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= psy200
         (490 letters)

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

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



>pdb|2QBY|A Chain A, Crystal Structure Of A Heterodimer Of Cdc6ORC1 INITIATORS
           Bound To Origin Dna (From S. Solfataricus)
          Length = 386

 Score = 60.8 bits (146), Expect = 2e-09,   Method: Compositional matrix adjust.
 Identities = 55/226 (24%), Positives = 103/226 (45%), Gaps = 8/226 (3%)

Query: 195 ELPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIK--DAFKTI 252
           ELP RE Q+  I   L      E   +++I G  GTGK+A +  ++S+   K    FK +
Sbjct: 21  ELPHREDQIRKIASILAPLYREEKPNNIFIYGLTGTGKTAVVKFVLSKLHKKFLGKFKHV 80

Query: 253 YINCNSVRNAASVYETIVNELKLKP--GGKSERHQLGAILKYF-DTKHKSXXXXXXXXXX 309
           YIN   +     V   ++  L +K    G S       ++K   D   +           
Sbjct: 81  YINTRQIDTPYRVLADLLESLDVKVPFTGLSIAELYRRLVKAVRDYGSQVVIVLDEIDAF 140

Query: 310 XXSRKQTILYTIFEWPS-IPGSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYS 368
                  ILY +    S +  SK+  +G+ N +   D + PR++++++ +  +  F PY+
Sbjct: 141 VKKYNDDILYKLSRINSEVNKSKISFIGITNDVKFVDLLDPRVKSSLSEEEII--FPPYN 198

Query: 369 REQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI 414
            E++ +I++++ +   K  +   + ++L A   A   GD R+A+D+
Sbjct: 199 AEELEDILTKRAQMAFKPGVLPDNVIKLCAALAAREHGDARRALDL 244


>pdb|2V1U|A Chain A, Structure Of The Aeropyrum Pernix Orc1 Protein In Complex
           With Dna
          Length = 387

 Score = 47.0 bits (110), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 56/235 (23%), Positives = 99/235 (42%), Gaps = 23/235 (9%)

Query: 196 LPGREVQLEGIRQFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDA-----FK 250
           LP RE +L  + + L   +  E   +  + G  GTGK+A   L++ R E + +      K
Sbjct: 21  LPHREAELRRLAEVLAPALRGEKPSNALLYGLTGTGKTAVARLVLRRLEARASSLGVLVK 80

Query: 251 TIYINCNS----VRNAASVYETI---VNELKLKPGGKSERHQLGAILKYFDTKHKSXXXX 303
            IY+N        R A+++ E +   V    L  G   ER     ++K            
Sbjct: 81  PIYVNARHRETPYRVASAIAEAVGVRVPFTGLSVGEVYER-----LVKRLSRLRGIYIIV 135

Query: 304 XXXXXXXXSR--KQTILYTIFEWPSIPGSKLV--LVGVANALDLTDRMLPRLQANVTLQP 359
                    R   Q +LY I       G ++   LVG+ N+L   + + PR+++  +L  
Sbjct: 136 LDEIDFLPKRPGGQDLLYRITRINQELGDRVWVSLVGITNSLGFVENLEPRVKS--SLGE 193

Query: 360 TLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGKVAAVSGDIRKAIDI 414
             + F PY+  Q+ +I+  + ++     + +   + L A   A   GD R+A+D+
Sbjct: 194 VELVFPPYTAPQLRDILETRAEEAFNPGVLDPDVVPLCAALAAREHGDARRALDL 248


>pdb|1FNN|A Chain A, Crystal Structure Of Cdc6p From Pyrobaculum Aerophilum
 pdb|1FNN|B Chain B, Crystal Structure Of Cdc6p From Pyrobaculum Aerophilum
          Length = 389

 Score = 38.5 bits (88), Expect = 0.010,   Method: Compositional matrix adjust.
 Identities = 46/200 (23%), Positives = 82/200 (41%), Gaps = 15/200 (7%)

Query: 226 GPPGTGKSASLNLLVSRAEIKDAFKTIYINCNSVRNAASVYETIVNELKLK-PGGKSERH 284
           G PGTGK+ +L  L    + K   + +YIN    RN  ++   I   L +  P     R 
Sbjct: 51  GRPGTGKTVTLRKLWELYKDKTTARFVYINGFIYRNFTAIIGEIARSLNIPFPRRGLSRD 110

