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= 000264
         (1764 letters)

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

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



>pdb|3NY1|A Chain A, Structure Of The Ubr-Box Of The Ubr1 Ubiquitin Ligase
 pdb|3NY1|B Chain B, Structure Of The Ubr-Box Of The Ubr1 Ubiquitin Ligase
          Length = 77

 Score = 58.9 bits (141), Expect = 2e-08,   Method: Composition-based stats.
 Identities = 26/70 (37%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSI-IYTXXXXXXXXXVTAW 175
           +CG V+ + +  Y CR C  DPTC +C+ CFQ+  HK H Y +   T           AW
Sbjct: 7   LCGRVFKSGETTYSCRDCAIDPTCVLCMDCFQDSVHKNHRYKMHTSTGGGFCDCGDTEAW 66

Query: 176 KREGFCSRHK 185
           K   FC  H+
Sbjct: 67  KTGPFCVNHE 76


>pdb|3NY2|A Chain A, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|B Chain B, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|C Chain C, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|D Chain D, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|E Chain E, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|F Chain F, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|G Chain G, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY2|H Chain H, Structure Of The Ubr-Box Of Ubr2 Ubiquitin Ligase
 pdb|3NY3|A Chain A, Structure Of The Ubr-Box Of Ubr2 In Complex With N-Degron
          Length = 75

 Score = 55.1 bits (131), Expect = 3e-07,   Method: Composition-based stats.
 Identities = 23/70 (32%), Positives = 35/70 (50%), Gaps = 1/70 (1%)

Query: 117 VCGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEHDYSIIYTXXXXXXXXXVT-AW 175
           +CG V+   +  Y CR C  DPTC +C+ CF    H++H Y +  +          T AW
Sbjct: 6   LCGRVFKVGEPTYSCRDCAVDPTCVLCMECFLGSIHRDHRYRMTTSGGGGFCDCGDTEAW 65

Query: 176 KREGFCSRHK 185
           K   +C +H+
Sbjct: 66  KEGPYCQKHE 75


>pdb|3NIH|A Chain A, The Structure Of Ubr Box (Riaaa)
 pdb|3NII|A Chain A, The Structure Of Ubr Box (Kiaa)
 pdb|3NIJ|A Chain A, The Structure Of Ubr Box (Hiaa)
 pdb|3NIK|A Chain A, The Structure Of Ubr Box (Reaa)
 pdb|3NIK|B Chain B, The Structure Of Ubr Box (Reaa)
 pdb|3NIK|D Chain D, The Structure Of Ubr Box (Reaa)
 pdb|3NIK|F Chain F, The Structure Of Ubr Box (Reaa)
 pdb|3NIL|A Chain A, The Structure Of Ubr Box (Rdaa)
 pdb|3NIL|B Chain B, The Structure Of Ubr Box (Rdaa)
 pdb|3NIL|D Chain D, The Structure Of Ubr Box (Rdaa)
 pdb|3NIL|F Chain F, The Structure Of Ubr Box (Rdaa)
 pdb|3NIM|A Chain A, The Structure Of Ubr Box (Rraa)
 pdb|3NIM|B Chain B, The Structure Of Ubr Box (Rraa)
 pdb|3NIM|D Chain D, The Structure Of Ubr Box (Rraa)
 pdb|3NIM|F Chain F, The Structure Of Ubr Box (Rraa)
 pdb|3NIN|A Chain A, The Structure Of Ubr Box (Rlges)
 pdb|3NIN|B Chain B, The Structure Of Ubr Box (Rlges)
 pdb|3NIS|A Chain A, The Structure Of Ubr Box (Native2)
 pdb|3NIS|B Chain B, The Structure Of Ubr Box (Native2)
 pdb|3NIS|D Chain D, The Structure Of Ubr Box (Native2)
 pdb|3NIS|F Chain F, The Structure Of Ubr Box (Native2)
          Length = 82

 Score = 37.7 bits (86), Expect = 0.064,   Method: Composition-based stats.
 Identities = 14/38 (36%), Positives = 19/38 (50%)

