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= 045516
(675 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 = 64.7 bits (156), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 50/200 (25%), Positives = 99/200 (49%), Gaps = 29/200 (14%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAE-----------VVDVRLSSDADGRFKGYGHVEF 464
++ L+VGN+PF + + + +FF+ V+ V+++ D K + +EF
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEF 58
Query: 465 ASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQ-----AAH 519
SV++ +A+ +G + +++++ R Y P G +E+ S G +AH
Sbjct: 59 RSVDETTQAMAFDGIIFQGQSLKI---RRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAH 115
Query: 520 TIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNK 579
+FI G + + +DQV+ E S G + ++ KD TG KG A+ ++ D + ++
Sbjct: 116 KLFIGGLPNYLNDDQVK----ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQ 171
Query: 580 ALE-MSGTEIGGYSLVVDEA 598
A+ ++G ++G L+V A
Sbjct: 172 AIAGLNGMQLGDKKLLVQRA 191
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 64.7 bits (156), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 50/78 (64%), Gaps = 2/78 (2%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIEL 476
T +VGNLPF+ Q D+ F +++ + VRL D D +FKG+ +VEF V+ +A+
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDLS-IRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY 75
Query: 477 NGQMLGNRAIRLDFARER 494
+G +LG+R++R+D A R
Sbjct: 76 DGALLGDRSLRVDIAEGR 93
>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 = 63.2 bits (152), Expect = 5e-10, Method: Compositional matrix adjust.
Identities = 48/197 (24%), Positives = 94/197 (47%), Gaps = 39/197 (19%)
Query: 414 GGSKTLFVGNLPFSVEQADVQNFFSEVAE-----------VVDVRLSSDADGRFKGYGHV 462
G ++ L+VGN+PF + + + +FF+ V+ V+++ D K + +
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFL 58
Query: 463 EFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIF 522
EF SV++ +A+ +G + +++++ R Y P G AH +F
Sbjct: 59 EFRSVDETTQAMAFDGIIFQGQSLKI---RRPHDYQPLPG---------------AHKLF 100
Query: 523 IKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE 582
I G + + +DQV+ E S G + ++ KD TG KG A+ ++ D + ++A+
Sbjct: 101 IGGLPNYLNDDQVK----ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 156
Query: 583 -MSGTEIGGYSLVVDEA 598
++G ++G L+V A
Sbjct: 157 GLNGMQLGDKKLLVQRA 173
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 62.8 bits (151), Expect = 6e-10, Method: Compositional matrix adjust.
Identities = 48/197 (24%), Positives = 94/197 (47%), Gaps = 39/197 (19%)
Query: 414 GGSKTLFVGNLPFSVEQADVQNFFSEVAE-----------VVDVRLSSDADGRFKGYGHV 462
G ++ L+VGN+PF + + + +FF+ V+ V+++ D K + +
Sbjct: 2 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFL 56
Query: 463 EFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIF 522
EF SV++ +A+ +G + +++++ R Y P G AH +F
Sbjct: 57 EFRSVDETTQAMAFDGIIFQGQSLKI---RRPHDYQPLPG---------------AHKLF 98
Query: 523 IKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE 582
I G + + +DQV+ E S G + ++ KD TG KG A+ ++ D + ++A+
Sbjct: 99 IGGLPNYLNDDQVK----ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIA 154
Query: 583 -MSGTEIGGYSLVVDEA 598
++G ++G L+V A
Sbjct: 155 GLNGMQLGDKKLLVQRA 171
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 60.5 bits (145), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 60/181 (33%), Positives = 88/181 (48%), Gaps = 36/181 (19%)
Query: 419 LFVGNLPFSVEQADVQNFFSEV-----AEVVDVRLSSDADGRFKGYGHVEFASVEDAHKA 473
LFVGNL F+ +++ S+V VVDVR+ G + +G+V+F S ED KA
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRI-----GMTRKFGYVDFESAEDLEKA 64
Query: 474 IELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGED 533
+EL G + I+L+ + G +S + + A T+ K V +D
Sbjct: 65 LELTGLKVFGNEIKLEKPK----------GKDSK------KERDARTLLAKNLPYKVTQD 108
Query: 534 QVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF-TDADSFNKALEMSGTEIGGYS 592
+ L+E F EI +S KD G KGIAY++F T+AD+ E GTEI G S
Sbjct: 109 E----LKEVFEDAAEIRLVS--KD---GKSKGIAYIEFKTEADAEKTFEEKQGTEIDGRS 159
Query: 593 L 593
+
Sbjct: 160 I 160
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 28/79 (35%), Positives = 43/79 (54%), Gaps = 5/79 (6%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
++TL NLP+ V Q +++ F + AE +RL S DG+ KG ++EF + DA K E
Sbjct: 93 ARTLLAKNLPYKVTQDELKEVFEDAAE---IRLVS-KDGKSKGIAYIEFKTEADAEKTFE 148
Query: 476 L-NGQMLGNRAIRLDFARE 493
G + R+I L + E
Sbjct: 149 EKQGTEIDGRSISLYYTGE 167
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 57.4 bits (137), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 46/75 (61%), Gaps = 2/75 (2%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE 475
+++FVGN+P+ + +++ FSEV VV RL D + G+ KGYG E+ E A A+
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMR 68
Query: 476 -LNGQMLGNRAIRLD 489
LNG+ RA+R+D
Sbjct: 69 NLNGREFSGRALRVD 83
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 54.7 bits (130), Expect = 2e-07, Method: Composition-based stats.
Identities = 35/94 (37%), Positives = 53/94 (56%), Gaps = 4/94 (4%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAH 471
S GS L+VG+L F++ + ++ F ++ ++ L D+D GR KGYG + F+ E A
Sbjct: 2 SSGSSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECAR 61
Query: 472 KAIE-LNGQMLGNRAIRLDFARER--GAYTPYSG 502
+A+E LNG L R +R+ ER G P SG
Sbjct: 62 RALEQLNGFELAGRPMRVGHVTERLDGGSGPSSG 95
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
+++ ++ ED +R E G+I I + KD DTG KG ++ F+D++ +A
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPF----GKIDNIVLMKDSDTGRSKGYGFITFSDSECARRA 63
Query: 581 LE-MSGTEIGGYSLVV 595
LE ++G E+ G + V
Sbjct: 64 LEQLNGFELAGRPMRV 79
>pdb|4ED5|A Chain A, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
pdb|4ED5|B Chain B, Crystal Structure Of The Two N-Terminal Rrm Domains Of Hur
Complexed With Rna
Length = 177
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 44/159 (27%), Positives = 72/159 (45%), Gaps = 24/159 (15%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
G L V LP ++ Q ++++ FS + EV +L D G GYG V + + +DA +A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 474 IE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGE 532
I LNG L ++ I++ +AR S+ K ++I G ++ +
Sbjct: 61 INTLNGLRLQSKTIKVSYAR------------PSSEVIKDA------NLYISGLPRTMTQ 102
Query: 533 DQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF 571
V E+ F G I V D TG +G+A++ F
Sbjct: 103 KDV----EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRF 137
Score = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI-EL 476
L++ LP ++ Q DV++ FS +++ R+ D G +G + F +A +AI
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 477 NGQ 479
NG
Sbjct: 151 NGH 153
>pdb|2DGO|A Chain A, Solution Structure Of The Rna Binding Domain In Cytotoxic
Granule-Associated Rna Binding Protein 1
pdb|2RNE|A Chain A, Solution Structure Of The Second Rna Recognition Motif
(Rrm) Of Tia-1
Length = 115
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 44/78 (56%), Gaps = 2/78 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI-EL 476
+FVG+L + D++ F+ + D R+ D A G+ KGYG V F + DA AI ++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 477 NGQMLGNRAIRLDFARER 494
GQ LG R IR ++A +
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
>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 = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 57/193 (29%), Positives = 89/193 (46%), Gaps = 44/193 (22%)
Query: 407 TPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEV-----AEVVDVRLSSDADGRFKGYGH 461
TPF LF+GNL + A+++ SE+ VVDVR ++ + +G+
Sbjct: 12 TPFN--------LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTN-----RKFGY 58
Query: 462 VEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTI 521
V+F S ED KA+EL G + I+L+ + R + + +AA T+
Sbjct: 59 VDFESAEDLEKALELTGLKVFGNEIKLEKPKGRDS----------------KKVRAARTL 102
Query: 522 FIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF-TDADSFNKA 580
K ++ ED+ L+E F EI +S G KGIAY++F ++AD+
Sbjct: 103 LAKNLSFNITEDE----LKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEADAEKNL 153
Query: 581 LEMSGTEIGGYSL 593
E G EI G S+
Sbjct: 154 EEKQGAEIDGRSV 166
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 44/159 (27%), Positives = 72/159 (45%), Gaps = 24/159 (15%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
G L V LP ++ Q ++++ FS + EV +L D G GYG V + + +DA +A
Sbjct: 1 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 60
Query: 474 IE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGE 532
I LNG L ++ I++ +AR S+ K ++I G ++ +
Sbjct: 61 INTLNGLRLQSKTIKVSYAR------------PSSEVIKDA------NLYISGLPRTMTQ 102
Query: 533 DQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF 571
V E+ F G I V D TG +G+A++ F
Sbjct: 103 KDV----EDMFSRFGRIINSRVLVDQTTGLSRGVAFIRF 137
Score = 33.5 bits (75), Expect = 0.40, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI-EL 476
L++ LP ++ Q DV++ FS +++ R+ D G +G + F +A +AI
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 477 NGQ 479
NG
Sbjct: 151 NGH 153
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 53.1 bits (126), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 2/78 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI-EL 476
+FVG+L + D+++ F+ ++ D R+ D A G+ KGYG V F + DA AI +
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 477 NGQMLGNRAIRLDFARER 494
GQ LG R IR ++A +
Sbjct: 78 GGQWLGGRQIRTNWATRK 95
Score = 31.2 bits (69), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD-ADSFNKALEMSGTEIGGYSLVVDE 597
++ F G+I+ V KD TG KG ++ F + D+ N + M G +GG + +
Sbjct: 32 IKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHMGGQWLGGRQIRTNW 91
Query: 598 AKQ 600
A +
Sbjct: 92 ATR 94
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 43/183 (23%), Positives = 79/183 (43%), Gaps = 17/183 (9%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
+ LF+G L F +++ F + + D + D + R +G+G V +A+VE+ A+
Sbjct: 12 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
+ R + P + +S Q+ G IF+ G + ED
Sbjct: 72 ARPHKVDGRVVE-----------PKRAVSREDS-QRPGAHLTVKKIFVGG----IKEDTE 115
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
L ++F G+I I + D +G +G A++ F D DS +K + + G++ V
Sbjct: 116 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 175
Query: 596 DEA 598
+A
Sbjct: 176 RKA 178
>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 = 52.8 bits (125), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 43/183 (23%), Positives = 79/183 (43%), Gaps = 17/183 (9%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
+ LF+G L F +++ F + + D + D + R +G+G V +A+VE+ A+
Sbjct: 13 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
+ R + P + +S Q+ G IF+ G + ED
Sbjct: 73 ARPHKVDGRVVE-----------PKRAVSREDS-QRPGAHLTVKKIFVGG----IKEDTE 116
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
L ++F G+I I + D +G +G A++ F D DS +K + + G++ V
Sbjct: 117 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 176
Query: 596 DEA 598
+A
Sbjct: 177 RKA 179
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 52.8 bits (125), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 43/183 (23%), Positives = 78/183 (42%), Gaps = 17/183 (9%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
+ LF+G L F +++ F + + D + D + R +G+G V +A+VE+ A+
Sbjct: 15 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
+ R + P + +S + G AH K F + ED
Sbjct: 75 ARPHKVDGRVVE-----------PKRAVSREDSQRPG-----AHLTVKKIFVGGIKEDTE 118
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
L ++F G+I I + D +G +G A++ F D DS +K + + G++ V
Sbjct: 119 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 178
Query: 596 DEA 598
+A
Sbjct: 179 RKA 181
>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 = 52.8 bits (125), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 43/183 (23%), Positives = 78/183 (42%), Gaps = 17/183 (9%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
+ LF+G L F +++ F + + D + D + R +G+G V +A+VE+ A+
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
+ R + P + +S + G AH K F + ED
Sbjct: 74 ARPHKVDGRVVE-----------PKRAVSREDSQRPG-----AHLTVKKIFVGGIKEDTE 117
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
L ++F G+I I + D +G +G A++ F D DS +K + + G++ V
Sbjct: 118 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 177
Query: 596 DEA 598
+A
Sbjct: 178 RKA 180
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 52.4 bits (124), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 43/183 (23%), Positives = 79/183 (43%), Gaps = 17/183 (9%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
+ LF+G L F +++ F + + D + D + R +G+G V +A+VE+ A+
Sbjct: 14 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
+ R + P + +S Q+ G IF+ G + ED
Sbjct: 74 ARPHKVDGRVVE-----------PKRAVSREDS-QRPGAHLTVKKIFVGG----IKEDTE 117
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
L ++F G+I I + D +G +G A++ F D DS +K + + G++ V
Sbjct: 118 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 177
Query: 596 DEA 598
+A
Sbjct: 178 RKA 180
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 32/88 (36%), Positives = 50/88 (56%), Gaps = 6/88 (6%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
SKTL + NL +S + +Q F + +++ + +G+ KGY +EFAS EDA +A+
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKA---TFIKVPQNQNGKSKGYAFIEFASFEDAKEALN 71
Query: 476 -LNGQMLGNRAIRLDFARERGAYTPYSG 502
N + + RAIRL+ RG +P SG
Sbjct: 72 SCNKREIEGRAIRLELQGPRG--SPNSG 97
>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 = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 43/183 (23%), Positives = 79/183 (43%), Gaps = 17/183 (9%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
+ LF+G L F +++ F + + D + D + R +G+G V +A+VE+ A+
Sbjct: 7 RKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
+ R + P + +S Q+ G IF+ G + ED
Sbjct: 67 ARPHKVDGRVVE-----------PKRAVSREDS-QRPGAHLTVKKIFVGG----IKEDTE 110
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
L ++F G+I I + D +G +G A++ F D DS +K + + G++ V
Sbjct: 111 EHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTVNGHNCEV 170
Query: 596 DEA 598
+A
Sbjct: 171 RKA 173
>pdb|3HI9|A Chain A, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|B Chain B, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|C Chain C, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
pdb|3HI9|D Chain D, The X-Ray Crystal Structure Of The First Rna Recognition
Motif (Rrm1) Of The Au-Rich Element (Are) Binding
Protein Hur At 2.0 Angstrom Resolution
Length = 84
Score = 50.1 bits (118), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 45/80 (56%), Gaps = 2/80 (2%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
G L V LP ++ Q ++++ FS + EV +L D G GYG V + + +DA +A
Sbjct: 3 GRTNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERA 62
Query: 474 IE-LNGQMLGNRAIRLDFAR 492
I LNG L ++ I++ +AR
Sbjct: 63 INTLNGLRLQSKTIKVSYAR 82
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 49.3 bits (116), Expect = 7e-06, Method: Composition-based stats.
