RPS-BLAST 2.2.26 [Sep-21-2011]

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

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

Query= psy13880
         (256 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 =  136 bits (345), Expect = 1e-38
 Identities = 56/156 (35%), Positives = 84/156 (53%), Gaps = 10/156 (6%)

Query: 68  PRGVYACEFVIESSSMGFMISDKDKNVVLFMYQPEARESNGGH-RLIKKTDFHLGQHVNT 126
           PR V A EF+++  +   + +DK  N+ +  Y PEA ES  G  RL+ + +FHLG  V +
Sbjct: 170 PRWVTAAEFLVDYDT--ILGADKFGNLHVLRYDPEAPESLDGDPRLLHRAEFHLGDIVTS 227

Query: 127 FFKIRCKPSPISDAPGARSRFLTWYASLDGALGFFLP-LPEKNYRRLLMLQNVMVTHTSH 185
           F K      P +    + S     Y +LDG++G  +P + E+ YRRL  LQ  +     H
Sbjct: 228 FQKG--SLVPKTGGAESTSSPQILYGTLDGSIGLLVPFISEEEYRRLQHLQQQLRDELPH 285

Query: 186 TGGLNPRAFRTYKGKGYYAGNPSRGIIDGSLVWKFL 221
             GL+PRAFR+Y  +      P + +IDG L+ +FL
Sbjct: 286 LCGLDPRAFRSYYSRSP----PVKNVIDGDLLERFL 317


>gnl|CDD|227490 COG5161, SFT1, Pre-mRNA cleavage and polyadenylation specificity
            factor [RNA processing and modification].
          Length = 1319

 Score = 91.2 bits (226), Expect = 9e-21
 Identities = 45/187 (24%), Positives = 77/187 (41%), Gaps = 5/187 (2%)

Query: 69   RGVYACEFVIESSSMGFMISDKDKNVVLFMYQPEARESNGGHRLIKKTDFHLGQHVNTFF 128
            R   + EF++  + + F+  D   N+    Y P    S  G RL+K++ F L    +   
Sbjct: 1136 RNATSTEFLVTGNELYFLCCDAKGNIHGLTYSPNNPISMSGARLVKRSSFTLH---SAEI 1192

Query: 129  KIRCKPSPISDAPGARSRFLTWYASLDGALGFFLPLPEKNYRRLLMLQNVMVTHTSHTGG 188
            K+   P       G +  F+  Y+  DG L   +P+ + +YRRLL +Q  ++      GG
Sbjct: 1193 KMNLLPRNSEFGAGFKKNFIMVYSRSDGMLIHVVPISDAHYRRLLGIQTAIMARLKSVGG 1252

Query: 189  LNPRAFRTYKGKGYYAGNPSRGIIDGSLVWKFLQLSLGERLEICKKIGSKHNDILDELYD 248
            LNPR +R      +      R  +D  ++  F    +  R  +  K G      + ++  
Sbjct: 1253 LNPRDYR-LNSDIHLHSLSLRSPLDLHIINLFSYFDMSTRESVASKAGRIDRKEISDMIA 1311

Query: 249  IE-ALSS 254
                L S
Sbjct: 1312 SLNLLRS 1318


>gnl|CDD|235646 PRK05925, PRK05925, aspartate kinase; Provisional.
          Length = 440

 Score = 30.9 bits (70), Expect = 0.58
 Identities = 15/37 (40%), Positives = 23/37 (62%), Gaps = 2/37 (5%)

Query: 210 GIIDGSLVWKFLQLSLGERLEICKKIGSKHNDILDEL 246
           G+ D  L+ +F +LS G+R  + +KI  KH +I  EL
Sbjct: 41  GVTD--LLEEFCRLSKGKREALTEKIREKHEEIAKEL 75


>gnl|CDD|224446 COG1529, CoxL, Aerobic-type carbon monoxide dehydrogenase, large
           subunit CoxL/CutL homologs [Energy production and
           conversion].
          Length = 731

 Score = 30.0 bits (68), Expect = 1.2
 Identities = 21/86 (24%), Positives = 31/86 (36%), Gaps = 12/86 (13%)

Query: 4   VQELLTVSLGLHGNRPLLLVRTQHELLIYQAFRHP-KGTLKLRFKK------LKVLFVSD 56
           V+E+L     +   RP+  + T+ EL +    R      +KL   K      +K    +D
Sbjct: 243 VEEILAALAAVVAGRPVKWIETREELFVATGHRRATLIDVKLGADKDGRLLAIKGTVAAD 302

Query: 57  RSKRANEQP-----GLPRGVYACEFV 77
                         GL RG Y  E V
Sbjct: 303 TGAYNGPTVPAAAAGLARGPYKIEAV 328


>gnl|CDD|236376 PRK09084, PRK09084, aspartate kinase III; Validated.
          Length = 448

 Score = 28.2 bits (64), Expect = 4.5
 Identities = 9/27 (33%), Positives = 12/27 (44%)

Query: 227 ERLEICKKIGSKHNDILDELYDIEALS 253
           ERL +  +I      ILD L D   + 
Sbjct: 57  ERLALLDEIRQIQYAILDRLGDPNVVR 83


>gnl|CDD|240359 PTZ00324, PTZ00324, glutamate dehydrogenase 2; Provisional.
          Length = 1002

 Score = 28.2 bits (63), Expect = 5.7
 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 6/69 (8%)

Query: 81  SSMGFMISDKDKNVVLFMYQPEARESNGGHRLIKKTDFHLGQHVNTFFKIRCKPSPISDA 140
           S  GF++   D++V L    P+      G R   + +FHL  + +    + C   P S  
Sbjct: 728 SPQGFLVLTDDRDVKL----PDGTIVESGLRF--RNEFHLLPYSDADVFVPCGGRPRSVT 781

Query: 141 PGARSRFLT 149
                RF  
Sbjct: 782 LFNVGRFFD 790


  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    0.140    0.422 

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: 13,216,880
Number of extensions: 1247900
Number of successful extensions: 840
Number of sequences better than 10.0: 1
Number of HSP's gapped: 834
Number of HSP's successfully gapped: 10
Length of query: 256
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 161
Effective length of database: 6,723,972
Effective search space: 1082559492
Effective search space used: 1082559492
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: 58 (26.0 bits)