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= psy6081
(226 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3FQD|A Chain A, Crystal Structure Of The S. Pombe Rat1-Rai1 Complex
Length = 899
Score = 178 bits (451), Expect = 3e-45, Method: Compositional matrix adjust.
Identities = 98/192 (51%), Positives = 124/192 (64%), Gaps = 19/192 (9%)
Query: 35 NGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVAIFECIDRLF 94
+G +I D S PNPNG+E DNLYLD NGI+HPC+HPED+PAP+ EDE VA+FE DR+
Sbjct: 34 DGTEIEPDLSLPNPNGVECDNLYLDXNGIVHPCSHPEDRPAPETEDEXXVAVFEYTDRIL 93
Query: 95 RIVRPRKLLYMAIDGVAPRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASKETAEKIA 154
VRPR+LL++AIDGVAPRAK NQ RSRRFR+S+E A K
Sbjct: 94 AXVRPRQLLFIAIDGVAPRAKXNQ-------------------QRSRRFRSSREAALKEE 134
Query: 155 EVARIREKLLADGCILPPEKEKGSHFDSNCITPGTPFMACLSACLHYYIHDRLNNDPGWK 214
E+ E+ G + K +DSNCITPGTPF L+ L YYI ++LN+DP W+
Sbjct: 135 ELQAFIEEAKQQGIPIDENATKKKSWDSNCITPGTPFXDTLAKSLRYYIINKLNSDPCWR 194
Query: 215 GIKVILSDANVP 226
++ ILSDA+VP
Sbjct: 195 NVRFILSDASVP 206
>pdb|3PIE|A Chain A, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIE|B Chain B, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIE|C Chain C, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIE|D Chain D, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant
pdb|3PIF|A Chain A, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
pdb|3PIF|B Chain B, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
pdb|3PIF|C Chain C, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
pdb|3PIF|D Chain D, Crystal Structure Of The 5'->3' Exoribonuclease Xrn1,
E178q Mutant In Complex With Manganese
Length = 1155
Score = 144 bits (364), Expect = 3e-35, Method: Compositional matrix adjust.
Identities = 81/199 (40%), Positives = 107/199 (53%), Gaps = 43/199 (21%)
Query: 30 LPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPK--DEDEMMVAIF 87
+ Q ++G +IP EFDNLYLDMN I+H CTH + E+E+ IF
Sbjct: 17 ISQLIDGSQIP-----------EFDNLYLDMNSILHNCTHGDGSEVNSRLSEEEVYSKIF 65
Query: 88 ECIDRLFRIVRPRKLLYMAIDGVAPRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASK 147
ID LF ++P++ YMAIDGVAPRAKMNQ R+RRFR +
Sbjct: 66 SYIDHLFHTIKPKQTFYMAIDGVAPRAKMNQ-------------------QRARRFRTAM 106
Query: 148 ETAEKIAEVARIREKLLADGCILPPEKEKGSHFDSNCITPGTPFMACLSACLHYYIHDRL 207
+ + + +K + +G LP KG FDSN ITPGT FMA L+ L Y+IHD++
Sbjct: 107 DAEKAL-------QKAIENGDELP----KGEPFDSNAITPGTEFMAKLTENLKYFIHDKI 155
Query: 208 NNDPGWKGIKVILSDANVP 226
ND W+ +KVI S VP
Sbjct: 156 TNDTRWQNVKVIFSGHEVP 174
>pdb|2Y35|A Chain A, Crystal Structure Of Xrn1-Substrate Complex
Length = 1140
Score = 129 bits (325), Expect = 1e-30, Method: Compositional matrix adjust.
