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= 027464
         (223 letters)

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

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



>pdb|4GR6|A Chain A, Crystal Structure Of Atrbcx2 From Arabidopsis Thaliana
 pdb|4GR6|B Chain B, Crystal Structure Of Atrbcx2 From Arabidopsis Thaliana
          Length = 126

 Score =  108 bits (271), Expect = 2e-24,   Method: Compositional matrix adjust.
 Identities = 48/71 (67%), Positives = 56/71 (78%)

Query: 98  VNEVGGQYEDSFEDVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKH 157
           + +V G Y+D+F DV+KQI NYFTYKAVRTVLHQLYEMNP QY WFYN + TN+P DGK 
Sbjct: 1   MEDVAGNYDDTFGDVQKQIVNYFTYKAVRTVLHQLYEMNPPQYTWFYNHIITNRPTDGKR 60

Query: 158 FIRILGKVVSE 168
           F+R LGK   E
Sbjct: 61  FLRALGKESQE 71


>pdb|2PEO|A Chain A, Crystal Structure Of Rbcx From Anabaena Ca
 pdb|2PEO|B Chain B, Crystal Structure Of Rbcx From Anabaena Ca
 pdb|2WVW|I Chain I, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|J Chain J, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|K Chain K, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|L Chain L, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|M Chain M, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|N Chain N, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|O Chain O, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|P Chain P, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|Q Chain Q, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|R Chain R, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|S Chain S, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|T Chain T, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|U Chain U, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|V Chain V, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|W Chain W, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|2WVW|X Chain X, Cryo-Em Structure Of The Rbcl-Rbcx Complex
 pdb|3HYB|A Chain A, Crystal Structure Of Rbcx From Anabaena, Crystal Form Ii
 pdb|3HYB|B Chain B, Crystal Structure Of Rbcx From Anabaena, Crystal Form Ii
 pdb|3RG6|C Chain C, Crystal Structure Of A Chaperone-Bound Assembly
           Intermediate Of Form I Rubisco
 pdb|3RG6|D Chain D, Crystal Structure Of A Chaperone-Bound Assembly
           Intermediate Of Form I Rubisco
 pdb|3RG6|E Chain E, Crystal Structure Of A Chaperone-Bound Assembly
           Intermediate Of Form I Rubisco
 pdb|3RG6|F Chain F, Crystal Structure Of A Chaperone-Bound Assembly
           Intermediate Of Form I Rubisco
          Length = 155

 Score = 51.2 bits (121), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 25/53 (47%), Positives = 34/53 (64%), Gaps = 1/53 (1%)

Query: 110 EDVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRIL 162
           +D  K +Q+Y TY+A+RTVL QL E NP   +W +NF A  K  DG+ +I  L
Sbjct: 28  KDTAKTLQSYLTYQALRTVLAQLGETNPPLALWLHNFSA-GKVQDGEKYIEEL 79


>pdb|3Q20|A Chain A, Crystal Structure Of Rbcx C103a Mutant From
           Thermosynechococcus Elongatus
 pdb|3Q20|B Chain B, Crystal Structure Of Rbcx C103a Mutant From
           Thermosynechococcus Elongatus
          Length = 126

 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 17/45 (37%), Positives = 28/45 (62%)

Query: 118 NYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRIL 162
           +Y TY+AVRTV+ QL E +P + +W + F +     DG+ ++  L
Sbjct: 16  SYLTYQAVRTVIGQLAETDPPRSLWLHQFTSQESIQDGERYLEAL 60


>pdb|4GR2|A Chain A, Structure Of Atrbcx1 From Arabidopsis Thaliana.
 pdb|4GR2|B Chain B, Structure Of Atrbcx1 From Arabidopsis Thaliana
          Length = 128

 Score = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 24/61 (39%), Positives = 30/61 (49%)

Query: 114 KQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKVVSETFVLF 173
           K + ++FTY AVR V  QL   NP  YM    F+ TN   DG  F+  L +  S    L 
Sbjct: 17  KHLHDFFTYVAVRIVSAQLESYNPEAYMELREFLDTNSVSDGDKFLATLMRRSSRHMNLA 76

