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= 018533
         (354 letters)

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

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



>pdb|4I1K|A Chain A, Crystal Structure Of Vrn1 (residues 208-341)
 pdb|4I1K|B Chain B, Crystal Structure Of Vrn1 (residues 208-341)
          Length = 146

 Score =  229 bits (583), Expect = 2e-60,   Method: Compositional matrix adjust.
 Identities = 108/131 (82%), Positives = 122/131 (93%), Gaps = 1/131 (0%)

Query: 216 RFYESASARKRTVTAEERERAINAAKAFEPSNPFCRVVLRPSYLYKGCIMYLPSCFAEKH 275
           +FYESASARKRTVTAEERERAINAAK FEP+NPF RVVLRPSYLY+GCIMYLPS FAEK+
Sbjct: 15  KFYESASARKRTVTAEERERAINAAKTFEPTNPFFRVVLRPSYLYRGCIMYLPSGFAEKY 74

Query: 276 LNGVCGFIKLQLSDGKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREF 335
           L+G+ GFIK+QL++ KQWPVRCLY+ GRAKFSQGWYEFT+EN LGEGDVCVFE+LR R+F
Sbjct: 75  LSGISGFIKVQLAE-KQWPVRCLYKAGRAKFSQGWYEFTLENNLGEGDVCVFELLRTRDF 133

Query: 336 VLKVTVFRVSE 346
           VLKVT FRV+E
Sbjct: 134 VLKVTAFRVNE 144


>pdb|1YEL|A Chain A, Structure Of The Hypothetical Arabidopsis Thaliana Protein
           At1g16640.1
          Length = 104

 Score = 32.7 bits (73), Expect = 0.34,   Method: Compositional matrix adjust.
 Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 2/59 (3%)

Query: 283 IKLQLSD--GKQWPVRCLYRGGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKV 339
           I + L D  G+ W VR   RG +   + GW  F  +N L +G    F   R R F + +
Sbjct: 40  ITVDLLDYSGRSWTVRMKKRGEKVFLTVGWENFVKDNNLEDGKYLQFIYDRDRTFYVII 98


>pdb|3LVT|A Chain A, The Crystal Structure Of A Protein In The Glycosyl
           Hydrolase Family 38 From Enterococcus Faecalis To 2.55a
          Length = 899

 Score = 29.6 bits (65), Expect = 2.5,   Method: Compositional matrix adjust.
 Identities = 24/116 (20%), Positives = 55/116 (47%), Gaps = 8/116 (6%)

Query: 17  DKRLRIPENFVRNFKDDLSAAATLIVPNGMVSRVGLRRLDNKVWFYDGWQEFMERYFIRI 76
           D+RL   +  VR F++ L+  +T + P  + + V   +  N+++F       ++ + +R+
Sbjct: 617 DERLEEEQKAVREFRERLAQRSTTLRPFEITTXVTXIKESNQLFFETTINNQIKDHRLRV 676

Query: 77  GYFLVFRYEGNSAFNVYIFNLPSSEINYQPNALSN-FEVPNHSKQYHIFAEMEDDD 131
            +      E + A ++Y       E+  +PN +S+ +E P + +    F  + D +
Sbjct: 677 LFPTGXVTETHEADSIY-------EVVTRPNQVSDTWENPTNPQHQQAFVNVHDQN 725


>pdb|1WID|A Chain A, Solution Structure Of The B3 Dna-Binding Domain Of Rav1
          Length = 130

 Score = 29.6 bits (65), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 25/85 (29%), Positives = 33/85 (38%), Gaps = 9/85 (10%)

Query: 253 VLRPSYLYKGCIMYLPSCFAEKHL-----NGVCGFIKLQLSD--GKQWPVRCLYRGGRAK 305
            + PS + K   + +P   AEKH      N     + L   D  GK W  R  Y      
Sbjct: 17  AVTPSDVGKLNRLVIPKHHAEKHFPLPSSNVSVKGVLLNFEDVNGKVWRFRYSYWNSSQS 76

