RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy17021
         (199 letters)



>gnl|CDD|217409 pfam03178, CPSF_A, CPSF A subunit region.  This family includes a
           region that lies towards the C-terminus of the cleavage
           and polyadenylation specificity factor (CPSF) A (160
           kDa) subunit. CPSF is involved in mRNA polyadenylation
           and binds the AAUAAA conserved sequence in pre-mRNA.
           CPSF has also been found to be necessary for splicing of
           single-intron pre-mRNAs. The function of the aligned
           region is unknown but may be involved in RNA/DNA
           binding.
          Length = 318

 Score =  149 bits (378), Expect = 3e-44
 Identities = 54/121 (44%), Positives = 76/121 (62%), Gaps = 1/121 (0%)

Query: 75  MEFVHKTSVDEVPYAMCPFQGALLVGVGRYLRLYDLGKKKLLRKCENKHLPNLIVKIESM 134
           ++ VHKT V     A+C FQG LL G G+ LR+YDLGK KLL K         +V ++  
Sbjct: 77  LKLVHKTEVKGAVTALCEFQGRLLAGQGQKLRVYDLGKDKLLPKAFLDTPITYVVSLKVF 136

Query: 135 GHRIYVSDVQESVFLVRYKRYENQLLIFADDTQPRWITTSCVL-DYNTVASADKFGNVCI 193
           G+RI V D+ +SV  + Y     +L++FA DTQPRW+T +  L DY+T+  ADKFGN+ +
Sbjct: 137 GNRIIVGDLMKSVTFLGYDEEPYRLILFARDTQPRWVTAAEFLVDYDTILGADKFGNLHV 196

Query: 194 V 194
           +
Sbjct: 197 L 197



 Score = 77.2 bits (191), Expect = 4e-17
 Identities = 35/93 (37%), Positives = 44/93 (47%), Gaps = 5/93 (5%)

Query: 1   MEFVHKTSVDEVPYAMCPFQGALLVGVGRYLRLYDLGKKKLLRKCENKVRIKGFRKAHQT 60
           ++ VHKT V     A+C FQG LL G G+ LR+YDLGK KLL K                
Sbjct: 77  LKLVHKTEVKGAVTALCEFQGRLLAGQGQKLRVYDLGKDKLLPKAFLD---TPITYVVSL 133

Query: 61  HTHSGRSDRLVGNAMEFVHKTSVDEVPYAMCPF 93
                R   +VG+ M+ V     DE PY +  F
Sbjct: 134 KVFGNRI--IVGDLMKSVTFLGYDEEPYRLILF 164


>gnl|CDD|225201 COG2319, COG2319, FOG: WD40 repeat [General function prediction
           only].
          Length = 466

 Score = 33.9 bits (76), Expect = 0.048
 Identities = 23/151 (15%), Positives = 48/151 (31%), Gaps = 16/151 (10%)

Query: 47  NKVRIKGFRKAHQTHTHSGRSDRLVGNAMEFVHKTSVDEVPYAMCPFQGALLVGVGRYLR 106
             +++   R      T +G +D +          +S+   P                 +R
Sbjct: 178 GTIKLWDLRTGKPLSTLAGHTDPV----------SSLAFSPDGGLLI---ASGSSDGTIR 224

Query: 107 LYDLGKKKLLRKCENKHLPNLIVKIESMGHRIYVSDVQESVFLVRYKRYENQLLIFADDT 166
           L+DL   KLLR   + H  +++      G  +       ++ L   +   + L   +  +
Sbjct: 225 LWDLSTGKLLRSTLSGHSDSVVSSFSPDGSLLASGSSDGTIRLWDLRSSSSLLRTLSGHS 284

Query: 167 QPRWITTSCVL-DYNTVASADKFGNVCIVST 196
               + +     D   +AS    G V +   
Sbjct: 285 S--SVLSVAFSPDGKLLASGSSDGTVRLWDL 313


>gnl|CDD|183779 PRK12830, PRK12830, UDP-N-acetylglucosamine
           1-carboxyvinyltransferase; Reviewed.
          Length = 417

 Score = 28.3 bits (64), Expect = 3.2
 Identities = 11/36 (30%), Positives = 22/36 (61%), Gaps = 2/36 (5%)

Query: 122 KHLPNLIVKIESMGHRIYVSDVQESVFLVRYKRYEN 157
           +HL + I K+E MG R+ V++  +S+F+ +    + 
Sbjct: 257 EHLESFIAKLEEMGVRVEVNE--DSIFVEKQGNLKA 290


>gnl|CDD|153431 cd07995, TPK, Thiamine pyrophosphokinase.  Thiamine
           pyrophosphokinase (TPK, EC:2.7.6.2, also spelled thiamin
           pyrophosphokinase) catalyzes the transfer of a
           pyrophosphate group from ATP to vitamin B1 (thiamine) to
           form the coenzyme thiamine pyrophosphate (TPP). TPP is
           required for central metabolic functions, and thiamine
           deficiency is associated with potentially fatal human
           diseases. The structure of thiamine pyrophosphokinase
           suggests that the enzyme may operate by a mechanism of
           pyrophosphoryl transfer similar to those described for
           pyrophosphokinases functioning in nucleotide
           biosynthesis.
          Length = 208

