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= psy2204
(231 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2YH0|A Chain A, Solution Structure Of The Closed Conformation Of Human
U2af65 Tandem Rrm1 And Rrm2 Domains
pdb|2YH1|A Chain A, Model Of Human U2af65 Tandem Rrm1 And Rrm2 Domains With
Eight-Site Uridine Binding
Length = 198
Score = 247 bits (631), Expect = 4e-66, Method: Compositional matrix adjust.
Identities = 128/196 (65%), Positives = 141/196 (71%), Gaps = 42/196 (21%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
ARRLYVGNIPFG+TE+ MM+FFN QM L GL QA GNPVLA QIN DKNFAFLEFRS+DE
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 106 TTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKIFIGGL 165
TTQAMAFDGI F+GQSLKIRRPHDYQP PG+++N +V VP GV+STVVPDS HK+FIGGL
Sbjct: 64 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGMSENPSVYVP-GVVSTVVPDSAHKLFIGGL 122
Query: 166 PNYLNE-----------------------------------------DQAIAGLNGMQLG 184
PNYLN+ DQAIAGLNGMQLG
Sbjct: 123 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG 182
Query: 185 DKKLIVQRASVGAKNA 200
DKKL+VQRASVGAKNA
Sbjct: 183 DKKLLVQRASVGAKNA 198
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 201 bits (511), Expect = 3e-52, Method: Compositional matrix adjust.
Identities = 109/190 (57%), Positives = 117/190 (61%), Gaps = 62/190 (32%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
ARRLYVGNIPFG+TE+ MM+FFN QM L GL QA GNPVLA QIN DKNFAFLEFRS+DE
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 106 TTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKIFIGGL 165
TTQAMAFDGI F+GQSLKIRRPHDYQP PG HK+FIGGL
Sbjct: 64 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGA---------------------HKLFIGGL 102
Query: 166 PNYLNE-----------------------------------------DQAIAGLNGMQLG 184
PNYLN+ DQAIAGLNGMQLG
Sbjct: 103 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG 162
Query: 185 DKKLIVQRAS 194
DKKL+VQRAS
Sbjct: 163 DKKLLVQRAS 172
>pdb|3VAF|A Chain A, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAF|B Chain B, Structure Of U2af65 Variant With Bru3 Dna
pdb|3VAG|A Chain A, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAG|B Chain B, Structure Of U2af65 Variant With Bru3c2 Dna
pdb|3VAH|A Chain A, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAH|B Chain B, Structure Of U2af65 Variant With Bru3c4 Dna
pdb|3VAI|A Chain A, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAI|B Chain B, Structure Of U2af65 Variant With Bru3c5 Dna
pdb|3VAJ|A Chain A, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAJ|B Chain B, Structure Of U2af65 Variant With Bru5c6 Dna
pdb|3VAK|A Chain A, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAK|B Chain B, Structure Of U2af65 Variant With Bru5 Dna
pdb|3VAL|A Chain A, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|B Chain B, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|D Chain D, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAL|I Chain I, Structure Of U2af65 Variant With Bru5c1 Dna
pdb|3VAM|A Chain A, Structure Of U2af65 Variant With Bru5c2 Dna
pdb|3VAM|B Chain B, Structure Of U2af65 Variant With Bru5c2 Dna
Length = 174
Score = 201 bits (510), Expect = 4e-52, Method: Compositional matrix adjust.
Identities = 109/190 (57%), Positives = 117/190 (61%), Gaps = 62/190 (32%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
ARRLYVGNIPFG+TE+ MM+FFN QM L GL QA GNPVLA QIN DKNFAFLEFRS+DE
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65
Query: 106 TTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKIFIGGL 165
TTQAMAFDGI F+GQSLKIRRPHDYQP PG HK+FIGGL
Sbjct: 66 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPGA---------------------HKLFIGGL 104
Query: 166 PNYLNE-----------------------------------------DQAIAGLNGMQLG 184
PNYLN+ DQAIAGLNGMQLG
Sbjct: 105 PNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAGLNGMQLG 164
Query: 185 DKKLIVQRAS 194
DKKL+VQRAS
Sbjct: 165 DKKLLVQRAS 174
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 160 bits (406), Expect = 4e-40, Method: Compositional matrix adjust.
