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= psy3343
(274 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 94.0 bits (232), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 45/77 (58%), Positives = 55/77 (71%)
Query: 96 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT 155
K +IL KNLP TL +++ F FG LGRVL+P GIT +VEFL+ +A+ AF LAY+
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS 69
Query: 156 KFKEVPLYLEWAPEGVF 172
KF VPLYLEWAP GVF
Sbjct: 70 KFHHVPLYLEWAPIGVF 86
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 30/87 (34%), Positives = 47/87 (54%), Gaps = 8/87 (9%)
Query: 89 QVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQ 141
QV + ++ ILV+N+P++ +++ LF FG+L V +P + G V+F+
Sbjct: 8 QVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFIT 67
Query: 142 KNQAKAAFNSLAY-TKFKEVPLYLEWA 167
K AK AFN+L + T L LEWA
Sbjct: 68 KQDAKKAFNALCHSTHLYGRRLVLEWA 94
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 43.9 bits (102), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 21/48 (43%), Positives = 33/48 (68%), Gaps = 2/48 (4%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM 274
+ L+IKNLNF++TE++++ F K G I S T+++KK+ G LSM
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNK--AGVLLSM 50
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 40.8 bits (94), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 152
I V NL T TDL+ LF PFG + R+ + TG + F ++ A A +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 153 AYTKFKEVPLYLEWA 167
+ + + L +EWA
Sbjct: 78 SGFGYDHLILNVEWA 92
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 39.3 bits (90), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 34/126 (26%), Positives = 50/126 (39%), Gaps = 8/126 (6%)
Query: 33 GTNAIAEAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVE 92
G E E +A AE + A GE + T+ F G + VE
Sbjct: 9 GKTLKGETTTEAVDAATAEKVFKQYANDNGVDGEWTYDDATKTFTVTEGSHHHHHHMDVE 68
Query: 93 ARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAK 146
+ + V NL YRT P L+ +FE +G +G V +P T V F K A+
Sbjct: 69 GMTS--LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAE 126
Query: 147 AAFNSL 152
A +++
Sbjct: 127 DAMDAM 132
Score = 32.3 bits (72), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 25/44 (56%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
T+L + NL + ++ D++RR F+K G + V + R + K F
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGF 114
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 35.8 bits (81), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 16/43 (37%), Positives = 26/43 (60%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
TL + NL + ++ DS+RR F+K G + V + R+ K+P F
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGF 57
Score = 35.0 bits (79), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 20/57 (35%), Positives = 28/57 (49%), Gaps = 8/57 (14%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFLQKNQAKAA 148
+ V NL YRT P L+ +FE +G +G V +P P G V F + A+ A
Sbjct: 16 LKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFA-FVRFHDRRDAQDA 71
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 35.8 bits (81), Expect = 0.027, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 152
+ V NL YRT P L+ +FE +G +G V +P T V F K A+ A +++
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Score = 32.7 bits (73), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 12/36 (33%), Positives = 23/36 (63%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
T+L + NL + ++ D++RR F+K G + V + R +
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDR 83
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 33.9 bits (76), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 5/81 (6%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL--VEFLQKNQAKAAFNS 151
R R +L KNLPY+ +LK +FE ++ R++ G+ +EF + A+ F
Sbjct: 91 RDARTLLAKNLPYKVTQDELKEVFEDAAEI-RLVSKDGKSKGIAYIEFKTEADAEKTFEE 149
Query: 152 LAYTKF--KEVPLYLEWAPEG 170
T+ + + LY P+G
Sbjct: 150 KQGTEIDGRSISLYYTGEPKG 170
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/43 (39%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP-KSPG 269
+T+Y+ NL F+ T + + R F K G + VT+ + KD KS G
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKG 59
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA 260
TT+ +KNL + ++ + ++FK CGPI V VA
Sbjct: 5 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA 37
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 33.1 bits (74), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA 260
TT+ +KNL + ++ + ++FK CGPI V VA
Sbjct: 42 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA 74
>pdb|4DBG|B Chain B, Crystal Structure Of Hoil-1l-Ubl Complexed With A Hoip-Uba
Derivative
Length = 162
Score = 33.1 bits (74), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 34/66 (51%)
Query: 63 AMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGD 122
+G E RA+L+ +G +A + V R +++ +++L + L+ALF+ GD
Sbjct: 71 GLGAFSCQEARRAWLDRHGNLDEAVEECVRTRRRKVQELQSLGFGPEEGSLQALFQHGGD 130
Query: 123 LGRVLV 128
+ R L
Sbjct: 131 VSRALT 136
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 33.1 bits (74), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 14/39 (35%), Positives = 26/39 (66%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
LY+ NL+ TED ++++F+ GPIA++ + K+ K+
Sbjct: 2 VLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKN 40
