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= psy17274
(184 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2ADC|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd34 Complexed With Cucucu Rna
pdb|2EVZ|A Chain A, Structure Of Rna Binding Domains 3 And 4 Of Polypyrimidine
Tract Binding Protein
Length = 229
Score = 253 bits (646), Expect = 5e-68, Method: Compositional matrix adjust.
Identities = 120/178 (67%), Positives = 145/178 (81%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F L GVYGDV RVKIL+NKK++AL+QMA+ +QA LAM H++ ++ GK +R+ +SKHQ
Sbjct: 52 LFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN 111
Query: 61 VQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEA 120
VQLP+EGQ D GLTKDY SPLHRFKKPGSKNFQNI+PPS TLHLSNIP SV+E++LK
Sbjct: 112 VQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVL 171
Query: 121 FTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKSNI 178
F+ G VKGFKFF KDRKMAL+Q+ S+EEA+ ALI +HNH L E HLRVSFSKS I
Sbjct: 172 FSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 229
>pdb|1QM9|A Chain A, Nmr, Representative Structure
Length = 198
Score = 253 bits (645), Expect = 5e-68, Method: Compositional matrix adjust.
Identities = 120/178 (67%), Positives = 145/178 (81%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F L GVYGDV RVKIL+NKK++AL+QMA+ +QA LAM H++ ++ GK +R+ +SKHQ
Sbjct: 21 LFILFGVYGDVQRVKILFNKKENALVQMADGNQAQLAMSHLNGHKLHGKPIRITLSKHQN 80
Query: 61 VQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEA 120
VQLP+EGQ D GLTKDY SPLHRFKKPGSKNFQNI+PPS TLHLSNIP SV+E++LK
Sbjct: 81 VQLPREGQEDQGLTKDYGNSPLHRFKKPGSKNFQNIFPPSATLHLSNIPPSVSEEDLKVL 140
Query: 121 FTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFSKSNI 178
F+ G VKGFKFF KDRKMAL+Q+ S+EEA+ ALI +HNH L E HLRVSFSKS I
Sbjct: 141 FSSNGGVVKGFKFFQKDRKMALIQMGSVEEAVQALIDLHNHDLGENHHLRVSFSKSTI 198
>pdb|3TYT|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein L (Hnrpl) From Mus Musculus At 1.60 A
Resolution
Length = 205
Score = 76.6 bits (187), Expect = 7e-15, Method: Compositional matrix adjust.
Identities = 51/170 (30%), Positives = 90/170 (52%), Gaps = 8/170 (4%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F++ +YG+V +VK + +K +A+++MA+ + A+ H++ +FG++M V +SK A
Sbjct: 22 VFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKMNVCVSKQPA 81
Query: 61 VQLPKE--GQPDAGLT-KDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDEL 117
+ +P + G D + KD++ S +RF P I PS LH N P VTE+
Sbjct: 82 I-MPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENF 140
Query: 118 KEAFTEKGF----TVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQL 163
E E G +VK F + LL+ DS +A+ L ++++Q+
Sbjct: 141 FEICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQM 190
>pdb|3TO8|A Chain A, Crystal Structure Of The Two C-Terminal Rrm Domains Of
Heterogeneous Nuclear Ribonucleoprotein L (Hnrnp L)
Length = 218
Score = 73.6 bits (179), Expect = 6e-14, Method: Compositional matrix adjust.
