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= psy4846
(279 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2WP8|J Chain J, Yeast Rrp44 Nuclease
Length = 977
Score = 134 bits (337), Expect = 6e-32, Method: Compositional matrix adjust.
Identities = 76/187 (40%), Positives = 97/187 (51%), Gaps = 23/187 (12%)
Query: 4 AMLRRHPVPPPANFEPLLHAAR-RQGFELSVGTGKELATSLD------------------ 44
AMLRRH PP NFE L R+ +S+ + K LA SLD
Sbjct: 726 AMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMS 785
Query: 45 ----AAAVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYP 100
AA YF SG DF HYGLA IYTHFTSPIRRY D++ HR LA IG +
Sbjct: 786 TRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSL 845
Query: 101 SLLDKKASTALCYNLNYRNRQAQYAGRASVALHTHLFFRSRVQDEDGYVLYVRKNALQIL 160
+ DK +C N+N ++R AQ+AGRAS+ + R+ E GYV+ V N + +L
Sbjct: 846 THRDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVL 905
Query: 161 IPKSRVQ 167
+PK V+
Sbjct: 906 VPKFGVE 912
>pdb|4IFD|J Chain J, Crystal Structure Of An 11-subunit Eukaryotic Exosome
Complex Bound To Rna
Length = 1003
Score = 134 bits (336), Expect = 6e-32, Method: Compositional matrix adjust.
Identities = 76/187 (40%), Positives = 97/187 (51%), Gaps = 23/187 (12%)
Query: 4 AMLRRHPVPPPANFEPLLHAAR-RQGFELSVGTGKELATSLD------------------ 44
AMLRRH PP NFE L R+ +S+ + K LA SLD
Sbjct: 752 AMLRRHAAPPSTNFEILNEMLNTRKNMSISLESSKALADSLDRCVDPEDPYFNTLVRIMS 811
Query: 45 ----AAAVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYP 100
AA YF SG DF HYGLA IYTHFTSPIRRY D++ HR LA IG +
Sbjct: 812 TRCMMAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSL 871
Query: 101 SLLDKKASTALCYNLNYRNRQAQYAGRASVALHTHLFFRSRVQDEDGYVLYVRKNALQIL 160
+ DK +C N+N ++R AQ+AGRAS+ + R+ E GYV+ V N + +L
Sbjct: 872 THRDKNKMDMICRNINRKHRNAQFAGRASIEYYVGQVMRNNESTETGYVIKVFNNGIVVL 931
Query: 161 IPKSRVQ 167
+PK V+
Sbjct: 932 VPKFGVE 938
>pdb|2VNU|D Chain D, Crystal Structure Of Sc Rrp44
Length = 760
Score = 130 bits (328), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 75/187 (40%), Positives = 96/187 (51%), Gaps = 23/187 (12%)
Query: 4 AMLRRHPVPPPANFEPLLHAAR-RQGFELSVGTGKELATSLD------------------ 44
A LRRH PP NFE L R+ +S+ + K LA SLD
Sbjct: 509 AXLRRHAAPPSTNFEILNEXLNTRKNXSISLESSKALADSLDRCVDPEDPYFNTLVRIXS 568
Query: 45 ----AAAVYFSSGMLQQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGADATYP 100
AA YF SG DF HYGLA IYTHFTSPIRRY D++ HR LA IG +
Sbjct: 569 TRCXXAAQYFYSGAYSYPDFRHYGLAVDIYTHFTSPIRRYCDVVAHRQLAGAIGYEPLSL 628
Query: 101 SLLDKKASTALCYNLNYRNRQAQYAGRASVALHTHLFFRSRVQDEDGYVLYVRKNALQIL 160
+ DK +C N+N ++R AQ+AGRAS+ + R+ E GYV+ V N + +L
Sbjct: 629 THRDKNKXDXICRNINRKHRNAQFAGRASIEYYVGQVXRNNESTETGYVIKVFNNGIVVL 688
Query: 161 IPKSRVQ 167
+PK V+
Sbjct: 689 VPKFGVE 695
>pdb|2IX0|A Chain A, Rnase Ii
Length = 663
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/40 (55%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 62 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI-GADATYP 100
H+GL Y +TSPIR+Y D+I HRLL A I G AT P
Sbjct: 503 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRP 542
>pdb|2IX1|A Chain A, Rnase Ii D209n Mutant
Length = 664
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/40 (55%), Positives = 26/40 (65%), Gaps = 1/40 (2%)
Query: 62 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI-GADATYP 100
H+GL Y +TSPIR+Y D+I HRLL A I G AT P
Sbjct: 504 HFGLGLEAYATWTSPIRKYGDMINHRLLKAVIKGETATRP 543
>pdb|2ID0|A Chain A, Escherichia Coli Rnase Ii
pdb|2ID0|B Chain B, Escherichia Coli Rnase Ii
pdb|2ID0|C Chain C, Escherichia Coli Rnase Ii
pdb|2ID0|D Chain D, Escherichia Coli Rnase Ii
Length = 644
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 22/40 (55%), Positives = 25/40 (62%), Gaps = 1/40 (2%)
Query: 62 HYGLATPIYTHFTSPIRRYADIIVHRLLAACI-GADATYP 100
H+GL Y +TSPIR+Y D I HRLL A I G AT P
Sbjct: 484 HFGLGLEAYATWTSPIRKYGDXINHRLLKAVIKGETATRP 523
