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= psy1724
         (473 letters)

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

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



>pdb|2YUJ|A Chain A, Solution Structure Of Human Ubiquitin Fusion Degradation
           Protein 1 Homolog Ufd1
          Length = 190

 Score =  274 bits (701), Expect = 7e-74,   Method: Compositional matrix adjust.
 Identities = 137/181 (75%), Positives = 155/181 (85%), Gaps = 5/181 (2%)

Query: 206 IPRPF-NR---SYKCFSVSMFPG-NEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLT 260
           IPR F NR    Y+CFSVSM  G N+R DVE+GGKIIMPPSAL+QL+RLNI YPMLFKLT
Sbjct: 8   IPRVFQNRFSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLT 67

Query: 261 NQKMGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTC 320
           N+   R+TH GVLEFVADEG  YLP+WMM+NLLL+EG LV +ESV+L VAT+SKFQPQ+ 
Sbjct: 68  NKNSDRMTHCGVLEFVADEGICYLPHWMMQNLLLEEGGLVQVESVNLQVATYSKFQPQSP 127

Query: 321 DFLDITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKPGNAVTIIECDMNVD 380
           DFLDITNPKAVLEN LRNFACLT+GD+IAINYN KIYEL V+ETKP  AV+IIECDMNVD
Sbjct: 128 DFLDITNPKAVLENALRNFACLTTGDVIAINYNEKIYELRVMETKPDKAVSIIECDMNVD 187

Query: 381 F 381
           F
Sbjct: 188 F 188



 Score =  124 bits (312), Expect = 9e-29,   Method: Compositional matrix adjust.
 Identities = 62/87 (71%), Positives = 70/87 (80%), Gaps = 5/87 (5%)

Query: 5  IPRPF-NR---SYKCFSVSMFPG-NEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLT 59
          IPR F NR    Y+CFSVSM  G N+R DVE+GGKIIMPPSAL+QL+RLNI YPMLFKLT
Sbjct: 8  IPRVFQNRFSTQYRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLT 67

Query: 60 NQKMGRITHSGVLEFVADEGKVYLPYW 86
          N+   R+TH GVLEFVADEG  YLP+W
Sbjct: 68 NKNSDRMTHCGVLEFVADEGICYLPHW 94



 Score = 96.7 bits (239), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 46/63 (73%), Positives = 52/63 (82%), Gaps = 1/63 (1%)

Query: 85  YWCFSVSMFPG-NEREDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGV 143
           Y CFSVSM  G N+R DVE+GGKIIMPPSAL+QL+RLNI YPMLFKLTN+   R+TH GV
Sbjct: 20  YRCFSVSMLAGPNDRSDVEKGGKIIMPPSALDQLSRLNITYPMLFKLTNKNSDRMTHCGV 79

Query: 144 LEL 146
           LE 
Sbjct: 80  LEF 82


>pdb|1ZC1|A Chain A, Ufd1 Exhibits The Aaa-Atpase Fold With Two Distinct
           Ubiquitin Interaction Sites
          Length = 208

 Score =  207 bits (527), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 97/191 (50%), Positives = 134/191 (70%), Gaps = 4/191 (2%)

Query: 205 DIPRPFNRSYKCFSVSMFPGNER-EDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQK 263
           ++P+ F   ++C+ ++M     R +D   GGKI +PPSAL +L+ LNI YPMLFKLT  +
Sbjct: 16  NMPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANE 75

Query: 264 MGRITHSGVLEFVADEGKVYLPYWMMRNLLLDEGELVNIESVSLPVATFSKFQPQTCDFL 323
            GR+TH GVLEF+A+EG+VYLP WMM  L +  G L+ I S  +P+  F K +PQ+ DFL
Sbjct: 76  TGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFL 135

Query: 324 DITNPKAVLENCLRNFACLTSGDMIAINYNSKIYELCVLETKP---GNAVTIIECDMNVD 380
           DI++PKAVLEN LRNF+ LT  D+I I+YN K +++ +LE KP     ++ +IE D+  D
Sbjct: 136 DISDPKAVLENVLRNFSTLTVDDVIEISYNGKTFKIKILEVKPESSSKSICVIETDLVTD 195

Query: 381 FAPPVGYTEPE 391
           FAPPVGY EP+
Sbjct: 196 FAPPVGYVEPD 206



 Score =  100 bits (248), Expect = 2e-21,   Method: Compositional matrix adjust.
 Identities = 51/120 (42%), Positives = 77/120 (64%), Gaps = 6/120 (5%)

Query: 4   DIPRPFNRSYKCFSVSMFPGNER-EDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQK 62
           ++P+ F   ++C+ ++M     R +D   GGKI +PPSAL +L+ LNI YPMLFKLT  +
Sbjct: 16  NMPQTFEEFFRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANE 75

Query: 63  MGRITHSGVLEFVADEGKVYLPYWCF-SVSMFPGN----EREDVERGGKIIMPPSALEQL 117
            GR+TH GVLEF+A+EG+VYLP W   ++ + PG+       DV  G  + + P +++ L
Sbjct: 76  TGRVTHGGVLEFIAEEGRVYLPQWMMETLGIQPGSLLQISSTDVPLGQFVKLEPQSVDFL 135



 Score = 68.9 bits (167), Expect = 5e-12,   Method: Compositional matrix adjust.
 Identities = 33/63 (52%), Positives = 43/63 (68%), Gaps = 1/63 (1%)

Query: 85  YWCFSVSMFPGNER-EDVERGGKIIMPPSALEQLTRLNICYPMLFKLTNQKMGRITHSGV 143
           + C+ ++M     R +D   GGKI +PPSAL +L+ LNI YPMLFKLT  + GR+TH GV
Sbjct: 25  FRCYPIAMMNDRIRKDDANFGGKIFLPPSALSKLSMLNIRYPMLFKLTANETGRVTHGGV 84

Query: 144 LEL 146
           LE 
Sbjct: 85  LEF 87


  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
   0.320    0.139    0.424 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 15,410,999
Number of Sequences: 62578
Number of extensions: 684843
Number of successful extensions: 1108
Number of sequences better than 100.0: 2
Number of HSP's better than 100.0 without gapping: 2
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 1096
Number of HSP's gapped (non-prelim): 6
length of query: 473
length of database: 14,973,337
effective HSP length: 102
effective length of query: 371
effective length of database: 8,590,381
effective search space: 3187031351
effective search space used: 3187031351
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: 53 (25.0 bits)