Identities = 75/90 (83%), Positives = 80/90 (88%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
ARRLYVGNIPFG+TE+ MM+FFN QM L GL QA GNPVLA QIN DKNFAFLEFRS+DE
Sbjct: 1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 60
Query: 106 TTQAMAFDGINFKGQSLKIRRPHDYQPTPG 135
TTQAMAFDGI F+GQSLKIRRPHDYQP PG
Sbjct: 61 TTQAMAFDGIIFQGQSLKIRRPHDYQPLPG 90
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 144 bits (362), Expect = 6e-35, Method: Compositional matrix adjust.
Identities = 68/82 (82%), Positives = 73/82 (89%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
ARRLYVGNIPFG+TE+ MM+FFN QM L GL QA GNPVLA QIN DKNFAFLEFRS+DE
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65
Query: 106 TTQAMAFDGINFKGQSLKIRRP 127
TTQAMAFDGI F+GQSLKIRRP
Sbjct: 66 TTQAMAFDGIIFQGQSLKIRRP 87
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 67.4 bits (163), Expect = 6e-12, Method: Compositional matrix adjust.
Identities = 40/84 (47%), Positives = 43/84 (51%), Gaps = 41/84 (48%)
Query: 158 HKIFIGGLPNYLNEDQ-----------------------------------------AIA 176
HK+FIGGLPNYLN+DQ AIA
Sbjct: 2 HKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 61
Query: 177 GLNGMQLGDKKLIVQRASVGAKNA 200
GLNGMQLGDKKL+VQRASVGAKNA
Sbjct: 62 GLNGMQLGDKKLLVQRASVGAKNA 85
>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 = 42.0 bits (97), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 22/81 (27%), Positives = 40/81 (49%), Gaps = 7/81 (8%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-KNFAFLEFRSI 103
AR +YVGN+ +G T +E+ + H G +L + + K FA++EF
Sbjct: 5 DARSIYVGNVDYGATAEEL------EAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDK 58
Query: 104 DETTQAMAFDGINFKGQSLKI 124
+ ++A D F+G+ +K+
Sbjct: 59 ESVRTSLALDESLFRGRQIKV 79
>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 = 41.6 bits (96), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 40/80 (50%), Gaps = 7/80 (8%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD-KNFAFLEFRSID 104
AR +YVGN+ +G T +E+ + H G +L + + K FA++EF +
Sbjct: 5 ARSIYVGNVDYGATAEEL------EAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE 58
Query: 105 ETTQAMAFDGINFKGQSLKI 124
++A D F+G+ +K+
Sbjct: 59 SVRTSLALDESLFRGRQIKV 78
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 39.7 bits (91), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/76 (28%), Positives = 39/76 (51%), Gaps = 5/76 (6%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
++++G + VT+D +ME F+ G + PV +L K +A++EF + DE
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTY----GKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61
Query: 108 QAMA-FDGINFKGQSL 122
+A+ DG GQ +
Sbjct: 62 KALKHMDGGQIDGQEI 77
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.9 bits (89), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 41/89 (46%), Gaps = 14/89 (15%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAF- 97
G Q RL+VGN+P +TE++ F + G P IN D+ F F
Sbjct: 15 GEKTYTQRCRLFVGNLPTDITEEDFKRLFER----------YGEPSEVF-INRDRGFGFI 63
Query: 98 -LEFRSIDETTQAMAFDGINFKGQSLKIR 125
LE R++ E +A DG K + L+IR
Sbjct: 64 RLESRTLAEIAKA-ELDGTILKSRPLRIR 91
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 28/89 (31%), Positives = 44/89 (49%), Gaps = 14/89 (15%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAF- 97
G Q RL+VGN+P +TE+EM + F + AG I+ DK F F
Sbjct: 15 GEKTFTQRSRLFVGNLPPDITEEEMRKLFEK-------YGKAGEVF----IHKDKGFGFI 63
Query: 98 -LEFRSIDETTQAMAFDGINFKGQSLKIR 125
LE R++ E + + D + +G+ L++R
Sbjct: 64 RLETRTLAEIAK-VELDNMPLRGKQLRVR 91
>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 = 38.5 bits (88), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 27/83 (32%), Positives = 43/83 (51%), Gaps = 14/83 (16%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAF--LEFRS 102
