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= 046123
         (108 letters)

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

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



>pdb|4FCG|A Chain A, Structure Of The Leucine-Rich Repeat Domain Of The Type
           Iii Effector Xcv3220 (Xopl)
          Length = 328

 Score = 44.3 bits (103), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 32/103 (31%), Positives = 50/103 (48%), Gaps = 2/103 (1%)

Query: 1   MKSLKTLVLSGCLKLKKFPD-IVGKSSQRKLQAGISSWSFILEGTAIRGLPASIELLSGS 59
           +  L+ L +  C +L + P+ +    +  + Q  ++  S  LE T IR LPASI  L   
Sbjct: 149 LNRLRELSIRACPELTELPEPLASTDASGEHQGLVNLQSLRLEWTGIRSLPASIANLQNL 208

Query: 60  VLLNLKDCKNLKSLPSTINGLRSLRTLYLSGCSKLKNVPETLG 102
             L +++   L +L   I+ L  L  L L GC+ L+N P   G
Sbjct: 209 KSLKIRNSP-LSALGPAIHHLPKLEELDLRGCTALRNYPPIFG 250



 Score = 36.2 bits (82), Expect = 0.004,   Method: Composition-based stats.
 Identities = 22/61 (36%), Positives = 30/61 (49%)

Query: 44  TAIRGLPASIELLSGSVLLNLKDCKNLKSLPSTINGLRSLRTLYLSGCSKLKNVPETLGK 103
           TA+R  P      +    L LKDC NL +LP  I+ L  L  L L GC  L  +P  + +
Sbjct: 240 TALRNYPPIFGGRAPLKRLILKDCSNLLTLPLDIHRLTQLEKLDLRGCVNLSRLPSLIAQ 299

Query: 104 V 104
           +
Sbjct: 300 L 300



 Score = 32.7 bits (73), Expect = 0.052,   Method: Composition-based stats.
 Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 1/66 (1%)

Query: 41  LEGTAIRGLPASIELLSGSVLLNLKDCKNLKSLPSTINGLRSLRTLYLSGCSKLKNVPET 100
           ++   +  LP + +  +G   L L     L++LP++I  L  LR L +  C +L  +PE 
Sbjct: 111 IDAAGLXELPDTXQQFAGLETLTLAR-NPLRALPASIASLNRLRELSIRACPELTELPEP 169

Query: 101 LGKVES 106
           L   ++
Sbjct: 170 LASTDA 175


>pdb|1P8T|A Chain A, Crystal Structure Of Nogo-66 Receptor
          Length = 285

 Score = 27.3 bits (59), Expect = 2.3,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 43/104 (41%), Gaps = 31/104 (29%)

Query: 19  PDIVGKSSQRKLQA---GI--SSWSFILEGTAIRGLPAS---------IELLSGSVL--- 61
           P +     Q+ LQA   GI  +S    L G  I  +PA+         I  L  +VL   
Sbjct: 11  PKVTTSCPQQGLQAVPVGIPAASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARI 70

Query: 62  -------------LNLKDCKNLKSL-PSTINGLRSLRTLYLSGC 91
                        L+L D   L+S+ P+T +GL  L TL+L  C
Sbjct: 71  DAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHLDRC 114


>pdb|1OZN|A Chain A, 1.5a Crystal Structure Of The Nogo Receptor Ligand Binding
           Domain Reveals A Convergent Recognition Scaffold
           Mediating Inhibition Of Myelination
          Length = 285

 Score = 27.3 bits (59), Expect = 2.4,   Method: Compositional matrix adjust.
 Identities = 31/104 (29%), Positives = 43/104 (41%), Gaps = 31/104 (29%)

Query: 19  PDIVGKSSQRKLQA---GI--SSWSFILEGTAIRGLPAS---------IELLSGSVL--- 61
           P +     Q+ LQA   GI  +S    L G  I  +PA+         I  L  +VL   
Sbjct: 12  PKVTTSCPQQGLQAVPVGIPAASQRIFLHGNRISHVPAASFRACRNLTILWLHSNVLARI 71

Query: 62  -------------LNLKDCKNLKSL-PSTINGLRSLRTLYLSGC 91
                        L+L D   L+S+ P+T +GL  L TL+L  C
Sbjct: 72  DAAAFTGLALLEQLDLSDNAQLRSVDPATFHGLGRLHTLHLDRC 115


