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= psy1423
         (125 letters)

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

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



>pdb|1WJT|A Chain A, Solution Structure Of The N-Terminal Domain I Of Mouse
           Transcription Elongation Factor S-Ii Protein 3
          Length = 103

 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 28/58 (48%), Positives = 39/58 (67%)

Query: 46  RQEQALDLLKALQTLNIDLNILTKTHIGMTVNNLRKSSKDDEVINLAKTLIKNWKKFI 103
           + E ALDLLK L +  + + +L  T IG+ VN +RK   D EV++LAK LIKNWK+ +
Sbjct: 29  KTEGALDLLKKLNSCQMSIQLLQTTRIGVAVNGVRKHCSDKEVVSLAKVLIKNWKRLL 86


>pdb|3V8X|A Chain A, The Crystal Structure Of Transferrin Binding Protein A
          (Tbpa) From Neisserial Meningitidis Serogroup B In
          Complex With Full Length Human Transferrin
          Length = 904

 Score = 28.5 bits (62), Expect = 0.94,   Method: Composition-based stats.
 Identities = 14/32 (43%), Positives = 21/32 (65%)

Query: 31 KKKRTSGDNKLTGLVRQEQALDLLKALQTLNI 62
          KK++T  DN++TGL +  ++ D L   Q LNI
Sbjct: 34 KKQKTRRDNEVTGLGKLVKSSDTLSKEQVLNI 65


>pdb|3V89|A Chain A, The Crystal Structure Of Transferrin Binding Protein A
          (Tbpa) From Neisseria Meningitidis Serogroup B In
          Complex With The C-Lobe Of Human Transferrin
          Length = 904

 Score = 28.5 bits (62), Expect = 0.95,   Method: Composition-based stats.
 Identities = 14/32 (43%), Positives = 21/32 (65%)

Query: 31 KKKRTSGDNKLTGLVRQEQALDLLKALQTLNI 62
          KK++T  DN++TGL +  ++ D L   Q LNI
Sbjct: 34 KKQKTRRDNEVTGLGKLVKSSDTLSKEQVLNI 65


>pdb|2YNS|A Chain A, Rimp_alpha_b54nls
 pdb|2YNS|B Chain B, Rimp_alpha_b54nls
 pdb|4B8O|A Chain A, Rimp_alpha_sv40tagnls
 pdb|4B8P|A Chain A, Rimp_alpha_a89nls
 pdb|4B8P|B Chain B, Rimp_alpha_a89nls
          Length = 490

 Score = 26.2 bits (56), Expect = 5.4,   Method: Composition-based stats.
 Identities = 22/74 (29%), Positives = 36/74 (48%), Gaps = 4/74 (5%)

Query: 19  PKRNLIGSAMLTKKKRTSGDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNN 78
           P  +++  A+ T     +GD+  T  +   QAL  L +L T N+  +I  K     T++N
Sbjct: 260 PSPSVLIPALRTVGNIVTGDDAQTQCIIDHQALPCLLSLLTQNLKKSI--KKEACWTISN 317

Query: 79  LRKSSKD--DEVIN 90
           +   +KD    VIN
Sbjct: 318 ITAGNKDQIQAVIN 331


>pdb|3R9C|A Chain A, Crystal Structure Of Mycobacterium Smegmatis Cyp164a2 With
           Econazole Bound
 pdb|3R9B|A Chain A, Crystal Structure Of Mycobacterium Smegmatis Cyp164a2 In
           Ligand Free State
 pdb|3R9B|B Chain B, Crystal Structure Of Mycobacterium Smegmatis Cyp164a2 In
           Ligand Free State
 pdb|3R9B|C Chain C, Crystal Structure Of Mycobacterium Smegmatis Cyp164a2 In
           Ligand Free State
          Length = 418

 Score = 25.8 bits (55), Expect = 6.1,   Method: Composition-based stats.
 Identities = 15/54 (27%), Positives = 32/54 (59%), Gaps = 3/54 (5%)

Query: 27  AMLTKKKRTSGDNKLTGLVRQEQALDLL---KALQTLNIDLNILTKTHIGMTVN 77
           A++ +++RT G++ ++GLV  E++ D L   + + T N+ L    +T + +  N
Sbjct: 214 ALIDERRRTPGEDLMSGLVAVEESGDQLTEDEIIATCNLLLIAGHETTVNLIAN 267


>pdb|3OOP|A Chain A, The Structure Of A Protein With Unknown Function From
          Listeria Innocua Clip11262
          Length = 143

 Score = 25.8 bits (55), Expect = 6.5,   Method: Compositional matrix adjust.
 Identities = 12/30 (40%), Positives = 18/30 (60%)

Query: 3  EPMSLRDSALWSKTRRPKRNLIGSAMLTKK 32
          EP+S ++ ALW+K   P  N I   +L K+
Sbjct: 50 EPISQKEIALWTKKDTPTVNRIVDVLLRKE 79


>pdb|4B8J|A Chain A, Rimp_alpha1a
          Length = 528

 Score = 25.4 bits (54), Expect = 8.5,   Method: Composition-based stats.
 Identities = 19/67 (28%), Positives = 33/67 (49%), Gaps = 2/67 (2%)

Query: 19  PKRNLIGSAMLTKKKRTSGDNKLTGLVRQEQALDLLKALQTLNIDLNILTKTHIGMTVNN 78
           P  +++  A+ T     +GD+  T  +   QAL  L +L T N+  +I  K     T++N
Sbjct: 298 PSPSVLIPALRTVGNIVTGDDAQTQCIIDHQALPCLLSLLTQNLKKSI--KKEACWTISN 355

Query: 79  LRKSSKD 85
           +   +KD
Sbjct: 356 ITAGNKD 362


  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
   0.317    0.131    0.373 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,259,876
Number of Sequences: 62578
Number of extensions: 104315
Number of successful extensions: 352
Number of sequences better than 100.0: 85
Number of HSP's better than 100.0 without gapping: 6
Number of HSP's successfully gapped in prelim test: 79
Number of HSP's that attempted gapping in prelim test: 346
Number of HSP's gapped (non-prelim): 85
length of query: 125
length of database: 14,973,337
effective HSP length: 86
effective length of query: 39
effective length of database: 9,591,629
effective search space: 374073531
effective search space used: 374073531
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: 45 (21.9 bits)