Identities = 40/186 (21%), Positives = 89/186 (47%), Gaps = 22/186 (11%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE- 475
+ L+VGNL ++ + ++ +F + ++++ D + + Y VE+ DA+ A++
Sbjct: 1 RVLYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQT 60
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
LNG+ + N +++++A + +S+S +F+ + +V ++ +
Sbjct: 61 LNGKQIENNIVKINWAFQ---------SQQSSS-------DDTFNLFVGDLNVNVDDETL 104
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV 594
R + ++ F S V D TGS +G ++ FT D A++ M G ++ G L
Sbjct: 105 RNAFKD-FPS---YLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLNGRPLR 160
Query: 595 VDEAKQ 600
++ A +
Sbjct: 161 INWAAK 166
>pdb|1FXL|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The C-Fos
Rna
pdb|1G2E|A Chain A, Crystal Structure Of Hud And Au-Rich Element Of The Tumor
Necrosis Factor Alpha Rna
Length = 167
Score = 49.3 bits (116), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 42/159 (26%), Positives = 72/159 (45%), Gaps = 25/159 (15%)
Query: 416 SKT-LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
SKT L V LP ++ Q + ++ F + E+ +L D G+ GYG V + +DA KA
Sbjct: 1 SKTNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKA 60
Query: 474 IE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGE 532
I LNG L + I++ +AR A ++N +++ G ++ +
Sbjct: 61 INTLNGLRLQTKTIKVSYARPSSASI-----RDAN-------------LYVSGLPKTMTQ 102
Query: 533 DQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF 571
+ LE+ F G I + D TG +G+ ++ F
Sbjct: 103 KE----LEQLFSQYGRIITSRILVDQVTGVSRGVGFIRF 137
Score = 36.2 bits (82), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 35/63 (55%), Gaps = 2/63 (3%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
L+V LP ++ Q +++ FS+ ++ R+ D G +G G + F +A +AI+ L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 477 NGQ 479
NGQ
Sbjct: 151 NGQ 153
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 49.3 bits (116), Expect = 8e-06, Method: Composition-based stats.
Identities = 29/84 (34%), Positives = 47/84 (55%), Gaps = 2/84 (2%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAH 471
S G L+VG+L F++ + ++ F + ++L D++ GR KGYG + F+ E A
Sbjct: 23 SAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAK 82
Query: 472 KAIE-LNGQMLGNRAIRLDFARER 494
KA+E LNG L R +++ ER
Sbjct: 83 KALEQLNGFELAGRPMKVGHVTER 106
Score = 40.4 bits (93), Expect = 0.003, Method: Composition-based stats.
Identities = 27/90 (30%), Positives = 45/90 (50%), Gaps = 7/90 (7%)
Query: 507 NSFQKGGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGI 566
N+ QKG G +++ ++ ED +R E G I I + D +TG KG
Sbjct: 17 NNLQKGSAGPM--RLYVGSLHFNITEDMLRGIFEPF----GRIESIQLMMDSETGRSKGY 70
Query: 567 AYLDFTDADSFNKALE-MSGTEIGGYSLVV 595
++ F+D++ KALE ++G E+ G + V
Sbjct: 71 GFITFSDSECAKKALEQLNGFELAGRPMKV 100
>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 = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 23/57 (40%), Positives = 34/57 (59%)
Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVV 595
LE HF SCG I RI++ D +G KG AY++F + +S + A+ M T G ++ V
Sbjct: 53 LEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVAMDETVFRGRTIKV 109
Score = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 17/73 (23%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE 475
++++VGN+ + D++ FS + + + D G KGY ++EFA A+
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKGYAYIEFAERNSVDAAVA 96
Query: 476 LNGQMLGNRAIRL 488
++ + R I++
Sbjct: 97 MDETVFRGRTIKV 109
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 34/116 (29%), Positives = 56/116 (48%), Gaps = 18/116 (15%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
GS +F+ NL S++ + + FS ++ ++ D +G KGYG V F + E A +AI
Sbjct: 4 GSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAI 62
Query: 475 E-LNGQMLGNRAI---RLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGF 526
E +NG +L +R + R +ER A + G R + ++IK F
Sbjct: 63 EKMNGMLLNDRKVFVGRFKSRKEREA-------------ELGARAKEFTNVYIKNF 105
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 44/76 (57%), Gaps = 3/76 (3%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG--RFKGYGHVEFASVEDAHKAIE 475
T F+GNLP+ V + ++ FF + + VRL + R KG+G+ EF ++ A+
Sbjct: 17 TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 75
Query: 476 LNGQMLGNRAIRLDFA 491
LN + LGN+ IR+D A
Sbjct: 76 LNEESLGNKRIRVDVA 91
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 27/74 (36%), Positives = 42/74 (56%), Gaps = 1/74 (1%)
Query: 409 FTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASV 467
+P+ ++T+F L + D+++FFS V +V DVR+ SD + R KG +VEF +
Sbjct: 18 LSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEI 77
Query: 468 EDAHKAIELNGQML 481
+ AI L GQ L
Sbjct: 78 QSVPLAIGLTGQRL 91
Score = 34.7 bits (78), Expect = 0.19, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 35/61 (57%)
Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEA 598
LE+ F + G++ + + D ++ KGIAY++F + S A+ ++G + G ++V +
Sbjct: 42 LEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQRLLGVPIIVQAS 101
Query: 599 K 599
+
Sbjct: 102 Q 102
>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 = 47.4 bits (111), Expect = 2e-05, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 47/80 (58%), Gaps = 2/80 (2%)
Query: 414 GGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHK 472
G S+ +++G++P+ + + + S V V+++++ D GR KGY +EF +E +
Sbjct: 1 GPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 60
Query: 473 AIE-LNGQMLGNRAIRLDFA 491
A+ LNG LG+R ++ ++
Sbjct: 61 AVRNLNGYQLGSRFLKCGYS 80
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 29/85 (34%), Positives = 48/85 (56%), Gaps = 3/85 (3%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDV-RLSSDAD-GRFKGYGHVEFASVEDA 470
S GS +F+GNL +++ + + FS ++ ++ D D G KGY + FAS + +
Sbjct: 2 SSGSSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDAS 61
Query: 471 HKAIE-LNGQMLGNRAIRLDFARER 494
AIE +NGQ L NR I + +A ++
Sbjct: 62 DAAIEAMNGQYLCNRPITVSYAFKK 86
Score = 29.3 bits (64), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 6/70 (8%)
Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRI-SVPKDYDTGSVKGIAYLDFTDADSFNK 579
IFI D + E L + F + G I + + +D DTG+ KG A+++F D+ +
Sbjct: 8 IFIGNLDPEIDEKL----LYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDA 63
Query: 580 ALE-MSGTEI 588
A+E M+G +
Sbjct: 64 AIEAMNGQYL 73
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 47.0 bits (110), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 40/159 (25%), Positives = 72/159 (45%), Gaps = 25/159 (15%)
Query: 416 SKT-LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
SKT L V LP ++ Q + ++ F + ++ +L D G+ GYG V ++ DA KA
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 474 IE-LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGE 532
I LNG L + I++ +AR A ++N +++ G ++ +
Sbjct: 63 INTLNGLKLQTKTIKVSYARPSSASI-----RDAN-------------LYVSGLPKTMSQ 104
Query: 533 DQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF 571
+ +E+ F G I + D TG +G+ ++ F
Sbjct: 105 KE----MEQLFSQYGRIITSRILLDQATGVSRGVGFIRF 139
Score = 37.7 bits (86), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
L+V LP ++ Q +++ FS+ ++ R+ D A G +G G + F +A +AI+ L
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 477 NGQ 479
NGQ
Sbjct: 153 NGQ 155
>pdb|4FXV|A Chain A, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|B Chain B, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|C Chain C, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
pdb|4FXV|D Chain D, Crystal Structure Of An Elav-Like Protein 1 (Elavl1) From
Homo Sapiens At 1.90 A Resolution
Length = 99
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 27/76 (35%), Positives = 43/76 (56%), Gaps = 2/76 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
L V LP + Q ++++ FS + EV +L D G GYG V + + +DA +AI L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 477 NGQMLGNRAIRLDFAR 492
NG L ++ I++ +AR
Sbjct: 82 NGLRLQSKTIKVSYAR 97
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI 474
S+ +++G++P+ + + + S V V+++++ D GR KGY +EF +E + A+
Sbjct: 2 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 61
Query: 475 E-LNGQMLGNRAIRLDFA 491
LNG LG+R ++ ++
Sbjct: 62 RNLNGYQLGSRFLKCGYS 79
>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 = 45.8 bits (107), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 42/183 (22%), Positives = 86/183 (46%), Gaps = 14/183 (7%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-L 476
++VG++ + + + ++ F+ + + +S D+ + KG+ VE+ E A A+E +
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 75
Query: 477 NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR 536
N MLG R I++ G P Q +A + I++ + +D ++
Sbjct: 76 NSVMLGGRNIKVGRPSNIGQAQPIID-------QLAEEARAFNRIYVASVHQDLSDDDIK 128
Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL-EMSGTEIGGYSLVV 595
+ E + G+I ++ +D TG KG ++++ A S A+ M+ ++GG L V
Sbjct: 129 SVFE----AFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 184
Query: 596 DEA 598
+A
Sbjct: 185 GKA 187
>pdb|4F02|A Chain A, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
pdb|4F02|D Chain D, Crystal Structure Of The Pabp-Binding Site Of Eif4g In
Complex With Rrm1-2 Of Pabp And Poly(A)
Length = 213
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
G +F+ NL S++ + + FS ++ ++ D +G KGYG V F + E A +AI
Sbjct: 102 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAI 160
Query: 475 E-LNGQMLGNRAI 486
E +NG +L +R +
Sbjct: 161 EKMNGMLLNDRKV 173
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 45/174 (25%), Positives = 81/174 (46%), Gaps = 25/174 (14%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK-GYGHVEFASVEDAHKAIE- 475
+L+VG+L V +A + FS ++ +R+ D R GY +V F DA +A++
Sbjct: 17 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 76
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
+N ++ + +R+ +++ S +K G G IFIK D S+
Sbjct: 77 MNFDVIKGKPVRIMWSQ------------RDPSLRKSGVGN----IFIKNLDKSIDN--- 117
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEI 588
+L + F + G I V D + GS KG ++ F ++ +A+E M+G +
Sbjct: 118 -KALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQEAAERAIEKMNGMLL 168
>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 = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 36/155 (23%), Positives = 67/155 (43%), Gaps = 24/155 (15%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-L 476
L V LP ++ F + + R+ D G GY V+F S D+ +AI+ L
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 477 NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR 536
NG + N+ +++ +AR GG +++ ++ +DQ
Sbjct: 77 NGITVRNKRLKVSYAR------------------PGGESIKDTNLYVTNLPRTITDDQ-- 116
Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF 571
L+ FG G I + ++ +D TG +G+A++ +
Sbjct: 117 --LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRY 149
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 4/85 (4%)
Query: 516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDAD 575
+A++T I + + +D L F + G I + +DY TG G A++DFT
Sbjct: 11 RASNTNLIVNY---LPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEX 67
Query: 576 SFNKALE-MSGTEIGGYSLVVDEAK 599
+A++ ++G + L V A+
Sbjct: 68 DSQRAIKVLNGITVRNKRLKVSYAR 92
>pdb|1CVJ|A Chain A, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|B Chain B, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|C Chain C, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|D Chain D, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|E Chain E, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|F Chain F, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|G Chain G, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