Identities = 68/177 (38%), Positives = 99/177 (55%), Gaps = 33/177 (18%)
Query: 52 EFDNLYLDMNGIIHPCTHPEDKPAP--KDEDEMMVAIFECIDRLFRIVRPRKLLYMAIDG 109
EFDNLYLDMNGI+H C+HP+D +E+++ IF +D+LF +++P++L ++++DG
Sbjct: 28 EFDNLYLDMNGIVHNCSHPDDNNIHFHLEEEQIFQEIFNYVDKLFYLIKPQRLFFLSVDG 87
Query: 110 VAPRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASKETAEKIAEVARIREKLLADGCI 169
VAPRAKMNQ RSRRFR ++E ++ A+ A+
Sbjct: 88 VAPRAKMNQ-------------------QRSRRFRTAREAEQQEAKAAQ----------- 117
Query: 170 LPPEKEKGSHFDSNCITPGTPFMACLSACLHYYIHDRLNNDPGWKGIKVILSDANVP 226
E + FDSNCITPGT FM L L ++ +++ DP W+ VILS P
Sbjct: 118 -RGELREHERFDSNCITPGTEFMVRLQEGLRAFLKTKISTDPLWQRCTVILSGQEAP 173
>pdb|1XXI|B Chain B, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|C Chain C, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|D Chain D, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|G Chain G, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|H Chain H, Adp Bound E. Coli Clamp Loader Complex
pdb|1XXI|I Chain I, Adp Bound E. Coli Clamp Loader Complex
Length = 368
Score = 32.3 bits (72), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 26 SLVSLPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVA 85
SLV E NG+++ ++ G+E++ L ++M G++H + PA D M A
Sbjct: 251 SLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGND--MAA 308
Query: 86 IFECIDRLFRIVRP 99
I + L R + P
Sbjct: 309 IELRMRELARTIPP 322
>pdb|1JR3|A Chain A, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1JR3|B Chain B, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1JR3|C Chain C, Crystal Structure Of The Processivity Clamp Loader Gamma
Complex Of E. Coli Dna Polymerase Iii
pdb|1XXH|B Chain B, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|C Chain C, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|D Chain D, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|G Chain G, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|H Chain H, Atpgs Bound E. Coli Clamp Loader Complex
pdb|1XXH|I Chain I, Atpgs Bound E. Coli Clamp Loader Complex
Length = 373
Score = 32.3 bits (72), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 26 SLVSLPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVA 85
SLV E NG+++ ++ G+E++ L ++M G++H + PA D M A
Sbjct: 251 SLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGND--MAA 308
Query: 86 IFECIDRLFRIVRP 99
I + L R + P
Sbjct: 309 IELRMRELARTIPP 322
>pdb|3GLG|B Chain B, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|C Chain C, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|D Chain D, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|G Chain G, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|H Chain H, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
pdb|3GLG|I Chain I, Crystal Structure Of A Mutant (Gammat157a) E. Coli Clamp
Loader Bound To Primer-Template Dna
Length = 395
Score = 32.3 bits (72), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 26 SLVSLPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVA 85
SLV E NG+++ ++ G+E++ L ++M G++H + PA D M A
Sbjct: 273 SLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGND--MAA 330
Query: 86 IFECIDRLFRIVRP 99
I + L R + P
Sbjct: 331 IELRMRELARTIPP 344
>pdb|3GLH|B Chain B, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|C Chain C, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|D Chain D, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|G Chain G, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|H Chain H, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|I Chain I, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|L Chain L, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|M Chain M, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
pdb|3GLH|N Chain N, Crystal Structure Of The E. Coli Clamp Loader Bound To Psi
Peptide
Length = 376
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 26 SLVSLPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVA 85
