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= psy9417
(161 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DIW|A Chain A, Solution Structure Of The Rpr Domain Of Putative Rna-
Binding Protein 16
Length = 152
Score = 130 bits (326), Expect = 5e-31, Method: Compositional matrix adjust.
Identities = 61/109 (55%), Positives = 83/109 (76%), Gaps = 1/109 (0%)
Query: 54 LYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKL 113
+ + +N EL S+N KPPISKAK+T I K A+KA +YK+VVQSVEKFI KCK +YK+
Sbjct: 10 MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 69
Query: 114 PGLYVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
PGLYVID+I+ Q+R QF + KDV+APRF+ N+ TF +++CP +D+ K
Sbjct: 70 PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 118
Score = 81.3 bits (199), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 40/57 (70%), Positives = 47/57 (82%)
Query: 1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 57
EL S+N KPPISKAK+T I K A+KA +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct: 19 ELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVI 75
>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 = 129 bits (325), Expect = 5e-31, Method: Compositional matrix adjust.
Identities = 61/109 (55%), Positives = 83/109 (76%), Gaps = 1/109 (0%)
Query: 54 LYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKL 113
+ + +N EL S+N KPPISKAK+T I K A+KA +YK+VVQSVEKFI KCK +YK+
Sbjct: 1 MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60
Query: 114 PGLYVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
PGLYVID+I+ Q+R QF + KDV+APRF+ N+ TF +++CP +D+ K
Sbjct: 61 PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109
Score = 81.6 bits (200), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 40/58 (68%), Positives = 47/58 (81%)
Query: 1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIG 58
EL S+N KPPISKAK+T I K A+KA +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct: 10 ELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVID 67
>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 = 129 bits (325), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 61/109 (55%), Positives = 83/109 (76%), Gaps = 1/109 (0%)
Query: 54 LYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKL 113
+ + +N EL S+N KPPISKAK+T I K A+KA +YK+VVQSVEKFI KCK +YK+
Sbjct: 1 MEAVKTFNSELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60
Query: 114 PGLYVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
PGLYVID+I+ Q+R QF + KDV+APRF+ N+ TF +++CP +D+ K
Sbjct: 61 PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109
Score = 81.6 bits (200), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 40/58 (68%), Positives = 47/58 (81%)
Query: 1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIG 58
EL S+N KPPISKAK+T I K A+KA +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct: 10 ELYSLNDYKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVID 67
>pdb|3D9I|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|3D9I|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 = 127 bits (320), Expect = 2e-30, Method: Compositional matrix adjust.
Identities = 60/109 (55%), Positives = 82/109 (75%), Gaps = 1/109 (0%)
Query: 54 LYVIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKL 113
+ + +N EL S+ KPPISKAK+T I K A+KA +YK+VVQSVEKFI KCK +YK+
Sbjct: 1 MEAVKTFNSELYSLMDMKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKV 60
Query: 114 PGLYVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
PGLYVID+I+ Q+R QF + KDV+APRF+ N+ TF +++CP +D+ K
Sbjct: 61 PGLYVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109
Score = 79.7 bits (195), Expect = 7e-16, Method: Compositional matrix adjust.
Identities = 39/58 (67%), Positives = 46/58 (79%)
Query: 1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIG 58
EL S+ KPPISKAK+T I K A+KA +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct: 10 ELYSLMDMKPPISKAKMTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVID 67
>pdb|3D9O|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|3D9O|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 = 126 bits (316), Expect = 7e-30, Method: Compositional matrix adjust.
Identities = 60/106 (56%), Positives = 80/106 (75%), Gaps = 1/106 (0%)
Query: 57 IGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGL 116
+ +N EL S+ KPPISKAK T I K A+KA +YK+VVQSVEKFI KCK +YK+PGL
Sbjct: 4 VKTFNSELYSLXDXKPPISKAKXTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGL 63
Query: 117 YVIDAIIHQARLQF-KYKDVYAPRFARNLYRTFGYVFQCPDEDRKK 161
YVID+I+ Q+R QF + KDV+APRF+ N+ TF +++CP +D+ K
Sbjct: 64 YVIDSIVRQSRHQFGQEKDVFAPRFSNNIISTFQNLYRCPGDDKSK 109
Score = 78.6 bits (192), Expect = 1e-15, Method: Compositional matrix adjust.
