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= 013052
(450 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3OTK|A Chain A, Structure And Mechanisim Of Core 2 Beta1,6-N-
Acetylglucosaminyltransferase: A Metal-Ion Independent
Gt-A Glycosyltransferase
pdb|3OTK|B Chain B, Structure And Mechanisim Of Core 2 Beta1,6-N-
Acetylglucosaminyltransferase: A Metal-Ion Independent
Gt-A Glycosyltransferase
pdb|3OTK|C Chain C, Structure And Mechanisim Of Core 2 Beta1,6-N-
Acetylglucosaminyltransferase: A Metal-Ion Independent
Gt-A Glycosyltransferase
pdb|3OTK|D Chain D, Structure And Mechanisim Of Core 2 Beta1,6-N-
Acetylglucosaminyltransferase: A Metal-Ion Independent
Gt-A Glycosyltransferase
Length = 391
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 53/205 (25%), Positives = 90/205 (43%), Gaps = 16/205 (7%)
Query: 122 RTLQAVYHPRNHYILHLDLEAPPRERLDLALSVKNDPIFFEVENVRVMLQSNLVTYKGPT 181
R L+A+Y P+N Y +H+D +A E LA +V+ F+ NV V Q V Y T
Sbjct: 101 RLLRAIYMPQNFYCIHVDRKA---EESFLA-AVQGIASCFD--NVFVASQLESVVYASWT 154
Query: 182 MIACTLQAIAILLKESLEWDWFINLSASDYPLVTQDDMLYVFSNMSKNLNFIEHTLISGW 241
+ L + L + + W + INLS D+P+ T +++ + N +
Sbjct: 155 RVKADLNCMKDLYRMNANWKYLINLSGMDFPIKTNLEIVRKLKCSTGENNLETEKMPPNK 214
Query: 242 KLNQRAKPIIVDPGLYLSKKSDIAWTTQRRSLPTSFQLFTGSAWVMLTRRFVEYCIWGWD 301
+ + + +VD L + I + P LF+GSA+ ++TR +V Y + +
Sbjct: 215 EERWKKRYAVVDGKL---TNTGIV----KAPPPLKTPLFSGSAYFVVTREYVGYVL---E 264
Query: 302 NLPRTLLMYYTNFISSPEGYFHTVI 326
N LM + SP+ + I
Sbjct: 265 NENIQKLMEWAQDTYSPDEFLWATI 289
>pdb|2GAK|A Chain A, X-ray Crystal Structure Of Murine Leukocyte-type Core 2
B1,6-n- Acetylglucosaminyltransferase (c2gnt-l)
pdb|2GAK|B Chain B, X-ray Crystal Structure Of Murine Leukocyte-type Core 2
B1,6-n- Acetylglucosaminyltransferase (c2gnt-l)
pdb|2GAM|A Chain A, X-Ray Crystal Structure Of Murine Leukocyte-Type Core 2
B1, 6-N-Acetylglucosaminyltransferase (C2gnt-L) In
Complex With Galb1,3galnac
pdb|2GAM|B Chain B, X-Ray Crystal Structure Of Murine Leukocyte-Type Core 2
B1, 6-N-Acetylglucosaminyltransferase (C2gnt-L) In
Complex With Galb1,3galnac
pdb|2GAM|C Chain C, X-Ray Crystal Structure Of Murine Leukocyte-Type Core 2
B1, 6-N-Acetylglucosaminyltransferase (C2gnt-L) In
Complex With Galb1,3galnac
pdb|2GAM|D Chain D, X-Ray Crystal Structure Of Murine Leukocyte-Type Core 2
B1, 6-N-Acetylglucosaminyltransferase (C2gnt-L) In
Complex With Galb1,3galnac
Length = 391
Score = 52.0 bits (123), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 52/205 (25%), Positives = 89/205 (43%), Gaps = 16/205 (7%)
Query: 122 RTLQAVYHPRNHYILHLDLEAPPRERLDLALSVKNDPIFFEVENVRVMLQSNLVTYKGPT 181
R L+A+Y P+N Y +H+D +A E LA +V+ F+ NV V Q V Y T
Sbjct: 101 RLLRAIYMPQNFYCIHVDRKA---EESFLA-AVQGIASCFD--NVFVASQLESVVYASWT 154
Query: 182 MIACTLQAIAILLKESLEWDWFINLSASDYPLVTQDDMLYVFSNMSKNLNFIEHTLISGW 241
+ L + L + + W + INL D+P+ T +++ + N +
Sbjct: 155 RVKADLNCMKDLYRMNANWKYLINLCGMDFPIKTNLEIVRKLKCSTGENNLETEKMPPNK 214
Query: 242 KLNQRAKPIIVDPGLYLSKKSDIAWTTQRRSLPTSFQLFTGSAWVMLTRRFVEYCIWGWD 301
+ + + +VD L + I + P LF+GSA+ ++TR +V Y + +
Sbjct: 215 EERWKKRYAVVDGKL---TNTGIV----KAPPPLKTPLFSGSAYFVVTREYVGYVL---E 264
Query: 302 NLPRTLLMYYTNFISSPEGYFHTVI 326
N LM + SP+ + I
Sbjct: 265 NENIQKLMEWAQDTYSPDEFLWATI 289
>pdb|3OBF|A Chain A, Crystal Structure Of Putative Transcriptional Regulator,
Iclr Family; Targeted Domain 129...302
pdb|3OBF|B Chain B, Crystal Structure Of Putative Transcriptional Regulator,
Iclr Family; Targeted Domain 129...302
Length = 176
Score = 33.1 bits (74), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 43/95 (45%), Gaps = 9/95 (9%)
Query: 130 PRNHYILHLDLEAPPRERLDLALSVKNDPIFFEVEN---VRVMLQSNLVTYKGPTMIACT 186
P H + HL AP R + ALS + +F EN VR +L+S +T G A
Sbjct: 41 PSRHQVKHL---APLGARYNEALS-SSVQVFLASENEDRVRQLLRSGSITLTGVDEDA-- 94
Query: 187 LQAIAILLKESLEWDWFINLSASDYPLVTQDDMLY 221
++A + LKES E W +N + V +Y
Sbjct: 95 VEAYLLRLKESXERGWAVNFGETSIEEVGVASPVY 129
>pdb|2DIW|A Chain A, Solution Structure Of The Rpr Domain Of Putative Rna-
Binding Protein 16
Length = 152
Score = 28.9 bits (63), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 207 SASDY-PLVTQDDMLYVFSNMSKNLNFIEHTLISGWKLNQRAKPIIVDPGLYL 258
S +DY P +++ M + K + F +H + S K Q+ KP PGLY+
Sbjct: 22 SLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYV 74
>pdb|3CW1|F Chain F, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|Z Chain Z, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|1 Chain 1, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|2 Chain 2, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3PGW|F Chain F, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|I Chain I, Crystal Structure Of Human U1 Snrnp
