e-37
 Identities = 55/114 (48%), Positives = 70/114 (61%), Gaps = 3/114 (2%)

Query: 55  AFYNYLSAWSTNDALSYGASQCSLRPEPKPWLHVSNDY---ELKIPKSAPLIYAQIPVSL 111
           AFY YLSAW +ND ++Y ASQ ++ P P  WLH  NDY    L+IP + PL YAQ P  L
Sbjct: 858 AFYIYLSAWVSNDPVAYAASQANIYPHPPEWLHDKNDYDPENLRIPAAEPLEYAQFPFYL 917

Query: 112 NNLYTTRDITELITQVRGICDEFESKGLPNYPSGIIFYFWQQFSQFKMYFFLAI 165
           N L  T    E I  VR IC+ +E  GLP+YPSG  F FW+Q+   + +  L+I
Sbjct: 918 NGLRETSQFVEAIEHVRAICNNYEGFGLPSYPSGYPFLFWEQYMGLRHWLLLSI 971


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

 Score = 33.2 bits (77), Expect = 0.079
 Identities = 12/31 (38%), Positives = 13/31 (41%), Gaps = 2/31 (6%)

Query: 17  PCLE--YKAANKRRSHPRLTARHGDTPLPTI 45
           P LE    A   R    RLT R G   LP +
Sbjct: 304 PSLESLANAQQGRYRLLRLTKRAGGARLPEV 334


>gnl|CDD|204078 pfam08832, SRC-1, Steroid receptor coactivator.  This domain is
           found in steroid/nuclear receptor coactivators and
           contains two LXXLL motifs that are involved in receptor
           binding. The family includes SRC-1/NcoA-1, NcoA-2/TIF2,
           pCIP/ACTR/GRIP-1/AIB1.
          Length = 78

 Score = 29.5 bits (66), Expect = 0.31
 Identities = 13/39 (33%), Positives = 15/39 (38%)

Query: 163 LAILMGAPGPSSSLPGGGASTCSSDSQSTTSSSSSTGGG 201
           L +L     P        + T   DS   T  SSSTGG 
Sbjct: 7   LQLLTTKTEPLEPPLMASSDTDCKDSLGVTGVSSSTGGC 45


>gnl|CDD|147207 pfam04924, Pox_A6, Poxvirus A6 protein. 
          Length = 371

 Score = 31.1 bits (71), Expect = 0.37
 Identities = 10/40 (25%), Positives = 21/40 (52%), Gaps = 12/40 (30%)

Query: 102 LIYAQIPVSLNNLYT------------TRDITELITQVRG 129
           L+  Q  +SLNN+Y+            ++ I E+++Q++ 
Sbjct: 109 LLNVQTLISLNNMYSNIKQDTAEIVSDSKKILEIVSQIKA 148


>gnl|CDD|233055 TIGR00617, rpa1, replication factor-a protein 1 (rpa1).  All
           proteins in this family for which functions are known
           are part of a multiprotein complex made up of homologs
           of RPA1, RPA2 and RPA3 that bind ssDNA and function in
           the recognition of DNA damage for nucleotide excision
           repairThis family is based on the phylogenomic analysis
           of JA Eisen (1999, Ph.D. Thesis, Stanford University)
           [DNA metabolism, DNA replication, recombination, and
           repair].
          Length = 608

 Score = 30.9 bits (70), Expect = 0.45
 Identities = 10/26 (38%), Positives = 16/26 (61%)

Query: 69  LSYGASQCSLRPEPKPWLHVSNDYEL 94
             Y  S+ SL+P  K + ++ NDYE+
Sbjct: 249 KVYYISKGSLKPANKQFTNLGNDYEM 274


>gnl|CDD|147982 pfam06112, Herpes_capsid, Gammaherpesvirus capsid protein.  This
           family consists of several Gammaherpesvirus capsid
           proteins. The exact function of this family is unknown.
          Length = 148

 Score = 29.4 bits (66), Expect = 0.75
 Identities = 17/36 (47%), Positives = 21/36 (58%)

Query: 168 GAPGPSSSLPGGGASTCSSDSQSTTSSSSSTGGGAG 203
           G PG ++ L G   S  SS   S +SSSS +G GAG
Sbjct: 101 GVPGGANQLSGSSGSALSSGPGSLSSSSSLSGSGAG 136


