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= psy11170
         (111 letters)

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

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



>pdb|2XND|I Chain I, Crystal Structure Of Bovine F1-C8 Sub-Complex Of Atp
          Synthase
          Length = 47

 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/36 (52%), Positives = 25/36 (69%)

Query: 39 YIQYSNIAARTLRRALKTEFRADAEKREESFIRITP 74
          YI+YS I A+ +R ALKTEF+A+A K   S I+I  
Sbjct: 11 YIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVK 46


>pdb|2W6I|I Chain I, Low Resolution Structures Of Bovine Mitochondrial
          F1-Atpase During Controlled Dehydration: Hydration
          State 4b.
 pdb|2W6J|I Chain I, Low Resolution Structures Of Bovine Mitochondrial
          F1-Atpase During Controlled Dehydration: Hydration
          State 5.
 pdb|2W6H|I Chain I, Low Resolution Structures Of Bovine Mitochondrial
          F1-Atpase During Controlled Dehydration: Hydration
          State 4a
          Length = 51

 Score = 40.0 bits (92), Expect = 3e-04,   Method: Compositional matrix adjust.
 Identities = 19/36 (52%), Positives = 25/36 (69%)

Query: 39 YIQYSNIAARTLRRALKTEFRADAEKREESFIRITP 74
          YI+YS I A+ +R ALKTEF+A+A K   S I+I  
Sbjct: 12 YIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVK 47


>pdb|1E79|I Chain I, Bovine F1-Atpase Inhibited By Dccd
          (Dicyclohexylcarbodiimide)
 pdb|1H8E|I Chain I, (Adp.Alf4)2(Adp.So4) Bovine F1-Atpase (All Three
          Catalytic Sites Occupied)
 pdb|2CK3|I Chain I, Azide Inhibited Bovine F1-Atpase
 pdb|2JDI|I Chain I, Ground State Structure Of F1-Atpase From Bovine Heart
          Mitochondria (Bovine F1-Atpase Crystallised In The
          Absence Of Azide)
 pdb|2V7Q|I Chain I, The Structure Of F1-Atpase Inhibited By I1-60his, A
          Monomeric Form Of The Inhibitor Protein, If1.
 pdb|2WSS|I Chain I, The Structure Of The Membrane Extrinsic Region Of Bovine
          Atp Synthase
 pdb|2WSS|R Chain R, The Structure Of The Membrane Extrinsic Region Of Bovine
          Atp Synthase
 pdb|4ASU|I Chain I, F1-Atpase In Which All Three Catalytic Sites Contain
          Bound Nucleotide, With Magnesium Ion Released In The
          Empty Site
          Length = 50

 Score = 40.0 bits (92), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 19/36 (52%), Positives = 25/36 (69%)

Query: 39 YIQYSNIAARTLRRALKTEFRADAEKREESFIRITP 74
          YI+YS I A+ +R ALKTEF+A+A K   S I+I  
Sbjct: 11 YIRYSQICAKAVRDALKTEFKANAMKTSGSTIKIVK 46


>pdb|2XOK|I Chain I, Refined Structure Of Yeast F1c10 Atpase Complex To 3 A
          Resolution
 pdb|3ZRY|I Chain I, Rotor Architecture In The F(1)-C(10)-Ring Complex Of The
          Yeast F-Atp Synthase
          Length = 61

 Score = 28.9 bits (63), Expect = 0.76,   Method: Compositional matrix adjust.
 Identities = 18/51 (35%), Positives = 27/51 (52%), Gaps = 4/51 (7%)

Query: 38 CYIQYSNIAARTLRRALKTEFR-ADAEKREESFIRITPWKDGKPIRHYSEP 87
           Y  Y N+AA+ +R +LKTE + A    R ++    T +K+G      SEP
Sbjct: 9  SYAAYLNVAAQAIRSSLKTELQTASVTNRSQTDAFYTQYKNGTAA---SEP 56


>pdb|2VZ8|A Chain A, Crystal Structure Of Mammalian Fatty Acid Synthase
 pdb|2VZ8|B Chain B, Crystal Structure Of Mammalian Fatty Acid Synthase
 pdb|2VZ9|A Chain A, Crystal Structure Of Mammalian Fatty Acid Synthase In
            Complex With Nadp
 pdb|2VZ9|B Chain B, Crystal Structure Of Mammalian Fatty Acid Synthase In
            Complex With Nadp
          Length = 2512

 Score = 28.5 bits (62), Expect = 1.0,   Method: Composition-based stats.
 Identities = 13/38 (34%), Positives = 18/38 (47%)