Q RL+VGN+P +TE+EM + F + AG I+ DK F F LE R+
Sbjct: 14 QRSRLFVGNLPPDITEEEMRKLFEK-------YGKAGEVF----IHKDKGFGFIRLETRT 62
Query: 103 IDETTQAMAFDGINFKGQSLKIR 125
+ E + + D + +G+ L++R
Sbjct: 63 LAEIAK-VELDNMPLRGKQLRVR 84
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 38.1 bits (87), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 22/90 (24%), Positives = 45/90 (50%), Gaps = 18/90 (20%)
Query: 42 ITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNF 95
+ R R ++VGNIP+ TE+++ + F++ PV++ ++ D K +
Sbjct: 4 VDRSLRSVFVGNIPYEATEEQLKDIFSEV-----------GPVVSFRLVYDRETGKPKGY 52
Query: 96 AFLEFRSIDETTQAMA-FDGINFKGQSLKI 124
F E++ + AM +G F G++L++
Sbjct: 53 GFCEYQDQETALSAMRNLNGREFSGRALRV 82
>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 = 37.4 bits (85), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 42/82 (51%), Gaps = 13/82 (15%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLA----QAAGNPVLACQINLDKNFAFLEFRS 102
R +YVGN+ +G T ++ F+ ++ + + +G+P K +A++EF
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHP---------KGYAYIEFAE 87
Query: 103 IDETTQAMAFDGINFKGQSLKI 124
+ A+A D F+G+++K+
Sbjct: 88 RNSVDAAVAMDETVFRGRTIKV 109
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 10/63 (15%)
Query: 40 STITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLE 99
S R AR L N+ F +TEDE+ E F + + L Q K A++E
Sbjct: 10 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR----------LVSQDGKSKGIAYIE 59
Query: 100 FRS 102
F+S
Sbjct: 60 FKS 62
>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 = 36.2 bits (82), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 28/63 (44%), Gaps = 10/63 (15%)
Query: 40 STITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLE 99
S R AR L N+ F +TEDE+ E F + + L Q K A++E
Sbjct: 93 SKKVRAARTLLAKNLSFNITEDELKEVFEDALEIR----------LVSQDGKSKGIAYIE 142
Query: 100 FRS 102
F+S
Sbjct: 143 FKS 145
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 35.8 bits (81), Expect = 0.020, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 55/129 (42%), Gaps = 20/129 (15%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDK-----NFAFLEF- 100
R LYVGN+ +TED + ++F G P+ +I +DK N+AF+E+
Sbjct: 1 RVLYVGNLDKAITEDILKQYF-----------QVGGPIANIKIMIDKNNKNVNYAFVEYH 49
Query: 101 RSIDETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSPHKI 160
+S D +G + +KI +Q +D+ + G ++ V D +
Sbjct: 50 QSHDANIALQTLNGKQIENNIVKINWA--FQSQQSSSDD-TFNLFVGDLNVNVDDETLRN 106
Query: 161 FIGGLPNYL 169
P+YL
Sbjct: 107 AFKDFPSYL 115
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 35.4 bits (80), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 50 YVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETTQA 109
YVGN+PF + ++ F L+ + V + K F ++EF +D +A
Sbjct: 19 YVGNLPFNTVQGDIDAIFKD------LSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEA 72
Query: 110 MAFDGINFKGQSLKI 124
+ +DG +SL++
Sbjct: 73 LTYDGALLGDRSLRV 87
>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 = 34.3 bits (77), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 34/71 (47%), Gaps = 6/71 (8%)
Query: 42 ITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFR 101
+ +++ LYVGN+ F TE+++ E F++ + + AC F F+E+
Sbjct: 14 LLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC------GFCFVEYY 67
Query: 102 SIDETTQAMAF 112
S + AM +
Sbjct: 68 SRADAENAMRY 78
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 33.1 bits (74), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 17/71 (23%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLE 99
+R +Y+G+IP+ TE+++++ L G PV+ ++ D K +AF+E