Query: 306 F--SQGWYEFTVENRLGEGDVCVFE 328
           +  ++GW  F  E  L  GDV  F 
Sbjct: 77  YVLTKGWSRFVKEKNLRAGDVVSFS 101


>pdb|3SHF|A Chain A, Crystal Structure Of The R265s Mutant Of Full-Length
           Murine Apaf-1
          Length = 1256

 Score = 28.1 bits (61), Expect = 6.8,   Method: Compositional matrix adjust.
 Identities = 35/138 (25%), Positives = 63/138 (45%), Gaps = 11/138 (7%)

Query: 16  RDKRLRIPENFVRNFKDDLSAAATLIVPNG-----MVSRVG--LRRLDNKVWFYDGWQEF 68
           R+K L I   FV   K+DL A A  I+        +VS +G  LR   N+  +Y   ++ 
Sbjct: 295 REKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYY--LRQL 352

Query: 69  MERYFIRIGYFLVFRYEG-NSAFNVYIFNLPSSEINYQPN-ALSNFEVPNHSKQYHIFAE 126
             + F RI     + YE  + A ++ +  L     +Y  + ++   +V   +K   +  +
Sbjct: 353 QNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWD 412

Query: 127 MEDDDSEHVDQPTVNKTF 144
           +E ++ E + Q  VNK+ 
Sbjct: 413 LETEEVEDILQEFVNKSL 430


>pdb|3SFZ|A Chain A, Crystal Structure Of Full-Length Murine Apaf-1
          Length = 1249

 Score = 28.1 bits (61), Expect = 7.6,   Method: Compositional matrix adjust.
 Identities = 35/138 (25%), Positives = 63/138 (45%), Gaps = 11/138 (7%)

Query: 16  RDKRLRIPENFVRNFKDDLSAAATLIVPNG-----MVSRVG--LRRLDNKVWFYDGWQEF 68
           R+K L I   FV   K+DL A A  I+        +VS +G  LR   N+  +Y   ++ 
Sbjct: 288 REKGLEILSLFVNMKKEDLPAEAHSIIKECKGSPLVVSLIGALLRDFPNRWAYY--LRQL 345

Query: 69  MERYFIRIGYFLVFRYEG-NSAFNVYIFNLPSSEINYQPN-ALSNFEVPNHSKQYHIFAE 126
             + F RI     + YE  + A ++ +  L     +Y  + ++   +V   +K   +  +
Sbjct: 346 QNKQFKRIRKSSSYDYEALDEAMSISVEMLREDIKDYYTDLSILQKDVKVPTKVLCVLWD 405

Query: 127 MEDDDSEHVDQPTVNKTF 144
           +E ++ E + Q  VNK+ 
Sbjct: 406 LETEEVEDILQEFVNKSL 423


>pdb|3OG2|A Chain A, Native Crystal Structure Of Trichoderma Reesei
           Beta-Galactosidase
 pdb|3OGR|A Chain A, Complex Structure Of Beta-Galactosidase From Trichoderma
           Reesei With Galactose
 pdb|3OGS|A Chain A, Complex Structure Of Beta-Galactosidase From Trichoderma
           Reesei With Iptg
 pdb|3OGV|A Chain A, Complex Structure Of Beta-Galactosidase From Trichoderma
           Reesei With Petg
          Length = 1003

 Score = 28.1 bits (61), Expect = 7.9,   Method: Compositional matrix adjust.
 Identities = 10/36 (27%), Positives = 20/36 (55%)

Query: 65  WQEFMERYFIRIGYFLVFRYEGNSAFNVYIFNLPSS 100
           W     R  +++G  +++  + NSA+N ++  LP S
Sbjct: 531 WTASSARQVVQLGSLVIYMVDRNSAYNYWVPTLPGS 566


