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= psy4687
         (339 letters)

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

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



>pdb|3AX1|A Chain A, Molecular Insights Into Mirna Processing By Arabidopsis
           Serrate
          Length = 358

 Score = 39.3 bits (90), Expect = 0.004,   Method: Compositional matrix adjust.
 Identities = 39/139 (28%), Positives = 63/139 (45%), Gaps = 23/139 (16%)

Query: 199 LRVLDRLILYLRIVHSVDYYNHCEYPNEDEMPNRCGIIHTRGSAPASKVTPQE-ITDYCS 257
           + +LD L+ YL  VH +DYY   E  NE +     G+ H R     S     E  + + S
Sbjct: 207 VELLDTLVTYLWRVHGLDYYGKVE-TNEAK-----GLRHVRAEGKVSDAKGDENESKFDS 260

Query: 258 TFQNKMSSLVSSPQEPTPEELDQLGAK-KTDAEVEKFIAANTQEISTD----KWLCPLSG 312
            +Q ++       Q+P    L+ + AK K DA   + +  + ++I  +    K+ C   G
Sbjct: 261 HWQERLKG-----QDP----LEVMAAKEKIDAAATEALDPHVRKIRDEKYGWKYGCGAKG 311

Query: 313 --KKFKGPDFIRKHIFNKH 329
             K F   +F+ KH+  KH
Sbjct: 312 CTKLFHAAEFVYKHLKLKH 330


>pdb|2PN1|A Chain A, Crystal Structure Of Carbamoylphosphate Synthase Large
           Subunit (Split Gene In Mj) (Zp_00538348.1) From
           Exiguobacterium Sp. 255-15 At 2.00 A Resolution
          Length = 331

 Score = 29.3 bits (64), Expect = 3.3,   Method: Compositional matrix adjust.
 Identities = 15/40 (37%), Positives = 25/40 (62%), Gaps = 2/40 (5%)

Query: 274 TPEELDQLGAKKTDAEVEKFIAANTQEISTDKWLCPLSGK 313
           T EE++QL +K TD  V++ +    QE+  D ++  +SGK
Sbjct: 170 TVEEVEQLFSKNTDLIVQELLVG--QELGVDAYVDLISGK 207


>pdb|3K11|A Chain A, Crystal Structure Of Putative Glycosyl Hydrolase
           (Np_813087.1) From Bacteroides Thetaiotaomicron Vpi-5482
           At 1.80 A Resolution
          Length = 445

 Score = 28.5 bits (62), Expect = 5.7,   Method: Compositional matrix adjust.
 Identities = 26/99 (26%), Positives = 42/99 (42%), Gaps = 11/99 (11%)

Query: 48  KAEVENLCKRYSGFLRVAIADPQPDRRWFRRGWVTFRRDVDIKEICWNLNN--IRLRDCE 105
           +A+ + L +    FL+ A     P++  +R GWV      D    CW   N    L  CE
Sbjct: 220 EAKNKYLAEAVKQFLQFADRXFIPEKGLYRHGWV--ESSTDHPAFCWARANGWALLTACE 277

Query: 106 LGAIVNRDLSRRVRT-------VSGLTSLKPVVQFDMKL 137
           L  ++  D  +R +        V G+T+L+    F  +L
Sbjct: 278 LLDVLPEDYPQRPKVXDYFRAHVRGVTALQSGEGFWHQL 316


>pdb|2XRH|A Chain A, Crystal Structure Of The Truncated Form Of Hp0721
          Length = 100

 Score = 27.7 bits (60), Expect = 8.5,   Method: Composition-based stats.
 Identities = 12/44 (27%), Positives = 21/44 (47%)

Query: 244 ASKVTPQEITDYCSTFQNKMSSLVSSPQEPTPEELDQLGAKKTD 287
           A  V PQ+I DY    + +M  +    ++   ++L +   K TD
Sbjct: 23  AGVVAPQDIVDYTKELKKRMEKMPEDKRKAFHKQLHEYATKNTD 66


  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
   0.319    0.135    0.412 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,081,112
Number of Sequences: 62578
Number of extensions: 334688
Number of successful extensions: 727
Number of sequences better than 100.0: 5
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 726
Number of HSP's gapped (non-prelim): 5
length of query: 339
length of database: 14,973,337
effective HSP length: 99
effective length of query: 240
effective length of database: 8,778,115
effective search space: 2106747600
effective search space used: 2106747600
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 52 (24.6 bits)