Sbjct: 3 SRVVYLGSIPYDQTEEQILD----------LCSNVG-PVINLKMMFDPQTGRSKGYAFIE 51
Query: 100 FRSIDETTQAM 110
FR ++ + A+
Sbjct: 52 FRDLESSASAV 62
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 29/63 (46%), Gaps = 10/63 (15%)
Query: 40 STITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLE 99
S R AR L N+P+ VT+DE+ E F + A L + K A++E
Sbjct: 87 SKKERDARTLLAKNLPYKVTQDELKEVF----------EDAAEIRLVSKDGKSKGIAYIE 136
Query: 100 FRS 102
F++
Sbjct: 137 FKT 139
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 33.1 bits (74), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 17/71 (23%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLE 99
+R +Y+G+IP+ TE+++++ L G PV+ ++ D K +AF+E
Sbjct: 2 SRVVYLGSIPYDQTEEQILD----------LCSNVG-PVINLKMMFDPQTGRSKGYAFIE 50
Query: 100 FRSIDETTQAM 110
FR ++ + A+
Sbjct: 51 FRDLESSASAV 61
>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 = 33.1 bits (74), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 38/71 (53%), Gaps = 17/71 (23%)
Query: 46 ARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLE 99
+R +Y+G+IP+ TE+++++ L G PV+ ++ D K +AF+E
Sbjct: 4 SRVVYLGSIPYDQTEEQILD----------LCSNVG-PVINLKMMFDPQTGRSKGYAFIE 52
Query: 100 FRSIDETTQAM 110
FR ++ + A+
Sbjct: 53 FRDLESSASAV 63
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 19/73 (26%), Positives = 32/73 (43%), Gaps = 17/73 (23%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFL 98
Q R+L++G + F TE+ + ++ Q L+ C + D + F F+
Sbjct: 26 QFRKLFIGGLSFETTEESLRNYYEQWGKLTD-----------CVVMRDPASKRSRGFGFV 74
Query: 99 EFRSIDETTQAMA 111
F S+ E AMA
Sbjct: 75 TFSSMAEVDAAMA 87
>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 = 31.2 bits (69), Expect = 0.44, Method: Compositional matrix adjust.
Identities = 18/65 (27%), Positives = 30/65 (46%), Gaps = 7/65 (10%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGN-PVLACQINLDKNFAFLEFRSIDETT 107
LYVGN+ F TE+++ E F++ + + AC F F+E+ S +
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTAC------GFCFVEYYSRADAE 95
Query: 108 QAMAF 112
AM +
Sbjct: 96 NAMRY 100
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 30.4 bits (67), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 38/78 (48%), Gaps = 6/78 (7%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
+L+VG + F E + + F++ +S + V + + F F+ F +ID+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVV-----VVKDRETQRSRGFGFVTFENIDDAK 68
Query: 108 QA-MAFDGINFKGQSLKI 124
A MA +G + G+ +++
Sbjct: 69 DAMMAMNGKSVDGRQIRV 86
>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 = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 38/85 (44%), Gaps = 17/85 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFLEFR 101
+++VG I V E EFF+Q ++ Q+ LDK+ F F+ +
Sbjct: 89 KIFVGGIGPDVRPKEFEEFFSQW-----------GTIIDAQLMLDKDTGQSRGFGFVTYD 137
Query: 102 SIDETTQAMAFDGINFKGQSLKIRR 126
S D + I+FK + ++I+R
Sbjct: 138 SADAVDRVCQNKFIDFKDRKIEIKR 162
>pdb|2QFJ|A Chain A, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
pdb|2QFJ|B Chain B, Crystal Structure Of First Two Rrm Domains Of Fir Bound To
Ssdna From A Portion Of Fuse
Length = 216
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 48/103 (46%), Gaps = 27/103 (26%)
Query: 39 GSTITRQA-----RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD- 92
GS RQ R+YVG+I + + ED + + F A P+ + ++ D
Sbjct: 16 GSAAQRQGALAIMSRVYVGSIYYELGEDTIRQAF-----------APFGPIKSIDMSWDS 64
Query: 93 -----KNFAFLEFRSIDETTQAMAFDGIN---FKGQSLKIRRP 127
K FAF+E+ + E Q +A + +N G+++K+ RP
Sbjct: 65 VTMKHKGFAFVEYE-VPEAAQ-LALEQMNSVMLGGRNIKVGRP 105
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 29.6 bits (65), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 36/84 (42%), Gaps = 13/84 (15%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLS--GLAQAAGNPVLACQINLDKNFAFLEFRSIDE 105
