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= 027229
         (226 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 =  206 bits (524), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 92/125 (73%), Positives = 108/125 (86%)

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

Query: 158 FIRILGKEKQDLAERVMITRLHLYGKWVKKCDHAQMYKAISDENLELMRERLIETVIWPS 217
           F+R LGKE Q+LAERVMITRLHLYGKW+KK DH ++Y+ ISDENL LMRERL+ETVIWPS
Sbjct: 61  FLRALGKESQELAERVMITRLHLYGKWIKKADHGKIYQEISDENLALMRERLMETVIWPS 120

Query: 218 DDSNT 222
           DD+N+
Sbjct: 121 DDTNS 125


>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 = 67.0 bits (162), Expect = 8e-12,   Method: Compositional matrix adjust.
 Identities = 39/100 (39%), Positives = 56/100 (56%), Gaps = 2/100 (2%)

Query: 110 EDVKKQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKEKQDL 169
           +D  K +Q+Y TY+A+RTVL QL E NP   +W +NF A  K  DG+ +I  L  EK DL
Sbjct: 28  KDTAKTLQSYLTYQALRTVLAQLGETNPPLALWLHNFSA-GKVQDGEKYIEELFLEKPDL 86

Query: 170 AERVMITRLHLYGKWVKKCDHAQMYKAISDENLELMRERL 209
           A R+M  R H+  + + +     +   I   N+E  R+ L
Sbjct: 87  ALRIMTVREHI-AEEIAEFLPEMVVTGIQQANMEKRRQHL 125


>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 = 57.8 bits (138), Expect = 4e-09,   Method: Compositional matrix adjust.
 Identities = 25/67 (37%), Positives = 41/67 (61%)

Query: 114 KQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKEKQDLAERV 173
           K + +Y TY+AVRTV+ QL E +P + +W + F +     DG+ ++  L +E+ DL  R+
Sbjct: 12  KTLISYLTYQAVRTVIGQLAETDPPRSLWLHQFTSQESIQDGERYLEALFREQPDLGFRI 71

Query: 174 MITRLHL 180
           +  R HL
Sbjct: 72  LTVREHL 78


>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 = 56.6 bits (135), Expect = 1e-08,   Method: Compositional matrix adjust.
 Identities = 37/104 (35%), Positives = 53/104 (50%), Gaps = 6/104 (5%)

Query: 114 KQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKEKQ---DLA 170
           K + ++FTY AVR V  QL   NP  YM    F+ TN   DG  F+  L +      +LA
Sbjct: 17  KHLHDFFTYVAVRIVSAQLESYNPEAYMELREFLDTNSVSDGDKFLATLMRRSSRHMNLA 76

Query: 171 ERVMITRLHLYGKWVKKCDHAQ--MYKAISDENLELMRERLIET 212
            R++  R   Y K   + D+ +   +K + D N  LMRE ++ET
Sbjct: 77  LRILEVR-SAYAKNDFEWDNMKRLAFKNVDDSNTRLMREYVLET 119


>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 = 49.7 bits (117), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 34/117 (29%), Positives = 60/117 (51%), Gaps = 8/117 (6%)

Query: 114 KQIQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKEKQDLAERV 173
           K +Q+Y TY+AV  +  +L E NP Q +W   ++A++   +G+ F+  L  E ++L  R+
Sbjct: 12  KVLQSYLTYQAVLRIQSELGETNPPQAIWLNQYLASHSIQNGETFLTELLDENKELVLRI 71

Query: 174 MITRLHLYGKWVKKCDHAQMYKAISDENLELMR---ERLIETVI----WPSDDSNTE 223
           +  R  +  + V          ++++ N+   R   ERL  TV     +PS+ SN E
Sbjct: 72  LAVREDI-AESVLDFLPGMTRNSLAESNIAHRRHLLERLTRTVAEVDNFPSETSNGE 127


>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 = 44.7 bits (104), Expect = 4e-05,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 40/76 (52%), Gaps = 4/76 (5%)

Query: 109 FEDVKKQ----IQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGK 164
           F+ V K+    +Q+Y TY+AVR +  QL E NP Q +W   F   +   +   ++  +  
Sbjct: 3   FKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMML 62