pdb|1CVJ|H Chain H, X-Ray Crystal Structure Of The Poly(A)-Binding Protein In
Complex With Polyadenylate Rna
Length = 190
Score = 45.4 bits (106), Expect = 9e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 41/73 (56%), Gaps = 2/73 (2%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
G +F+ NL S++ + + FS ++ ++ D +G KGYG V F + E A +AI
Sbjct: 97 GVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAERAI 155
Query: 475 E-LNGQMLGNRAI 486
E +NG +L +R +
Sbjct: 156 EKMNGMLLNDRKV 168
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 47/185 (25%), Positives = 84/185 (45%), Gaps = 25/185 (13%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK-GYGHVEFASVEDAHKAIE- 475
+L+VG+L V +A + FS ++ +R+ D R GY +V F DA +A++
Sbjct: 12 SLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDT 71
Query: 476 LNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQV 535
+N ++ + +R+ +++ S +K G G IFIK D S+
Sbjct: 72 MNFDVIKGKPVRIMWSQ------------RDPSLRKSGVG----NIFIKNLDKSIDN--- 112
Query: 536 RASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLV 594
+L + F + G I V D + GS KG ++ F ++ +A+E M+G + +
Sbjct: 113 -KALYDTFSAFGNILSCKVVCD-ENGS-KGYGFVHFETQEAAERAIEKMNGMLLNDRKVF 169
Query: 595 VDEAK 599
V K
Sbjct: 170 VGRFK 174
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 45.4 bits (106), Expect = 9e-05, Method: Composition-based stats.
Identities = 37/165 (22%), Positives = 72/165 (43%), Gaps = 24/165 (14%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
L V LP + ++ F + + R+ D G GY V+F S D+ +AI+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 477 NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR 536
NG + N+ +++ +AR GG +++ ++ +DQ
Sbjct: 66 NGITVRNKRLKVSYAR------------------PGGESIKDTNLYVTNLPRTITDDQ-- 105
Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL 581
L+ FG G I + ++ +D TG +G+A++ + + +A+
Sbjct: 106 --LDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAI 148
Score = 28.9 bits (63), Expect = 8.7, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 532 EDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG 590
+D L F + G I + +DY TG G A++DFT +A++ ++G +
Sbjct: 13 QDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN 72
Query: 591 YSLVVDEAK 599
L V A+
Sbjct: 73 KRLKVSYAR 81
>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 = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 46/78 (58%), Gaps = 2/78 (2%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI 474
S+ +++G++P+ + + + S V V+++++ D GR KGY +EF +E + A+
Sbjct: 4 SRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAV 63
Query: 475 E-LNGQMLGNRAIRLDFA 491
LNG LG+R ++ ++
Sbjct: 64 RNLNGYQLGSRFLKCGYS 81
>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 = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 42/183 (22%), Positives = 86/183 (46%), Gaps = 14/183 (7%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-L 476
++VG++ + + + ++ F+ + + +S D+ + KG+ VE+ E A A+E +
Sbjct: 31 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQM 90
Query: 477 NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR 536
N MLG R I++ G P Q +A + I++ + +D ++
Sbjct: 91 NSVMLGGRNIKVGRPSNIGQAQPIID-------QLAEEARAFNRIYVASVHQDLSDDDIK 143
Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL-EMSGTEIGGYSLVV 595
+ E + G+I ++ +D TG KG ++++ A S A+ M+ ++GG L V
Sbjct: 144 SVFE----AFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSMNLFDLGGQYLRV 199
Query: 596 DEA 598
+A
Sbjct: 200 GKA 202
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 26/96 (27%), Positives = 44/96 (45%), Gaps = 14/96 (14%)
Query: 510 QKGGRGQAAHT---------IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDT 560
Q+ GRG AA +++ +GED +R + F G I I + D T
Sbjct: 11 QQMGRGSAAQRQGALAIMSRVYVGSIYYELGEDTIR----QAFAPFGPIKSIDMSWDSVT 66
Query: 561 GSVKGIAYLDFTDADSFNKALE-MSGTEIGGYSLVV 595
KG A++++ ++ ALE M+ +GG ++ V
Sbjct: 67 MKHKGFAFVEYEVPEAAQLALEQMNSVMLGGRNIKV 102
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 43/73 (58%), Gaps = 2/73 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKA-IEL 476
LFVG L F + ++ FS+ ++ +V + D + R +G+G V F +++DA A + +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAM 74
Query: 477 NGQMLGNRAIRLD 489
NG+ + R IR+D
Sbjct: 75 NGKSVDGRQIRVD 87
Score = 36.2 bits (82), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 538 SLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA-LEMSGTEIGGYSLVVD 596
SLE+ F G+I+ + V KD +T +G ++ F + D A + M+G + G + VD
Sbjct: 28 SLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMAMNGKSVDGRQIRVD 87
Query: 597 EA 598
+A
Sbjct: 88 QA 89
>pdb|2HGN|A Chain A, Nmr Structure Of The Third Qrrm Domain Of Human Hnrnp F
pdb|2KG1|A Chain A, Structure Of The Third Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 139
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 34/114 (29%), Positives = 53/114 (46%), Gaps = 5/114 (4%)
Query: 399 ESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKG 458
+ G+ + + FT QS + + LP+ + D+ NFFS + V V + DGR G
Sbjct: 29 QMGRGSGDSEFTVQSTTGHCVHMRGLPYKATENDIYNFFSPL-NPVRVHIEIGPDGRVTG 87
Query: 459 YGHVEFASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKG 512
VEFA+ E+A A+ + + +R I L GA S G S+ +G
Sbjct: 88 EADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTGA----SNGAYSSQVMQG 137
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 29/78 (37%), Positives = 45/78 (57%), Gaps = 3/78 (3%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG--RFKGYGHVEFASVEDAHKAIE 475
T F+GNLP+ V + ++ FF + + VRL + R KG+G+ EF ++ A+
Sbjct: 21 TAFLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALS 79
Query: 476 LNGQMLGNRAIRLDFARE 493
LN + LGNR IR+D A +
Sbjct: 80 LNEESLGNRRIRVDVADQ 97
>pdb|1HD0|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
pdb|1HD1|A Chain A, Heterogeneous Nuclear Ribonucleoprotein D0 (Hnrnp D0
Rbd1), Nmr
Length = 75
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 6/69 (8%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-- 475
+F+G L + + D++++FS+ EVVD L D GR +G+G V F E K ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMDQK 61
Query: 476 ---LNGQML 481
LNG+++
Sbjct: 62 EHKLNGKVI 70
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 44.3 bits (103), Expect = 2e-04, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
LFV + + D+ + F+E E+ ++ L+ D G KGY VE+ + ++A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 477 NGQMLGNRAIRLDFARERG 495
NGQ L + I +D+ RG
Sbjct: 70 NGQDLMGQPISVDWCFVRG 88
Score = 32.3 bits (72), Expect = 0.86, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 526 FDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS 584
F + V E+ + + F GEI I + D TG +KG +++ A+E ++
Sbjct: 11 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 70
Query: 585 GTEIGGYSLVVD 596
G ++ G + VD
Sbjct: 71 GQDLMGQPISVD 82
>pdb|1P27|B Chain B, Crystal Structure Of The Human Y14MAGOH COMPLEX
pdb|1P27|D Chain D, Crystal Structure Of The Human Y14MAGOH COMPLEX
Length = 106
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 31/101 (30%), Positives = 52/101 (51%), Gaps = 2/101 (1%)
Query: 397 DAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGR 455
D +S ++ P +S LFV + + D+ + F+E E+ ++ L+ D G
Sbjct: 4 DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 63
Query: 456 FKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARERG 495
KGY VE+ + ++A A+E LNGQ L + I +D+ RG
Sbjct: 64 LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDWCFVRG 104
Score = 31.2 bits (69), Expect = 1.8, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 526 FDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS 584
F + V E+ + + F GEI I + D TG +KG +++ A+E ++
Sbjct: 27 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 86
Query: 585 GTEIGGYSLVVD 596
G ++ G + VD
Sbjct: 87 GQDLMGQPISVD 98
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
LFV + + D+ + F+E E+ ++ L+ D G KGY VE+ + ++A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 477 NGQMLGNRAIRLDFARERG 495
NGQ L + I +D+ RG
Sbjct: 70 NGQDLMGQPISVDWCFVRG 88
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 526 FDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS 584
F + V E+ + + F GEI I + D TG +KG +++ A+E ++
Sbjct: 11 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 70
Query: 585 GTEIGGYSLVVD 596
G ++ G + VD
Sbjct: 71 GQDLMGQPISVD 82
>pdb|3MD1|A Chain A, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
pdb|3MD1|B Chain B, Crystal Structure Of The Second Rrm Domain Of Yeast
Poly(U)-Binding Protein (Pub1)
Length = 83
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 2/75 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE-L 476
LFVG+L +V+ ++N F + + + D G +GYG V F S +DA A++ +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 477 NGQMLGNRAIRLDFA 491
GQ L R +R+++A
Sbjct: 64 QGQDLNGRPLRINWA 78
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 44/79 (55%), Gaps = 2/79 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
LFV + + D+ + F+E E+ ++ L+ D G KGY VE+ + ++A A+E L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 477 NGQMLGNRAIRLDFARERG 495
NGQ L + I +D+ RG
Sbjct: 72 NGQDLMGQPISVDWCFVRG 90
Score = 32.0 bits (71), Expect = 1.3, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 526 FDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS 584
F + V E+ + + F GEI I + D TG +KG +++ A+E ++
Sbjct: 13 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 72
Query: 585 GTEIGGYSLVVD 596
G ++ G + VD
Sbjct: 73 GQDLMGQPISVD 84
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 50/104 (48%), Gaps = 10/104 (9%)
Query: 396 VDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR 455
+D +S K + +T + LFVGNLP + + D + F E +V ++ D
Sbjct: 6 IDIKSFLKPGEKTYTQRC----RLFVGNLPTDITEEDFKRLFERYGEPSEVFINRD---- 57
Query: 456 FKGYGHVEFASVEDAHKA-IELNGQMLGNRAIRLDFARERGAYT 498
+G+G + S A A EL+G +L +R +R+ FA A T
Sbjct: 58 -RGFGFIRLESRTLAEIAKAELDGTILKSRPLRIRFATHGAALT 100
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 44/80 (55%), Gaps = 3/80 (3%)
Query: 416 SKT-LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
SKT L V LP ++ Q + ++ F + ++ +L D G+ GYG V ++ DA KA
Sbjct: 3 SKTNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKA 62
Query: 474 IE-LNGQMLGNRAIRLDFAR 492
I LNG L + I++ +AR
Sbjct: 63 INTLNGLKLQTKTIKVSYAR 82
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
T+FVG + +++ ++++FF+ V +V++ +D G KGYG V F + D K +E
Sbjct: 12 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 69
>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 = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 41/173 (23%), Positives = 75/173 (43%), Gaps = 34/173 (19%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEF---ASVEDAH 471
S +F+G L + + +++ +F + V D+++ D A GR +G+G + F +SV++
Sbjct: 3 SCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVV 62
Query: 472 KAIE-LNGQMLG-NRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSS 529
K L+G+++ RAI D + G IF+ G
Sbjct: 63 KTQHILDGKVIDPKRAIPRDEQDKTGK------------------------IFVGG---- 94
Query: 530 VGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE 582
+G D EE F G I + D DTG +G ++ + AD+ ++ +
Sbjct: 95 IGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTYDSADAVDRVCQ 147
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 43.1 bits (100), Expect = 4e-04, Method: Composition-based stats.