>pdb|2J3F|A Chain A, L-Ficolin Complexed To N-Acetyl-D-Galactosamine
 pdb|2J3F|B Chain B, L-Ficolin Complexed To N-Acetyl-D-Galactosamine
 pdb|2J3F|C Chain C, L-Ficolin Complexed To N-Acetyl-D-Galactosamine
 pdb|2J3F|E Chain E, L-Ficolin Complexed To N-Acetyl-D-Galactosamine
 pdb|2J3F|F Chain F, L-Ficolin Complexed To N-Acetyl-D-Galactosamine
 pdb|2J3O|A Chain A, L-Ficolin Complexed To N-Acetyl-D-Glucosamine
 pdb|2J3O|B Chain B, L-Ficolin Complexed To N-Acetyl-D-Glucosamine
 pdb|2J3O|C Chain C, L-Ficolin Complexed To N-Acetyl-D-Glucosamine
 pdb|2J3O|D Chain D, L-Ficolin Complexed To N-Acetyl-D-Glucosamine
 pdb|2J3O|E Chain E, L-Ficolin Complexed To N-Acetyl-D-Glucosamine
 pdb|2J3O|F Chain F, L-Ficolin Complexed To N-Acetyl-D-Glucosamine
          Length = 219

 Score = 28.1 bits (61), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 14/91 (15%)

Query: 53  RRLDNKVWFYDGWQEFMERYFIRIGYFLV-------FRYEGNSAFNVYIFNLPSSEINYQ 105
           RR+D  V FY  W  + + +  R+G F +          +G S       +L   E NYQ
Sbjct: 53  RRVDGSVDFYRDWATYKQGFGSRLGEFWLGNDNIHALTAQGTSELRT---DLVDFEDNYQ 109

Query: 106 PNALSNFEVPNHSKQYHI----FAEMEDDDS 132
                +F+V + +++Y++    F E    DS
Sbjct: 110 FAKYRSFKVADEAEKYNLVLGAFVEGSAGDS 140


>pdb|2J0G|A Chain A, L-Ficolin Complexed To N-Acetyl-Mannosamine
 pdb|2J0G|B Chain B, L-Ficolin Complexed To N-Acetyl-Mannosamine
 pdb|2J0G|C Chain C, L-Ficolin Complexed To N-Acetyl-Mannosamine
 pdb|2J0G|D Chain D, L-Ficolin Complexed To N-Acetyl-Mannosamine
 pdb|2J0G|E Chain E, L-Ficolin Complexed To N-Acetyl-Mannosamine
 pdb|2J0G|F Chain F, L-Ficolin Complexed To N-Acetyl-Mannosamine
 pdb|2J0H|A Chain A, L-Ficolin Complexed To Acetyl-Choline
 pdb|2J0H|B Chain B, L-Ficolin Complexed To Acetyl-Choline
 pdb|2J0H|C Chain C, L-Ficolin Complexed To Acetyl-Choline
 pdb|2J0H|D Chain D, L-Ficolin Complexed To Acetyl-Choline
 pdb|2J0H|E Chain E, L-Ficolin Complexed To Acetyl-Choline
 pdb|2J0H|F Chain F, L-Ficolin Complexed To Acetyl-Choline
 pdb|2J0Y|A Chain A, L-ficolin Complexed To B-1,3-d-glucan
 pdb|2J0Y|B Chain B, L-ficolin Complexed To B-1,3-d-glucan
 pdb|2J0Y|C Chain C, L-ficolin Complexed To B-1,3-d-glucan
 pdb|2J0Y|D Chain D, L-ficolin Complexed To B-1,3-d-glucan
 pdb|2J0Y|E Chain E, L-ficolin Complexed To B-1,3-d-glucan
 pdb|2J0Y|F Chain F, L-ficolin Complexed To B-1,3-d-glucan
 pdb|2J1G|A Chain A, L-Ficolin Complexed To N-Acetyl-Cystein
 pdb|2J1G|B Chain B, L-Ficolin Complexed To N-Acetyl-Cystein
 pdb|2J1G|C Chain C, L-Ficolin Complexed To N-Acetyl-Cystein
 pdb|2J1G|D Chain D, L-Ficolin Complexed To N-Acetyl-Cystein
 pdb|2J1G|E Chain E, L-Ficolin Complexed To N-Acetyl-Cystein
 pdb|2J1G|F Chain F, L-Ficolin Complexed To N-Acetyl-Cystein
 pdb|2J2P|A Chain A, L-Ficolin Complexed To N-Acetyl-Cystein (150mm)
 pdb|2J2P|B Chain B, L-Ficolin Complexed To N-Acetyl-Cystein (150mm)
 pdb|2J2P|C Chain C, L-Ficolin Complexed To N-Acetyl-Cystein (150mm)
 pdb|2J2P|D Chain D, L-Ficolin Complexed To N-Acetyl-Cystein (150mm)
 pdb|2J2P|E Chain E, L-Ficolin Complexed To N-Acetyl-Cystein (150mm)
 pdb|2J2P|F Chain F, L-Ficolin Complexed To N-Acetyl-Cystein (150mm)
 pdb|2J3G|A Chain A, L-ficolin
 pdb|2J3G|B Chain B, L-ficolin
 pdb|2J3G|C Chain C, L-ficolin
 pdb|2J3G|D Chain D, L-ficolin
 pdb|2J3G|E Chain E, L-ficolin
 pdb|2J3G|F Chain F, L-ficolin
 pdb|2J3U|A Chain A, L-Ficolin Complexed To Galactose
 pdb|2J3U|B Chain B, L-Ficolin Complexed To Galactose
 pdb|2J3U|C Chain C, L-Ficolin Complexed To Galactose
 pdb|2J3U|D Chain D, L-Ficolin Complexed To Galactose
 pdb|2J3U|E Chain E, L-Ficolin Complexed To Galactose
 pdb|2J3U|F Chain F, L-Ficolin Complexed To Galactose
 pdb|2J61|B Chain B, L-ficolin Complexed To N-acetylglucosamine (forme C)
          Length = 218