R+YVGN+P + ++ + F + + L G P FAF+EF +
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP----------FAFVEFEDPRD 73
Query: 106 TTQAM-AFDGINFKGQSLKIRRPH 128
A+ DG ++ G L++ P
Sbjct: 74 AEDAVYGRDGYDYDGYRLRVEFPR 97
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 29.6 bits (65), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 11/62 (17%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFL 98
GS+ + +LY+GN+ VT D++ + F + LA Q+ L +AF+
Sbjct: 1 GSSGSSGMNKLYIGNLSPAVTADDLRQLFGDR-----------KLPLAGQVLLKSGYAFV 49
Query: 99 EF 100
++
Sbjct: 50 DY 51
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 23/101 (22%), Positives = 39/101 (38%), Gaps = 15/101 (14%)
Query: 39 GSTITRQARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFL 98
GS+ + +L++GN+P TE E+ F Q VL C I + F +
Sbjct: 1 GSSGSSGMVKLFIGNLPREATEQEIRSLFEQY-----------GKVLECDIIKNYGFVHI 49
Query: 99 EFRSIDETT----QAMAFDGINFKGQSLKIRRPHDYQPTPG 135
E ++ E G+N ++ K + P+ G
Sbjct: 50 EDKTAAEDAIRNLHHYKLHGVNINVEASKNKSKASSGPSSG 90
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 28.9 bits (63), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 9/53 (16%)
Query: 50 YVGNIPFGVTEDEMMEFFNQQMHLSG--LAQAAGNPVLACQINLDKNFAFLEF 100
++GN+P+ VTE+ + EFF + +++S L + NP K F + EF
Sbjct: 19 FLGNLPYDVTEESIKEFF-RGLNISAVRLPREPSNPERL------KGFGYAEF 64
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 28.9 bits (63), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 16/85 (18%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN----FAFLEF 100
Q R LYVGN+ VTE +++ F+Q P +C++ + + F+EF
Sbjct: 14 QPRTLYVGNLSRDVTEVLILQLFSQI-----------GPCKSCKMITEHTSNDPYCFVEF 62
Query: 101 -RSIDETTQAMAFDGINFKGQSLKI 124
D A +G G+ +K+
Sbjct: 63 YEHRDAAAALAAMNGRKILGKEVKV 87
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 28.5 bits (62), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 9/53 (16%)
Query: 50 YVGNIPFGVTEDEMMEFFNQQMHLSG--LAQAAGNPVLACQINLDKNFAFLEF 100
++GN+P+ VTE+ + EFF + +++S L + NP K F + EF
Sbjct: 23 FLGNLPYDVTEESIKEFF-RGLNISAVRLPREPSNPERL------KGFGYAEF 68
>pdb|2KXF|A Chain A, Solution Structure Of The First Two Rrm Domains Of
Fbp-Interacting Repressor (Fir)
pdb|2KXH|A Chain A, Solution Structure Of The First Two Rrm Domains Of Fir In
The Complex With Fbp Nbox Peptide
Length = 199
Score = 28.5 bits (62), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 44/89 (49%), Gaps = 22/89 (24%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
R+YVG+I + + ED + + F A P+ + ++ D K FAF+E+
Sbjct: 15 RVYVGSIYYELGEDTIRQAF-----------APFGPIKSIDMSWDSVTMKHKGFAFVEY- 62
Query: 102 SIDETTQAMAFDGIN---FKGQSLKIRRP 127
+ E Q +A + +N G+++K+ RP
Sbjct: 63 EVPEAAQ-LALEQMNSVMLGGRNIKVGRP 90
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 28.1 bits (61), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 31/66 (46%), Gaps = 9/66 (13%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
+++ L + N+ + TE+ + E F + + V Q K +AF+EF S +
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEKATFIK---------VPQNQNGKSKGYAFIEFASFE 64
Query: 105 ETTQAM 110
+ +A+
Sbjct: 65 DAKEAL 70
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 28.1 bits (61), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 23/83 (27%), Positives = 40/83 (48%), Gaps = 10/83 (12%)
Query: 49 LYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNF------AFLEFRS 102
+YV + VT D++ +FF +Q + + + G P++ I LDK A + +
Sbjct: 18 IYVQGLNDSVTLDDLADFF-KQCGVVKMNKRTGQPMI--HIYLDKETGKPKGDATVSYED 74
Query: 103 IDETTQAM-AFDGINFKGQSLKI 124
A+ FDG +F+G LK+
Sbjct: 75 PPTAKAAVEWFDGKDFQGSKLKV 97