Identities = 28/89 (31%), Positives = 47/89 (52%), Gaps = 5/89 (5%)
Query: 412 QSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAH 471
+ G +F+ NL S++ + + FS ++ ++ D +G KGYG V F + E A
Sbjct: 7 RKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS-KGYGFVHFETQEAAE 65
Query: 472 KAIE-LNGQMLGNRAI---RLDFARERGA 496
+AIE +NG +L +R + R +ER A
Sbjct: 66 RAIEKMNGMLLNDRKVFVGRFKSRKEREA 94
>pdb|2XS5|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS5|B Chain B, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Mvh Rna, Uguuc
pdb|2XS7|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Sycp3 Rna, Uuguuu
Length = 87
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
T+FVG + +++ ++++FF+ V +V++ +D G KGYG V F + D K +E
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRL--SSDADGRFKGYGHVEFASVEDAHKAIE- 475
+ V N+PF Q +++ FS E+ VRL G +G+G V+F + +DA KA
Sbjct: 18 ILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFNA 77
Query: 476 -LNGQMLGNRAIRLDFA 491
+ L R + L++A
Sbjct: 78 LCHSTHLYGRRLVLEWA 94
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 39/87 (44%), Gaps = 9/87 (10%)
Query: 396 VDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR 455
V A+ K+ Q P L++ NLP S+++ +++N +V+ R+ D+ G
Sbjct: 13 VQAQMAKQQEQDP--------TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGT 64
Query: 456 FKGYGHVEFASVEDAHKAI-ELNGQML 481
+G G S E I NG+ +
Sbjct: 65 SRGVGFARMESTEKCEAVIGHFNGKFI 91
>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 = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 39/76 (51%), Gaps = 1/76 (1%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
S TL+VGNL F + + FS+ ++ + + D G+ VE+ S DA A+
Sbjct: 18 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMR 77
Query: 476 -LNGQMLGNRAIRLDF 490
+NG L +R IR D+
Sbjct: 78 YINGTRLDDRIIRTDW 93
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 29/96 (30%), Positives = 50/96 (52%), Gaps = 2/96 (2%)
Query: 397 DAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGR 455
D +S ++ P +S LFV + + D+ + F+E E+ ++ L+ D G
Sbjct: 3 DYDSVEQDGDEPGPQRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGY 62
Query: 456 FKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDF 490
KGY VE+ + ++A A+E LNGQ L + I +D+
Sbjct: 63 LKGYTLVEYETYKEAQAAMEGLNGQDLMGQPISVDW 98
Score = 32.0 bits (71), Expect = 1.1, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 526 FDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS 584
F + V E+ + + F GEI I + D TG +KG +++ A+E ++
Sbjct: 26 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 85
Query: 585 GTEIGGYSLVVD 596
G ++ G + VD
Sbjct: 86 GQDLMGQPISVD 97
>pdb|2XS2|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like In Complex With Rna, Uuguucuu
Length = 102
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 35/58 (60%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
T+FVG + +++ ++++FF+ V +V++ +D G KGYG V F + D K +E
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTGVSKGYGFVSFYNDVDVQKIVE 68
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 42.7 bits (99), Expect = 7e-04, Method: Composition-based stats.
Identities = 34/93 (36%), Positives = 49/93 (52%), Gaps = 8/93 (8%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVV--DVRLSSDADGRFKGYGHVEFASVEDA 470
S GS +FV NLPF +++ F+E V+ D+++ +G+ KG G V+F S E A
Sbjct: 2 SSGSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME---NGKSKGCGVVKFESPEVA 58
Query: 471 HKAIE-LNGQMLGNRAIRLDFARERGAYTPYSG 502
+A +NG L R I D +R A P SG
Sbjct: 59 ERACRMMNGMKLSGREI--DVRIDRNASGPSSG 89
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 42.4 bits (98), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 25/72 (34%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIEL- 476
T+FV NL + V ++ FS VV + D DG+ +G G V F +A +AI +
Sbjct: 17 TVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMF 76
Query: 477 NGQMLGNRAIRL 488
NGQ+L +R + +
Sbjct: 77 NGQLLFDRPMHV 88
>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 = 42.4 bits (98), Expect = 9e-04, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSF 577
A +I++ D ++ LE HF CG + R+++ D +G KG AY++F+D +S
Sbjct: 5 ARSIYVGNVDYGATAEE----LEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 60
Query: 578 NKALEMSGTEIGGYSLVV 595
+L + + G + V
Sbjct: 61 RTSLALDESLFRGRQIKV 78
Score = 32.3 bits (72), Expect = 1.0, Method: Composition-based stats.
Identities = 16/74 (21%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAI 474
+++++VGN+ + +++ F V V + D G KG+ ++EF+ E ++
Sbjct: 5 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 64
Query: 475 ELNGQMLGNRAIRL 488
L+ + R I++
Sbjct: 65 ALDESLFRGRQIKV 78
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 42.4 bits (98), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 45/81 (55%), Gaps = 5/81 (6%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
++TL NL F++ + +++ F + E+ RL S DG+ KG ++EF S DA K +E
Sbjct: 16 ARTLLAKNLSFNITEDELKEVFEDALEI---RLVSQ-DGKSKGIAYIEFKSEADAEKNLE 71
Query: 476 L-NGQMLGNRAIRLDFARERG 495
G + R++ L + E+G
Sbjct: 72 EKQGAEIDGRSVSLYYTGEKG 92
Score = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 27/79 (34%), Positives = 40/79 (50%), Gaps = 10/79 (12%)
Query: 516 QAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF-TDA 574
+AA T+ K ++ ED+ L+E F EI +S G KGIAY++F ++A
Sbjct: 14 RAARTLLAKNLSFNITEDE----LKEVFEDALEIRLVS-----QDGKSKGIAYIEFKSEA 64
Query: 575 DSFNKALEMSGTEIGGYSL 593
D+ E G EI G S+
Sbjct: 65 DAEKNLEEKQGAEIDGRSV 83
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE- 475
K L V N+PF D++ F + +++DV + + G KG+G V F + DA +A E
Sbjct: 16 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADADRAREK 74
Query: 476 LNGQMLGNRAIRLDFARER 494
L+G ++ R I ++ A R
Sbjct: 75 LHGTVVEGRKIEVNNATAR 93
>pdb|3S7R|A Chain A, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
pdb|3S7R|B Chain B, Crystal Structure Of A Heterogeneous Nuclear
Ribonucleoprotein AB (Hnrpab) From Homo Sapiens At 2.15
A Resolution
Length = 87
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 1/68 (1%)
Query: 420 FVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIELNG 478
FVG L + + D++++F++ EVVD + D + GR +G+G + F K ++
Sbjct: 15 FVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQKE 74
Query: 479 QMLGNRAI 486
L R I
Sbjct: 75 HRLDGRVI 82
Score = 33.9 bits (76), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 18/67 (26%), Positives = 32/67 (47%)
Query: 524 KGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEM 583
K F + D + L+++F GE+ ++ D +TG +G ++ F DA S K L+
Sbjct: 13 KXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKVLDQ 72
Query: 584 SGTEIGG 590
+ G
Sbjct: 73 KEHRLDG 79
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 25/74 (33%), Positives = 42/74 (56%), Gaps = 2/74 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
LFV + + D+ + F+E E+ ++ L+ D G KGY VE+ + ++A A+E L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 477 NGQMLGNRAIRLDF 490
NGQ L + I +D+
Sbjct: 70 NGQDLMGQPISVDW 83
Score = 32.3 bits (72), Expect = 0.80, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 526 FDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MS 584
F + V E+ + + F GEI I + D TG +KG +++ A+E ++
Sbjct: 11 FVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGLN 70
Query: 585 GTEIGGYSLVVD 596
G ++ G + VD
Sbjct: 71 GQDLMGQPISVD 82
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 29/87 (33%), Positives = 42/87 (48%), Gaps = 8/87 (9%)
Query: 514 RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD 573
R Q + T+F+KG + ED +L+E F R + D +TGS KG ++DF
Sbjct: 11 RSQPSKTLFVKG----LSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNS 63
Query: 574 ADSFNKALE-MSGTEIGGYSLVVDEAK 599
+ A E M EI G + +D AK
Sbjct: 64 EEDAKAAKEAMEDGEIDGNKVTLDWAK 90
Score = 36.2 bits (82), Expect = 0.057, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 44/80 (55%), Gaps = 7/80 (8%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAI 474
SKTLFV L + ++ F V R+ +D + G KG+G V+F S EDA A
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFDGS---VRARIVTDRETGSSKGFGFVDFNSEEDAKAAK 71
Query: 475 EL--NGQMLGNRAIRLDFAR 492
E +G++ GN+ + LD+A+
Sbjct: 72 EAMEDGEIDGNK-VTLDWAK 90
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 27/74 (36%), Positives = 40/74 (54%), Gaps = 6/74 (8%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR-FKGYGHVEFA---SVEDAHKA 473
T++V NLPFS+ D+ FS+ +VV V + D D R KG + F S ++ +A
Sbjct: 18 TVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRA 77
Query: 474 IELNGQMLGNRAIR 487
I N Q+ G R I+
Sbjct: 78 IN-NKQLFG-RVIK 89
Score = 33.9 bits (76), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 14/38 (36%), Positives = 23/38 (60%)
Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADS 576
L F G++ ++++ KD DT KG+A++ F D DS
Sbjct: 33 LYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDS 70
>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 = 0.001, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 40/78 (51%), Gaps = 4/78 (5%)
Query: 518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSF 577
A +I++ D ++ LE HF CG + R+++ D +G KG AY++F+D +S
Sbjct: 6 ARSIYVGNVDYGATAEE----LEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESV 61
Query: 578 NKALEMSGTEIGGYSLVV 595
+L + + G + V
Sbjct: 62 RTSLALDESLFRGRQIKV 79
Score = 31.6 bits (70), Expect = 1.3, Method: Composition-based stats.
Identities = 16/74 (21%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAI 474
+++++VGN+ + +++ F V V + D G KG+ ++EF+ E ++
Sbjct: 6 ARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL 65
Query: 475 ELNGQMLGNRAIRL 488
L+ + R I++
Sbjct: 66 ALDESLFRGRQIKV 79
>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 = 41.6 bits (96), Expect = 0.001, Method: Composition-based stats.
