RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy16395
         (157 letters)



>gnl|CDD|220655 pfam10255, Paf67, RNA polymerase I-associated factor PAF67.  RNA
           polymerase I is a multisubunit enzyme and its
           transcription competence is dependent on the presence of
           PAF67. This family of proteins is conserved from worms
           to humans.
          Length = 402

 Score =  148 bits (375), Expect = 9e-44
 Identities = 61/122 (50%), Positives = 79/122 (64%), Gaps = 15/122 (12%)

Query: 25  QVFMDEVNQQKMLPTIRSYLKLYTTLPLSKLATFMGNARAGQDSEIERDVDKETKSLITH 84
           Q+F+ EV QQ+ +  +RSYLKLYTT+ L KLA+ +             DVD E   L + 
Sbjct: 296 QLFLKEVKQQQDINKLRSYLKLYTTITLEKLASLL-------------DVDDEE--LRSQ 340

Query: 85  LLAFKHKMKNVVWTRGPSGLEGTFQSGSELDFYIDNEMIHIADTKVAHRYGDFFIRKIIK 144
           LLA+KHK + + W+ G S L G F S S+LDFYID +MIHI +TKV  RYGDFFIR+I K
Sbjct: 341 LLAYKHKSRQLEWSSGASLLSGEFVSSSDLDFYIDGDMIHIKETKVQKRYGDFFIRQINK 400

Query: 145 FE 146
            +
Sbjct: 401 CK 402


>gnl|CDD|223020 PHA03246, PHA03246, large tegument protein UL36; Provisional.
          Length = 3095

 Score = 28.8 bits (64), Expect = 1.6
 Identities = 18/57 (31%), Positives = 29/57 (50%), Gaps = 5/57 (8%)

Query: 90  HKMKNVVWTRGPSG-LEGTFQSG-SELDFYIDNEMIHIADTKVAHRYGDFFIRKIIK 144
           H + N + ++ P G L   F S   E +FY+D     I DT+++ R    FI ++ K
Sbjct: 148 HDLPNRILSKDPGGNLCVAFSSSYGESEFYLDENTPTILDTQISART---FIERVWK 201


>gnl|CDD|233781 TIGR02212, lolCE, lipoprotein releasing system, transmembrane
           protein, LolC/E family.  This model describes the LolC
           protein, and its paralog LolE found in some species.
           These proteins are homologous to permease proteins of
           ABC transporters. In some species, two paralogs occur,
           designated LolC and LolE. In others, a single form is
           found and tends to be designated LolC [Protein fate,
           Protein and peptide secretion and trafficking].
          Length = 411

 Score = 28.4 bits (64), Expect = 1.7
 Identities = 11/31 (35%), Positives = 18/31 (58%), Gaps = 2/31 (6%)

Query: 106 GTFQSGSELDFYIDNEMIHIADTKVAHRYGD 136
           G F +G E+D Y+   ++ + D +   RYGD
Sbjct: 188 GIFSTGGEVDGYL--ALMPLEDAQRFLRYGD 216


>gnl|CDD|215402 PLN02754, PLN02754, chorismate synthase.
          Length = 413

 Score = 28.2 bits (63), Expect = 2.1
 Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 2/22 (9%)

Query: 102 SGLEGTFQSGSEL--DFYIDNE 121
           SG  GT  +GSE   +FY+D  
Sbjct: 277 SGFAGTLLTGSEHNDEFYMDEH 298


>gnl|CDD|173541 PTZ00348, PTZ00348, tyrosyl-tRNA synthetase; Provisional.
          Length = 682

 Score = 27.2 bits (60), Expect = 5.2
 Identities = 13/39 (33%), Positives = 20/39 (51%)

Query: 20  ISPFRQVFMDEVNQQKMLPTIRSYLKLYTTLPLSKLATF 58
           + P RQ F       ++L  ++SY K   TLPL++ A  
Sbjct: 330 LEPVRQHFASNPEAHELLEAVKSYRKGGATLPLAETALP 368


>gnl|CDD|148689 pfam07230, Phage_T4_Gp20, Bacteriophage T4-like capsid assembly
           protein (Gp20).  This family consists of several
           bacteriophage T4-like capsid assembly (or portal)
           proteins. The exact mechanism by which the
           double-stranded (ds) DNA bacteriophages incorporate the
           portal protein at a unique vertex of the icosahedral
           capsid is unknown. In phage T4, there is evidence that
           this vertex, constituted by 12 subunits of gp20, acts as
           an initiator for the assembly of the major capsid
           protein and the scaffolding proteins into a prolate
           icosahedron of precise dimensions. The regulation of
           portal protein gene expression is an important regulator
           of prohead assembly in bacteriophage T4.
          Length = 500