Identities = 39/58 (67%), Positives = 45/58 (77%)
Query: 1 ELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIG 58
EL S+ KPPISKAK T I K A+KA +YK+VVQSVEKFI KCK +YK+PGLYVI
Sbjct: 10 ELYSLXDXKPPISKAKXTQITKAAIKAIKFYKHVVQSVEKFIQKCKPEYKVPGLYVID 67
>pdb|2XTL|A Chain A, Structure Of The Major Pilus Backbone Protein From
Streptococcus Agalactiae
pdb|2XTL|B Chain B, Structure Of The Major Pilus Backbone Protein From
Streptococcus Agalactiae
Length = 452
Score = 36.6 bits (83), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 10/81 (12%)
Query: 25 LKATHYYKYV----VQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKPPISKAKIT 80
+KA + Y++V ++V K I K Q+++ GL G++ S+ T+ P AK++
Sbjct: 358 VKANYSYEWVEDKNAKNVVKLISNDKGQFEITGL-TEGQY-----SLEETQAPTGYAKLS 411
Query: 81 GIVKLALKATHYYKYVVQSVE 101
G V + AT Y K Q +E
Sbjct: 412 GDVSFNVNATSYSKGSAQDIE 432
Score = 28.5 bits (62), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 19/36 (52%)
Query: 4 SINSTKPPISKAKITGIVKLALKATHYYKYVVQSVE 39
S+ T+ P AK++G V + AT Y K Q +E
Sbjct: 397 SLEETQAPTGYAKLSGDVSFNVNATSYSKGSAQDIE 432
>pdb|1SZ9|A Chain A, The Rna Polymerase Ii Ctd In Mrna Processing: Beta-Turn
Recognition And Beta-Spiral Model
pdb|1SZ9|B Chain B, The Rna Polymerase Ii Ctd In Mrna Processing: Beta-Turn
Recognition And Beta-Spiral Model
pdb|1SZ9|C Chain C, The Rna Polymerase Ii Ctd In Mrna Processing: Beta-Turn
Recognition And Beta-Spiral Model
pdb|1SZA|A Chain A, The Rna Polymerase Ii Ctd In Mrna Processing: Beta-Turn
Recognition And Beta-Spiral Model
pdb|1SZA|B Chain B, The Rna Polymerase Ii Ctd In Mrna Processing: Beta-Turn
Recognition And Beta-Spiral Model
pdb|1SZA|C Chain C, The Rna Polymerase Ii Ctd In Mrna Processing: Beta-Turn
Recognition And Beta-Spiral Model
Length = 144
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 45/96 (46%), Gaps = 16/96 (16%)
Query: 56 VIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPG 115
++ ++N L + PI IT + KLA + +Y V ++E I KC + KL
Sbjct: 8 IVKDFNSILEELTFNSRPI----ITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYA 63
Query: 116 LYVIDAIIHQARLQFKYKDVYAP---RFARNLYRTF 148
Y +D+I K+V +P F+RNL+ +
Sbjct: 64 FYALDSIC---------KNVGSPYTIYFSRNLFNLY 90
Score = 27.3 bits (59), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 23/46 (50%)
Query: 13 SKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIG 58
S+ IT + KLA + +Y V ++E I KC + KL Y +
Sbjct: 23 SRPIITTLTKLAEENISCAQYFVDAIESRIEKCMPKQKLYAFYALD 68
>pdb|2BF0|X Chain X, Crystal Structure Of The Rpr Of Pcf11
Length = 143
Score = 35.0 bits (79), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 27/96 (28%), Positives = 45/96 (46%), Gaps = 16/96 (16%)
Query: 56 VIGEWNQELLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPG 115
++ ++N L + PI IT + KLA + +Y V ++E I KC + KL
Sbjct: 13 IVKDFNSILEELTFNSRPI----ITTLTKLAEENISCAQYFVDAIESRIEKCXPKQKLYA 68
Query: 116 LYVIDAIIHQARLQFKYKDVYAP---RFARNLYRTF 148
Y +D+I K+V +P F+RNL+ +
Sbjct: 69 FYALDSIC---------KNVGSPYTIYFSRNLFNLY 95
Score = 27.3 bits (59), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 15/45 (33%), Positives = 23/45 (51%)
Query: 13 SKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVI 57
S+ IT + KLA + +Y V ++E I KC + KL Y +
Sbjct: 28 SRPIITTLTKLAEENISCAQYFVDAIESRIEKCXPKQKLYAFYAL 72