 Score = 27.7 bits (60), Expect = 9.3,   Method: Compositional matrix adjust.
 Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 14/91 (15%)

Query: 53  RRLDNKVWFYDGWQEFMERYFIRIGYFLV-------FRYEGNSAFNVYIFNLPSSEINYQ 105
           RR+D  V FY  W  + + +  R+G F +          +G S       +L   E NYQ
Sbjct: 52  RRVDGSVDFYRDWATYKQGFGSRLGEFWLGNDNIHALTAQGTSELRT---DLVDFEDNYQ 108

Query: 106 PNALSNFEVPNHSKQYHI----FAEMEDDDS 132
                +F+V + +++Y++    F E    DS
Sbjct: 109 FAKYRSFKVADEAEKYNLVLGAFVEGSAGDS 139


>pdb|2J3F|D Chain D, L-Ficolin Complexed To N-Acetyl-D-Galactosamine
          Length = 219

 Score = 27.7 bits (60), Expect = 9.8,   Method: Compositional matrix adjust.
 Identities = 24/91 (26%), Positives = 40/91 (43%), Gaps = 14/91 (15%)

Query: 53  RRLDNKVWFYDGWQEFMERYFIRIGYFLV-------FRYEGNSAFNVYIFNLPSSEINYQ 105
           RR+D  V FY  W  + + +  R+G F +          +G S       +L   E NYQ
Sbjct: 53  RRVDGSVDFYRDWATYKQGFGSRLGEFWLGNDNIHALTAQGTSELRT---DLVDFEDNYQ 109

Query: 106 PNALSNFEVPNHSKQYHI----FAEMEDDDS 132
                +F+V + +++Y++    F E    DS
Sbjct: 110 FAKYRSFKVADEAEKYNLVLGAFVEGSAGDS 140


  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
   0.322    0.138    0.421 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 10,136,668
Number of Sequences: 62578
Number of extensions: 406347
Number of successful extensions: 950
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 9
Number of HSP's that attempted gapping in prelim test: 946
Number of HSP's gapped (non-prelim): 12
length of query: 354
length of database: 14,973,337
effective HSP length: 100
effective length of query: 254
effective length of database: 8,715,537
effective search space: 2213746398
effective search space used: 2213746398
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 52 (24.6 bits)