Query: 174 L 174
           L
Sbjct: 77  L 77


>pdb|2PY8|A Chain A, Rbcx
 pdb|2PY8|B Chain B, Rbcx
 pdb|2PY8|C Chain C, Rbcx
 pdb|2PY8|D Chain D, Rbcx
          Length = 147

 Score = 41.2 bits (95), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 24/79 (30%), Positives = 41/79 (51%), Gaps = 3/79 (3%)

Query: 114 KQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKVVSETFVLF 173
           K +Q+Y TY+AV  +  +L E NP Q +W   ++A++   +G+ F   L +++ E   L 
Sbjct: 12  KVLQSYLTYQAVLRIQSELGETNPPQAIWLNQYLASHSIQNGETF---LTELLDENKELV 68

Query: 174 LFLNIKRNASTEDVVCVFP 192
           L +   R    E V+   P
Sbjct: 69  LRILAVREDIAESVLDFLP 87


>pdb|2Z44|A Chain A, Crystal Structure Of Selenomethionine-Labeled Orf134
          Length = 134

 Score = 39.3 bits (90), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 4/42 (9%)

Query: 109 FEDVKKQ----IQNYFTYKAVRTVLHQLYEMNPTQYMWFYNF 146
           F+ V K+    +Q+Y TY+AVR +  QL E NP Q +W   F
Sbjct: 3   FKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEF 44


>pdb|2PEM|A Chain A, Crystal Structure Of Rbcx In Complex With Substrate
 pdb|2PEM|B Chain B, Crystal Structure Of Rbcx In Complex With Substrate
 pdb|2PEM|C Chain C, Crystal Structure Of Rbcx In Complex With Substrate
 pdb|2PEM|D Chain D, Crystal Structure Of Rbcx In Complex With Substrate
 pdb|2PEM|E Chain E, Crystal Structure Of Rbcx In Complex With Substrate
 pdb|2PEM|F Chain F, Crystal Structure Of Rbcx In Complex With Substrate
 pdb|2PEN|A Chain A, Crystal Structure Of Rbcx, Crystal Form I
 pdb|2PEN|B Chain B, Crystal Structure Of Rbcx, Crystal Form I
 pdb|2PEN|C Chain C, Crystal Structure Of Rbcx, Crystal Form I
 pdb|2PEN|D Chain D, Crystal Structure Of Rbcx, Crystal Form I
 pdb|2PEN|E Chain E, Crystal Structure Of Rbcx, Crystal Form I
 pdb|2PEN|F Chain F, Crystal Structure Of Rbcx, Crystal Form I
 pdb|2PEQ|A Chain A, Crystal Structure Of Rbcx, Crystal Form Ii
 pdb|2PEQ|B Chain B, Crystal Structure Of Rbcx, Crystal Form Ii
 pdb|2Z45|A Chain A, Crystal Structure Of Zn-bound Orf134
 pdb|2Z45|B Chain B, Crystal Structure Of Zn-bound Orf134
 pdb|2Z46|A Chain A, Crystal Structure Of Native-Orf134
 pdb|2Z46|B Chain B, Crystal Structure Of Native-Orf134
 pdb|2Z46|C Chain C, Crystal Structure Of Native-Orf134
 pdb|2Z46|D Chain D, Crystal Structure Of Native-Orf134
 pdb|2Z46|E Chain E, Crystal Structure Of Native-Orf134
 pdb|2Z46|F Chain F, Crystal Structure Of Native-Orf134
          Length = 134

 Score = 38.9 bits (89), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 18/42 (42%), Positives = 25/42 (59%), Gaps = 4/42 (9%)

Query: 109 FEDVKKQ----IQNYFTYKAVRTVLHQLYEMNPTQYMWFYNF 146
           F+ V K+    +Q+Y TY+AVR +  QL E NP Q +W   F
Sbjct: 3   FKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEF 44