>gnl|CDD|190271 pfam02296, Alpha_adaptin_C, Alpha adaptin AP2, C-terminal domain.
           Alpha adaptin is a hetero tetramer which regulates
           clathrin-bud formation. The carboxyl-terminal appendage
           of the alpha subunit regulates translocation of
           endocytic accessory proteins to the bud site.
          Length = 113

 Score = 28.8 bits (65), Expect = 0.79
 Identities = 12/43 (27%), Positives = 16/43 (37%)

Query: 4   CCCCIPTGSGGQWPCLEYKAANKRRSHPRLTARHGDTPLPTIV 46
               I T   G+  CL     N +    RLT R  D  +P  +
Sbjct: 68  GAGVIHTSVSGKVGCLLRLEPNYQAQMYRLTIRATDESVPAAL 110


>gnl|CDD|223660 COG0587, DnaE, DNA polymerase III, alpha subunit [DNA replication,
           recombination, and repair].
          Length = 1139

 Score = 30.3 bits (69), Expect = 0.80
 Identities = 19/68 (27%), Positives = 28/68 (41%), Gaps = 14/68 (20%)

Query: 79  RPEPKPWLHVSNDYELKIPKSAPLIYAQIPVSLNNLYTTRDITELITQVRGICDEFESK- 137
             + K   + S +  LK P+    ++A IP +L N   T +I E           FE   
Sbjct: 225 LSDDKRLRYSSAEQYLKSPEEMARLFADIPEALAN---TVEIAERC--------NFELDL 273

Query: 138 --GLPNYP 143
              LPN+P
Sbjct: 274 GPRLPNFP 281


>gnl|CDD|204658 pfam11477, PM0188, Sialyltransferase PMO188.  PMO188 is a
           sialyltransferase from P.multocida. It transfers sialic
           acid from cytidine 5'-monophosphonuraminic acid to an
           acceptor sugar. It has important catalytic residues such
           as Asp141, His311, Glu338, Ser355 and Ser356.
          Length = 381

 Score = 29.8 bits (67), Expect = 0.83
 Identities = 14/54 (25%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 109 VSLNNLYTTRDITELITQVRGICDEFESKGLPNYPSGIIF-YFWQQFSQFKMYF 161
           V+L +L    D+ + I Q + +  E+ + G PN+P+  +  Y W      + +F
Sbjct: 124 VTLYSLCKIPDLEQEILQHKNVLLEYLTGGTPNFPNPTLNRYLWNNLYDTQYHF 177


>gnl|CDD|204269 pfam09578, Spore_YabQ, Spore cortex protein YabQ (Spore_YabQ).
           This protein is predicted to span the membrane several
           times. It is only found in genomes of species that
           perform sporulation, such as Bacillus subtilis,
           Clostridium tetani, and other members of the Firmicutes
           (low-GC Gram-positive bacteria). Mutation of this
           sigmaE-dependent gene blocks development of the spore
           cortex. The length of the C-terminal region, which
           includes some hydrophobic regions, is variable.
          Length = 80

 Score = 27.5 bits (62), Expect = 1.5
 Identities = 10/28 (35%), Positives = 18/28 (64%), Gaps = 2/28 (7%)

Query: 144 SGIIFYF--WQQFSQFKMYFFLAILMGA 169
           + I+FYF  +  + + + Y FLA+L+G 
Sbjct: 44  ALIVFYFLLYTNYGEIRFYVFLALLLGI 71


>gnl|CDD|224529 COG1613, Sbp, ABC-type sulfate transport system, periplasmic
           component [Inorganic ion transport and metabolism].
          Length = 348

 Score = 28.5 bits (64), Expect = 2.8
 Identities = 10/21 (47%), Positives = 16/21 (76%), Gaps = 1/21 (4%)

Query: 45  IVSAQP-PSGGAFYNYLSAWS 64
           +++  P  SGGA +NYL+AW+
Sbjct: 158 VITPNPKTSGGARWNYLAAWA 178


>gnl|CDD|182700 PRK10752, PRK10752, sulfate transporter subunit; Provisional.
          Length = 329

 Score = 28.2 bits (63), Expect = 2.9
 Identities = 11/24 (45%), Positives = 17/24 (70%), Gaps = 1/24 (4%)