Query: 285 QLGAILKYFDTKHKSXXXXXXXXXXXXSRKQTILYTIF----EWPSIPGSKLVLVGVANA 340
           +  A+L   +   +             +    IL T      E   +   ++ LV V + 
Sbjct: 111 EFLALL--VEHLRERDLYMFLVLDDAFNLAPDILSTFIRLGQEADKLGAFRIALVIVGHN 168

Query: 341 LDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTDKFNMFNASALQLLAGK 400
             + + + P  +    +   ++ F+PY+++QI +I+  + K       ++   LQ++A  
Sbjct: 169 DAVLNNLDPSTRG--IMGKYVIRFSPYTKDQIFDILLDRAKAGLAEGSYSEDILQMIADI 226

Query: 401 VAAVS------GDIRKAIDI 414
             A +      GD R AIDI
Sbjct: 227 TGAQTPLDTNRGDARLAIDI 246


>pdb|1UQW|A Chain A, Crystal Structure Of Ylib Protein From Escherichia Coi
 pdb|1UQW|B Chain B, Crystal Structure Of Ylib Protein From Escherichia Coi
          Length = 509

 Score = 32.7 bits (73), Expect = 0.46,   Method: Compositional matrix adjust.
 Identities = 18/56 (32%), Positives = 27/56 (48%)

Query: 329 GSKLVLVGVANALDLTDRMLPRLQANVTLQPTLMNFAPYSREQILEIISQKLKQTD 384
           G +    G + +    D  L  L A+    PTL N A YS +Q+ + ++Q LK  D
Sbjct: 398 GVRXFYTGWSASTGEADWALSPLFASQNWPPTLFNTAFYSNKQVDDFLAQALKTND 453


>pdb|2CHQ|A Chain A, Replication Factor C Adpnp Complex
 pdb|2CHQ|B Chain B, Replication Factor C Adpnp Complex
 pdb|2CHQ|C Chain C, Replication Factor C Adpnp Complex
 pdb|2CHV|A Chain A, Replication Factor C Adpnp Complex
 pdb|2CHV|B Chain B, Replication Factor C Adpnp Complex
 pdb|2CHV|C Chain C, Replication Factor C Adpnp Complex
 pdb|2CHV|D Chain D, Replication Factor C Adpnp Complex
 pdb|2CHV|E Chain E, Replication Factor C Adpnp Complex
 pdb|2CHV|F Chain F, Replication Factor C Adpnp Complex
          Length = 319

 Score = 30.8 bits (68), Expect = 1.7,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 208 QFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS 258
           Q L G+V  +    +  SGPPGTGK+A+  + ++R    + ++  +I  N+
Sbjct: 27  QRLKGYVERKNIPHLLFSGPPGTGKTAT-AIALARDLFGENWRDNFIEMNA 76


>pdb|2CHG|A Chain A, Replication Factor C Domains 1 And 2
 pdb|2CHG|B Chain B, Replication Factor C Domains 1 And 2
 pdb|2CHG|C Chain C, Replication Factor C Domains 1 And 2
 pdb|2CHG|D Chain D, Replication Factor C Domains 1 And 2
          Length = 226

 Score = 30.4 bits (67), Expect = 2.1,   Method: Compositional matrix adjust.
 Identities = 16/51 (31%), Positives = 29/51 (56%), Gaps = 1/51 (1%)

Query: 208 QFLLGHVNNETSGSMYISGPPGTGKSASLNLLVSRAEIKDAFKTIYINCNS 258
           Q L G+V  +    +  SGPPGTGK+A+  + ++R    + ++  +I  N+
Sbjct: 27  QRLKGYVERKNIPHLLFSGPPGTGKTAT-AIALARDLFGENWRDNFIEMNA 76


  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    0.379 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 12,029,750
Number of Sequences: 62578
Number of extensions: 434226
Number of successful extensions: 1076
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 1066
Number of HSP's gapped (non-prelim): 11
length of query: 490
length of database: 14,973,337
effective HSP length: 103
effective length of query: 387
effective length of database: 8,527,803
effective search space: 3300259761
effective search space used: 3300259761
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)