Identities = 34/116 (29%), Positives = 53/116 (45%), Gaps = 12/116 (10%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFK-GYGHVEFASVEDAHKAI 474
S TL+VGNL F + + FS+ ++ + + D + G+ VE+ S DA A+
Sbjct: 39 SCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAM 98
Query: 475 E-LNGQMLGNRAIRLD----FARERGAYTPYSGGNESNSFQ------KGGRGQAAH 519
+NG L +R IR D F R SGG + ++ +GG G+ A
Sbjct: 99 RYINGTRLDDRIIRTDWDAGFKEGRQYGRGRSGGQVRDEYRQDYDAGRGGYGKLAQ 154
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/79 (32%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE- 475
K L V N+PF D++ F + +++DV + + G KG+G V F + DA +A E
Sbjct: 30 KRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS-KGFGFVTFENSADADRAREK 88
Query: 476 LNGQMLGNRAIRLDFARER 494
L+G ++ R I ++ A R
Sbjct: 89 LHGTVVEGRKIEVNNATAR 107
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 33/93 (35%), Positives = 49/93 (52%), Gaps = 8/93 (8%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVV--DVRLSSDADGRFKGYGHVEFASVEDA 470
S G+ +FV NLPF +++ F+E V+ D+++ +G+ KG G V+F S E A
Sbjct: 5 SSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME---NGKSKGCGVVKFESPEVA 61
Query: 471 HKAIE-LNGQMLGNRAIRLDFARERGAYTPYSG 502
+A +NG L R I D +R A P SG
Sbjct: 62 ERACRMMNGMKLSGREI--DVRIDRNASGPSSG 92
>pdb|3BS9|A Chain A, X-Ray Structure Of Human Tia-1 Rrm2
pdb|3BS9|B Chain B, X-Ray Structure Of Human Tia-1 Rrm2
Length = 87
Score = 40.8 bits (94), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/54 (42%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 440 VAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFA 491
+ D R+ D A G+ KGYG V F + DA AI+ + GQ LG R IR ++A
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWA 83
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 45/82 (54%), Gaps = 5/82 (6%)
Query: 518 AHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSF 577
AH +FI G + + +DQV+ E S G + ++ KD TG KG A+ ++ D +
Sbjct: 1 AHKLFIGGLPNYLNDDQVK----ELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVT 56
Query: 578 NKALE-MSGTEIGGYSLVVDEA 598
++A+ ++G ++G L+V A
Sbjct: 57 DQAIAGLNGMQLGDKKLLVQRA 78
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 46/81 (56%), Gaps = 6/81 (7%)
Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTD-ADSFNK 579
+FI G + E ++A FG G I+ + + KD + S +G A++ F + AD+ N
Sbjct: 10 LFIGGLNRETNEKMLKAV----FGKHGPISEVLLIKDRTSKS-RGFAFITFENPADAKNA 64
Query: 580 ALEMSGTEIGGYSLVVDEAKQ 600
A +M+G + G ++ V++AK+
Sbjct: 65 AKDMNGKSLHGKAIKVEQAKK 85
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 25/97 (25%), Positives = 46/97 (47%), Gaps = 14/97 (14%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
LF+G L + ++ F + + +V L D + +G+ + F + DA A ++N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMN 69
Query: 478 GQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGR 514
G+ L +AI+++ A++ SFQ GGR
Sbjct: 70 GKSLHGKAIKVEQAKK-------------PSFQSGGR 93
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 23/89 (25%), Positives = 43/89 (48%), Gaps = 3/89 (3%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE 475
+ LF+G L F + ++N++ + ++ D + D A R +G+G V F+S+ + A+
Sbjct: 28 RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMA 87
Query: 476 LNGQMLGNRAI--RLDFARERGAYTPYSG 502
+ R + + ARE P SG
Sbjct: 88 ARPHSIDGRVVEPKRAVAREESGSGPSSG 116
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 30/95 (31%), Positives = 45/95 (47%), Gaps = 4/95 (4%)
Query: 400 SGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGY 459
SG P P + V +PFS + DV++FF + V V L D GR G
Sbjct: 3 SGSSGKPLPINPDD---LYVSVHGMPFSAMENDVRDFFHGL-RVDAVHLLKDHVGRNNGN 58
Query: 460 GHVEFASVEDAHKAIELNGQMLGNRAIRLDFARER 494
G V+F S +D +A++ N ++ R + + A ER
Sbjct: 59 GLVKFLSPQDTFEALKRNRMLMIQRYVEVSPATER 93
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 39.3 bits (90), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIEL 476
T++VG L V + + F + VV+ + D G+ +GYG VEF S EDA AI++
Sbjct: 17 TVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKI 76
Query: 477 NGQM-LGNRAIRLD 489
+ L + IR++
Sbjct: 77 MDMIKLYGKPIRVN 90
Score = 34.7 bits (78), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 35/73 (47%), Gaps = 8/73 (10%)
Query: 514 RGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFT- 572
R Q A T+++ G D V E L E F G + +PKD TG +G +++F
Sbjct: 12 RNQDA-TVYVGGLDEKVSE----PLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLS 66
Query: 573 --DADSFNKALEM 583
DAD K ++M
Sbjct: 67 EEDADYAIKIMDM 79
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR-FKGYGHVEFASVEDAHKAIE-L 476
L V L + D++ FS+ + DV + D R +G+ V F +V+DA +A E
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 477 NGQMLGNRAIRLDFARERGAYT 498
NG L R IR+DF+ + +T
Sbjct: 75 NGMELDGRRIRVDFSITKRPHT 96
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR-FKGYGHVEFASVEDAHKAIE-L 476
L V L + D++ FS+ + DV + D R +G+ V F +V+DA +A E
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 477 NGQMLGNRAIRLDFA 491
NG L R IR+DF+
Sbjct: 109 NGMELDGRRIRVDFS 123
>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 = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 40/183 (21%), Positives = 81/183 (44%), Gaps = 14/183 (7%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAIE-L 476
++VG++ + + + ++ F+ + + S D+ + KG+ VE+ E A A+E
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQX 74
Query: 477 NGQMLGNRAIRLDFARERGAYTPYSGGNESNSFQKGGRGQAAHTIFIKGFDSSVGEDQVR 536
N LG R I++ G P Q +A + I++ + +D ++
Sbjct: 75 NSVXLGGRNIKVGRPSNIGQAQPIID-------QLAEEARAFNRIYVASVHQDLSDDDIK 127
Query: 537 ASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALEMSGT-EIGGYSLVV 595
+ E + G+I ++ +D TG KG ++++ A S A+ ++GG L V
Sbjct: 128 SVFE----AFGKIKSCTLARDPTTGKHKGYGFIEYEKAQSSQDAVSSXNLFDLGGQYLRV 183
Query: 596 DEA 598
+A
Sbjct: 184 GKA 186
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR-FKGYGHVEFASVEDAHKAIE-L 476
L V L + D++ FS+ + DV + D R +G+ V F +V+DA +A E
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 477 NGQMLGNRAIRLDFARERGAYT 498
NG L R IR+DF+ + +T
Sbjct: 78 NGMELDGRRIRVDFSITKRPHT 99
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 38.9 bits (89), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 18/47 (38%), Positives = 29/47 (61%), Gaps = 1/47 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEF 464
LFVG L +S Q ++++FS+ EVVD + D + +G+G V+F
Sbjct: 19 LFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKF 65
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 15/61 (24%), Positives = 28/61 (45%), Gaps = 4/61 (6%)
Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
+F+ G D S ++ +R+ +F GE+ + KD T +G ++ F D +
Sbjct: 19 LFVGGLDWSTTQETLRS----YFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDPNCVGTV 74
Query: 581 L 581
L
Sbjct: 75 L 75
>pdb|1FJ7|A Chain A, Solution Structure Of Nucleolin Rbd1
Length = 101
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 46/90 (51%), Gaps = 18/90 (20%)
Query: 405 AQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEV-----AEVVDVRLSSDADGRFKGY 459
+ TPF LF+GNL + A+++ SE+ VVDVR ++ + +
Sbjct: 14 STTPFN--------LFIGNLNPNKSVAELKVAISELFAKNDLAVVDVRTGTN-----RKF 60
Query: 460 GHVEFASVEDAHKAIELNGQMLGNRAIRLD 489
G+V+F S ED KA+EL G + I+L+
Sbjct: 61 GYVDFESAEDLEKALELTGLKVFGNEIKLE 90
Score = 31.2 bits (69), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 26/43 (60%)
Query: 557 DYDTGSVKGIAYLDFTDADSFNKALEMSGTEIGGYSLVVDEAK 599
D TG+ + Y+DF A+ KALE++G ++ G + +++ K
Sbjct: 51 DVRTGTNRKFGYVDFESAEDLEKALELTGLKVFGNEIKLEKPK 93
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein H'
Length = 102
Score = 38.1 bits (87), Expect = 0.014, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 412 QSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAH 471
QS + + LP+ + D+ NFFS + + V + DGR G VEFA+ EDA
Sbjct: 11 QSTTGHCVHMRGLPYRATENDIYNFFSPL-NPMRVHIEIGPDGRVTGEADVEFATHEDAV 69
Query: 472 KAIELNGQMLGNRAIRL 488
A+ + + +R + L
Sbjct: 70 AAMAKDKANMQHRYVEL 86
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 38.1 bits (87), Expect = 0.015, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
+ L+VG L V+ + F ++ D+++ D + + +G+ VEF EDA AI+
Sbjct: 64 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 123
Query: 476 -LNGQMLGNRAIRLDFA 491
+N L R IR++ A
Sbjct: 124 NMNESELFGRTIRVNLA 140
Score = 35.8 bits (81), Expect = 0.076, Method: Composition-based stats.
Identities = 24/79 (30%), Positives = 45/79 (56%), Gaps = 5/79 (6%)
Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
+++ G V +D+V L F G+IT I +P DY+T +G A+++F A+ A
Sbjct: 66 LYVGGLAEEV-DDKV---LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 121
Query: 581 LE-MSGTEIGGYSLVVDEA 598
++ M+ +E+ G ++ V+ A
Sbjct: 122 IDNMNESELFGRTIRVNLA 140
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 19/64 (29%), Positives = 37/64 (57%), Gaps = 1/64 (1%)
Query: 425 PFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQMLGNR 484
PF+V + +V F + + V +R+ +A G GY V+F++ E+ +A++ N + +G R
Sbjct: 19 PFNVTEKNVMEFLAPLKPVA-IRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGR 77
Query: 485 AIRL 488
I +
Sbjct: 78 YIEV 81
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 38.1 bits (87), Expect = 0.017, Method: Composition-based stats.
Identities = 26/81 (32%), Positives = 37/81 (45%), Gaps = 1/81 (1%)
Query: 409 FTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVE 468
F Q +T+FVGNL V + + F + + V + D +G+ K +G V F E
Sbjct: 9 FPAQEEADRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPE 68
Query: 469 DAHKAIE-LNGQMLGNRAIRL 488
AI LNG L R I +
Sbjct: 69 SVSYAIALLNGIRLYGRPINV 89
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 38.1 bits (87), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 24/67 (35%), Positives = 38/67 (56%), Gaps = 3/67 (4%)
Query: 424 LPFSVEQADVQNFFSEVAEVV--DVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQML 481
LPF + ++ FFS + E+V + L D GR G V+FAS E A KA++ + + +
Sbjct: 23 LPFGCSKEEIVQFFSGL-EIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERI 81
Query: 482 GNRAIRL 488
G+R I +
Sbjct: 82 GHRYIEI 88
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 37.7 bits (86), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 25/71 (35%), Positives = 33/71 (46%), Gaps = 1/71 (1%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
L V NL F V AD+Q F+E + + D GR G V F DA KA+ + N
Sbjct: 31 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYN 90
Query: 478 GQMLGNRAIRL 488
G L R + +
Sbjct: 91 GVPLDGRPMNI 101
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 37.7 bits (86), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 26/56 (46%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
L V NL F V AD+Q F+E + + D GR G V F DA KA+
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAM 93
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 37.7 bits (86), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 44/77 (57%), Gaps = 2/77 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
L+V NL ++ ++ FS + ++ + GR KG+G V F+S E+A KA+ E+N
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEG-GRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 478 GQMLGNRAIRLDFARER 494
G+++ + + + A+ +
Sbjct: 77 GRIVATKPLYVALAQRK 93
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain (Rbd2)
Of Hu Antigen C (Huc)
Length = 85
Score = 37.7 bits (86), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 36/63 (57%), Gaps = 2/63 (3%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
L+V LP ++ Q +++ FS+ ++ R+ D A G +G G + F +A +AI+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 477 NGQ 479
NGQ
Sbjct: 64 NGQ 66
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 37.4 bits (85), Expect = 0.025, Method: Composition-based stats.