>pdb|4GFH|F Chain F, Topoisomerase Ii-Dna-Amppnp Complex
          Length = 1099

 Score = 25.8 bits (55), Expect = 7.3,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 4/62 (6%)

Query: 46  IRGLPASIELLSGSVLLNLKDCKNLKSLPSTINGLRSLRTLYLSGCSKLKNVPETLGKVE 105
           ++ +P S  +    +L +L D  N++S+P+ ++G +  +   L GC K KN+   L KV 
Sbjct: 624 LKEIPISDFINKELILFSLAD--NIRSIPNVLDGFKPGQRKVLYGCFK-KNLKSEL-KVA 679

Query: 106 SL 107
            L
Sbjct: 680 QL 681


>pdb|4GFH|A Chain A, Topoisomerase Ii-Dna-Amppnp Complex
          Length = 1103

 Score = 25.8 bits (55), Expect = 7.3,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 4/62 (6%)

Query: 46  IRGLPASIELLSGSVLLNLKDCKNLKSLPSTINGLRSLRTLYLSGCSKLKNVPETLGKVE 105
           ++ +P S  +    +L +L D  N++S+P+ ++G +  +   L GC K KN+   L KV 
Sbjct: 628 LKEIPISDFINKELILFSLAD--NIRSIPNVLDGFKPGQRKVLYGCFK-KNLKSEL-KVA 683

Query: 106 SL 107
            L
Sbjct: 684 QL 685


>pdb|1BGW|A Chain A, Topoisomerase Residues 410-1202
 pdb|1BJT|A Chain A, Topoisomerase Ii Residues 409-1201
          Length = 793

 Score = 25.4 bits (54), Expect = 8.7,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 4/62 (6%)

Query: 46  IRGLPASIELLSGSVLLNLKDCKNLKSLPSTINGLRSLRTLYLSGCSKLKNVPETLGKVE 105
           ++ +P S  +    +L +L D  N++S+P+ ++G +  +   L GC K KN+   L KV 
Sbjct: 259 LKEIPISDFINKELILFSLAD--NIRSIPNVLDGFKPGQRKVLYGCFK-KNLKSEL-KVA 314

Query: 106 SL 107
            L
Sbjct: 315 QL 316


>pdb|2RGR|A Chain A, Topoisomerase Iia Bound To G-segment Dna
          Length = 759

 Score = 25.4 bits (54), Expect = 8.7,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 4/62 (6%)

Query: 46  IRGLPASIELLSGSVLLNLKDCKNLKSLPSTINGLRSLRTLYLSGCSKLKNVPETLGKVE 105
           ++ +P S  +    +L +L D  N++S+P+ ++G +  +   L GC K KN+   L KV 
Sbjct: 249 LKEIPISDFINKELILFSLAD--NIRSIPNVLDGFKPGQRKVLYGCFK-KNLKSEL-KVA 304

Query: 106 SL 107
            L
Sbjct: 305 QL 306


>pdb|3L4J|A Chain A, Topoisomerase Ii-Dna Cleavage Complex, Apo
 pdb|3L4K|A Chain A, Topoisomerase Ii-Dna Cleavage Complex, Metal-Bound
          Length = 722

 Score = 25.4 bits (54), Expect = 8.7,   Method: Composition-based stats.
 Identities = 19/62 (30%), Positives = 34/62 (54%), Gaps = 4/62 (6%)

Query: 46  IRGLPASIELLSGSVLLNLKDCKNLKSLPSTINGLRSLRTLYLSGCSKLKNVPETLGKVE 105
           ++ +P S  +    +L +L D  N++S+P+ ++G +  +   L GC K KN+   L KV 
Sbjct: 247 LKEIPISDFINKELILFSLAD--NIRSIPNVLDGFKPGQRKVLYGCFK-KNLKSEL-KVA 302

Query: 106 SL 107
            L
Sbjct: 303 QL 304


  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
   0.315    0.133    0.370 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,777,092
Number of Sequences: 62578
Number of extensions: 90900
Number of successful extensions: 194
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 185
Number of HSP's gapped (non-prelim): 14
length of query: 108
length of database: 14,973,337
effective HSP length: 72
effective length of query: 36
effective length of database: 10,467,721
effective search space: 376837956
effective search space used: 376837956
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)
S2: 45 (21.9 bits)