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 27.7 bits (60), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 18/79 (22%), Positives = 41/79 (51%), Gaps = 7/79 (8%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDET 106
R +YVGN+ + T +++ E F+Q + + + + K F F+E + +
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNV-----KLIYDRETKKPKGFGFVEMQE-ESV 55
Query: 107 TQAMA-FDGINFKGQSLKI 124
++A+A D +F G+++++
Sbjct: 56 SEAIAKLDNTDFMGRTIRV 74
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 30/139 (21%), Positives = 48/139 (34%), Gaps = 44/139 (31%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
Q R+L++G + F T++ + F Q L+ C + D N F F+
Sbjct: 13 QLRKLFIGGLSFETTDESLRSHFEQWGTLTD-----------CVVMRDPNTKRSRGFGFV 61
Query: 99 EFRSIDETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSP- 157
+ +++E AM RPH + V P +S P
Sbjct: 62 TYATVEEVDAAMNA-------------RPHKV--------DGRVVEPKRAVSREDSQRPG 100
Query: 158 -----HKIFIGGLPNYLNE 171
KIF+GG+ E
Sbjct: 101 AHLTVKKIFVGGIKEDTEE 119
>pdb|1NML|A Chain A, Di-Haemic Cytochrome C Peroxidase From Pseudomonas Nautica
617, Form In (Ph 4.0)
pdb|1RZ5|A Chain A, Di-Haem Cytochrome C Peroxidase, Form Out
pdb|1RZ6|A Chain A, Di-Haem Cytochrome C Peroxidase, Form In
Length = 326
Score = 27.7 bits (60), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 23/43 (53%)
Query: 131 QPTPGVTDNAAVAVPAGVISTVVPDSPHKIFIGGLPNYLNEDQ 173
Q P DN AVA+ A + + P++P ++ G + LNE +
Sbjct: 143 QENPVTFDNMAVAIEAYEATLITPEAPFDKYLRGDTSALNESE 185
>pdb|3UWT|A Chain A, Crystal Structure Of A Rna Binding Domain Of Poly-U
Binding Splicing Factor 60kda (Puf60) From Homo Sapiens
At 2.50 A Resolution
Length = 200
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 40/87 (45%), Gaps = 18/87 (20%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
R+YVG+I + + ED + + F A P+ + + D K FAF+E+
Sbjct: 14 RVYVGSIYYELGEDTIRQAF-----------APFGPIKSIDXSWDSVTXKHKGFAFVEYE 62
Query: 102 SIDETTQAMA-FDGINFKGQSLKIRRP 127
+ A+ + + G+++K+ RP
Sbjct: 63 VPEAAQLALEQXNSVXLGGRNIKVGRP 89
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 27.7 bits (60), Expect = 5.5, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 39/84 (46%), Gaps = 18/84 (21%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLD------KNFAFLEFR 101
RLYVG++ F +TED L G+ + G + + Q+ +D K + F+ F
Sbjct: 28 RLYVGSLHFNITED----------MLRGIFEPFGR-IESIQLMMDSETGRSKGYGFITFS 76
Query: 102 SIDETTQAMA-FDGINFKGQSLKI 124
+ +A+ +G G+ +K+
Sbjct: 77 DSECAKKALEQLNGFELAGRPMKV 100
>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 = 27.7 bits (60), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 30/139 (21%), Positives = 48/139 (34%), Gaps = 44/139 (31%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
Q R+L++G + F T++ + F Q L+ C + D N F F+
Sbjct: 11 QLRKLFIGGLSFETTDESLRSHFEQWGTLTD-----------CVVMRDPNTKRSRGFGFV 59
Query: 99 EFRSIDETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSP- 157
+ +++E AM RPH + V P +S P
Sbjct: 60 TYATVEEVDAAMNA-------------RPHKV--------DGRVVEPKRAVSREDSQRPG 98
Query: 158 -----HKIFIGGLPNYLNE 171
KIF+GG+ E
Sbjct: 99 AHLTVKKIFVGGIKEDTEE 117
>pdb|1EB7|A Chain A, Crystal Structure Of The Di-Haem Cytochrome C Peroxidase
From Pseudomonas Aeruginosa
pdb|2VHD|A Chain A, Crystal Structure Of The Di-Haem Cytochrome C Peroxidase
From Pseudomonas Aeruginosa - Mixed Valence Form
pdb|2VHD|B Chain B, Crystal Structure Of The Di-Haem Cytochrome C Peroxidase
From Pseudomonas Aeruginosa - Mixed Valence Form
Length = 323
Score = 27.7 bits (60), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 13/36 (36%), Positives = 20/36 (55%)
Query: 138 DNAAVAVPAGVISTVVPDSPHKIFIGGLPNYLNEDQ 173
DN A+A+ A + V PDSP +++ G L+ Q
