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= psy2138
         (208 letters)

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

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



>pdb|2GLI|A Chain A, Five-Finger GliDNA COMPLEX
          Length = 155

 Score = 29.6 bits (65), Expect = 1.3,   Method: Compositional matrix adjust.
 Identities = 19/81 (23%), Positives = 35/81 (43%), Gaps = 2/81 (2%)

Query: 64  CHAFWRKYGGLKIPGKLSDGELDYLKPNKKSGSSSLSEEDRIGPSGLV--GHRPHRCSVP 121
           C   + +   LK   +   GE  Y+  ++    +  +  DR           +P+ C +P
Sbjct: 75  CRKSYSRLENLKTHLRSHTGEKPYMCEHEGCSKAFSNASDRAKHQNRTHSNEKPYVCKLP 134

Query: 122 GCSKEFKLKAHLHRHLATGHG 142
           GC+K +   + L +H+ T HG
Sbjct: 135 GCTKRYTDPSSLRKHVKTVHG 155


>pdb|3G5B|A Chain A, The Structure Of Unc5b Cytoplasmic Domain
          Length = 405

 Score = 28.9 bits (63), Expect = 2.0,   Method: Compositional matrix adjust.
 Identities = 20/63 (31%), Positives = 30/63 (47%), Gaps = 14/63 (22%)

Query: 87  YLKPNKKSGSSSLSEEDRI--------GPSGLVGHRPHRCSVPGCSKE------FKLKAH 132
           YL+ NK   +  LSE  +         GP+GL+  RP   +VP C++       F+LK  
Sbjct: 41  YLRINKTESTLPLSEGSQTVLSPSVTCGPTGLLLCRPVVLTVPHCAEVIAGDWIFQLKTQ 100

Query: 133 LHR 135
            H+
Sbjct: 101 AHQ 103


>pdb|2EBT|A Chain A, Solution Structure Of Three Tandem Repeats Of Zf-C2h2
           Domains From Human Kruppel-Like Factor 5
          Length = 100

 Score = 28.5 bits (62), Expect = 2.7,   Method: Compositional matrix adjust.
 Identities = 17/39 (43%), Positives = 20/39 (51%), Gaps = 2/39 (5%)

Query: 106 GPSG--LVGHRPHRCSVPGCSKEFKLKAHLHRHLATGHG 142
           G SG  L   R H C  PGC+K +   +HL  HL T  G
Sbjct: 4   GSSGPDLEKRRIHYCDYPGCTKVYTKSSHLKAHLRTHTG 42


>pdb|4FZ2|A Chain A, Crystal Structure Of The Fourth Type Of Archaeal Trna
           Splicing Endonuclease From Candidatus Micrarchaeum
           Acidiphilum Arman-2
 pdb|4FZ2|B Chain B, Crystal Structure Of The Fourth Type Of Archaeal Trna
           Splicing Endonuclease From Candidatus Micrarchaeum
           Acidiphilum Arman-2
          Length = 395

 Score = 28.5 bits (62), Expect = 2.8,   Method: Compositional matrix adjust.
 Identities = 19/52 (36%), Positives = 27/52 (51%), Gaps = 10/52 (19%)

Query: 59  KICINCHAFWRKYGGLKIPGKLSDGELDYLKPNKKSGSSSLSEEDRIGPSGL 110
           K+ I+   + R+ G ++IPGK S           + G  SLSE +RIG S L
Sbjct: 296 KLAIDFELYHRRGGDIEIPGKNS----------PRFGMLSLSENERIGGSEL 337


>pdb|2EM3|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
           640- 672) Of Human Zinc Finger Protein 28 Homolog
          Length = 46

 Score = 26.9 bits (58), Expect = 8.3,   Method: Composition-based stats.
 Identities = 16/37 (43%), Positives = 20/37 (54%), Gaps = 4/37 (10%)

Query: 114 RPHRCSVPGCSKEFKLKAHLHRHLATGHGLVARPGSP 150
           +P+ C V  CSK F  KAHL +H  T  G   +P  P
Sbjct: 11  KPYECKV--CSKAFTQKAHLAQHQKTHTG--EKPSGP 43


>pdb|1MEY|C Chain C, Crystal Structure Of A Designed Zinc Finger Protein Bound
           To Dna
 pdb|1MEY|F Chain F, Crystal Structure Of A Designed Zinc Finger Protein Bound
           To Dna
 pdb|1MEY|G Chain G, Crystal Structure Of A Designed Zinc Finger Protein Bound
           To Dna
          Length = 87

 Score = 26.9 bits (58), Expect = 9.1,   Method: Compositional matrix adjust.
 Identities = 24/82 (29%), Positives = 32/82 (39%), Gaps = 9/82 (10%)

Query: 61  CINCHAFWRKYGGLKIPGKLSDGELDYLKPN---KKSGSSSLSEEDRIGPSGLVGHRPHR 117
           C  C   + +   L+   +   GE  Y  P      S SS L +  R       G +P++
Sbjct: 7   CPECGKSFSQSSNLQKHQRTHTGEKPYKCPECGKSFSQSSDLQKHQRT----HTGEKPYK 62

Query: 118 CSVPGCSKEFKLKAHLHRHLAT 139
           C  P C K F    HL RH  T
Sbjct: 63  C--PECGKSFSRSDHLSRHQRT 82


>pdb|2EOZ|A Chain A, Solution Structure Of The C2h2 Type Zinc Finger (Region
           809- 841) Of Human Zinc Finger Protein 473
          Length = 46

 Score = 26.6 bits (57), Expect = 9.2,   Method: Composition-based stats.
 Identities = 12/24 (50%), Positives = 17/24 (70%), Gaps = 2/24 (8%)

Query: 114 RPHRCSVPGCSKEFKLKAHLHRHL 137
           +P+ C+V  C K F L AHL++HL
Sbjct: 11  KPYSCNV--CGKAFVLSAHLNQHL 32


  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
   0.321    0.138    0.455 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,014,925
Number of Sequences: 62578
Number of extensions: 295744
Number of successful extensions: 602
Number of sequences better than 100.0: 43
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 22
Number of HSP's that attempted gapping in prelim test: 555
Number of HSP's gapped (non-prelim): 65
length of query: 208
length of database: 14,973,337
effective HSP length: 94
effective length of query: 114
effective length of database: 9,091,005
effective search space: 1036374570
effective search space used: 1036374570
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)