>pdb|2R7D|A Chain A, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7D|B Chain B, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7D|C Chain C, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Triclinic Crystal Form.
Northeast Structural Genomics Target Drr63
pdb|2R7F|A Chain A, Crystal Structure Of Ribonuclease Ii Family Protein From
Deinococcus Radiodurans, Hexagonal Crystal Form.
Northeast Structural Genomics Target Drr63
Length = 469
Score = 35.4 bits (80), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 16/40 (40%), Positives = 22/40 (55%)
Query: 56 QQSDFHHYGLATPIYTHFTSPIRRYADIIVHRLLAACIGA 95
Q S H+G +Y TSP RRY D++VH+ L A +
Sbjct: 321 QPSPGPHHGXGLDLYAQATSPXRRYLDLVVHQQLRAFLAG 360
>pdb|3ASY|A Chain A, Ligand-Free Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASY|B Chain B, Ligand-Free Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASZ|A Chain A, Cmp-Complex Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
pdb|3ASZ|B Chain B, Cmp-Complex Structure Of Uridine Kinase From Thermus
Thermophilus Hb8
Length = 211
Score = 31.2 bits (69), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 11/20 (55%), Positives = 15/20 (75%)
Query: 68 PIYTHFTSPIRRYADIIVHR 87
P++ HF P +RYAD+IV R
Sbjct: 167 PMHLHFVEPTKRYADVIVPR 186
>pdb|2XNT|A Chain A, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|B Chain B, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|C Chain C, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|D Chain D, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|E Chain E, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|F Chain F, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|G Chain G, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|H Chain H, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|I Chain I, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNT|J Chain J, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNU|A Chain A, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNU|B Chain B, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNU|C Chain C, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNU|D Chain D, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNU|E Chain E, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|A Chain A, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|B Chain B, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|C Chain C, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|D Chain D, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|E Chain E, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|F Chain F, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|G Chain G, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|H Chain H, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|I Chain I, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
pdb|2XNV|J Chain J, Acetylcholine Binding Protein (Achbp) As Template For
Hierarchical In Silico Screening Procedures To Identify
Structurally Novel Ligands For The Nicotinic Receptors
Length = 236
Score = 27.3 bits (59), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 26/61 (42%)
Query: 151 YVRKNALQILIPKSRVQDEDGYVLYVRKNALQILIPKYGLEGTLFLRCDSPSVSWTYNEK 210
Y +Q+L P+ V DG V+++ L + G++ + C SW Y+
Sbjct: 110 YSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGVTCAVKFGSWVYSGF 169
Query: 211 E 211
E
Sbjct: 170 E 170
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 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,682,809
Number of Sequences: 62578
Number of extensions: 294741
Number of successful extensions: 609
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 22
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 581
Number of HSP's gapped (non-prelim): 26
length of query: 279
length of database: 14,973,337
effective HSP length: 98
effective length of query: 181
effective length of database: 8,840,693
effective search space: 1600165433
effective search space used: 1600165433
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: 51 (24.3 bits)