Query: 165 EKQDLAERVMITRLHL 180
           E ++L  R++  R +L
Sbjct: 63  ENKELVLRILTVRENL 78


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

 Score = 43.9 bits (102), Expect = 7e-05,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 109 FEDVKKQ----IQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGK 164
           F+ V K+    +Q+Y TY+AVR +  QL E NP Q +W   F   +   +   ++     
Sbjct: 3   FKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAXXL 62

Query: 165 EKQDLAERVMITRLHL 180
           E ++L  R++  R +L
Sbjct: 63  ENKELVLRILTVRENL 78


>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 = 42.7 bits (99), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 109 FEDVKKQ----IQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGK 164
           F+ V K+    +Q+Y TY+AVR +  QL E NP Q +W   F   +   +   ++     
Sbjct: 3   FKKVAKETAITLQSYLTYQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAXXL 62

Query: 165 EKQDLAERVMITRLHL 180
           E ++L  R++  R +L
Sbjct: 63  ENKELVLRILTVRENL 78


>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 = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 4/76 (5%)

Query: 109 FEDVKKQ----IQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGK 164
           F+ V K+    +Q+Y TY+AVR +   L E NP Q +W   F   +   +   ++  +  
Sbjct: 3   FKKVAKETAITLQSYLTYQAVRLISQALSETNPGQAIWLGEFSKRHPIQESDLYLEAMML 62

Query: 165 EKQDLAERVMITRLHL 180
           E ++L  R++  R +L
Sbjct: 63  ENKELVLRILTVRENL 78


>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 = 38.9 bits (89), Expect = 0.002,   Method: Compositional matrix adjust.
 Identities = 21/76 (27%), Positives = 38/76 (50%), Gaps = 4/76 (5%)

Query: 109 FEDVKKQ----IQNYFTYKAVRTVLHQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGK 164
           F+ V K+    +Q+  T +AVR +  QL E NP Q +W   F   +   +   ++  +  
Sbjct: 3   FKKVAKETAITLQSALTLQAVRLISQQLSETNPGQAIWLGEFSKRHPIQESDLYLEAMML 62

Query: 165 EKQDLAERVMITRLHL 180
           E ++L  R++  R +L
Sbjct: 63  ENKELVLRILTVRENL 78


>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 = 27.3 bits (59), Expect = 6.6,   Method: Composition-based stats.
 Identities = 13/45 (28%), Positives = 21/45 (46%)

Query: 130 HQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKEKQDLAERVM 174
           H LY++N T   WFYN  +     +   ++R L      L+  V+
Sbjct: 481 HSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFASTLSNDVL 525


>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 = 6.6,   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|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 = 6.6,   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|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 = 27.3 bits (59), Expect = 6.8,   Method: Composition-based stats.
 Identities = 13/45 (28%), Positives = 21/45 (46%)

Query: 130 HQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKEKQDLAERVM 174
           H LY++N T   WFYN  +     +   ++R L      L+  V+
Sbjct: 481 HSLYKLNTTVENWFYNMHSETDGSELFKYLRTLNGFASTLSNDVL 525


>pdb|3HXR|A Chain A, Nucleoporin Nup120 From S.Cerevisiae (Aa 1-757)
          Length = 761

 Score = 26.9 bits (58), Expect = 8.8,   Method: Composition-based stats.
 Identities = 13/45 (28%), Positives = 21/45 (46%)

Query: 130 HQLYEMNPTQYMWFYNFVATNKPGDGKHFIRILGKEKQDLAERVM 174
           H LY++N T   WFYN  +     +   ++R L      L+  V+
Sbjct: 485 HSLYKLNTTVENWFYNXHSETDGSELFKYLRTLNGFASTLSNDVL 529


  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
   0.318    0.135    0.411 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,808,665
Number of Sequences: 62578
Number of extensions: 198809
Number of successful extensions: 421
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 16
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 403
Number of HSP's gapped (non-prelim): 18
length of query: 226
length of database: 14,973,337
effective HSP length: 95
effective length of query: 131
effective length of database: 9,028,427
effective search space: 1182723937
effective search space used: 1182723937
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)