 Score = 26.9 bits (60), Expect = 5.8
 Identities = 17/37 (45%), Positives = 20/37 (54%), Gaps = 2/37 (5%)

Query: 45  KLYTTL--PLSKLATFMGNARAGQDSEIERDVDKETK 79
           KLY  L  PLS+L    G    G+ +EI RD  K TK
Sbjct: 361 KLYEALRIPLSRLPDEDGGFNFGRGTEITRDELKFTK 397


>gnl|CDD|235535 PRK05621, PRK05621, F0F1 ATP synthase subunit gamma; Validated.
          Length = 284

 Score = 26.2 bits (59), Expect = 7.2
 Identities = 6/25 (24%), Positives = 13/25 (52%), Gaps = 4/25 (16%)

Query: 14  LFYSHFISPFRQVFMDEVNQQKMLP 38
           + Y+ F++   Q    E   +++LP
Sbjct: 169 IVYNKFVNTLSQ----EPTVEQLLP 189


>gnl|CDD|131042 TIGR01987, HI0074, nucleotidyltransferase substrate binding
           protein, HI0074 family.  The member of this family from
           Haemophilus influenzae, HI0074, has been shown by
           crystal structure to resemble nucleotidyltransferase
           substrate binding proteins. It forms a complex with
           HI0073, encoded by the adjacent gene and containing a
           nucleotidyltransferase nucleotide binding domain
           (pfam01909).
          Length = 123

 Score = 25.6 bits (56), Expect = 8.5
 Identities = 11/51 (21%), Positives = 18/51 (35%), Gaps = 2/51 (3%)

Query: 106 GTFQSGSELDFYID--NEMIHIADTKVAHRYGDFFIRKIIKFEELNKKLQA 154
           G     S     +D  N   H  D + A          + +FE L ++L+ 
Sbjct: 73  GLIGDESLWIAMLDDRNITSHTYDQEKAREIYAQIRDYVPEFEFLLEQLRQ 123


>gnl|CDD|181362 PRK08296, PRK08296, hypothetical protein; Provisional.
          Length = 603

 Score = 26.2 bits (58), Expect = 9.2
 Identities = 8/28 (28%), Positives = 14/28 (50%), Gaps = 2/28 (7%)

Query: 49  TLPLSKLATFMGNARAGQDSEIERDVDK 76
            +PL  +  ++G  R G+   IER  + 
Sbjct: 308 EIPLGYIKDYIGRLRRGET--IERPTEA 333


>gnl|CDD|233087 TIGR00678, holB, DNA polymerase III, delta' subunit.  This model
           describes the N-terminal half of the delta' subunit of
           DNA polymerase III. Delta' is homologous to the gamma
           and tau subunits, which form an outgroup for
           phylogenetic comparison. The gamma/tau branch of the
           tree is much more tighly conserved than the delta'
           branch, and some members of that branch score more
           highly against this model than some proteins
           classisified as delta'. The noise cutoff is set to
           detect weakly scoring delta' subunits rather than to
           exclude gamma/tau subunits. At position 126-127 of the
           seed alignment, this family lacks the HM motif of
           gamma/tau; at 132 it has a near-invariant A vs. an
           invariant F in gamma/tau [DNA metabolism, DNA
           replication, recombination, and repair].
          Length = 188

 Score = 25.7 bits (57), Expect = 9.8
 Identities = 7/11 (63%), Positives = 10/11 (90%)

Query: 32  NQQKMLPTIRS 42
           + +K+LPTIRS
Sbjct: 135 SPEKLLPTIRS 145


  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
   0.323    0.139    0.399 

Gapped
Lambda     K      H
   0.267   0.0787    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,034,778
Number of extensions: 720130
Number of successful extensions: 651
Number of sequences better than 10.0: 1
Number of HSP's gapped: 650
Number of HSP's successfully gapped: 25
Length of query: 157
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 68
Effective length of database: 6,990,096
Effective search space: 475326528
Effective search space used: 475326528
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (24.9 bits)