Query: 118 CGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEH 155
           CG  +   +  YRC  C  D TC +C+ CF   +H  H
Sbjct: 11  CGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNH 48


>pdb|3NIT|A Chain A, The Structure Of Ubr Box (Native1)
          Length = 90

 Score = 37.7 bits (86), Expect = 0.065,   Method: Composition-based stats.
 Identities = 14/38 (36%), Positives = 19/38 (50%)

Query: 118 CGAVWGNNDIAYRCRTCEHDPTCAICVPCFQNGNHKEH 155
           CG  +   +  YRC  C  D TC +C+ CF   +H  H
Sbjct: 19  CGRKFKIGEPLYRCHECGCDDTCVLCIHCFNPKDHVNH 56


>pdb|3GRA|A Chain A, Crystal Structure Of Arac Family Transcriptional Regulator
            From Pseudomonas Putida
 pdb|3GRA|B Chain B, Crystal Structure Of Arac Family Transcriptional Regulator
            From Pseudomonas Putida
          Length = 202

 Score = 32.3 bits (72), Expect = 2.7,   Method: Composition-based stats.
 Identities = 30/91 (32%), Positives = 39/91 (42%), Gaps = 8/91 (8%)

Query: 1331 SSMEMFEQDLYLSICREMRKNMTYPDLMKEDEECSVAEGGLKNRGNSDSFL-----LGKY 1385
            S+  + E DL L +C  +R  + YP+L +   +C+     L    N   FL     L  Y
Sbjct: 65   SAAALKELDL-LVVCGGLRTPLKYPELDRLLNDCAAHGXALGGLWNGAWFLGRAGVLDDY 123

Query: 1386 VASISKEMRENASASEVSRGDRIAAESLVYD 1416
              SI  E R  AS SE S   RI   S   D
Sbjct: 124  GCSIHPEQR--ASLSERSPQTRITPASFTLD 152


>pdb|2Q1F|A Chain A, Crystal Structure Of Chondroitin Sulfate Lyase Abc From
            Bacteroides Thetaiotaomicron Wal2926
 pdb|2Q1F|B Chain B, Crystal Structure Of Chondroitin Sulfate Lyase Abc From
            Bacteroides Thetaiotaomicron Wal2926
          Length = 1022

 Score = 31.6 bits (70), Expect = 3.6,   Method: Compositional matrix adjust.
 Identities = 22/82 (26%), Positives = 39/82 (47%), Gaps = 3/82 (3%)

Query: 1169 FKFLSSISSNIEDAPKSAPEVTNYDAEHVSEESVQDVCALCHDPNSRTPVSY-LILLQKS 1227
             + +SS SS+ E AP+  P+V+N     +++  V++      DP     + Y  + +Q+ 
Sbjct: 551  LRLVSSDSSSAEQAPEYXPKVSNAQERKIAKRLVENGFRAEPDPQGNLSLGYGCVSVQRR 610

Query: 1228 RLLSFVDRGSPS--WDQDQWLG 1247
               S V RG     W  + +LG
Sbjct: 611  ENWSAVARGHSRYLWAAEHYLG 632


>pdb|2FX0|A Chain A, Crystal Structure Of Hlyiir, A Hemolysin Ii
           Transcriptional Regulator
          Length = 201

 Score = 30.8 bits (68), Expect = 7.6,   Method: Composition-based stats.
 Identities = 28/105 (26%), Positives = 50/105 (47%), Gaps = 20/105 (19%)

Query: 810 LAPADLYVN-------RIIERFGLSNYLSLNLERPSEYEPI-LVQEMLTLIIQILQERRF 861
           +A A  Y N        + +++GL+N L   LE+ +++ PI  ++E LT+    ++E   
Sbjct: 41  VAXASYYFNGKENLYYEVFKKYGLANELPNFLEK-NQFNPINALREYLTVFTTHIKENPE 99