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 32.7 bits (73), Expect = 0.24, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 153
RS +LV LP DLK GD+ V G+ G+VE+L+K + A L
Sbjct: 13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGM-GMVEYLRKEDMEYALRKLD 71
Query: 154 YTKFK 158
TKF+
Sbjct: 72 DTKFR 76
>pdb|3PGW|S Chain S, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|L Chain L, Crystal Structure Of Human U1 Snrnp
Length = 437
Score = 32.3 bits (72), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
TL++ +N+++TE +RR F+ GPI + + K
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSK 138
>pdb|3CW1|K Chain K, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|6 Chain 6, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|7 Chain 7, Crystal Structure Of Human Spliceosomal U1 Snrnp
pdb|3CW1|8 Chain 8, Crystal Structure Of Human Spliceosomal U1 Snrnp
Length = 216
Score = 32.3 bits (72), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 12/35 (34%), Positives = 22/35 (62%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
TL++ +N+++TE +RR F+ GPI + + K
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSK 138
>pdb|2UP1|A Chain A, Structure Of Up1-Telomeric Dna Complex
pdb|1PO6|A Chain A, Crystal Structure Of Up1 Complexed With
D(Tagg(6mi)ttaggg): A Human Telomeric Repeat Containing
6-Methyl-8-(2-Deoxy-
Beta-Ribofuranosyl)isoxanthopteridine (6mi)
Length = 183
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L+I L+F +T++S+R HF++ G + V R + K F
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGF 50
>pdb|3B4D|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|A Chain A, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|B Chain B, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|C Chain C, Crystal Structure Of Human Pabpn1 Rrm
pdb|3B4M|D Chain D, Crystal Structure Of Human Pabpn1 Rrm
Length = 96
Score = 32.3 bits (72), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 12/43 (27%), Positives = 23/43 (53%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
++Y+ N+++ +T + + HF CG + VT+ K P F
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGF 49
>pdb|1H2T|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|X Chain X, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2U|Y Chain Y, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
In Complex With A Cap Analogue M7gpppg
pdb|1H2V|Z Chain Z, Structure Of The Human Nuclear Cap-Binding-Complex (Cbc)
pdb|1N52|B Chain B, Cap Binding Complex
pdb|1N54|B Chain B, Cap Binding Complex M7gpppg Free
pdb|3FEX|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex.
pdb|3FEY|B Chain B, Crystal Structure Of The Cbc-Importin Alpha Complex
Length = 156
Score = 32.0 bits (71), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 16/45 (35%), Positives = 23/45 (51%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFL 272
TLY+ NL+F +TE+ I F K G I + + K K+ F
Sbjct: 40 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFC 84
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 32.0 bits (71), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L+I L+F +T++S+R HF++ G + V R + K F
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGF 57
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L+I L+F +T++S+R HF++ G + V R + K F
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGF 55
>pdb|2JWN|A Chain A, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
pdb|2JWN|B Chain B, Solution Nmr Structure Of The Protease-Resistent Domain Of
Xenopus Laevis Epabp2
Length = 124
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 10/31 (32%), Positives = 19/31 (61%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
++Y+ N+++ ST + HF CG I +T+
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITI 68
>pdb|1L3K|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
pdb|1U1K|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt 7da
Ggg); A Human Telomeric Repeat Containing
7-Deaza-Adenine
pdb|1U1L|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtt Prn
Ggg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1M|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 7gu
Gg); A Human Telomeric Repeat Containing 7-Deaza-Guanine
pdb|1U1N|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta (Prn)
Gg); A Human Telomeric Repeat Containing Nebularine
pdb|1U1O|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggttag(Di)g); A Human Telomeric Repeat Containing
Inosine
pdb|1U1P|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggtta 2pr
Gg); A Human Telomeric Repeat Containing 2-Aminopurine
pdb|1U1Q|A Chain A, Crystal Structure Of Up1 Complexed With
D(Ttagggtta(Di)gg); A Human Telomeric Repeat Containing
Inosine
pdb|1U1R|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(2pr)
G); A Human Telomeric Repeat Containing 2-Aminopurine
Length = 196
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L+I L+F +T++S+R HF++ G + V R + K F
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGF 57
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 32.0 bits (71), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L+I L+F +T++S+R HF++ G + V R + K F
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGF 58
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 32.0 bits (71), Expect = 0.41, Method: Composition-based stats.