Identities = 20/69 (28%), Positives = 35/69 (50%), Gaps = 1/69 (1%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIELN 477
+FVG L + DV+++F + +V D L D R +G+G V F S + K E++
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEIH 61
Query: 478 GQMLGNRAI 486
+ N+ +
Sbjct: 62 FHEINNKMV 70
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 37.4 bits (85), Expect = 0.025, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 42/82 (51%), Gaps = 2/82 (2%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAH 471
S + L+VG L V+ + F ++ D+++ D + + +G+ VEF EDA
Sbjct: 2 STTKRVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAA 61
Query: 472 KAIE-LNGQMLGNRAIRLDFAR 492
AI+ +N L R IR++ A+
Sbjct: 62 AAIDNMNESELFGRTIRVNLAK 83
Score = 35.8 bits (81), Expect = 0.080, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 46/80 (57%), Gaps = 5/80 (6%)
Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
+++ G V +D+V L F G+IT I +P DY+T +G A+++F A+ A
Sbjct: 8 LYVGGLAEEV-DDKV---LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAA 63
Query: 581 LE-MSGTEIGGYSLVVDEAK 599
++ M+ +E+ G ++ V+ AK
Sbjct: 64 IDNMNESELFGRTIRVNLAK 83
>pdb|3MDF|A Chain A, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
pdb|3MDF|B Chain B, Crystal Structure Of The Rrm Domain Of Cyclophilin 33
Length = 85
Score = 37.4 bits (85), Expect = 0.026, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
+ L+VG L V+ + F ++ D+++ D + + +G+ VEF EDA AI+
Sbjct: 8 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 67
Query: 476 -LNGQMLGNRAIRLDFAR 492
+N L R IR++ A+
Sbjct: 68 NMNESELFGRTIRVNLAK 85
Score = 37.0 bits (84), Expect = 0.040, Method: Composition-based stats.
Identities = 26/89 (29%), Positives = 47/89 (52%), Gaps = 5/89 (5%)
Query: 512 GGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF 571
G +++ G V +D+V L F G+IT I +P DY+T +G A+++F
Sbjct: 1 GSMATTKRVLYVGGLAEEV-DDKV---LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEF 56
Query: 572 TDADSFNKALE-MSGTEIGGYSLVVDEAK 599
A+ A++ M+ +E+ G ++ V+ AK
Sbjct: 57 ELAEDAAAAIDNMNESELFGRTIRVNLAK 85
>pdb|3LPY|A Chain A, Crystal Structure Of The Rrm Domain Of Cyp33
pdb|3LPY|B Chain B, Crystal Structure Of The Rrm Domain Of Cyp33
Length = 79
Score = 37.4 bits (85), Expect = 0.029, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
+ L+VG L V+ + F ++ D+++ D + + +G+ VEF EDA AI+
Sbjct: 3 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 62
Query: 476 -LNGQMLGNRAIRLDFA 491
+N L R IR++ A
Sbjct: 63 NMNESELFGRTIRVNLA 79
Score = 35.0 bits (79), Expect = 0.15, Method: Composition-based stats.
Identities = 24/83 (28%), Positives = 46/83 (55%), Gaps = 5/83 (6%)
Query: 517 AAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADS 576
+ +++ G V +D+V L F G+IT I +P DY+T +G A+++F A+
Sbjct: 1 SKRVLYVGGLAEEV-DDKV---LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAED 56
Query: 577 FNKALE-MSGTEIGGYSLVVDEA 598
A++ M+ +E+ G ++ V+ A
Sbjct: 57 AAAAIDNMNESELFGRTIRVNLA 79
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 37.4 bits (85), Expect = 0.030, Method: Composition-based stats.
Identities = 28/97 (28%), Positives = 46/97 (47%), Gaps = 13/97 (13%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVD-VRLSSDADGRFKGYGHVEFASVEDAHKAIELN 477
+++ LPF E V +FF ++ V D + ++ +G+ G G VEF + D A+ +
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRH 87
Query: 478 GQMLGNRAI------------RLDFARERGAYTPYSG 502
Q +GNR I ++D R+R P SG
Sbjct: 88 KQYMGNRFIQVHPITKKGMLEKIDMIRKRLQSGPSSG 124
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 37.0 bits (84), Expect = 0.032, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 27/57 (47%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
L V NL F V AD+Q F+E + + D GR G V F DA KA++
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 94
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 37.0 bits (84), Expect = 0.033, Method: Composition-based stats.
Identities = 24/87 (27%), Positives = 44/87 (50%), Gaps = 2/87 (2%)
Query: 407 TPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR-FKGYGHVEFA 465
T P+ + L V +P +V++ ++ F + V++ D + R +GYG V+F
Sbjct: 33 TQMNPEPDVLRNLMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQ 92
Query: 466 SVEDAHKAIE-LNGQMLGNRAIRLDFA 491
S A +AI LNG + N+ +++ A
Sbjct: 93 SGSSAQQAIAGLNGFNILNKRLKVALA 119
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 37.0 bits (84), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 41/78 (52%), Gaps = 2/78 (2%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADG-RFKGYGHVEFASVEDAHKAIE 475
+ L+VG L V+ + F ++ D+++ D + + +G+ VEF EDA AI+
Sbjct: 13 RVLYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAID 72
Query: 476 -LNGQMLGNRAIRLDFAR 492
+N L R IR++ A+
Sbjct: 73 NMNESELFGRTIRVNLAK 90
Score = 35.8 bits (81), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 47/88 (53%), Gaps = 5/88 (5%)
Query: 513 GRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFT 572
G +++ G V +D+V L F G+IT I +P DY+T +G A+++F
Sbjct: 7 GMATTKRVLYVGGLAEEV-DDKV---LHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFE 62
Query: 573 DADSFNKALE-MSGTEIGGYSLVVDEAK 599
A+ A++ M+ +E+ G ++ V+ AK
Sbjct: 63 LAEDAAAAIDNMNESELFGRTIRVNLAK 90
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 37.0 bits (84), Expect = 0.036, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
IF+ G E+++R E+FG GE+ I +P D T +G ++ F + + K
Sbjct: 2 IFVGGLSPDTPEEKIR----EYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 57
Query: 581 LEMSGTEIG 589
+E +G
Sbjct: 58 MEKKYHNVG 66
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 37.0 bits (84), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 39/71 (54%), Gaps = 1/71 (1%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
LF+ LPFS + +++ V D+RL ++ G+ KG +VE+ + A +A+ +++
Sbjct: 20 LFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMD 79
Query: 478 GQMLGNRAIRL 488
G + I++
Sbjct: 80 GMTIKENIIKV 90
>pdb|3ULH|A Chain A, Crystal Structure Of A Rna Binding Domain Of Tho Complex
Subunit 4 Protein (Thoc4) From Homo Sapiens At 2.54 A
Resolution
Length = 107
Score = 36.6 bits (83), Expect = 0.046, Method: Compositional matrix adjust.
Identities = 25/67 (37%), Positives = 30/67 (44%), Gaps = 1/67 (1%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
L V NL F V AD+Q F+E + + D GR G V F DA KA + N
Sbjct: 32 LLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQYN 91
Query: 478 GQMLGNR 484
G L R
Sbjct: 92 GVPLDGR 98
>pdb|2HGM|A Chain A, Nmr Structure Of The Second Qrrm Domain Of Human Hnrnp F
pdb|2KG0|A Chain A, Structure Of The Second Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 126
Score = 36.6 bits (83), Expect = 0.047, Method: Compositional matrix adjust.
Identities = 23/67 (34%), Positives = 38/67 (56%), Gaps = 3/67 (4%)
Query: 424 LPFSVEQADVQNFFSEVAEVV--DVRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQML 481
LPF + ++ FFS + E+V + L D +G+ G V+FAS E A KA+ + + +
Sbjct: 50 LPFGCTKEEIVQFFSGL-EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERI 108
Query: 482 GNRAIRL 488
G+R I +
Sbjct: 109 GHRYIEV 115
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 36.6 bits (83), Expect = 0.049, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 33/69 (47%), Gaps = 4/69 (5%)
Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
IF+ G E+++R E+FG GE+ I +P D T +G ++ F + + K
Sbjct: 4 IFVGGLSPDTPEEKIR----EYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKI 59
Query: 581 LEMSGTEIG 589
+E +G
Sbjct: 60 MEKKYHNVG 68
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 36.2 bits (82), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 27/104 (25%), Positives = 51/104 (49%), Gaps = 10/104 (9%)
Query: 396 VDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR 455
+D ++ +K + FT +S LFVGNLP + + +++ F + + +V + D
Sbjct: 6 IDLKNFRKPGEKTFTQRS----RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD---- 57
Query: 456 FKGYGHVEFASVEDAHKA-IELNGQMLGNRAIRLDFARERGAYT 498
KG+G + + A A +EL+ L + +R+ FA + T
Sbjct: 58 -KGFGFIRLETRTLAEIAKVELDNMPLRGKQLRVRFACHSASLT 100
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 36.2 bits (82), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 29/57 (50%), Gaps = 1/57 (1%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKAI 474
L V LP+ + D++ +FS EV+ V++ D G KG+G V F E K +
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74
Score = 35.4 bits (80), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 15/43 (34%), Positives = 26/43 (60%)
Query: 539 LEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL 581
L+E+F + GE+ + V KD TG KG ++ FT+ ++ K +
Sbjct: 32 LKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVM 74
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 36.2 bits (82), Expect = 0.065, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 27/57 (47%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
L V NL F V AD+Q F+E + + D GR G V F DA KA++
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMK 147
>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 = 35.8 bits (81), Expect = 0.070, Method: Compositional matrix adjust.
Identities = 22/82 (26%), Positives = 38/82 (46%), Gaps = 4/82 (4%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + ++G A++ F + S
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSSAT 66
Query: 579 KALE-MSGTEIGGYSLVVDEAK 599
AL M G + + AK
Sbjct: 67 NALRSMQGFPFYDKPMRIQYAK 88
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 35.4 bits (80), Expect = 0.092, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRF-KGYGHVEF--ASVEDAHKA 473
+ ++VGNL +S V+ FS+ +V +V+L D + + KG+G VE SV +A
Sbjct: 2 RNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQEESVSEAIAK 61
Query: 474 IELNGQMLGNRAIRL 488
++ N +G R IR+
Sbjct: 62 LD-NTDFMG-RTIRV 74
>pdb|2DB1|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein F Homolog
Length = 118
Score = 35.4 bits (80), Expect = 0.092, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 38/81 (46%), Gaps = 3/81 (3%)
Query: 411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVA---EVVDVRLSSDADGRFKGYGHVEFASV 467
P+ G + + LP+S DVQNF S+ V V +GR G VE S
Sbjct: 12 PEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESE 71
Query: 468 EDAHKAIELNGQMLGNRAIRL 488
+D A++ + + +G+R I +
Sbjct: 72 DDVKLALKKDRESMGHRYIEV 92
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 35.4 bits (80), Expect = 0.096, Method: Composition-based stats.
Identities = 23/79 (29%), Positives = 39/79 (49%), Gaps = 2/79 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE-L 476
L V LP + ++ F + + R+ D G GY V+F S D+ +AI+ L
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 477 NGQMLGNRAIRLDFARERG 495
NG + N+ +++ +AR G
Sbjct: 66 NGITVRNKRLKVSYARPGG 84
Score = 29.6 bits (65), Expect = 5.1, Method: Composition-based stats.
Identities = 19/69 (27%), Positives = 32/69 (46%), Gaps = 1/69 (1%)
Query: 532 EDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKALE-MSGTEIGG 590
+D L F + G I + +DY TG G A++DFT +A++ ++G +
Sbjct: 13 QDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVLNGITVRN 72
Query: 591 YSLVVDEAK 599
L V A+
Sbjct: 73 KRLKVSYAR 81
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 35.4 bits (80), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 30/95 (31%), Positives = 46/95 (48%), Gaps = 7/95 (7%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD--GRF--KGYGHVEFASVE 468
S GS LF+ NL FS + ++ FS+V + +S + G G+G VE+ E
Sbjct: 2 SSGSSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 469 DAHKAI-ELNGQMLGNRAIRLDFARERGAYTPYSG 502
A KA+ +L G + + + + ER A P SG
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRIS-ER-ATKPASG 94
>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 = 35.4 bits (80), Expect = 0.10, Method: Compositional matrix adjust.