Query: 41  PLPTIVSAQPP-SGGAFYNYLSAW 63
           P  ++++  P  SGGA +NYL+AW
Sbjct: 137 PGVSVITPNPKSSGGARWNYLAAW 160


>gnl|CDD|131199 TIGR02144, LysX_arch, Lysine biosynthesis enzyme LysX.  The family
           of proteins found in this equivalog include the
           characterized LysX from Thermus thermophilus which is
           part of a well-organized lysine biosynthesis gene
           cluster. LysX is believed to carry out an ATP-dependent
           acylation of the amino group of alpha-aminoadipate in
           the prokaryotic version of the fungal AAA lysine
           biosynthesis pathway. No species having a sequence in
           this equivalog contains the elements of the more common
           diaminopimelate lysine biosythesis pathway, and none has
           been shown to be a lysine auxotroph. These sequences
           have mainly recieved the name of the related enzyme,
           "ribosomal protein S6 modification protein RimK". RimK
           has been characterized in E. coli, and acts by
           ATP-dependent condensation of S6 with glutamate
           residues.
          Length = 280

 Score = 27.8 bits (62), Expect = 4.6
 Identities = 11/28 (39%), Positives = 12/28 (42%)

Query: 54  GAFYNYLSAWSTNDALSYGASQCSLRPE 81
            A Y Y + W TN A    A  C L  E
Sbjct: 189 AAIYRYSNHWRTNTARGGKAEPCPLDEE 216


>gnl|CDD|130044 TIGR00971, 3a0106s03, sulfate/thiosulfate-binding protein.  This
           model describes binding proteins functionally associated
           with the sulfate ABC transporter. In the model bacterium
           E. coli, two different members work with the same
           transporter; mutation analysis says each enables the
           uptake of both sulfate and thiosulfate. In many species,
           a single binding protein is found, and may be referred
           to in general terms as a sulfate ABC transporter
           sulfate-binding protein [Transport and binding proteins,
           Anions].
          Length = 315

 Score = 26.9 bits (59), Expect = 7.7
 Identities = 9/16 (56%), Positives = 11/16 (68%)

Query: 52  SGGAFYNYLSAWSTND 67
           SGGA +NYL+AW    
Sbjct: 138 SGGARWNYLAAWGYAL 153


>gnl|CDD|114217 pfam05481, Myco_19_kDa, Mycobacterium 19 kDa lipoprotein antigen.
           Most of the antigens of Mycobacterium leprae and M.
           tuberculosis that have been identified are members of
           stress protein families, which are highly conserved
           throughout many diverse species. Of the M. leprae and M.
           tuberculosis antigens identified by monoclonal
           antibodies, all except the 18-kDa M. leprae antigen and
           the 19-kDa M. tuberculosis antigen are strongly
           cross-reactive between these two species and are coded
           within very similar genes.
          Length = 160

 Score = 26.5 bits (58), Expect = 7.8
 Identities = 12/19 (63%), Positives = 15/19 (78%)

Query: 180 GASTCSSDSQSTTSSSSST 198
           GAS CSS ++ST SSS +T
Sbjct: 18  GASGCSSGNKSTPSSSKTT 36


>gnl|CDD|220589 pfam10129, OpgC_C, OpgC protein.  This domain, found in various
           hypothetical and OpgC prokaryotic proteins. It is likely
           to act as an acyltransferase enzyme.
          Length = 358

 Score = 26.8 bits (60), Expect = 9.1
 Identities = 12/35 (34%), Positives = 17/35 (48%), Gaps = 10/35 (28%)

Query: 139 LPNYPSGIIFYF----WQQFSQFKMYFFLAILMGA 169
           LP YPSG  ++F    WQ      + F L + +G 
Sbjct: 180 LPAYPSGGGWFFNPFAWQ------LLFVLGLWLGL 208


  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
   0.317    0.134    0.431 

Gapped
Lambda     K      H
   0.267   0.0638    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 10,107,477
Number of extensions: 896707
Number of successful extensions: 1113
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1108
Number of HSP's successfully gapped: 24
Length of query: 204
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 112
Effective length of database: 6,857,034
Effective search space: 767987808
Effective search space used: 767987808
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: 41 (21.7 bits)
S2: 57 (25.9 bits)