Query: 63   EKREESFIRITPWKDGKPIRHYSEPLHYVTPILLQDDL 100
            ++ E +F+ +    D   IR    PLHY  P   QD L
Sbjct: 1526 KQTEHAFVNVLSRGDLSSIRWVCSPLHYALPASCQDRL 1563


>pdb|4B2Q|I Chain I, Model Of The Yeast F1fo-Atp Synthase Dimer Based On
          Subtomogram Average
 pdb|4B2Q|II Chain i, Model Of The Yeast F1fo-Atp Synthase Dimer Based On
          Subtomogram Average
          Length = 59

 Score = 28.5 bits (62), Expect = 1.0,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 8/58 (13%)

Query: 38 CYIQYSNIAARTLRRALKTEFR-ADAEKREESFIRITPWKDGKPIRHYSEPLHYVTPI 94
           Y  Y N+AA+ +R +LKTE + A    R ++    T +K+G      SEP    TPI
Sbjct: 9  SYAAYLNVAAQAIRSSLKTELQTASVLNRSQTDAFYTQYKNGTAA---SEP----TPI 59


>pdb|2HLD|I Chain I, Crystal Structure Of Yeast Mitochondrial F1-Atpase
 pdb|2HLD|R Chain R, Crystal Structure Of Yeast Mitochondrial F1-Atpase
 pdb|2HLD|1 Chain 1, Crystal Structure Of Yeast Mitochondrial F1-Atpase
 pdb|3FKS|I Chain I, Yeast F1 Atpase In The Absence Of Bound Nucleotides
 pdb|3FKS|R Chain R, Yeast F1 Atpase In The Absence Of Bound Nucleotides
 pdb|3FKS|1 Chain 1, Yeast F1 Atpase In The Absence Of Bound Nucleotides
 pdb|2WPD|I Chain I, The Mg.Adp Inhibited State Of The Yeast F1c10 Atp
          Synthase
 pdb|3OE7|I Chain I, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
          Gamma-I270t
 pdb|3OE7|R Chain R, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
          Gamma-I270t
 pdb|3OE7|1 Chain 1, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
          Gamma-I270t
 pdb|3OEE|I Chain I, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
          Alpha-F405s
 pdb|3OEE|R Chain R, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
          Alpha-F405s
 pdb|3OEE|1 Chain 1, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
          Alpha-F405s
 pdb|3OEH|I Chain I, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
          Beta-V279f
 pdb|3OEH|R Chain R, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
          Beta-V279f
 pdb|3OEH|1 Chain 1, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
          Beta-V279f
 pdb|3OFN|I Chain I, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
          Alpha-N67i
 pdb|3OFN|R Chain R, Structure Of Four Mutant Forms Of Yeast F1 Atpase:
          Alpha-N67i
 pdb|3ZIA|I Chain I, The Structure Of F1-atpase From Saccharomyces Cerevisiae
          Inhibited By Its Regulatory Protein If1
 pdb|3ZIA|S Chain S, The Structure Of F1-atpase From Saccharomyces Cerevisiae
          Inhibited By Its Regulatory Protein If1
          Length = 61

 Score = 28.1 bits (61), Expect = 1.2,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 8/58 (13%)

Query: 38 CYIQYSNIAARTLRRALKTEFR-ADAEKREESFIRITPWKDGKPIRHYSEPLHYVTPI 94
           Y  Y N+AA+ +R +LKTE + A    R ++    T +K+G      SEP    TPI
Sbjct: 9  SYAAYLNVAAQAIRSSLKTELQTASVLNRSQTDAFYTQYKNGTAA---SEP----TPI 59


>pdb|3THC|A Chain A, Crystal Structure Of Human Beta-Galactosidase In Complex
          With Galactose
 pdb|3THC|B Chain B, Crystal Structure Of Human Beta-Galactosidase In Complex
          With Galactose
 pdb|3THC|C Chain C, Crystal Structure Of Human Beta-Galactosidase In Complex
          With Galactose
 pdb|3THC|D Chain D, Crystal Structure Of Human Beta-Galactosidase In Complex
          With Galactose
 pdb|3THD|A Chain A, Crystal Structure Of Human Beta-Galactosidase In Complex
          With 1- Deoxygalactonojirimycin
 pdb|3THD|B Chain B, Crystal Structure Of Human Beta-Galactosidase In Complex
          With 1- Deoxygalactonojirimycin
 pdb|3THD|C Chain C, Crystal Structure Of Human Beta-Galactosidase In Complex
          With 1- Deoxygalactonojirimycin
 pdb|3THD|D Chain D, Crystal Structure Of Human Beta-Galactosidase In Complex
          With 1- Deoxygalactonojirimycin
          Length = 654