Identities = 49/170 (28%), Positives = 90/170 (52%), Gaps = 8/170 (4%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F++ +YG+V +VK + +K +A+++MA+ + A+ H++ +FG+++ V +SK A
Sbjct: 28 VFNVFCLYGNVEKVKFMKSKPGAAMVEMADGYAVDRAITHLNNNFMFGQKLNVCVSKQPA 87
Query: 61 VQLPKE--GQPDAGLT-KDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDEL 117
+ +P + G D + KD++ S +RF P I PS LH N P VTE+
Sbjct: 88 I-MPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENF 146
Query: 118 KEAFTEKGF----TVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQL 163
E E G +VK F + LL+ +S +A+ L ++++Q+
Sbjct: 147 FEICDELGVKRPSSVKVFSGKSERSSSGLLEWESKSDALETLGFLNHYQM 196
>pdb|3S01|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein L (Hnrpl) From Mus Musculus At 2.15 A
Resolution
Length = 212
Score = 67.4 bits (163), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 48/168 (28%), Positives = 82/168 (48%), Gaps = 6/168 (3%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F++ +YG+V +VK +K +A ++ A+ + A+ H++ FG++ V +SK A
Sbjct: 22 VFNVFCLYGNVEKVKFXKSKPGAAXVEXADGYAVDRAITHLNNNFXFGQKXNVCVSKQPA 81
Query: 61 VQLPKE-GQPDAGLT-KDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELK 118
+ + G D + KD++ S +RF P I PS LH N P VTE+
Sbjct: 82 IXPGQSYGLEDGSCSYKDFSESRNNRFSTPEQAAKNRIQHPSNVLHFFNAPLEVTEENFF 141
Query: 119 EAFTEKGF----TVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQ 162
E E G +VK F + LL+ DS +A+ L ++++Q
Sbjct: 142 EICDELGVKRPTSVKVFSGKSERSSSGLLEWDSKSDALETLGFLNHYQ 189
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 42.4 bits (98), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 32/103 (31%), Positives = 51/103 (49%), Gaps = 12/103 (11%)
Query: 72 GLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGF 131
GLT D L F+KPG K F L + N+P +TE+E+++ F + G G
Sbjct: 3 GLTID-----LKNFRKPGEKTFTQ----RSRLFVGNLPPDITEEEMRKLFEKYGKA--GE 51
Query: 132 KFFPKDRKMALLQLDSIEEAITALIQMHNHQLSEQSHLRVSFS 174
F KD+ ++L++ A A +++ N L + LRV F+
Sbjct: 52 VFIHKDKGFGFIRLETRTLAEIAKVELDNMPLRGK-QLRVRFA 93
Score = 28.9 bits (63), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F G G+V ++ K I++ A +A + +D + + GKQ+RV + H A
Sbjct: 42 LFEKYGKAGEVF----IHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA 97
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 34.7 bits (78), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 37/74 (50%), Gaps = 3/74 (4%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNH 161
T ++ NIP TE +L F GF + FK +P ++ ++ D+ E+A ++ + N
Sbjct: 29 TAYIGNIPHFATEADLIPLFQNFGFILD-FKHYP-EKGCCFIKYDTHEQAAVCIVALANF 86
Query: 162 QLSEQSHLRVSFSK 175
+ +LR + K
Sbjct: 87 PF-QGRNLRTGWGK 99
>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 = 33.5 bits (75), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 43/80 (53%), Gaps = 9/80 (11%)
Query: 85 FKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGF----KFFPKDRKM 140
+ +PG ++ ++ L+++N+P ++T+D+L F + G V+ K + R +
Sbjct: 3 YARPGGESIKDT-----NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV 57
Query: 141 ALLQLDSIEEAITALIQMHN 160
A ++ + EEA A+ ++N
Sbjct: 58 AFVRYNKREEAQEAISALNN 77
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 33.5 bits (75), Expect = 0.073, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 43/80 (53%), Gaps = 9/80 (11%)
Query: 85 FKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGF----KFFPKDRKM 140
+ +PG ++ ++ L+++N+P ++T+D+L F + G V+ K + R +
Sbjct: 79 YARPGGESIKDT-----NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV 133
Query: 141 ALLQLDSIEEAITALIQMHN 160
A ++ + EEA A+ ++N
Sbjct: 134 AFVRYNKREEAQEAISALNN 153
>pdb|2CPJ|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
pdb|2RS8|A Chain A, Solution Structure Of The N-Terminal Rna Recognition Motif
Of Nono
Length = 99
Score = 33.5 bits (75), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 103 LHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNHQ 162
L + N+P +TE+E+++ F + G G F KD+ ++L++ A A +++ N
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYG--KAGEVFIHKDKGFGFIRLETRTLAEIAKVELDNMP 75
Query: 163 LSEQSHLRVSFS 174
L + LRV F+
Sbjct: 76 LRGK-QLRVRFA 86
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 29/60 (48%), Gaps = 4/60 (6%)
Query: 1 MFSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQA 60
+F G G+V ++ K I++ A +A + +D + + GKQ+RV + H A
Sbjct: 35 LFEKYGKAGEVF----IHKDKGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSA 90
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From Drosophila
Melanogaster
Length = 184
Score = 33.1 bits (74), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 43/80 (53%), Gaps = 9/80 (11%)
Query: 85 FKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGF----KFFPKDRKM 140
+ +PG ++ ++ L+++N+P ++T+D+L F + G V+ K + R +
