BLASTP 2.2.26 [Sep-21-2011]


Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schaffer, 
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997), 
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs",  Nucleic Acids Res. 25:3389-3402.


Reference for compositional score matrix adjustment: Altschul, Stephen F., 
John C. Wootton, E. Michael Gertz, Richa Agarwala, Aleksandr Morgulis,
Alejandro A. Schaffer, and Yi-Kuo Yu (2005) "Protein database searches
using compositionally adjusted substitution matrices", FEBS J. 272:5101-5109.

Query= 023906
         (275 letters)

Database: pdbaa 
           62,578 sequences; 14,973,337 total letters

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



>pdb|1WLJ|A Chain A, Human Isg20
          Length = 189

 Score =  112 bits (279), Expect = 3e-25,   Method: Compositional matrix adjust.
 Identities = 62/162 (38%), Positives = 97/162 (59%), Gaps = 7/162 (4%)

Query: 81  DVVAMDCEMVGISQGNKSALGRVSLVNKWGNLIYDEFVRPLERVVDFRTRISGIRPRDLR 140
           +VVAMDCEMVG+    +S L R SLVN  G ++YD+F+RP   + D+RTR+SG+ P+ + 
Sbjct: 6   EVVAMDCEMVGLGPHRESGLARCSLVNVHGAVLYDKFIRPEGEITDYRTRVSGVTPQHMV 65

Query: 141 KAKDFPTVQKKVAELIEGRILVGHALHNDLKALLLTHSKKDLRDTSEYQPF-----LKNG 195
            A  F   + ++ +L++G+++VGH L +D +AL    S   + DTS  +       L + 
Sbjct: 66  GATPFAVARLEILQLLKGKLVVGHDLKHDFQALKEDMSGYTIYDTSTDRLLWREAKLDHC 125

Query: 196 RSKALRHLAAEILAVEIQNG--EHCPIDDARAAMLLYMKNRK 235
           R  +LR L+  +L   IQN    H  ++DARA M LY  +++
Sbjct: 126 RRVSLRVLSERLLHKSIQNSLLGHSSVEDARATMELYQISQR 167


>pdb|1ZBU|A Chain A, Crystal Structure Of Full-Length 3'-Exonuclease
 pdb|1ZBU|B Chain B, Crystal Structure Of Full-Length 3'-Exonuclease
 pdb|1ZBU|C Chain C, Crystal Structure Of Full-Length 3'-Exonuclease
 pdb|1ZBU|D Chain D, Crystal Structure Of Full-Length 3'-Exonuclease
          Length = 349

 Score = 30.8 bits (68), Expect = 0.83,   Method: Compositional matrix adjust.
 Identities = 33/136 (24%), Positives = 53/136 (38%), Gaps = 30/136 (22%)

Query: 114 YDEFVRPL--ERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRILVGHALHNDLK 171
           + ++VRP    ++ DF   ++GI    + +A  FP V KKV +L + +      L    K
Sbjct: 170 FQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDLXKLK-----ELGTKYK 224

Query: 172 ALLLT-----------------------HSKKDLRDTSEYQPFLKNGRSKALRHLAAEIL 208
             LLT                        +KK +     Y  F K  RS+    +  E L
Sbjct: 225 YSLLTDGSWDXSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIXLEKL 284

Query: 209 AVEIQNGEHCPIDDAR 224
             +     HC +DD++
Sbjct: 285 GXDYDGRPHCGLDDSK 300


>pdb|1ZBH|A Chain A, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By
           3'- Exonuclease
 pdb|1ZBH|B Chain B, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By
           3'- Exonuclease
 pdb|1ZBH|C Chain C, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By
           3'- Exonuclease
 pdb|1ZBH|D Chain D, 3'-End Specific Recognition Of Histone Mrna Stem-Loop By
           3'- Exonuclease
          Length = 299

 Score = 30.4 bits (67), Expect = 1.1,   Method: Compositional matrix adjust.
 Identities = 32/136 (23%), Positives = 55/136 (40%), Gaps = 30/136 (22%)

Query: 114 YDEFVRPL--ERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAELIEGRILVGHALHNDLK 171
           + ++VRP    ++ DF   ++GI    + +A  FP V KKV +L++ +      L    K
Sbjct: 120 FQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDLMKLK-----ELGTKYK 174

