RPS-BLAST 2.2.26 [Sep-21-2011]

Database: pdb70 
           27,921 sequences; 6,701,793 total letters

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

Query= psy6209
         (115 letters)



>3qwz_A Transitional endoplasmic reticulum ATPase; UBX, P97 binding,
           transport protein; HET: MLY; 2.00A {Homo sapiens} PDB:
           2pjh_B
          Length = 211

 Score =  107 bits (269), Expect = 9e-31
 Identities = 73/95 (76%), Positives = 84/95 (88%)

Query: 20  QIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIV 79
            + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEF +V
Sbjct: 110 DVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFXVV 169

Query: 80  DTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           +TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 170 ETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 204


>3hu3_A Transitional endoplasmic reticulum ATPase; VCP, transport protein;
           HET: AGS; 2.20A {Homo sapiens} PDB: 3hu2_A* 3hu1_A*
           1e32_A* 1s3s_A* 2pjh_B
          Length = 489

 Score =  111 bits (278), Expect = 4e-30
 Identities = 73/96 (76%), Positives = 84/96 (87%)

Query: 20  QIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIV 79
            + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+V GGMRAVEFK+V
Sbjct: 107 DVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVHGGMRAVEFKVV 166

Query: 80  DTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGVR 115
           +TDP+PYCIVA DTVIHCEG+PIKRE EE   N V 
Sbjct: 167 ETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEVG 202


>3tiw_A Transitional endoplasmic reticulum ATPase; beta-barrel alpha-helix,
           transport protein ATPase ubiquitin ubiquitin,
           phosphorylation; 1.80A {Homo sapiens} PDB: 3qq8_A 3qq7_A
           3qc8_A
          Length = 187

 Score =  102 bits (254), Expect = 8e-29
 Identities = 65/78 (83%), Positives = 75/78 (96%)

Query: 23  YGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIVDTD 82
           YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V+TD
Sbjct: 110 YGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVVETD 169

Query: 83  PAPYCIVAADTVIHCEGD 100
           P+PYCIVA DTVIHCEG+
Sbjct: 170 PSPYCIVAPDTVIHCEGE 187


>1ypw_A Transitional endoplasmic reticulum ATPase; AAA, P97/VCP, ERAD,
           CDC48; HET: ADP ANP; 3.50A {Mus musculus} PDB: 1oz4_A*
           1yq0_A* 1yqi_A* 1r7r_A* 3cf2_A* 3cf1_A* 3cf3_A*
          Length = 806

 Score =  101 bits (254), Expect = 1e-26
 Identities = 74/95 (77%), Positives = 85/95 (89%)

Query: 20  QIVYGKRIHVLPIDDSVQGLTGNLFEVYLKPYFLEAYRPVHKDDLFIVRGGMRAVEFKIV 79
            + YGKRIHVLPIDD+V+G+TGNLFEVYLKPYFLEAYRP+ K D+F+VRGGMRAVEFK+V
Sbjct: 107 DVKYGKRIHVLPIDDTVEGITGNLFEVYLKPYFLEAYRPIRKGDIFLVRGGMRAVEFKVV 166

Query: 80  DTDPAPYCIVAADTVIHCEGDPIKREGEENKPNGV 114
           +TDP+PYCIVA DTVIHCEG+PIKRE EE   N V
Sbjct: 167 ETDPSPYCIVAPDTVIHCEGEPIKREDEEESLNEV 201


>1cz4_A VCP-like ATPase; double-PSI beta-barrel, beta-CLAM, substrate
           recognition DOM hydrolase; NMR {Thermoplasma
           acidophilum} SCOP: b.52.2.3 d.31.1.1 PDB: 1cz5_A
          Length = 185

 Score = 81.5 bits (201), Expect = 8e-21
 Identities = 25/98 (25%), Positives = 41/98 (41%), Gaps = 8/98 (8%)

Query: 17  RDIQIVYGKRIHVLPIDDSVQGLT-GNLFEVYLKPYFLEAYRPVHKDDLFIVRG----GM 71
           R ++    K++ + PI    Q L  G   E Y++   +   RP+ + D   V G    G 
Sbjct: 88  RKVRTEIAKKVTLAPIIRKDQRLKFGEGIEEYVQRALI--RRPMLEQDNISVPGLTLAGQ 145

Query: 72  RAVEFKIVDTDPAPYC-IVAADTVIHCEGDPIKREGEE 108
             + FK+V T P+     +  +T I    +P     EE
Sbjct: 146 TGLLFKVVKTLPSKVPVEIGEETKIEIREEPASEVLEE 183


>2yuj_A Ubiquitin fusion degradation 1-like; ubiquitin-dependent
           proteolytic, structural genomics, NPPSFA; NMR {Homo
           sapiens}
          Length = 190

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 13/102 (12%), Positives = 32/102 (31%), Gaps = 9/102 (8%)

Query: 1   MSFRLTTPCRDLLDRQRDIQIVYGKRIHVLPIDDSVQGLTG--NLFEVYLKPYFLEAYRP 58
           M   L      L+ +   + +         P       +T    + E  L+ +       
Sbjct: 95  MMQNLLLEEGGLV-QVESVNLQVATYSKFQPQSPDFLDITNPKAVLENALRNFAC----- 148

Query: 59  VHKDDLFIVRGGMRAVEFKIVDTDPAPY-CIVAADTVIHCEG 99
           +   D+  +    +  E ++++T P     I+  D  +  + 
Sbjct: 149 LTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVDFDA 190


  Database: pdb70
    Posted date:  Sep 4, 2012  3:40 AM
  Number of letters in database: 6,701,793
  Number of sequences in database:  27,921
  
Lambda     K      H
   0.324    0.145    0.447 

Gapped
Lambda     K      H
   0.267   0.0515    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 1,871,830
Number of extensions: 108664
Number of successful extensions: 204
Number of sequences better than 10.0: 1
Number of HSP's gapped: 201
Number of HSP's successfully gapped: 20
Length of query: 115
Length of database: 6,701,793
Length adjustment: 78
Effective length of query: 37
Effective length of database: 4,523,955
Effective search space: 167386335
Effective search space used: 167386335
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: 41 (22.0 bits)
S2: 51 (23.9 bits)