 Score = 26.2 bits (56), Expect = 5.0,   Method: Composition-based stats.
 Identities = 15/41 (36%), Positives = 22/41 (53%), Gaps = 7/41 (17%)

Query: 50 LRRALKTEFRADAEKREESFIRITPWKDGKPIRHYSEPLHY 90
          LR A +  F  D  +  +SF+     KDG+P R+ S  +HY
Sbjct: 1  LRNATQRMFEIDYSR--DSFL-----KDGQPFRYISGSIHY 34


>pdb|2X75|A Chain A, Staphylococcus Aureus Adenylosuccinate Lyase
          Length = 431

 Score = 25.8 bits (55), Expect = 5.9,   Method: Compositional matrix adjust.
 Identities = 12/42 (28%), Positives = 22/42 (52%), Gaps = 5/42 (11%)

Query: 65  REESFIRITP-----WKDGKPIRHYSEPLHYVTPILLQDDLD 101
           REE++ ++ P     W+   P R   E    +T +L +++LD
Sbjct: 368 REEAYDKVQPKAMISWETKTPFRELIEQDESITSVLTKEELD 409


>pdb|3PXN|A Chain A, Crystal Structure Of The Drosophila Kinesin Family
          Member Kin10NOD IN Complex With Divalent Manganese And
          Adp
          Length = 344

 Score = 25.8 bits (55), Expect = 6.3,   Method: Compositional matrix adjust.
 Identities = 9/24 (37%), Positives = 14/24 (58%)

Query: 58 FRADAEKREESFIRITPWKDGKPI 81
          +R    +RE S ++  PW DGK +
Sbjct: 33 YRQFLGRREPSVVQFPPWSDGKSL 56


>pdb|3DC4|A Chain A, Crystal Structure Of The Drosophila Kinesin Family
          Member Nod In Complex With Adp
 pdb|3DCB|A Chain A, Crystal Structure Of The Drosophila Kinesin Family
          Member Nod In Complex With Amppnp
 pdb|3DCO|N Chain N, Drosophila Nod (3dc4) And Bovine Tubulin (1jff) Docked
          Into The 11-Angstrom Cryo-Em Map Of Nucleotide-Free Nod
          Complexed To The Microtubule
          Length = 344

 Score = 25.8 bits (55), Expect = 6.5,   Method: Composition-based stats.
 Identities = 10/33 (30%), Positives = 16/33 (48%)

Query: 58 FRADAEKREESFIRITPWKDGKPIRHYSEPLHY 90
          +R    +RE S ++  PW DGK +       H+
Sbjct: 33 YRQFLGRREPSVVQFPPWSDGKSLIVDQNEFHF 65


>pdb|1VK5|A Chain A, X-Ray Structure Of Gene Product From Arabidopsis
          Thaliana At3g22680
 pdb|2Q3T|A Chain A, Ensemble Refinement Of The Protein Crystal Structure Of
          Gene Product From Arabidopsis Thaliana At3g22680
          Length = 157

 Score = 25.4 bits (54), Expect = 8.7,   Method: Compositional matrix adjust.
 Identities = 9/14 (64%), Positives = 12/14 (85%)

Query: 84 YSEPLHYVTPILLQ 97
          Y +PLHY+T +LLQ
Sbjct: 78 YGQPLHYLTNVLLQ 91


>pdb|3GAN|A Chain A, Crystal Structure Of Gene Product From Arabidopsis
          Thaliana At3g22680 With Bound Suramin
          Length = 157

 Score = 25.4 bits (54), Expect = 9.0,   Method: Compositional matrix adjust.
 Identities = 9/14 (64%), Positives = 12/14 (85%)

Query: 84 YSEPLHYVTPILLQ 97
          Y +PLHY+T +LLQ
Sbjct: 78 YGQPLHYLTNVLLQ 91


  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
   0.324    0.138    0.410 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 2,965,931
Number of Sequences: 62578
Number of extensions: 99053
Number of successful extensions: 241
Number of sequences better than 100.0: 27
Number of HSP's better than 100.0 without gapping: 24
Number of HSP's successfully gapped in prelim test: 3
Number of HSP's that attempted gapping in prelim test: 217
Number of HSP's gapped (non-prelim): 27
length of query: 111
length of database: 14,973,337
effective HSP length: 75
effective length of query: 36
effective length of database: 10,279,987
effective search space: 370079532
effective search space used: 370079532
T: 11
A: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 45 (21.9 bits)