pdb|2Y9A|F Chain F, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9A|M Chain M, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9A|T Chain T, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9B|F Chain F, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9B|M Chain M, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9B|T Chain T, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9C|F Chain F, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9C|M Chain M, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9C|T Chain T, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9D|F Chain F, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9D|M Chain M, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|2Y9D|T Chain T, Structure Of The Spliceosomal U4 Snrnp Core Domain
pdb|3S6N|F Chain F, Crystal Structure Of The Gemin2-Binding Domain Of Smn,
Gemin2 In Complex With Smd1D2FEG FROM HUMAN
pdb|4F7U|F Chain F, Macromolecular Machine 6
pdb|4F7U|I Chain I, Macromolecular Machine 6
pdb|1VU2|D Chain D, The 8s Snrnp Assembly Intermediate
pdb|1VU2|L Chain L, The 8s Snrnp Assembly Intermediate
pdb|1VU2|T Chain T, The 8s Snrnp Assembly Intermediate
pdb|1VU2|BB Chain b, The 8s Snrnp Assembly Intermediate
pdb|1VU2|JJ Chain j, The 8s Snrnp Assembly Intermediate
pdb|1VU2|RR Chain r, The 8s Snrnp Assembly Intermediate
pdb|1VU2|ZZ Chain z, The 8s Snrnp Assembly Intermediate
pdb|1VU3|D Chain D, The 8s Snrnp Assembly Intermediate
pdb|1VU3|L Chain L, The 8s Snrnp Assembly Intermediate
pdb|1VU3|T Chain T, The 8s Snrnp Assembly Intermediate
pdb|1VU3|BB Chain b, The 8s Snrnp Assembly Intermediate
pdb|1VU3|JJ Chain j, The 8s Snrnp Assembly Intermediate
pdb|1VU3|RR Chain r, The 8s Snrnp Assembly Intermediate
pdb|4F77|L Chain L, The 8s Snrnp Assembly Intermediate
pdb|4F77|D Chain D, The 8s Snrnp Assembly Intermediate
pdb|4F77|T Chain T, The 8s Snrnp Assembly Intermediate
pdb|4F77|BB Chain b, The 8s Snrnp Assembly Intermediate
pdb|4F77|JJ Chain j, The 8s Snrnp Assembly Intermediate
pdb|4F77|RR Chain r, The 8s Snrnp Assembly Intermediate
pdb|4F77|ZZ Chain z, The 8s Snrnp Assembly Intermediate
Length = 86
Score = 28.5 bits (62), Expect = 8.2, Method: Composition-based stats.
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 309 MYYTNFISSPEGYFHTVICNTEEFRNTAISNDL 341
M Y ++ S +GY + + NTEE+ + A+S L
Sbjct: 27 MEYKGYLVSVDGYMNMQLANTEEYIDGALSGHL 59
>pdb|3D9P|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9P|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
Length = 145
Score = 28.5 bits (62), Expect = 8.8, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 207 SASDY-PLVTQDDMLYVFSNMSKNLNFIEHTLISGWKLNQRAKPIIVDPGLYL 258
S +DY P +++ M + K + F +H + S K Q+ KP PGLY+
Sbjct: 13 SLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYV 65
>pdb|3D9J|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9J|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9K|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9K|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9L|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9L|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9M|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9M|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9N|A Chain A, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
pdb|3D9N|B Chain B, Snapshots Of The Rna Processing Factor Scaf8 Bound To
Different Phosphorylated Forms Of The Carboxy-Terminal
Domain Of Rna-Polymerase Ii
Length = 145
Score = 28.5 bits (62), Expect = 8.8, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 27/53 (50%), Gaps = 1/53 (1%)
Query: 207 SASDY-PLVTQDDMLYVFSNMSKNLNFIEHTLISGWKLNQRAKPIIVDPGLYL 258
S +DY P +++ M + K + F +H + S K Q+ KP PGLY+
Sbjct: 13 SLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYV 65
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
0.322 0.136 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,743,360
Number of Sequences: 62578
Number of extensions: 565488
Number of successful extensions: 1389
Number of sequences better than 100.0: 8
Number of HSP's better than 100.0 without gapping: 4
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 1381
Number of HSP's gapped (non-prelim): 8
length of query: 450
length of database: 14,973,337
effective HSP length: 102
effective length of query: 348
effective length of database: 8,590,381
effective search space: 2989452588
effective search space used: 2989452588
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: 53 (25.0 bits)