Sbjct: 150 DNMALAIEAYEATLVTPDSPFDLYLKGDDKALDAQQ 185
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 27.3 bits (59), Expect = 6.4, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 39/85 (45%), Gaps = 13/85 (15%)
Query: 47 RRLYVGNIPFGVTEDEMMEFFNQQMHLSGLA---QAAGNPVLACQINLDKNFAFLEFRSI 103
R ++VGN+ V E+ + E F Q L+ + G P K+F F+ F+
Sbjct: 17 RTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKP---------KSFGFVCFKHP 67
Query: 104 DETTQAMA-FDGINFKGQSLKIRRP 127
+ + A+A +GI G+ + + P
Sbjct: 68 ESVSYAIALLNGIRLYGRPINVSGP 92
>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 = 27.3 bits (59), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 30/139 (21%), Positives = 48/139 (34%), Gaps = 44/139 (31%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
Q R+L++G + F T++ + F Q L+ C + D N F F+
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTD-----------CVVMRDPNTKRSRGFGFV 60
Query: 99 EFRSIDETTQAMAFDGINFKGQSLKIRRPHDYQPTPGVTDNAAVAVPAGVISTVVPDSP- 157
+ +++E AM RPH + V P +S P
Sbjct: 61 TYATVEEVDAAMNA-------------RPHKV--------DGRVVEPKRAVSREDSQRPG 99
Query: 158 -----HKIFIGGLPNYLNE 171
KIF+GG+ E
Sbjct: 100 AHLTVKKIFVGGIKEDTEE 118
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
Q R+L++G + F T++ + F Q L+ +P + F F+ + +++
Sbjct: 10 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV-VMRDP----NTKRSRGFGFVTYATVE 64
Query: 105 ETTQAM 110
E AM
Sbjct: 65 EVDAAM 70
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 27.3 bits (59), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 30/66 (45%), Gaps = 5/66 (7%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSID 104
Q R+L++G + F T++ + F Q L+ +P + F F+ + +++
Sbjct: 12 QLRKLFIGGLSFETTDESLRSHFEQWGTLTDCV-VMRDP----NTKRSRGFGFVTYATVE 66
Query: 105 ETTQAM 110
E AM
Sbjct: 67 EVDAAM 72
>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 = 27.3 bits (59), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 17/72 (23%)
Query: 45 QARRLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKN------FAFL 98
Q R+L++G + F T++ + F Q L+ C + D N F F+
Sbjct: 5 QLRKLFIGGLSFETTDESLRSHFEQWGTLTD-----------CVVMRDPNTKRSRGFGFV 53
Query: 99 EFRSIDETTQAM 110
+ +++E AM
Sbjct: 54 TYATVEEVDAAM 65
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 27.3 bits (59), Expect = 8.0, Method: Compositional matrix adjust.
Identities = 17/34 (50%), Positives = 20/34 (58%), Gaps = 6/34 (17%)
Query: 173 QAIAGLNGMQLGDKKLIVQRASVGAKNASGQQAP 206
QAIAGLNG + +K+L V A ASG Q P
Sbjct: 99 QAIAGLNGFNILNKRLKVALA------ASGHQRP 126
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 26.9 bits (58), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 39/78 (50%), Gaps = 6/78 (7%)
Query: 48 RLYVGNIPFGVTEDEMMEFFNQQMHLSGLAQAAGNPVLACQINLDKNFAFLEFRSIDETT 107
RL+V N+ + +E+++ + F+ LS L P+ + K FAF+ F +
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHY----PIDSL-TKKPKGFAFVTFMFPEHAV 64
Query: 108 QAMA-FDGINFKGQSLKI 124
+A A DG F+G+ L +
Sbjct: 65 KAYAEVDGQVFQGRMLHV 82
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: 6,481,073
Number of Sequences: 62578
Number of extensions: 249769
Number of successful extensions: 600
Number of sequences better than 100.0: 54
Number of HSP's better than 100.0 without gapping: 25
Number of HSP's successfully gapped in prelim test: 29
Number of HSP's that attempted gapping in prelim test: 556
Number of HSP's gapped (non-prelim): 60
length of query: 231
length of database: 14,973,337
effective HSP length: 96
effective length of query: 135
effective length of database: 8,965,849
effective search space: 1210389615
effective search space used: 1210389615
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: 50 (23.9 bits)