Query: 862 CGLTTAESLKRELVHRLAIGDATHSQLVKSLPRDLSKFDQLQEIL 906
            G    E + +E            ++L K  P  +  F+QL+EIL
Sbjct: 100 IGTLAYEEIIKE-----------SARLEKIKPYFIGSFEQLKEIL 133


>pdb|2WV1|A Chain A, Crystal Structure Of The Hlyiir Mutant Protein With
           Residues 169-186 Substituted By A Linker Containing Two
           Thrombin Sites
 pdb|2WV1|B Chain B, Crystal Structure Of The Hlyiir Mutant Protein With
           Residues 169-186 Substituted By A Linker Containing Two
           Thrombin Sites
          Length = 202

 Score = 30.4 bits (67), Expect = 8.4,   Method: Composition-based stats.
 Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 13/88 (14%)

Query: 820 IIERFGLSNYLSLNLERPSEYEPI-LVQEMLTLIIQILQERRFCGLTTAESLKRELVHRL 878
           + +++GL+N L   LE+ +++ PI  ++E LT+    ++E    G    E + +E     
Sbjct: 60  VFKKYGLANELPNFLEK-NQFNPINALREYLTVFTTHIKENPEIGTLAYEEIIKE----- 113

Query: 879 AIGDATHSQLVKSLPRDLSKFDQLQEIL 906
                  ++L K  P  +  F+QL+EIL
Sbjct: 114 ------SARLEKIKPYFIGSFEQLKEIL 135


>pdb|2JK3|A Chain A, Crystal Structure Of The Hlyiir Mutant Protein With
           Residues 169-186 Substituted By Gssgssg Linker
 pdb|2JK3|B Chain B, Crystal Structure Of The Hlyiir Mutant Protein With
           Residues 169-186 Substituted By Gssgssg Linker
          Length = 188

 Score = 30.4 bits (67), Expect = 8.4,   Method: Composition-based stats.
 Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 13/88 (14%)

Query: 820 IIERFGLSNYLSLNLERPSEYEPI-LVQEMLTLIIQILQERRFCGLTTAESLKRELVHRL 878
           + +++GL+N L   LE+ +++ PI  ++E LT+    ++E    G    E + +E     
Sbjct: 56  VFKKYGLANELPNFLEK-NQFNPINALREYLTVFTTHIKENPEIGTLAYEEIIKE----- 109

Query: 879 AIGDATHSQLVKSLPRDLSKFDQLQEIL 906
                  ++L K  P  +  F+QL+EIL
Sbjct: 110 ------SARLEKIKPYFIGSFEQLKEIL 131


>pdb|2JJ7|A Chain A, Crystal Structure Of The Hlyiir Mutant Protein With
           Residues 170-185 Substituted By Alanine
 pdb|2JJ7|B Chain B, Crystal Structure Of The Hlyiir Mutant Protein With
           Residues 170-185 Substituted By Alanine
          Length = 186

 Score = 30.4 bits (67), Expect = 8.7,   Method: Composition-based stats.
 Identities = 24/88 (27%), Positives = 45/88 (51%), Gaps = 13/88 (14%)

Query: 820 IIERFGLSNYLSLNLERPSEYEPI-LVQEMLTLIIQILQERRFCGLTTAESLKRELVHRL 878
           + +++GL+N L   LE+ +++ PI  ++E LT+    ++E    G    E + +E     
Sbjct: 58  VFKKYGLANELPNFLEK-NQFNPINALREYLTVFTTHIKENPEIGTLAYEEIIKE----- 111

Query: 879 AIGDATHSQLVKSLPRDLSKFDQLQEIL 906
                  ++L K  P  +  F+QL+EIL
Sbjct: 112 ------SARLEKIKPYFIGSFEQLKEIL 133


  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
   0.319    0.134    0.400 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 47,979,750
Number of Sequences: 62578
Number of extensions: 1860338
Number of successful extensions: 4056
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 4052
Number of HSP's gapped (non-prelim): 10
length of query: 1764
length of database: 14,973,337
effective HSP length: 113
effective length of query: 1651
effective length of database: 7,902,023
effective search space: 13046239973
effective search space used: 13046239973
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 59 (27.3 bits)