Sbjct: 90 YARPGGESIKDT-----NLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGV 144
Query: 141 ALLQLDSIEEAITALIQMHN 160
A ++ + EEA A+ ++N
Sbjct: 145 AFVRYNKREEAQEAISALNN 164
>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 = 0.17, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 7 VYGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAV 61
VYG + R+ ++Y+K+ A I+ H A H D ++ G+++ V + + + V
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV 184
Query: 62 Q 62
+
Sbjct: 185 K 185
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 31.2 bits (69), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 25/90 (27%), Positives = 40/90 (44%), Gaps = 7/90 (7%)
Query: 85 FKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQ 144
F KPG K Y L + N+P +TE++ K F G + F +DR ++
Sbjct: 11 FLKPGEKT----YTQRCRLFVGNLPTDITEEDFKRLFERYGEPSE--VFINRDRGFGFIR 64
Query: 145 LDSIEEAITALIQMHNHQLSEQSHLRVSFS 174
L+S A A ++ L + LR+ F+
Sbjct: 65 LESRTLAEIAKAELDGTILKSRP-LRIRFA 93
>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 = 31.2 bits (69), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 31/61 (50%), Gaps = 5/61 (8%)
Query: 7 VYGDVLRVKILYNKKDS-----ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAV 61
VYG + R+ ++Y+K+ A I+ H A H D ++ G+++ V + + + V
Sbjct: 125 VYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGRTV 184
Query: 62 Q 62
+
Sbjct: 185 K 185
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 31.2 bits (69), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTE-KGFTVKGFKFFPKDRKMALLQLDSIEEAITALI 156
PP+ L L+N+P E L F + GF K + P +A ++ D+ +A A
Sbjct: 11 PPNHILFLTNLPEETNELMLSMLFNQFPGF--KEVRLVPGRHDIAFVEFDNEVQAGAARD 68
Query: 157 QMHNHQLSEQSHLRVSFSK 175
+ ++++ + +++SF+K
Sbjct: 69 ALQGFKITQNNAMKISFAK 87
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 31.2 bits (69), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 40/79 (50%), Gaps = 3/79 (3%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTE-KGFTVKGFKFFPKDRKMALLQLDSIEEAITALI 156
PP+ L L+N+P E L F + GF K + P +A ++ D+ +A A
Sbjct: 205 PPNHILFLTNLPEETNELMLSMLFNQFPGF--KEVRLVPGRHDIAFVEFDNEVQAGAARD 262
Query: 157 QMHNHQLSEQSHLRVSFSK 175
+ ++++ + +++SF+K
Sbjct: 263 ALQGFKITQNNAMKISFAK 281
>pdb|3R27|A Chain A, Crystal Structure Of The First Rrm Domain Of Heterogeneous
Nuclear Ribonucleoprotein L (Hnrnp L)
pdb|3R27|B Chain B, Crystal Structure Of The First Rrm Domain Of Heterogeneous
Nuclear Ribonucleoprotein L (Hnrnp L)
Length = 100
Score = 30.8 bits (68), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 39/80 (48%), Gaps = 3/80 (3%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQ 157
P SP +H+ + V E +L EA E G + PK R+ AL++ + + A A+
Sbjct: 19 PASPVVHIRGLIDGVVEADLVEALQEFG-PISYVVVMPKKRQ-ALVEFEDVLGACNAVNY 76
Query: 158 MHNHQLSEQSHLR-VSFSKS 176
++Q+ H V++S S
Sbjct: 77 AADNQIYIAGHPAFVNYSTS 96
>pdb|3RED|A Chain A, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|B Chain B, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|C Chain C, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|D Chain D, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|E Chain E, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|F Chain F, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|G Chain G, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|H Chain H, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|I Chain I, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|J Chain J, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|K Chain K, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
pdb|3RED|L Chain L, 3.0 A Structure Of The Prunus Mume Hydroxynitrile Lyase
Isozyme-1
Length = 521
Score = 30.4 bits (67), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 14/46 (30%), Positives = 24/46 (52%)
Query: 91 KNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPK 136
+NF NI PP+P + +T + + +F+ F++ F FFP
Sbjct: 301 RNFINILPPNPIEPSTVTVLGITSNFYQCSFSSLPFSIPPFAFFPN 346
>pdb|1JU2|A Chain A, Crystal Structure Of The Hydroxynitrile Lyase From Almond
pdb|1JU2|B Chain B, Crystal Structure Of The Hydroxynitrile Lyase From Almond
Length = 536
Score = 30.4 bits (67), Expect = 0.65, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 22/46 (47%)
Query: 91 KNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPK 136
+NF NI PP+P ++ D + +F+ FT F FFP
Sbjct: 300 RNFINILPPNPIEPTIVTVLGISNDFYQCSFSSLPFTTPPFGFFPS 345
>pdb|3GDN|A Chain A, Almond Hydroxynitrile Lyase In Complex With Benzaldehyde
pdb|3GDN|B Chain B, Almond Hydroxynitrile Lyase In Complex With Benzaldehyde
pdb|3GDP|A Chain A, Hydroxynitrile Lyase From Almond, Monoclinic Crystal Form
pdb|3GDP|B Chain B, Hydroxynitrile Lyase From Almond, Monoclinic Crystal Form
Length = 521
Score = 30.0 bits (66), Expect = 0.75, Method: Compositional matrix adjust.