Identities = 14/36 (38%), Positives = 22/36 (61%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
TTLY+ L TE +R HF + G I ++TV +++
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQ 48
>pdb|1PGZ|A Chain A, Crystal Structure Of Up1 Complexed With D(Ttagggttag(6-Mi)
G); A Human Telomeric Repeat Containing 6-Methyl-8-(2-
Deoxy-Beta-Ribofuranosyl)isoxanthopteridine (6-Mi)
Length = 195
Score = 32.0 bits (71), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L+I L+F +T++S+R HF++ G + V R + K F
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGF 56
>pdb|1WEX|A Chain A, Solution Structure Of Rrm Domain In Protein Bab28521
Length = 104
Score = 31.6 bits (70), Expect = 0.50, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 31/67 (46%), Gaps = 5/67 (7%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKF 157
++ V+ L + DL E FG + V++ P+ LVEF + AK A
Sbjct: 17 VVHVRGLCESVVEADLVEALEKFGTICYVMMMPFKRQALVEFENIDSAKECVTFAA---- 72
Query: 158 KEVPLYL 164
+VP+Y+
Sbjct: 73 -DVPVYI 78
>pdb|3UCG|A Chain A, Crystal Structure Of A Rna Binding Domain Of Hypothetical
Polyadenylate-Binding Protein (Pabpn1) From Homo Sapiens
At 1.95 A Resolution
Length = 89
Score = 31.6 bits (70), Expect = 0.52, Method: Composition-based stats.
Identities = 12/43 (27%), Positives = 23/43 (53%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
++Y+ N+++ +T + + HF CG + VT+ K P F
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGF 50
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 31.6 bits (70), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 24/36 (66%), Gaps = 2/36 (5%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDP 265
++I LN+++TED++R +F K G + + + KDP
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYGTVTDLKIM--KDP 39
>pdb|2O3D|A Chain A, Structure Of Human Sf2ASF RNA RECOGNITION MOTIF 2 (RRM2)
Length = 113
Score = 31.2 bits (69), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 153
RS+ ++V LP DLK GD+ V G TG+VEF++K A L
Sbjct: 13 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKEDMTYAVRKLD 71
Query: 154 YTKFK 158
TKF+
Sbjct: 72 NTKFR 76
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 31.2 bits (69), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 24/38 (63%), Gaps = 2/38 (5%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKS 267
L+I L+F +TE+S+R ++++ G + V R DP S
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMR--DPAS 65
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 31.2 bits (69), Expect = 0.69, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 30/72 (41%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
+ V NLP D K LFE +G+ V + G + + A+ A L T K
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 84
Query: 159 EVPLYLEWAPEG 170
PL + +A G
Sbjct: 85 SRPLRIRFATHG 96
>pdb|3BEG|B Chain B, Crystal Structure Of Sr Protein Kinase 1 Complexed To Its
Substrate AsfSF2
Length = 115
Score = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 94 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 153
RS+ ++V LP DLK GD+ V G TG+VEF++K A L
Sbjct: 14 RSENRVVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKEDMTYAVRKLD 72
Query: 154 YTKFK 158
TKF+
Sbjct: 73 NTKFR 77
>pdb|2J7Q|A Chain A, Crystal Structure Of The Ubiquitin-Specific Protease
Encoded By Murine Cytomegalovirus Tegument Protein M48
In Complex With A Ubquitin-Based Suicide Substrate
Length = 232
Score = 30.8 bits (68), Expect = 0.79, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 6/87 (6%)
Query: 79 ENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFE-PFGDLGRVLVPPYGITGLV 137
++G +LDA + + + KR L + PYR L T++ + E P G G L P+ T
Sbjct: 53 DSGARLDA---IADEKVKRQALTDH-PYR-LGTEIPTVIETPAGITGHALSRPFNGTAET 107
Query: 138 EFLQKNQAKAAFNSLAYTKFKEVPLYL 164
+ L + + L Y + K +P+Y+
Sbjct: 108 QDLGGYKCLGILDFLTYARGKPLPVYI 134