Identities = 25/106 (23%), Positives = 46/106 (43%), Gaps = 9/106 (8%)
Query: 391 TDVKMVDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRL-S 449
T++KM D + A F KTLFV + + ++ ++ F + + +
Sbjct: 84 TELKMWDPHNDPNAQGDAF-------KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136
Query: 450 SDADGRFKGYGHVEFASVEDAHKAI-ELNGQMLGNRAIRLDFARER 494
S G+ +GY +E+ D H A +G+ + R + +D R R
Sbjct: 137 SKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGR 182
>pdb|2HGL|A Chain A, Nmr Structure Of The First Qrrm Domain Of Human Hnrnp F
pdb|2KFY|A Chain A, Nmr Structure Of The First Qrrm Of Hnrnp F In Complex With
Agggau G- Tract Rna
Length = 136
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 37/81 (45%), Gaps = 3/81 (3%)
Query: 411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVA---EVVDVRLSSDADGRFKGYGHVEFASV 467
P+ G + + LP+S DVQNF S+ V +GR G VE S
Sbjct: 39 PEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSE 98
Query: 468 EDAHKAIELNGQMLGNRAIRL 488
+D A++ + + +G+R I +
Sbjct: 99 DDVKMALKKDRESMGHRYIEV 119
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 35/74 (47%), Gaps = 15/74 (20%)
Query: 424 LPFSVEQADVQNFFSEVAEVVDVRLSS---------DADGRFKGYGHVEFASVEDAHKAI 474
LP+S DV NFFS D R+ + + DG+ +G +E S +D KA+
Sbjct: 19 LPWSCTMEDVLNFFS------DCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL 72
Query: 475 ELNGQMLGNRAIRL 488
E + +G R + +
Sbjct: 73 EKHRMYMGQRYVEV 86
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 35.0 bits (79), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + + ++G A++ F + S
Sbjct: 9 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 65
Query: 579 KALE-MSG 585
AL M G
Sbjct: 66 NALRSMQG 73
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + + ++G A++ F + S
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 65
Query: 579 KALE-MSG 585
AL M G
Sbjct: 66 NALRSMQG 73
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 21/79 (26%), Positives = 39/79 (49%), Gaps = 4/79 (5%)
Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
IF+ G + GE ++R E+F G +T + + D + +G ++ F D S ++A
Sbjct: 13 IFVGGIPHNCGETELR----EYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA 68
Query: 581 LEMSGTEIGGYSLVVDEAK 599
+ M +I G + V A+
Sbjct: 69 VNMHFHDIMGKKVEVKRAE 87
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/60 (23%), Positives = 34/60 (56%), Gaps = 1/60 (1%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIELN 477
+FVG +P + + +++ +F + V +V + DA+ R +G+G + F + +A+ ++
Sbjct: 13 IFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMH 72
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 34.7 bits (78), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + + ++G A++ F + S
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 66
Query: 579 KALE-MSG 585
AL M G
Sbjct: 67 NALRSMQG 74
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af Large
Subunit
Length = 87
Score = 34.7 bits (78), Expect = 0.20, Method: Composition-based stats.
Identities = 19/86 (22%), Positives = 45/86 (52%), Gaps = 16/86 (18%)
Query: 414 GGSKTLFVGNLPFSVEQADVQNFFSEVAE-----------VVDVRLSSDADGRFKGYGHV 462
G ++ L+VGN+PF + + + +FF+ V+ V+++ D K + +
Sbjct: 4 GSARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFL 58
Query: 463 EFASVEDAHKAIELNGQMLGNRAIRL 488
EF SV++ +A+ +G + +++++
Sbjct: 59 EFRSVDETTQAMAFDGIIFQGQSLKI 84
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 33/64 (51%), Gaps = 3/64 (4%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + + ++G A++ F + S
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 66
Query: 579 KALE 582
AL
Sbjct: 67 NALR 70
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 34.3 bits (77), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + + ++G A++ F + S
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 65
Query: 579 KALE-MSG 585
AL M G
Sbjct: 66 NALRSMQG 73
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 34.3 bits (77), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 27/82 (32%), Positives = 42/82 (51%), Gaps = 3/82 (3%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVA-EVVDVRLSSDADGRFKGYGHVEFASVEDAH 471
SG +LFVG+L V+ + FF +V ++ D G KGYG V+F +
Sbjct: 6 SGPEYSLFVGDLTPDVDDGMLYEFFVKVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQK 65
Query: 472 KAI-ELNGQM-LGNRAIRLDFA 491
+A+ E G + LG++ +RL A
Sbjct: 66 RALTECQGAVGLGSKPVRLSVA 87
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 34.3 bits (77), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 20/68 (29%), Positives = 35/68 (51%), Gaps = 4/68 (5%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + + ++G A++ F + S
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKMRGQAFVIFKEVSSAT 65
Query: 579 KALE-MSG 585
AL M G
Sbjct: 66 NALRSMQG 73
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 33.9 bits (76), Expect = 0.31, Method: Composition-based stats.
Identities = 22/98 (22%), Positives = 48/98 (48%), Gaps = 19/98 (19%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAE-----------VVDVRLSSDADGRFKGYGHVEF 464
++ L+VGN+PF + + + +FF+ V+ V+++ D K + +EF
Sbjct: 1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQD-----KNFAFLEF 55
Query: 465 ASVEDAHKAIELNGQMLGNRAIRLDFARERGAYTPYSG 502
SV++ +A+ +G + +++++ R Y P G
Sbjct: 56 RSVDETTQAMAFDGIIFQGQSLKI---RRPHDYQPLPG 90
>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 = 0.35, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 43/87 (49%), Gaps = 8/87 (9%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKA-IELN 477
LFVGNLP + + +++ F + + +V + D KG+G + + A A +EL+
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD-----KGFGFIRLETRTLAEIAKVELD 72
Query: 478 GQMLGNRAIRLDFARERGAYT--PYSG 502
L + +R+ FA + T P SG
Sbjct: 73 NMPLRGKQLRVRFACHSASLTSGPSSG 99
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 33.5 bits (75), Expect = 0.39, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 29/54 (53%)
Query: 528 SSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKAL 581
+++ ED L+E F G I+RI + KD TG KG A++ F + +A+
Sbjct: 21 TNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
Score = 30.0 bits (66), Expect = 4.2, Method: Composition-based stats.
Identities = 18/58 (31%), Positives = 28/58 (48%), Gaps = 1/58 (1%)
Query: 418 TLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAI 474
T+ V NL + D+Q F + + L+ D G+ KG+ + F EDA +AI
Sbjct: 17 TIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
>pdb|1DRZ|A Chain A, U1a Spliceosomal ProteinHEPATITIS DELTA VIRUS GENOMIC
Ribozyme Complex
Length = 97
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + + +G A++ F + S
Sbjct: 9 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKXRGQAFVIFKEVSSAT 65
Query: 579 KALE 582
AL
Sbjct: 66 NALR 69
>pdb|3CUL|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUL|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|A Chain A, Aminoacyl-Trna Synthetase Ribozyme
pdb|3CUN|B Chain B, Aminoacyl-Trna Synthetase Ribozyme
pdb|3EGZ|A Chain A, Crystal Structure Of An In Vitro Evolved Tetracycline
Aptamer And Artificial Riboswitch
Length = 98
Score = 33.5 bits (75), Expect = 0.43, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + + +G A++ F + S
Sbjct: 10 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKXRGQAFVIFKEVSSAT 66
Query: 579 KALE 582
AL
Sbjct: 67 NALR 70
>pdb|1CX0|A Chain A, Hepatitis Delta Virus Ribozyme
Length = 95
Score = 33.1 bits (74), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 18/64 (28%), Positives = 32/64 (50%), Gaps = 3/64 (4%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + + +G A++ F + S
Sbjct: 7 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSR---SLKXRGQAFVIFKEVSSAT 63
Query: 579 KALE 582
AL
Sbjct: 64 NALR 67
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 32.7 bits (73), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 16/58 (27%), Positives = 30/58 (51%), Gaps = 1/58 (1%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDAD-GRFKGYGHVEFASVEDAHKAIE 475
+FVG LP+ A ++ +F ++ + + +D G+ +GYG V A A +A +
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 32.7 bits (73), Expect = 0.77, Method: Composition-based stats.
Identities = 24/72 (33%), Positives = 36/72 (50%), Gaps = 2/72 (2%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGR-FKGYGHVEFASVEDAHKAIE-L 476
L V L + D++ FS+ + DV + D R +G+ V F +V+DA +A E
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 477 NGQMLGNRAIRL 488
NG L R IR+
Sbjct: 78 NGMELDGRRIRV 89
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 32.3 bits (72), Expect = 0.80, Method: Composition-based stats.
Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 8/75 (10%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
LFV P V+++++ F + +V++ G+ VEF E A KAI E++
Sbjct: 34 LFVRPFPLDVQESELNEIFGPFGPMKEVKI-------LNGFAFVEFEEAESAAKAIEEVH 86
Query: 478 GQMLGNRAIRLDFAR 492
G+ N+ + + +++
Sbjct: 87 GKSFANQPLEVVYSK 101
>pdb|2EK6|A Chain A, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|B Chain B, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|C Chain C, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|D Chain D, Crystal Structure Of Human Rna-Binding Protein 12
Length = 95
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 415 GSKTLFVGNLPFSVEQADVQNFFSEVAEVV--DVRLSSDADGRFKGYGHVEFASVEDAHK 472
G + V N+PF+V ++ +FF +V+ V L + G G V F S ++A
Sbjct: 14 GPTVIKVQNMPFTVSIDEILDFFYGY-QVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
Query: 473 A-IELNGQMLGNRAIRL 488
A I+LN + +G+R ++L
Sbjct: 73 AVIDLNDRPIGSRKVKL 89
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-E 475
K LFV NL +V + ++ FS+ ++ V+ + K Y + F + A KA+ E
Sbjct: 12 KVLFVRNLANTVTEEILEKAFSQFGKLERVK-------KLKDYAFIHFDERDGAVKAMEE 64
Query: 476 LNGQMLGNRAIRLDFAR 492
+NG+ L I + FA+
Sbjct: 65 MNGKDLEGENIEIVFAK 81
>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 = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 2/85 (2%)
Query: 409 FTPQSGGSKTLFVGNLPFSVEQAD-VQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASV 467
TP S+ L V LP D + S V +L+ DG+ KG+ +E+ +
Sbjct: 175 LTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETA 234
Query: 468 EDAHKA-IELNGQMLGNRAIRLDFA 491
E A +A + +G LG +R+ F
Sbjct: 235 EMAEEAQQQADGLSLGGSHLRVSFC 259
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDA-DGRFKGYGHVEFASVEDAHKA 473
LF+G +P ++++ D++ F E ++ ++ + D G KG + + E A KA
Sbjct: 16 LFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKA 71
Score = 30.4 bits (67), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 34/69 (49%), Gaps = 4/69 (5%)
Query: 512 GGRGQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDF 571
G + A +FI ++ E ++ EE G+I ++V KD TG KG A+L +
Sbjct: 7 GMKDHDAIKLFIGQIPRNLDEKDLKPLFEEF----GKIYELTVLKDRFTGMHKGCAFLTY 62
Query: 572 TDADSFNKA 580
+ +S KA
Sbjct: 63 CERESALKA 71
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + ++G A++ F + S
Sbjct: 4 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSSAT 60
Query: 579 KAL 581
AL
Sbjct: 61 NAL 63
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 2/85 (2%)
Query: 409 FTPQSGGSKTLFVGNLPFSVEQAD-VQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASV 467
TP S+ L V LP D + S V +L+ DG+ KG+ +E+ +
Sbjct: 177 LTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETA 236
Query: 468 EDAHKA-IELNGQMLGNRAIRLDFA 491
E A +A + +G LG +R+ F
Sbjct: 237 EMAEEAQQQADGLSLGGSHLRVSFC 261
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 38/85 (44%), Gaps = 2/85 (2%)
Query: 409 FTPQSGGSKTLFVGNLPFSVEQAD-VQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASV 467
TP S+ L V LP D + S V +L+ DG+ KG+ +E+ +
Sbjct: 177 LTPALLHSRCLCVDRLPPGFNDVDALCRALSAVHSPTFCQLACGQDGQLKGFAVLEYETA 236
Query: 468 EDAHKA-IELNGQMLGNRAIRLDFA 491
E A +A + +G LG +R+ F
Sbjct: 237 EMAEEAQQQADGLSLGGSHLRVSFC 261
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 31.6 bits (70), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/56 (26%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKA 473
LFVG +P +++ D++ F E + ++ + D G KG + + + + A KA
Sbjct: 18 LFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKA 73
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 31.2 bits (69), Expect = 1.7, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + ++G A++ F + S
Sbjct: 5 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSSAT 61
Query: 579 KAL 581
AL
Sbjct: 62 NAL 64
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 31.2 bits (69), Expect = 1.8, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + ++G A++ F + S
Sbjct: 6 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSSAT 62
Query: 579 KAL 581
AL
Sbjct: 63 NAL 65
>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 = 1.8, Method: Composition-based stats.