>pdb|2PEI|A Chain A, Crystal Structure Of Selenomethionine-Labeled Rbcx
 pdb|2PEI|B Chain B, Crystal Structure Of Selenomethionine-Labeled Rbcx
 pdb|2PEI|C Chain C, Crystal Structure Of Selenomethionine-Labeled Rbcx
 pdb|2PEI|D Chain D, Crystal Structure Of Selenomethionine-Labeled Rbcx
 pdb|2PEI|E Chain E, Crystal Structure Of Selenomethionine-Labeled Rbcx
 pdb|2PEI|F Chain F, Crystal Structure Of Selenomethionine-Labeled Rbcx
 pdb|2PEI|G Chain G, Crystal Structure Of Selenomethionine-Labeled Rbcx
 pdb|2PEI|H Chain H, Crystal Structure Of Selenomethionine-Labeled Rbcx
 pdb|2PEI|I Chain I, Crystal Structure Of Selenomethionine-Labeled Rbcx
 pdb|2PEI|J Chain J, Crystal Structure Of Selenomethionine-Labeled Rbcx
 pdb|2PEI|K Chain K, Crystal Structure Of Selenomethionine-Labeled Rbcx
 pdb|2PEI|L Chain L, Crystal Structure Of Selenomethionine-Labeled Rbcx
          Length = 109

 Score = 38.5 bits (88), Expect = 0.003,   Method: Compositional matrix adjust.
 Identities = 18/43 (41%), Positives = 25/43 (58%), Gaps = 4/43 (9%)

Query: 108 SFEDVKKQ----IQNYFTYKAVRTVLHQLYEMNPTQYMWFYNF 146
            F+ V K+    +Q+Y TY+AVR +  QL E NP Q +W   F
Sbjct: 2   EFKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEF 44


>pdb|2PEK|A Chain A, Crystal Structure Of Rbcx Point Mutant Q29a
 pdb|2PEK|B Chain B, Crystal Structure Of Rbcx Point Mutant Q29a
 pdb|2PEK|C Chain C, Crystal Structure Of Rbcx Point Mutant Q29a
 pdb|2PEK|D Chain D, Crystal Structure Of Rbcx Point Mutant Q29a
 pdb|2PEK|E Chain E, Crystal Structure Of Rbcx Point Mutant Q29a
 pdb|2PEK|F Chain F, Crystal Structure Of Rbcx Point Mutant Q29a
          Length = 134

 Score = 36.6 bits (83), Expect = 0.012,   Method: Compositional matrix adjust.
 Identities = 17/42 (40%), Positives = 24/42 (57%), Gaps = 4/42 (9%)

Query: 109 FEDVKKQ----IQNYFTYKAVRTVLHQLYEMNPTQYMWFYNF 146
           F+ V K+    +Q+Y TY+AVR +   L E NP Q +W   F
Sbjct: 3   FKKVAKETAITLQSYLTYQAVRLISQALSETNPGQAIWLGEF 44


>pdb|2PEJ|A Chain A, Crystal Structure Of Rbcx Point Mutant Y17aY20L
 pdb|2PEJ|B Chain B, Crystal Structure Of Rbcx Point Mutant Y17aY20L
 pdb|2PEJ|C Chain C, Crystal Structure Of Rbcx Point Mutant Y17aY20L
 pdb|2PEJ|D Chain D, Crystal Structure Of Rbcx Point Mutant Y17aY20L
 pdb|2PEJ|E Chain E, Crystal Structure Of Rbcx Point Mutant Y17aY20L
 pdb|2PEJ|F Chain F, Crystal Structure Of Rbcx Point Mutant Y17aY20L
          Length = 134

 Score = 33.9 bits (76), Expect = 0.083,   Method: Compositional matrix adjust.
 Identities = 16/42 (38%), Positives = 23/42 (54%), Gaps = 4/42 (9%)

Query: 109 FEDVKKQ----IQNYFTYKAVRTVLHQLYEMNPTQYMWFYNF 146
           F+ V K+    +Q+  T +AVR +  QL E NP Q +W   F
Sbjct: 3   FKKVAKETAITLQSALTLQAVRLISQQLSETNPGQAIWLGEF 44