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 30.8 bits (68), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 13/37 (35%), Positives = 23/37 (62%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD 264
+ LY+ +L+FN TED +R F+ G I ++ + + D
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSD 42
>pdb|1H6K|Z Chain Z, Nuclear Cap Binding Complex
pdb|1H6K|X Chain X, Nuclear Cap Binding Complex
pdb|1H6K|Y Chain Y, Nuclear Cap Binding Complex
Length = 98
Score = 30.8 bits (68), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 15/42 (35%), Positives = 22/42 (52%)
Query: 228 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
TLY+ NL+F +TE+ I F K G I + + K + G
Sbjct: 19 CTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACG 60
>pdb|2J7Q|C Chain C, Crystal Structure Of The Ubiquitin-Specific Protease
Encoded By Murine Cytomegalovirus Tegument Protein M48
In Complex With A Ubquitin-Based Suicide Substrate
Length = 232
Score = 30.8 bits (68), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 46/95 (48%), Gaps = 7/95 (7%)
Query: 79 ENGVQLDAFNQVVEARSKRIILVKNLPYRTLPTDLKALFE-PFGDLGRVLVPPYGITGLV 137
++G +LDA + + + KR L + PYR L T++ + E P G G L P+ T
Sbjct: 53 DSGARLDA---IADEKVKRQALTDH-PYR-LGTEIPTVIETPAGITGHALSRPFNGTAET 107
Query: 138 EFLQKNQAKAAFNSLAYTKFKEVPLYLEWAPEGVF 172
+ L + + L Y + K +P+Y+ GVF
Sbjct: 108 QDLGGYKCLGILDFLTYARGKPLPVYI-IVTVGVF 141
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 15/40 (37%), Positives = 21/40 (52%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
L++ LN +ED +RR F+ G I T+ R D S G
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKG 57
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 6/79 (7%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 151
++ V NLP + L PFG L R + TG E+++K+ A A +
Sbjct: 97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 152 LAYTKFKEVPLYLEWAPEG 170
L LY+ W G
Sbjct: 157 LLGKPLGPRTLYVHWTDAG 175
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 30.4 bits (67), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 6/79 (7%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 151
++ V NLP + L PFG L R + TG E+++K+ A A +
Sbjct: 97 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 156
Query: 152 LAYTKFKEVPLYLEWAPEG 170
L LY+ W G
Sbjct: 157 LLGKPLGPRTLYVHWTDAG 175
>pdb|3H2U|B Chain B, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
pdb|3H2U|D Chain D, Human Raver1 Rrm1, Rrm2, And Rrm3 Domains In Complex With
Human Vinculin Tail Domain Vt
Length = 283
Score = 30.4 bits (67), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 31/79 (39%), Gaps = 6/79 (7%)
Query: 98 IILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNS 151
++ V NLP + L PFG L R + TG E+++K+ A A +
Sbjct: 95 LLCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSD 154
Query: 152 LAYTKFKEVPLYLEWAPEG 170
L LY+ W G
Sbjct: 155 LLGKPLGPRTLYVHWTDAG 173
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 30.0 bits (66), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 16/30 (53%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLV 128
I V LPY T L+ FE FGD+ +V
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVV 49
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 30.0 bits (66), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
D +Y+ NL N + + R F GP+ SV VAR
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR 107
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 14/35 (40%), Positives = 19/35 (54%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVAR 261
D +Y+ NL N + + R F GP+ SV VAR
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVAR 107
>pdb|1X4C|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 2
Length = 108
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 99 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 158
++V LP DLK GD+ V G TG+VEF++K A L TKF+
Sbjct: 18 VVVSGLPPSGSWQDLKDHMREAGDVCYADVYRDG-TGVVEFVRKEDMTYAVRKLDNTKFR 76
>pdb|2NQ9|A Chain A, High Resolution Crystal Structure Of Escherichia Coli