Identities = 25/106 (23%), Positives = 47/106 (44%), Gaps = 9/106 (8%)
Query: 391 TDVKMVDAESGKKAAQTPFTPQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLS- 449
T++KM D + A F KTLFV + + ++ ++ F + + +
Sbjct: 84 TELKMWDPHNDPNAQGDAF-------KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVY 136
Query: 450 SDADGRFKGYGHVEFASVEDAHKAIE-LNGQMLGNRAIRLDFARER 494
S G+ +GY +E+ D H A + +G+ + R + +D R R
Sbjct: 137 SKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRVLVDVERGR 182
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 31.2 bits (69), Expect = 2.2, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 31/68 (45%), Gaps = 4/68 (5%)
Query: 521 IFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFNKA 580
+FI G ++ +R E+FG GE+ V +D T +G ++ F D +K
Sbjct: 3 MFIGGLSWQTTQEGLR----EYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQAGVDKV 58
Query: 581 LEMSGTEI 588
L S E+
Sbjct: 59 LAQSRHEL 66
>pdb|2VOD|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VOD|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auauuuu
pdb|2VON|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VON|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auaauuu
pdb|2VOO|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOO|B Chain B, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Uuuuuuuu
pdb|2VOP|A Chain A, Crystal Structure Of N-Terminal Domains Of Human La
Protein Complexed With Rna Oligomer Auuuu
Length = 193
Score = 30.8 bits (68), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 33/64 (51%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
++++++ P D++ + + +V+++++ FKG V F S+E A K +E
Sbjct: 109 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 168
Query: 476 LNGQ 479
GQ
Sbjct: 169 TPGQ 172
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + ++G A++ F + S
Sbjct: 7 HTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSL---KMRGQAFVIFKEVSSAT 63
Query: 579 KAL 581
AL
Sbjct: 64 NAL 66
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 30.8 bits (68), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 21/67 (31%), Positives = 35/67 (52%), Gaps = 5/67 (7%)
Query: 421 VGNLPFSVEQADVQNFFSEVAEVVD---VRLSSDADGRFKGYGHVEFASVEDAHKAIELN 477
+ N+PFS+ + DV F + VD V + D +G+ G V+F + +DA K+ L+
Sbjct: 20 ITNIPFSITKMDVLQFLEGIP--VDENAVHVLVDNNGQGLGQALVQFKNEDDARKSERLH 77
Query: 478 GQMLGNR 484
+ L R
Sbjct: 78 RKKLNGR 84
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 30.8 bits (68), Expect = 2.4, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 3/63 (4%)
Query: 519 HTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDADSFN 578
HTI+I + + +D+++ SL F G+I I V + ++G A++ F + S
Sbjct: 10 HTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSL---KMRGQAFVIFKEVSSAT 66
Query: 579 KAL 581
AL
Sbjct: 67 NAL 69
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.8 bits (68), Expect = 2.6, Method: Composition-based stats.
Identities = 25/95 (26%), Positives = 42/95 (44%), Gaps = 4/95 (4%)
Query: 411 PQSGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDA 470
P ++VGNLP + D+++ F + + D+ L + G + VEF DA
Sbjct: 17 PAGNNDCRIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGG--PPFAFVEFEDPRDA 74
Query: 471 HKAIE-LNGQMLGNRAIRLDFARE-RGAYTPYSGG 503
A+ +G +R++F R RG + S G
Sbjct: 75 EDAVYGRDGYDYDGYRLRVEFPRSGRGTGSGPSSG 109
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 30.8 bits (68), Expect = 2.6, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 515 GQAAHTIFIKGFDSSVGEDQVRASLEEHFGSCGEITRISVPKDYDTGSVKGIAYLDFTDA 574
G + +FI G ++ +R E+FG GE+ V +D T +G ++ F D
Sbjct: 22 GSSGCKMFIGGLSWQTTQEGLR----EYFGQFGEVKECLVMRDPLTKRSRGFGFVTFMDQ 77
Query: 575 DSFNKALEMSGTEI 588
+K L S E+
Sbjct: 78 AGVDKVLAQSRHEL 91
>pdb|3N9U|C Chain C, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
pdb|3N9U|I Chain I, Crystal Structure Of The Complex Between The 25 Kda
Subunit And The 59 Kda Subunit (Rrm Domain) Of Human
Cleavage Factor Im
Length = 156
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 36/61 (59%), Gaps = 3/61 (4%)
Query: 419 LFVGNLPF-SVEQADVQNFFSE-VAEVVDVRLSSD-ADGRFKGYGHVEFASVEDAHKAIE 475
++VG+ + + +Q +Q S V +VV+++ + + A+G+ KGY V AS HK +E
Sbjct: 58 VYVGSFSWWTTDQQLIQVIRSIGVYDVVELKFAENRANGQSKGYAEVVVASENSVHKLLE 117
Query: 476 L 476
L
Sbjct: 118 L 118
>pdb|3NMR|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
pdb|3NNA|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/63 (25%), Positives = 29/63 (46%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIEL 476
+ LF+G + + D++ FS ++ + R+ DG +G V F + A AI+
Sbjct: 96 RKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIKA 155
Query: 477 NGQ 479
Q
Sbjct: 156 XHQ 158
>pdb|1S79|A Chain A, Solution Structure Of The Central Rrm Of Human La Protein
Length = 103
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 33/64 (51%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
++++++ P D++ + + +V+++++ FKG V F S+E A K +E
Sbjct: 11 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQMRRTLHKAFKGSIFVVFDSIESAKKFVE 70
Query: 476 LNGQ 479
GQ
Sbjct: 71 TPGQ 74
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 30.0 bits (66), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 27/58 (46%)
Query: 417 KTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI 474
+ LFVG L + DV+ F + + + DG KG V+++S +A AI
Sbjct: 16 RKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAI 73
>pdb|2DNP|A Chain A, Solution Structure Of Rna Binding Domain 2 In Rna-Binding
Protein 14
Length = 90
Score = 30.0 bits (66), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHK 472
SG + +FVGN+ + ++++ F V++ + D Y V DA
Sbjct: 6 SGNTWKIFVGNVSAACTSQELRSLFERRGRVIECDVVKD-------YAFVHMEKEADAKA 58
Query: 473 AI-ELNGQMLGNRAIRLDFA 491
AI +LNG+ + + I ++ +
Sbjct: 59 AIAQLNGKEVKGKRINVELS 78
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 29.6 bits (65), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 38/75 (50%), Gaps = 8/75 (10%)
Query: 419 LFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAI-ELN 477
LFV P V+++++ F + +V++ G+ VEF E A KAI E++
Sbjct: 7 LFVRPFPLDVQESELNEIFGPFGPMKEVKI-------LNGFAFVEFEEAESAAKAIEEVH 59
Query: 478 GQMLGNRAIRLDFAR 492
G+ N+ + + +++
Sbjct: 60 GKSFANQPLEVVYSK 74
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Hypothetical Protein Flj201171
Length = 123
Score = 29.6 bits (65), Expect = 6.2, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 30/69 (43%), Gaps = 4/69 (5%)
Query: 424 LPFSVEQADVQNFFSEVAEVVD----VRLSSDADGRFKGYGHVEFASVEDAHKAIELNGQ 479
LPF+ +V FF + + + + DGR G V FA E A A+ +
Sbjct: 31 LPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKD 90
Query: 480 MLGNRAIRL 488
+LG R I L
Sbjct: 91 LLGKRYIEL 99
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 29.3 bits (64), Expect = 8.0, Method: Composition-based stats.
Identities = 24/90 (26%), Positives = 41/90 (45%), Gaps = 7/90 (7%)
Query: 413 SGGSKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHK 472
S GS +FVG + + +++ FFS+ +V+DV + F+ + V FA D
Sbjct: 2 SSGSSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIPKP----FRAFAFVTFA---DDQI 54
Query: 473 AIELNGQMLGNRAIRLDFARERGAYTPYSG 502
A L G+ L + I + + + SG
Sbjct: 55 AQSLCGEDLIIKGISVHISNAEPKHNSNSG 84
>pdb|2LXU|A Chain A, Solution Nmr Structure Of The Eukaryotic Rna Recognition
Motif, Rrm1, From The Heterogeneous Nuclear
Ribonucleoprotein H From Homo Sapiens, Northeast
Structural Genomics Consortium (Nesg) Target Hr8614a
Length = 108
Score = 29.3 bits (64), Expect = 8.5, Method: Composition-based stats.
Identities = 19/71 (26%), Positives = 34/71 (47%), Gaps = 3/71 (4%)
Query: 421 VGNLPFSVEQADVQNFFSEVA---EVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIELN 477
V LP+S +VQ FFS+ +R +GR G VE S ++ A++ +
Sbjct: 12 VRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLALKKD 71
Query: 478 GQMLGNRAIRL 488
+ +G+R + +
Sbjct: 72 RETMGHRYVEV 82
>pdb|1ZH5|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1ZH5|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 195
Score = 28.9 bits (63), Expect = 9.0, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 32/64 (50%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
++++++ P D++ + + +V++++ FKG V F S+E A K +E
Sbjct: 111 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKAFKGSIFVVFDSIESAKKFVE 170
Query: 476 LNGQ 479
GQ
Sbjct: 171 TPGQ 174
>pdb|1YTY|A Chain A, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
pdb|1YTY|B Chain B, Structural Basis For Recognition Of Uuuoh 3'-Terminii Of
Nascent Rna Pol Iii Transcripts By La Autoantigen
Length = 194
Score = 28.9 bits (63), Expect = 9.1, Method: Compositional matrix adjust.
Identities = 15/64 (23%), Positives = 32/64 (50%)
Query: 416 SKTLFVGNLPFSVEQADVQNFFSEVAEVVDVRLSSDADGRFKGYGHVEFASVEDAHKAIE 475
++++++ P D++ + + +V++++ FKG V F S+E A K +E
Sbjct: 110 NRSVYIKGFPTDATLDDIKEWLEDKGQVLNIQXRRTLHKAFKGSIFVVFDSIESAKKFVE 169
Query: 476 LNGQ 479
GQ
Sbjct: 170 TPGQ 173
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 28.9 bits (63), Expect = 9.8, Method: Compositional matrix adjust.
Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 538 SLEEHFGSCGEITRISVPKDYDTGSV-KGIAYLDFTDADSFNKAL-EMSGTEIGG 590
+ E F + G+I I +P + + KG AY++F + D KAL M G +I G
Sbjct: 20 HIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHMDGGQIDG 74
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
0.308 0.127 0.353
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,919,285
Number of Sequences: 62578
Number of extensions: 362173
Number of successful extensions: 743
Number of sequences better than 100.0: 178
Number of HSP's better than 100.0 without gapping: 81
Number of HSP's successfully gapped in prelim test: 97
Number of HSP's that attempted gapping in prelim test: 546
Number of HSP's gapped (non-prelim): 241
length of query: 675
length of database: 14,973,337
effective HSP length: 105
effective length of query: 570
effective length of database: 8,402,647
effective search space: 4789508790
effective search space used: 4789508790
T: 11
A: 40
X1: 16 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.6 bits)
S2: 55 (25.8 bits)