 Score = 27.1 bits (61), Expect = 5.4
 Identities = 9/31 (29%), Positives = 16/31 (51%)

Query: 126 NLIVKIESMGHRIYVSDVQESVFLVRYKRYE 156
           NL++K    G +I + D Q  +FL+    + 
Sbjct: 112 NLLLKYAKDGIKIVLIDEQNEIFLLLPGSHT 142


>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
           [Transcription].
          Length = 450

 Score = 27.3 bits (61), Expect = 6.1
 Identities = 19/63 (30%), Positives = 28/63 (44%), Gaps = 8/63 (12%)

Query: 106 RLYDLGKKKLLRKCENKHLPNLIVKIESMGHRIYVSDVQE--SVFL-----VRY-KRYEN 157
            L D+G++  LR       P  I+       R+ V DV+    +FL     V Y ++YE 
Sbjct: 388 YLTDIGEETSLRYAVQLLTPASIIAKRRGSKRVEVEDVERAKELFLDVKRSVEYVEKYEG 447

Query: 158 QLL 160
            LL
Sbjct: 448 LLL 450


>gnl|CDD|236421 PRK09231, PRK09231, fumarate reductase flavoprotein subunit;
           Validated.
          Length = 582

 Score = 27.3 bits (61), Expect = 7.3
 Identities = 20/57 (35%), Positives = 29/57 (50%), Gaps = 7/57 (12%)

Query: 75  MEFV--HKTSVDEVPYAM---CPFQGALLVGVG--RYLRLYDLGKKKLLRKCENKHL 124
           MEFV  H T +      M   C  +G +LV     RYL+ Y LG +  L + +NK++
Sbjct: 226 MEFVQYHPTGLPGSGILMTEGCRGEGGILVNKDGYRYLQDYGLGPETPLGEPKNKYM 282


>gnl|CDD|223618 COG0544, Tig, FKBP-type peptidyl-prolyl cis-trans isomerase
          (trigger factor) [Posttranslational modification,
          protein turnover, chaperones].
          Length = 441

 Score = 26.9 bits (60), Expect = 8.6
 Identities = 10/20 (50%), Positives = 12/20 (60%)

Query: 39 KKLLRKCENKVRIKGFRKAH 58
           K L+K   KV+I GFRK  
Sbjct: 29 DKALKKLAKKVKIPGFRKGK 48


>gnl|CDD|234956 PRK01490, tig, trigger factor; Provisional.
          Length = 435

 Score = 26.7 bits (60), Expect = 8.7
 Identities = 10/18 (55%), Positives = 11/18 (61%)

Query: 39 KKLLRKCENKVRIKGFRK 56
           K L+K    VRI GFRK
Sbjct: 29 DKALKKLAKTVRIPGFRK 46


>gnl|CDD|218700 pfam05697, Trigger_N, Bacterial trigger factor protein (TF).  In
          the E. coli cytosol, a fraction of the newly
          synthesised proteins requires the activity of molecular
          chaperones for folding to the native state. The major
          chaperones implicated in this folding process are the
          ribosome-associated Trigger Factor (TF), and the DnaK
          and GroEL chaperones with their respective
          co-chaperones. Trigger Factor is an ATP-independent
          chaperone and displays chaperone and
          peptidyl-prolyl-cis-trans-isomerase (PPIase) activities
          in vitro. It is composed of at least three domains, an
          N-terminal domain which mediates association with the
          large ribosomal subunit, a central substrate binding
          and PPIase domain with homology to FKBP proteins, and a
          C-terminal domain of unknown function. The positioning
          of TF at the peptide exit channel, together with its
          ability to interact with nascent chains as short as 57
          residues renders TF a prime candidate for being the
          first chaperone that binds to the nascent polypeptide
          chains. This family represents the N-terminal region of
          the protein.
          Length = 145

 Score = 26.0 bits (58), Expect = 9.2
 Identities = 9/18 (50%), Positives = 12/18 (66%)

Query: 39 KKLLRKCENKVRIKGFRK 56
           K L++   KV+I GFRK
Sbjct: 29 DKALKELAKKVKIPGFRK 46


  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
   0.324    0.140    0.423 

Gapped
Lambda     K      H
   0.267   0.0795    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 9,953,682
Number of extensions: 907114
Number of successful extensions: 867
Number of sequences better than 10.0: 1
Number of HSP's gapped: 865
Number of HSP's successfully gapped: 15
Length of query: 199
Length of database: 10,937,602
Length adjustment: 92
Effective length of query: 107
Effective length of database: 6,857,034
Effective search space: 733702638
Effective search space used: 733702638
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: 40 (21.6 bits)
S2: 56 (25.2 bits)