Endonuclease Iv (Endo Iv) Y72a Mutant Bound To Damaged
Dna
Length = 285
Score = 29.6 bits (65), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 29/56 (51%), Gaps = 3/56 (5%)
Query: 27 WNSLFLGTNAIAE--AMAETYNATKAEVLTGSGAATRLAMGETEIVEKTR-AFLEE 79
W + L T I E A E Y+ T A++L A L TE +EK+R AF++E
Sbjct: 39 WRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSALINLGHPVTEALEKSRDAFIDE 94
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 29.3 bits (64), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 13/30 (43%), Positives = 20/30 (66%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTV 259
LY+ +L+FN TED +R F+ G I S+ +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQL 58
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 23/37 (62%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPK 266
L++ L+F++ E S+ + F K G I+ V V + ++ +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQ 51
>pdb|2UXT|A Chain A, Sufi Protein From Escherichia Coli
pdb|2UXT|B Chain B, Sufi Protein From Escherichia Coli
pdb|2UXV|A Chain A, Sufi Protein From Escherichia Coli
pdb|2UXV|B Chain B, Sufi Protein From Escherichia Coli
Length = 451
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 16/77 (20%), Positives = 32/77 (41%), Gaps = 9/77 (11%)
Query: 39 EAMAETYNATKAEVLTGSGAATRLAMGETEIVEKTRAFLEENGVQLDAFNQVVEARSKRI 98
E + + N + + G A+ IV++ R F E + + + +
Sbjct: 253 EILVDMSNGDEVSITCGEAAS---------IVDRIRGFFEPSSILVSTLVLTLRPTGLLP 303
Query: 99 ILVKNLPYRTLPTDLKA 115
++ +LP R LPT++ A
Sbjct: 304 LVTDSLPMRLLPTEIMA 320
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
TL KNL+FN TED ++ F+ I V+ +D KS G
Sbjct: 101 TLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKG 137
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 28.9 bits (63), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 14/45 (31%), Positives = 25/45 (55%), Gaps = 2/45 (4%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD--PKSPG 269
D T+++ NL E+ + F + GP+ VT+ + ++ PKS G
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFG 60
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 28.5 bits (62), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%), Gaps = 4/41 (9%)
Query: 229 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPG 269
TL KNL+FN TED ++ F+ I V+ +D KS G
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSKG 54
>pdb|4A5W|A Chain A, Crystal Structure Of C5b6
Length = 1580
Score = 28.1 bits (61), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 141 QKNQAKAAFNSLAYTKFKEVPLYLEW 166
++NQA+ + ++AY+ + LY++W
Sbjct: 426 EENQAREGYRAIAYSSLSQSYLYIDW 451
>pdb|3CU7|A Chain A, Human Complement Component 5
pdb|3CU7|B Chain B, Human Complement Component 5
pdb|3KLS|A Chain A, Structure Of Complement C5 In Complex With Ssl7
pdb|3KLS|B Chain B, Structure Of Complement C5 In Complex With Ssl7
pdb|3KM9|A Chain A, Structure Of Complement C5 In Complex With The C-Terminal
Beta-Grasp Domain Of Ssl7
pdb|3KM9|B Chain B, Structure Of Complement C5 In Complex With The C-Terminal
Beta-Grasp Domain Of Ssl7
pdb|4E0S|A Chain A, Crystal Structure Of C5b-6
Length = 1676
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 141 QKNQAKAAFNSLAYTKFKEVPLYLEW 166
++NQA+ + ++AY+ + LY++W
Sbjct: 444 EENQAREGYRAIAYSSLSQSYLYIDW 469
>pdb|3PRX|A Chain A, Structure Of Complement C5 In Complex With Cvf And Ssl7
pdb|3PRX|C Chain C, Structure Of Complement C5 In Complex With Cvf And Ssl7
pdb|3PVM|A Chain A, Structure Of Complement C5 In Complex With Cvf
pdb|3PVM|C Chain C, Structure Of Complement C5 In Complex With Cvf
Length = 1676
Score = 28.1 bits (61), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 8/26 (30%), Positives = 18/26 (69%)
Query: 141 QKNQAKAAFNSLAYTKFKEVPLYLEW 166
++NQA+ + ++AY+ + LY++W
Sbjct: 444 EENQAREGYRAIAYSSLSQSYLYIDW 469
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 27.7 bits (60), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 11/42 (26%), Positives = 23/42 (54%)