Identities = 15/46 (32%), Positives = 22/46 (47%)
Query: 91 KNFQNIYPPSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPK 136
+NF NI PP+P ++ D + +F+ FT F FFP
Sbjct: 300 RNFINILPPNPIEPTIVTVLGISNDFYQCSFSSLPFTTPPFGFFPS 345
>pdb|3B6U|A Chain A, Crystal Structure Of The Motor Domain Of Human Kinesin
Family Member 3b In Complex With Adp
pdb|3B6U|B Chain B, Crystal Structure Of The Motor Domain Of Human Kinesin
Family Member 3b In Complex With Adp
Length = 372
Score = 30.0 bits (66), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 38/72 (52%), Gaps = 1/72 (1%)
Query: 2 FSLTGVYGDVLRVKILYNKKDSALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAV 61
+++ G+ GD + ++ N D ++ S Q ++ L ++ +++R ++SK Q
Sbjct: 117 YTMEGIRGDPEKRGVIPNSFDHIFTHISRS-QNQQYLVRASYLEIYQEEIRDLLSKDQTK 175
Query: 62 QLPKEGQPDAGL 73
+L + +PD G+
Sbjct: 176 RLELKERPDTGV 187
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 30.0 bits (66), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 21/80 (26%), Positives = 40/80 (50%), Gaps = 7/80 (8%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFF-----PKDRKMALLQLDSIEEAITALI 156
++ + NIP TE++LK+ F+E G V F+ K + + E A++A+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVS-FRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 157 QMHNHQLSEQSHLRVSFSKS 176
++ + S ++ LRV + S
Sbjct: 69 NLNGREFSGRA-LRVDNAAS 87
>pdb|2KM8|B Chain B, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 84
Score = 29.6 bits (65), Expect = 0.91, Method: Compositional matrix adjust.
Identities = 18/84 (21%), Positives = 43/84 (51%), Gaps = 5/84 (5%)
Query: 98 PPSPTLHLSNIPASVTEDELKEAFTEKGFTVK-GFKFFP---KDRKMALLQLDSIEEAIT 153
PPS ++L +IP TE+++ + + G + F P + + A ++ +E + +
Sbjct: 2 PPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 61
Query: 154 ALIQMHNHQLSEQSHLRVSFSKSN 177
A+ ++ +QL + L+ +S ++
Sbjct: 62 AVRNLNGYQLGSR-FLKCGYSSNS 84
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 29.3 bits (64), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 5/77 (6%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMH 159
S LH+ NI + T EL+ F E G ++ KD A + ++ E+A+ A+ +
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIEC--DIVKD--YAFVHMERAEDAVEAIRGLD 65
Query: 160 NHQL-SEQSHLRVSFSK 175
N + ++ H+++S S+
Sbjct: 66 NTEFQGKRMHVQLSTSR 82
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 28.9 bits (63), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 31/64 (48%)
Query: 100 SPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMH 159
S TL LSN+ S TE+ L+E F + F K + A ++ S E+A AL +
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 160 NHQL 163
++
Sbjct: 75 KREI 78
>pdb|2CQ1|A Chain A, Solution Structure Of Rna Binding Domain In Ptb-Like
Protein L
Length = 101
Score = 27.7 bits (60), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 31/72 (43%), Gaps = 6/72 (8%)
Query: 99 PSPTLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQM 158
PS LH+ +P VTE E+ G K + A L+L + E AIT M
Sbjct: 14 PSRVLHIRKLPGEVTETEVIALGLPFGKVTNILML--KGKNQAFLELATEEAAIT----M 67
Query: 159 HNHQLSEQSHLR 170
N+ + HLR
Sbjct: 68 VNYYSAVTPHLR 79
>pdb|2DR1|A Chain A, Crystal Structure Of The Ph1308 Protein From Pyrococcus
Horikoshii Ot3
pdb|2DR1|B Chain B, Crystal Structure Of The Ph1308 Protein From Pyrococcus