Query: 172 ALLLT-----------------------HSKKDLRDTSEYQPFLKNGRSKALRHLAAEIL 208
             LLT                        +KK +     Y  F K  RS+    +  E L
Sbjct: 175 YSLLTDGSWDMSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIMLEKL 234

Query: 209 AVEIQNGEHCPIDDAR 224
            ++     +C +DD++
Sbjct: 235 GMDYDGRPNCGLDDSK 250


>pdb|1W0H|A Chain A, Crystallographic Structure Of The Nuclease Domain Of
           3'hexo, A Deddh Family Member, Bound To Ramp
          Length = 204

 Score = 29.6 bits (65), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 31/131 (23%), Positives = 53/131 (40%), Gaps = 20/131 (15%)

Query: 114 YDEFVRPL--ERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE---------------LI 156
           + ++VRP    ++ DF   ++GI    + +A  FP V KKV +               L 
Sbjct: 52  FQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWXKLKELGTKYKYSLLT 111

Query: 157 EGRILVGHALHNDLKALLLTH---SKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQ 213
           +G       L+   +   L +   +KK +     Y  F K  RS+    +  E L  +  
Sbjct: 112 DGSWDXSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIXLEKLGXDYD 171

Query: 214 NGEHCPIDDAR 224
              HC +DD++
Sbjct: 172 GRPHCGLDDSK 182


>pdb|4HXH|B Chain B, Structure Of Mrna Stem-loop, Human Stem-loop Binding
           Protein And 3'hexo Ternary Complex
 pdb|4HXH|E Chain E, Structure Of Mrna Stem-loop, Human Stem-loop Binding
           Protein And 3'hexo Ternary Complex
          Length = 303

 Score = 29.6 bits (65), Expect = 1.8,   Method: Compositional matrix adjust.
 Identities = 31/131 (23%), Positives = 53/131 (40%), Gaps = 20/131 (15%)

Query: 114 YDEFVRPL--ERVVDFRTRISGIRPRDLRKAKDFPTVQKKVAE---------------LI 156
           + ++VRP    ++ DF   ++GI    + +A  FP V KKV +               L 
Sbjct: 116 FQQYVRPEINTQLSDFCISLTGITQDQVDRADTFPQVLKKVIDWXKLKELGTKYKYSLLT 175

Query: 157 EGRILVGHALHNDLKALLLTH---SKKDLRDTSEYQPFLKNGRSKALRHLAAEILAVEIQ 213
           +G       L+   +   L +   +KK +     Y  F K  RS+    +  E L  +  
Sbjct: 176 DGSWDXSKFLNIQCQLSRLKYPPFAKKWINIRKSYGNFYKVPRSQTKLTIXLEKLGXDYD 235

Query: 214 NGEHCPIDDAR 224
              HC +DD++
Sbjct: 236 GRPHCGLDDSK 246


>pdb|1X79|B Chain B, Crystal Structure Of Human Gga1 Gat Domain Complexed With
           The Gat-Binding Domain Of Rabaptin5
 pdb|1X79|C Chain C, Crystal Structure Of Human Gga1 Gat Domain Complexed With
           The Gat-Binding Domain Of Rabaptin5
          Length = 112

 Score = 29.3 bits (64), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 19/66 (28%), Positives = 32/66 (48%), Gaps = 8/66 (12%)

Query: 179 KKDLRDTSEYQPFLKNGRSKA--------LRHLAAEILAVEIQNGEHCPIDDARAAMLLY 230
           +K ++D  E + F+K     +        LR  A+EIL  E+Q G      D +  M + 
Sbjct: 23  EKTMKDKQELEDFIKQSSEDSSHQISALVLRAQASEILLEELQQGLSQAKRDVQEQMAVL 82

Query: 231 MKNRKQ 236
           M++R+Q
Sbjct: 83  MQSREQ 88


  Database: pdbaa
    Posted date:  Mar 3, 2013 10:34 PM
  Number of letters in database: 14,973,337
  Number of sequences in database:  62,578
  
Lambda     K      H
   0.314    0.130    0.369 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,327,556
Number of Sequences: 62578
Number of extensions: 283015
Number of successful extensions: 551
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 545
Number of HSP's gapped (non-prelim): 11
length of query: 275
length of database: 14,973,337
effective HSP length: 97
effective length of query: 178
effective length of database: 8,903,271
effective search space: 1584782238
effective search space used: 1584782238
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (22.0 bits)
S2: 51 (24.3 bits)