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= psy6373
         (199 letters)

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

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



>pdb|2FFU|A Chain A, Crystal Structure Of Human Ppgalnact-2 Complexed With Udp
           And Ea2
 pdb|2FFV|A Chain A, Human Ppgalnact-2 Complexed With Manganese And Udp
 pdb|2FFV|B Chain B, Human Ppgalnact-2 Complexed With Manganese And Udp
          Length = 501

 Score =  202 bits (515), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 88/108 (81%), Positives = 99/108 (91%)

Query: 3   RTPMIAGGLFSIDRKYFEKLGKYDMAMSVWGGENLEISFRVWQCGGSLEIVPCSRVGHVF 62
           +TPMIAGGLF +D+ YFE+LGKYDM M VWGGENLEISFRVWQCGGSLEI+PCSRVGHVF
Sbjct: 232 KTPMIAGGLFVMDKFYFEELGKYDMMMDVWGGENLEISFRVWQCGGSLEIIPCSRVGHVF 291

Query: 63  RKRHPYTFPGGSGNVFARNTRRAAEVWMDNYKHYYYAEVPLAKTIPFG 110
           RK+HPYTFPGGSG VFARNTRRAAEVWMD YK++YYA VP A+ +P+G
Sbjct: 292 RKQHPYTFPGGSGTVFARNTRRAAEVWMDEYKNFYYAAVPSARNVPYG 339


>pdb|1XHB|A Chain A, The Crystal Structure Of Udp-Galnac: Polypeptide Alpha-N-
           Acetylgalactosaminyltransferase-T1
          Length = 472

 Score =  163 bits (413), Expect = 5e-41,   Method: Compositional matrix adjust.
 Identities = 68/109 (62%), Positives = 85/109 (77%)

Query: 3   RTPMIAGGLFSIDRKYFEKLGKYDMAMSVWGGENLEISFRVWQCGGSLEIVPCSRVGHVF 62
           RTP +AGGLFSIDR YF+++G YD  M +WGGENLEISFR+WQCGG+LEIV CS VGHVF
Sbjct: 200 RTPTMAGGLFSIDRDYFQEIGTYDAGMDIWGGENLEISFRIWQCGGTLEIVTCSHVGHVF 259

Query: 63  RKRHPYTFPGGSGNVFARNTRRAAEVWMDNYKHYYYAEVPLAKTIPFGE 111
           RK  PYTFPGG+G +  +N RR AEVWMD +K+++Y   P    + +G+
Sbjct: 260 RKATPYTFPGGTGQIINKNNRRLAEVWMDEFKNFFYIISPGVTKVDYGD 308


>pdb|2D7I|A Chain A, Crsytal Structure Of Pp-Galnac-T10 With Udp, Galnac And
           Mn2+
 pdb|2D7R|A Chain A, Crystal Structure Of Pp-galnac-t10 Complexed With
           Galnac-ser On Lectin Domain
          Length = 570

 Score =  128 bits (322), Expect = 2e-30,   Method: Compositional matrix adjust.
 Identities = 56/109 (51%), Positives = 74/109 (67%), Gaps = 2/109 (1%)

Query: 4   TPMIAGGLFSIDRKYFEKLGKYDMAMSVWGGENLEISFRVWQCGGSLEIVPCSRVGHVFR 63
           +P++AGGLF++DRK+F +LG YD  + +WGGE  EISF+VW CGG +E +PCSRVGH++R
Sbjct: 281 SPVMAGGLFAVDRKWFWELGGYDPGLEIWGGEQYEISFKVWMCGGRMEDIPCSRVGHIYR 340

Query: 64  KRHPYTFPGGSGNVFARNTRRAAEVWMDNYKHYYYAEVPLAKTIPFGET 112
           K  PY  P G     ARN +R AEVWMD Y  Y Y   P  + +  G+ 
Sbjct: 341 KYVPYKVPAGVS--LARNLKRVAEVWMDEYAEYIYQRRPEYRHLSAGDV 387


>pdb|2Z87|A Chain A, Crystal Structure Of Chondroitin Polymerase From
           Escherichia Coli Strain K4 (K4cp) Complexed With Udp-
           Galnac And Udp
 pdb|2Z87|B Chain B, Crystal Structure Of Chondroitin Polymerase From
           Escherichia Coli Strain K4 (K4cp) Complexed With Udp-
           Galnac And Udp
          Length = 624

 Score = 31.2 bits (69), Expect = 0.38,   Method: Composition-based stats.
 Identities = 12/40 (30%), Positives = 24/40 (60%)

Query: 8   AGGLFSIDRKYFEKLGKYDMAMSVWGGENLEISFRVWQCG 47
           +GG  +  +K+  + G +D   + WGGE+ E  +R+++ G
Sbjct: 276 SGGNVAFAKKWLFRAGWFDEEFTHWGGEDNEFGYRLYREG 315


>pdb|2Z86|A Chain A, Crystal Structure Of Chondroitin Polymerase From
           Escherichia Coli Strain K4 (K4cp) Complexed With
           Udp-Glcua And Udp
 pdb|2Z86|B Chain B, Crystal Structure Of Chondroitin Polymerase From
           Escherichia Coli Strain K4 (K4cp) Complexed With
           Udp-Glcua And Udp
 pdb|2Z86|C Chain C, Crystal Structure Of Chondroitin Polymerase From
           Escherichia Coli Strain K4 (K4cp) Complexed With
           Udp-Glcua And Udp
 pdb|2Z86|D Chain D, Crystal Structure Of Chondroitin Polymerase From
           Escherichia Coli Strain K4 (K4cp) Complexed With
           Udp-Glcua And Udp
          Length = 625

 Score = 31.2 bits (69), Expect = 0.40,   Method: Composition-based stats.
 Identities = 12/40 (30%), Positives = 24/40 (60%)

Query: 8   AGGLFSIDRKYFEKLGKYDMAMSVWGGENLEISFRVWQCG 47
           +GG  +  +K+  + G +D   + WGGE+ E  +R+++ G
Sbjct: 277 SGGNVAFAKKWLFRAGWFDEEFTHWGGEDNEFGYRLYREG 316


  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    0.136    0.425 

Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,283,166
Number of Sequences: 62578
Number of extensions: 190383
Number of successful extensions: 314
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 306
Number of HSP's gapped (non-prelim): 8
length of query: 199
length of database: 14,973,337
effective HSP length: 94
effective length of query: 105
effective length of database: 9,091,005
effective search space: 954555525
effective search space used: 954555525
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)