Horikoshii Ot3
Length = 386
Score = 27.7 bits (60), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 41/164 (25%), Positives = 76/164 (46%), Gaps = 29/164 (17%)
Query: 6 GVYGDV-LRVKILYNKKDS-ALIQMAESHQAHLAMMHMDKLRVFGKQMRVMISKHQAVQL 63
G Y D+ L VK L K+ + + M + ++A+ ++K+ GK+ + + + +A ++
Sbjct: 236 GWYFDIPLYVKYLKEKESTPSTPPMPQVFGINVALRIIEKMG--GKEKWLEMYEKRA-KM 292
Query: 64 PKEGQPDAGLTKDYTASPLHRFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAFTE 123
+EG + GL D A P H SPT+ P + DE+ EA +
Sbjct: 293 VREGVREIGL--DILAEPGHE---------------SPTITAVLTPPGIKGDEVYEAMRK 335
Query: 124 KGFTV-KGF-----KFFPKDRKMALLQLDSIEEAITALIQMHNH 161
+GF + KG+ K F + M ++ + I+E + L ++ N
Sbjct: 336 RGFELAKGYGSVKEKTF-RIGHMGYMKFEDIQEMLDNLREVINE 378
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 27.3 bits (59), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 102 TLHLSNIPASVTEDELKEAF 121
TL N+P VT+DELKE F
Sbjct: 95 TLLAKNLPYKVTQDELKEVF 114
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 26.9 bits (58), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 5/74 (6%)
Query: 102 TLHLSNIPASVTEDELKEAFTEKGFTVKGFKFFPKDRKMALLQLDSIEEAITALIQMHNH 161
L + N+ +VTE+ L++AF++ G + K + A + D + A+ A+ +M+
Sbjct: 13 VLFVRNLANTVTEEILEKAFSQFG----KLERVKKLKDYAFIHFDERDGAVKAMEEMNGK 68
Query: 162 QLSEQSHLRVSFSK 175
L E ++ + F+K
Sbjct: 69 DL-EGENIEIVFAK 81
>pdb|4DKT|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With
N-Acetyl-L-Threonyl-L-Alpha-Aspartyl-N5-[(1e)-2-
Fluoroethanimidoyl]-L-Ornithinamide
Length = 668
Score = 26.9 bits (58), Expect = 6.6, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 30/79 (37%), Gaps = 14/79 (17%)
Query: 35 HLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQ 94
H+A MDK+RVF + SK V PK P H PG K+
Sbjct: 207 HVARSEMDKVRVFQATRGKLSSKCSVVLGPK--------------WPSHYLMVPGGKHNM 252
Query: 95 NIYPPSPTLHLSNIPASVT 113
+ Y + ++ P +T
Sbjct: 253 DFYVEALAFPDTDFPGLIT 271
>pdb|3APM|A Chain A, Crystal Structure Of The Human Snp Pad4 Protein
Length = 666
Score = 26.9 bits (58), Expect = 6.6, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 30/79 (37%), Gaps = 14/79 (17%)
Query: 35 HLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQ 94
H+A MDK+RVF + SK V PK P H PG K+
Sbjct: 205 HVARSEMDKVRVFQATRGKLSSKCSVVLGPK--------------WPSHYLMVPGGKHNM 250
Query: 95 NIYPPSPTLHLSNIPASVT 113
+ Y + ++ P +T
Sbjct: 251 DFYVEALAFPDTDFPGLIT 269
>pdb|1WD8|A Chain A, Calcium Free Form Of Human Peptidylarginine Deiminase
Type4 (Pad4)
Length = 670
Score = 26.9 bits (58), Expect = 6.8, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 30/79 (37%), Gaps = 14/79 (17%)
Query: 35 HLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQ 94
H+A MDK+RVF + SK V PK P H PG K+
Sbjct: 209 HVARSEMDKVRVFQATRGKLSSKCSVVLGPK--------------WPSHYLMVPGGKHNM 254
Query: 95 NIYPPSPTLHLSNIPASVT 113
+ Y + ++ P +T
Sbjct: 255 DFYVEALAFPDTDFPGLIT 273
>pdb|3APN|A Chain A, Crystal Structure Of The Human Wild-Type Pad4 Protein
Length = 666
Score = 26.9 bits (58), Expect = 6.8, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 30/79 (37%), Gaps = 14/79 (17%)
Query: 35 HLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQ 94
H+A MDK+RVF + SK V PK P H PG K+
Sbjct: 205 HVARSEMDKVRVFQATRGKLSSKCSVVLGPK--------------WPSHYLMVPGGKHNM 250
