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= 025425
         (253 letters)

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

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



>pdb|2YU4|A Chain A, Solution Structure Of The Sp-Ring Domain In Non-Smc
           Element 2 Homolog (Mms21, S. Cerevisiae)
          Length = 94

 Score = 34.7 bits (78), Expect = 0.046,   Method: Compositional matrix adjust.
 Identities = 18/53 (33%), Positives = 30/53 (56%), Gaps = 6/53 (11%)

Query: 157 NISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKS---KNANARCPVAGC 206
             +CP++ +   E+ +PV++  C H YE++AI   I+S   +   A CP  GC
Sbjct: 7   GFTCPITKE---EMKKPVKNKVCGHTYEEDAIVRMIESRQKRKKKAYCPQIGC 56


>pdb|3I2D|A Chain A, Crystal Structure Of S. Cerevisiae Sumo E3 Ligase Siz1
          Length = 371

 Score = 32.3 bits (72), Expect = 0.28,   Method: Compositional matrix adjust.
 Identities = 19/66 (28%), Positives = 36/66 (54%), Gaps = 8/66 (12%)

Query: 142 EQEDIVMTSTQSNILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQAYIKSKNANARC 201
           E E++ +T+T S I+++ CP+S    T +  P +S+ CKH+   +A+       ++  + 
Sbjct: 235 EDEEMGLTTT-STIMSLQCPIS---YTRMKYPSKSINCKHLQCFDALWFL----HSQLQI 286

Query: 202 PVAGCP 207
           P   CP
Sbjct: 287 PTWQCP 292


>pdb|2OVP|B Chain B, Structure Of The Skp1-Fbw7 Complex
 pdb|2OVQ|B Chain B, Structure Of The Skp1-Fbw7-Cyclinedegc Complex
 pdb|2OVR|B Chain B, Structure Of The Skp1-Fbw7-Cyclinedegn Complex
          Length = 445

 Score = 31.2 bits (69), Expect = 0.54,   Method: Compositional matrix adjust.
 Identities = 16/70 (22%), Positives = 34/70 (48%), Gaps = 3/70 (4%)

Query: 131 VHHAGELMPGEEQEDIVMTSTQSNILNISCPLSGKPITELAEPVRSVECKHIYEKNAIQA 190
           V H G +   + +++I+++ +    L +    +G+ I  L     +V C H++EK  +  
Sbjct: 156 VGHTGGVWSSQMRDNIIISGSTDRTLKVWNAETGECIHTLYGHTSTVRCMHLHEKRVVSG 215

Query: 191 YIKSKNANAR 200
              S++A  R
Sbjct: 216 ---SRDATLR 222


>pdb|3HBM|A Chain A, Crystal Structure Of Pseg From Campylobacter Jejuni
 pdb|3HBN|A Chain A, Crystal Structure Pseg-Udp Complex From Campylobacter
           Jejuni
          Length = 282

 Score = 28.5 bits (62), Expect = 4.0,   Method: Compositional matrix adjust.
 Identities = 14/45 (31%), Positives = 22/45 (48%)

Query: 140 GEEQEDIVMTSTQSNILNISCPLSGKPITELAEPVRSVECKHIYE 184
           G  + D+V+    S++     PL G  I E+  PV  +  + IYE
Sbjct: 16  GHIKRDLVLAKQYSDVSFACLPLEGSLIDEIPYPVYELSSESIYE 60


  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
   0.313    0.127    0.357 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,950,786
Number of Sequences: 62578
Number of extensions: 259858
Number of successful extensions: 524
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 521
Number of HSP's gapped (non-prelim): 5
length of query: 253
length of database: 14,973,337
effective HSP length: 97
effective length of query: 156
effective length of database: 8,903,271
effective search space: 1388910276
effective search space used: 1388910276
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: 50 (23.9 bits)