>pdb|3CV0|A Chain A, Structure Of Peroxisomal Targeting Signal 1 (Pts1) Binding
           Domain Of Trypanosoma Brucei Peroxin 5 (Tbpex5)complexed
           To T. Brucei Phosphoglucoisomerase (Pgi) Pts1 Peptide
 pdb|3CVL|A Chain A, Structure Of Peroxisomal Targeting Signal 1 (Pts1) Binding
           Domain Of Trypanosoma Brucei Peroxin 5 (Tbpex5)complexed
           To T. Brucei Phosphofructokinase (Pfk) Pts1 Peptide
 pdb|3CVN|A Chain A, Structure Of Peroxisomal Targeting Signal 1 (Pts1) Binding
           Domain Of Trypanosoma Brucei Peroxin 5 (Tbpex5)complexed
           To T. Brucei Glyceraldehyde-3-Phosphate Dehydrogenase
           (Gapdh) Pts1 Peptide
 pdb|3CVP|A Chain A, Structure Of Peroxisomal Targeting Signal 1 (Pts1) Binding
           Domain Of Trypanosoma Brucei Peroxin 5 (Tbpex5)complexed
           To Pts1 Peptide (10-Skl)
          Length = 327

 Score = 27.3 bits (59), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 5/43 (11%)

Query: 101 VGGQYEDSFEDVKKQIQNYF-----TYKAVRTVLHQLYEMNPT 138
           V  Q +   +D+  Q +++F      Y+  RT+LH   EMNP 
Sbjct: 128 VNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPN 170


>pdb|3CVQ|A Chain A, Structure Of Peroxisomal Targeting Signal 1 (pts1) Binding
           Domain Of Trypanosoma Brucei Peroxin 5 (tbpex5)complexed
           To Pts1 Peptide (7- Skl)
          Length = 327

 Score = 27.3 bits (59), Expect = 7.5,   Method: Compositional matrix adjust.
 Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 5/43 (11%)

Query: 101 VGGQYEDSFEDVKKQIQNYF-----TYKAVRTVLHQLYEMNPT 138
           V  Q +   +D+  Q +++F      Y+  RT+LH   EMNP 
Sbjct: 128 VNLQADVDIDDLNVQSEDFFFAAPNEYRECRTLLHAALEMNPN 170


>pdb|3F7F|A Chain A, Structure Of Nup120
 pdb|3F7F|B Chain B, Structure Of Nup120
 pdb|3F7F|C Chain C, Structure Of Nup120
 pdb|3F7F|D Chain D, Structure Of Nup120
          Length = 729

 Score = 26.9 bits (58), Expect = 8.6,   Method: Compositional matrix adjust.
 Identities = 12/38 (31%), Positives = 18/38 (47%)

Query: 130 HQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKVVS 167
           H LY++N T   WFYN  +     +   ++R L    S
Sbjct: 481 HSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFAS 518


>pdb|3H7N|A Chain A, Structure Of Nup120
 pdb|3H7N|B Chain B, Structure Of Nup120
 pdb|3H7N|C Chain C, Structure Of Nup120
 pdb|3H7N|D Chain D, Structure Of Nup120
          Length = 729

 Score = 26.9 bits (58), Expect = 8.8,   Method: Compositional matrix adjust.
 Identities = 12/38 (31%), Positives = 18/38 (47%)

Query: 130 HQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKVVS 167
           H LY++N T   WFYN  +     +   ++R L    S
Sbjct: 481 HSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFAS 518


  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    0.139    0.418 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,438,242
Number of Sequences: 62578
Number of extensions: 180761
Number of successful extensions: 363
Number of sequences better than 100.0: 14
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 351
Number of HSP's gapped (non-prelim): 14
length of query: 223
length of database: 14,973,337
effective HSP length: 95
effective length of query: 128
effective length of database: 9,028,427
effective search space: 1155638656
effective search space used: 1155638656
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: 49 (23.5 bits)