Query: 95 NIYPPSPTLHLSNIPASVT 113
+ Y + ++ P +T
Sbjct: 251 DFYVEALAFPDTDFPGLIT 269
>pdb|2DEW|X Chain X, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With Histone H3 N-Terminal Tail Including Arg8
pdb|2DEX|X Chain X, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With Histone H3 N-Terminal Peptide Including
Arg17
pdb|2DEY|X Chain X, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With Histone H4 N-Terminal Tail Including Arg3
Length = 671
Score = 26.9 bits (58), Expect = 6.8, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 30/79 (37%), Gaps = 14/79 (17%)
Query: 35 HLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQ 94
H+A MDK+RVF + SK V PK P H PG K+
Sbjct: 210 HVARSEMDKVRVFQATRGKLSSKCSVVLGPK--------------WPSHYLMVPGGKHNM 255
Query: 95 NIYPPSPTLHLSNIPASVT 113
+ Y + ++ P +T
Sbjct: 256 DFYVEALAFPDTDFPGLIT 274
>pdb|2DW5|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With
N-Alpha-Benzoyl-N5-(2-Fluoro-1-Iminoethyl)-L-Ornithine
Amide
pdb|3B1T|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With O-Cl-Amidine
pdb|3B1U|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase 4 In
Complex With O-F-Amidine
Length = 671
Score = 26.9 bits (58), Expect = 6.9, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 30/79 (37%), Gaps = 14/79 (17%)
Query: 35 HLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQ 94
H+A MDK+RVF + SK V PK P H PG K+
Sbjct: 210 HVARSEMDKVRVFQATRGKLSSKCSVVLGPK--------------WPSHYLMVPGGKHNM 255
Query: 95 NIYPPSPTLHLSNIPASVT 113
+ Y + ++ P +T
Sbjct: 256 DFYVEALAFPDTDFPGLIT 274
>pdb|1WD9|A Chain A, Calcium Bound Form Of Human Peptidylarginine Deiminase
Type4 (pad4)
pdb|1WDA|A Chain A, Crystal Structure Of Human Peptidylarginine Deiminase
Type4 (Pad4) In Complex With Benzoyl-L-Arginine Amide
Length = 670
Score = 26.9 bits (58), Expect = 7.1, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 30/79 (37%), Gaps = 14/79 (17%)
Query: 35 HLAMMHMDKLRVFGKQMRVMISKHQAVQLPKEGQPDAGLTKDYTASPLHRFKKPGSKNFQ 94
H+A MDK+RVF + SK V PK P H PG K+
Sbjct: 209 HVARSEMDKVRVFQATRGKLSSKCSVVLGPK--------------WPSHYLMVPGGKHNM 254
Query: 95 NIYPPSPTLHLSNIPASVT 113
+ Y + ++ P +T
Sbjct: 255 DFYVEALAFPDTDFPGLIT 273
>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 = 26.6 bits (57), Expect = 9.6, Method: Compositional matrix adjust.
Identities = 13/38 (34%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 84 RFKKPGSKNFQNIYPPSPTLHLSNIPASVTEDELKEAF 121
+ +KP ++ + + + TL N+ ++TEDELKE F
Sbjct: 84 KLEKPKGRDSKKV-RAARTLLAKNLSFNITEDELKEVF 120
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
0.319 0.132 0.372
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,160,649
Number of Sequences: 62578
Number of extensions: 192925
Number of successful extensions: 553
Number of sequences better than 100.0: 41
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 31
Number of HSP's that attempted gapping in prelim test: 537
Number of HSP's gapped (non-prelim): 44
length of query: 184
length of database: 14,973,337
effective HSP length: 93
effective length of query: 91
effective length of database: 9,153,583
effective search space: 832976053
effective search space used: 832976053
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)