>pdb|3MD7|A Chain A, Crystal Structure Of A Beta-Lactamase-Like Protein Bound
To Gmp From Brucella Melitensis
Length = 293
Score = 33.1 bits (74), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 122 IIHQARLQFKYKDVYAPRFARN-LYRTFGYVFQCP 155
++ RL DVYA R RN LY TFGY F+ P
Sbjct: 123 VVDNGRLM----DVYANRLTRNRLYDTFGYCFETP 153
>pdb|3PY6|A Chain A, Crystal Structure Of A Beta-Lactamase-Like Protein From
Brucella Melitensis Bound To Gmp
pdb|3PY5|A Chain A, Crystal Structure Of A Beta-Lactamase-Like Protein From
Brucella Melitensis Bound To Amp
pdb|3QH8|A Chain A, Crystal Structure Of A Beta-Lactamase-Like Protein Bound
To Amp From Brucella Melitensis, Long Wavelength
Synchrotron Data
Length = 274
Score = 33.1 bits (74), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 17/35 (48%), Positives = 20/35 (57%), Gaps = 5/35 (14%)
Query: 122 IIHQARLQFKYKDVYAPRFARN-LYRTFGYVFQCP 155
++ RL DVYA R RN LY TFGY F+ P
Sbjct: 104 VVDNGRLM----DVYANRLTRNRLYDTFGYCFETP 134
>pdb|2LO6|A Chain A, Structure Of Nrd1 Cid Bound To Phosphorylated Rnap Ii Ctd
Length = 161
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 26/59 (44%)
Query: 64 LLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAI 122
L S K IS ++I + AL ++ + + C +KL LY+ID+I
Sbjct: 14 LESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYIIDSI 72
>pdb|3KCZ|A Chain A, Human Poly(Adp-Ribose) Polymerase 2, Catalytic Fragment In
Complex With An Inhibitor 3-Aminobenzamide
pdb|3KCZ|B Chain B, Human Poly(Adp-Ribose) Polymerase 2, Catalytic Fragment In
Complex With An Inhibitor 3-Aminobenzamide
pdb|3KJD|A Chain A, Human Poly(Adp-Ribose) Polymerase 2, Catalytic Fragment In
Complex With An Inhibitor Abt-888
pdb|3KJD|B Chain B, Human Poly(Adp-Ribose) Polymerase 2, Catalytic Fragment In
Complex With An Inhibitor Abt-888
Length = 368
Score = 27.3 bits (59), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 18/85 (21%), Positives = 40/85 (47%)
Query: 13 SKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIGEWNQELLSINSTKP 72
S+ K TG++ L+ A ++++ K + ++ GL + + +++N +
Sbjct: 266 SRLKNTGLLLLSEVALGQCNELLEANPKAEGLLQGKHSTKGLGKMAPSSAHFVTLNGSTV 325
Query: 73 PISKAKITGIVKLALKATHYYKYVV 97
P+ A TGI+ +Y +Y+V
Sbjct: 326 PLGPASDTGILNPDGYTLNYNEYIV 350
>pdb|3CLJ|A Chain A, Structure Of The Rna Polymerase Ii Ctd-Interacting Domain
Of Nrd1
Length = 157
Score = 26.9 bits (58), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 26/59 (44%)
Query: 64 LLSINSTKPPISKAKITGIVKLALKATHYYKYVVQSVEKFIWKCKSQYKLPGLYVIDAI 122
L S K IS ++I + AL ++ + + C +KL LY+ID+I
Sbjct: 10 LESFKDLKSGISGSRIKKLTTYALDHIDIESKIISLIIDYSRLCPDSHKLGSLYIIDSI 68
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 0.137 0.416
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,671,799
Number of Sequences: 62578
Number of extensions: 165210
Number of successful extensions: 326
Number of sequences better than 100.0: 13
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 2
Number of HSP's that attempted gapping in prelim test: 299
Number of HSP's gapped (non-prelim): 24
length of query: 161
length of database: 14,973,337
effective HSP length: 91
effective length of query: 70
effective length of database: 9,278,739
effective search space: 649511730
effective search space used: 649511730
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: 47 (22.7 bits)