Query: 230 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQF 271
L+++NL++ S+E+ + + F GP++ + K P F
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGF 52
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 27.7 bits (60), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 9/32 (28%), Positives = 21/32 (65%)
Query: 97 RIILVKNLPYRTLPTDLKALFEPFGDLGRVLV 128
RI++++NLPY+ ++ +F +G + ++ V
Sbjct: 19 RILMIRNLPYKITAEEMYDIFGKYGPIRQIRV 50
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 27.7 bits (60), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 33/79 (41%), Gaps = 6/79 (7%)
Query: 95 SKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAA 148
SK ++V LP + K+LF GD+ + IT G V + N A A
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 149 FNSLAYTKFKEVPLYLEWA 167
N+L K + + + +A
Sbjct: 63 INTLNGLKLQTKTIKVSYA 81
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 27.3 bits (59), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 14/37 (37%), Positives = 18/37 (48%)
Query: 227 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKK 263
DT LY+ NL T+D + F K G I + R K
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDK 49
>pdb|2LCT|A Chain A, Solution Structure Of The Vav1 Sh2 Domain Complexed With A
Syk-Derived Doubly Phosphorylated Peptide
Length = 107
Score = 27.3 bits (59), Expect = 8.3, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 132 GITGLVEFLQKNQAKAAFNSLAYT 155
G+T LVEF Q+N K F SL T
Sbjct: 77 GLTELVEFYQQNSLKDCFKSLDTT 100
>pdb|2NQH|A Chain A, High Resolution Crystal Structure Of Escherichia Coli
Endonuclease Iv (Endo Iv) E261q Mutant
pdb|2NQJ|A Chain A, Crystal Structure Of Escherichia Coli Endonuclease Iv
(Endo Iv) E261q Mutant Bound To Damaged Dna
pdb|2NQJ|B Chain B, Crystal Structure Of Escherichia Coli Endonuclease Iv
(Endo Iv) E261q Mutant Bound To Damaged Dna
Length = 285
Score = 27.3 bits (59), Expect = 8.9, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 27 WNSLFLGTNAIAE--AMAETYNATKAEVLTGSGAATRLAMGETEIVEKTR-AFLEE 79
W + L T I E A E Y+ T A++L L TE +EK+R AF++E
Sbjct: 39 WRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSYLINLGHPVTEALEKSRDAFIDE 94
>pdb|2CRH|A Chain A, Solution Structure Of The Sh2 Domain Of Human Proto-
Oncogene Protein Vav1
pdb|2ROR|A Chain A, Solution Structure Of The Vav1 Sh2 Domain Complexed With A
Tyrosine-Phosphorylated Peptide From Slp76
Length = 138
Score = 27.3 bits (59), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 13/24 (54%), Positives = 15/24 (62%)
Query: 132 GITGLVEFLQKNQAKAAFNSLAYT 155
G+T LVEF Q+N K F SL T
Sbjct: 94 GLTELVEFYQQNSLKDCFKSLDTT 117
>pdb|1QUM|A Chain A, Crystal Structure Of Escherichia Coli Endonuclease Iv In
Complex With Damaged Dna
pdb|1QTW|A Chain A, High-resolution Crystal Structure Of The Escherichia
Coli Dna Repair Enzyme Endonuclease Iv
Length = 285
Score = 27.3 bits (59), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 3/56 (5%)
Query: 27 WNSLFLGTNAIAE--AMAETYNATKAEVLTGSGAATRLAMGETEIVEKTR-AFLEE 79
W + L T I E A E Y+ T A++L L TE +EK+R AF++E
Sbjct: 39 WRAAPLTTQTIDEFKAACEKYHYTSAQILPHDSYLINLGHPVTEALEKSRDAFIDE 94
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
0.316 0.134 0.386
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 6,013,486
Number of Sequences: 62578
Number of extensions: 196295
Number of successful extensions: 807
Number of sequences better than 100.0: 69
Number of HSP's better than 100.0 without gapping: 48
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 742
Number of HSP's gapped (non-prelim): 82
length of query: 274
length of database: 14,973,337
effective HSP length: 97
effective length of query: 177
effective length of database: 8,903,271
effective search space: 1575878967
effective search space used: 1575878967
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 bits)