SLV E NG+++ ++ G+E++ L ++M G++H + PA D M A
Sbjct: 254 SLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGND--MAA 311
Query: 86 IFECIDRLFRIVRP 99
I + L R + P
Sbjct: 312 IELRMRELARTIPP 325
>pdb|3GLF|B Chain B, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|C Chain C, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|D Chain D, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|G Chain G, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|H Chain H, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLF|I Chain I, Crystal Structure Of The Ecoli Clamp Loader Bound To
Primer-template Dna
pdb|3GLI|B Chain B, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|C Chain C, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|D Chain D, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|G Chain G, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|H Chain H, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
pdb|3GLI|I Chain I, Crystal Structure Of The E. Coli Clamp Loader Bound To
Primer-template Dna And Psi Peptide
Length = 395
Score = 32.0 bits (71), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/74 (28%), Positives = 36/74 (48%), Gaps = 2/74 (2%)
Query: 26 SLVSLPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIHPCTHPEDKPAPKDEDEMMVA 85
SLV E NG+++ ++ G+E++ L ++M G++H + PA D M A
Sbjct: 273 SLVEAMVEANGERVMALINEAAARGIEWEALLVEMLGLLHRIAMVQLSPAALGND--MAA 330
Query: 86 IFECIDRLFRIVRP 99
I + L R + P
Sbjct: 331 IELRMRELARTIPP 344
>pdb|3NKH|A Chain A, Crystal Structure Of Integrase From Mrsa Strain
Staphylococcus Aureus
pdb|3NKH|B Chain B, Crystal Structure Of Integrase From Mrsa Strain
Staphylococcus Aureus
Length = 244
Score = 30.4 bits (67), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 16/44 (36%), Positives = 26/44 (59%), Gaps = 1/44 (2%)
Query: 22 YSFASLVSLPQEVNGQKIPFDSSKPNPNGMEFDNLYLDMNGIIH 65
Y F +L + Q +NG +I + N + ++FDN L++NG IH
Sbjct: 54 YLFVALXTEFQALNGXRIGEXLAIQNED-IDFDNKSLNINGTIH 96
>pdb|3IK2|A Chain A, Crystal Structure Of A Glycoside Hydrolase Family 44
Endoglucanase Produced By Clostridium Acetobutylium Atcc
824
Length = 517
Score = 28.9 bits (63), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 28/109 (25%), Positives = 46/109 (42%), Gaps = 11/109 (10%)
Query: 112 PRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASKETAEKIAEVARIREKLLADGCILP 171
P+ K N+P +VY+ +D+ L + S T + VA + LA+ + P
Sbjct: 73 PKEKYNEPASVYTAFHDK------SLAMGVPY--SLVTLQAGGYVAADQSGPLANTDVAP 124
Query: 172 PEKEKGSHFDSN---CITPGTPFMACLSACLHYYIHDRLNNDPGWKGIK 217
K K F+ N +TP T + Y+ ++ + G KGIK
Sbjct: 125 SSKWKKVEFNKNGPLSLTPDTTDGSVYMDEFVNYLVNKYGSASGSKGIK 173
>pdb|2I4K|A Chain A, Solution Structure Of The Px Domain Of Sorting Nexin 1
Length = 128
Score = 27.7 bits (60), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 26/109 (23%), Positives = 45/109 (41%), Gaps = 9/109 (8%)
Query: 109 GVAPRAKMNQPLTVYSVLYDRGNYSTWQLMRSRRFRASKETAEKIAEVARIREKLLADGC 168
G+ K+ + Y V Y ++ L RS++F + ++ + ++ EK +G
Sbjct: 7 GITDPEKIGDGMNAY-VAYKVTTQTSLPLFRSKQFAVKRRFSDFLGLYEKLSEKHSQNGF 65
Query: 169 ILPPEKEKGSHFDSNCITPG------TPFMACLSACLHYYIHDRLNNDP 211
I+PP EK S + G F+ A L Y+ R+ N P
Sbjct: 66 IVPPPPEK-SLIGMTKVKVGKEDSSSAEFLEKRRAALERYLQ-RIVNHP 112
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
0.318 0.135 0.414
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,185,137
Number of Sequences: 62578
Number of extensions: 290886
Number of successful extensions: 578
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 563
Number of HSP's gapped (non-prelim): 13
length of query: 226
length of database: 14,973,337
effective HSP length: 95
effective length of query: 131
effective length of database: 9,028,427
effective search space: 1182723937
effective search space used: 1182723937
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: 50 (23.9 bits)