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= psy3345
(787 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 142 bits (359), Expect = 5e-34, Method: Compositional matrix adjust.
Identities = 66/91 (72%), Positives = 73/91 (80%)
Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
KQT SKILVRNIPFQA Q E+ ELF FGELK VRLPKKM G+G HRGFGFV+FITK +A
Sbjct: 12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71
Query: 742 KRAMKALCQSTHLYGRRLVLEWAEEADNVED 772
K+A ALC STHLYGRRLVLEWA+ V+
Sbjct: 72 KKAFNALCHSTHLYGRRLVLEWADSEVTVQS 102
Score = 49.3 bits (116), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 30/88 (34%), Positives = 47/88 (53%), Gaps = 8/88 (9%)
Query: 439 NQVVEARSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVP-------PYGITGLVEFL 491
QV + ++ ILV+N+P++ +++ LF FG+L V +P + G V+F+
Sbjct: 7 GQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFI 66
Query: 492 QKNQAKAAFNSLAY-TKFKEVPLYLEWA 518
K AK AFN+L + T L LEWA
Sbjct: 67 TKQDAKKAFNALCHSTHLYGRRLVLEWA 94
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 38/75 (50%), Gaps = 2/75 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKE-TDKTKGFALVTFLMPEHATQAYQ 396
+I VRN+ + + ++ +LF +G L V LP T +GF V F+ + A +A+
Sbjct: 17 KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAFN 76
Query: 397 HLDGTVFL-GRMLHL 410
L + L GR L L
Sbjct: 77 ALCHSTHLYGRRLVL 91
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 107 bits (268), Expect = 2e-23, Method: Compositional matrix adjust.
Identities = 48/75 (64%), Positives = 58/75 (77%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+FVRNLSYT +E+DL KLF YGPL+E+ PID T K KGFA VTF+ PEHA +AY
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 398 LDGTVFLGRMLHLIP 412
+DG VF GRMLH++P
Sbjct: 70 VDGQVFQGRMLHVLP 84
Score = 33.9 bits (76), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
++ VRN+ + + + ++E+LF A+G L + P + + +GF FV F+ A +A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSL-TKKPKGFAFVTFMFPEHAVKA 66
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 22/103 (21%), Positives = 43/103 (41%), Gaps = 14/103 (13%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+++NL++ S+E+ + + F GP++ + K P G+ FV F E +
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKP-----KGFAFVTFMFPEHAVK 65
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTG 685
A + R L +T+K+++S +G
Sbjct: 66 AYAEVDGQVFQ---------GRMLHVLPSTIKKEASQSGPSSG 99
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 95.1 bits (235), Expect = 1e-19, Method: Compositional matrix adjust.
Identities = 45/77 (58%), Positives = 55/77 (71%)
Query: 447 KRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYT 506
K +IL KNLP TL +++ F FG LGRVL+P GIT +VEFL+ +A+ AF LAY+
Sbjct: 10 KTVILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYS 69
Query: 507 KFKEVPLYLEWAPEGVF 523
KF VPLYLEWAP GVF
Sbjct: 70 KFHHVPLYLEWAPIGVF 86
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 39/77 (50%), Gaps = 8/77 (10%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
IL +N+P +E++E F FG L V LP+ + + VEF+ EA++A +
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITA-------IVEFLEPLEARKAFRH 65
Query: 748 LCQSTHLYGRRLVLEWA 764
L S + L LEWA
Sbjct: 66 LAYSK-FHHVPLYLEWA 81
Score = 33.9 bits (76), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 30/60 (50%), Gaps = 6/60 (10%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
I +NL ++ + F ++G L V+LP T A+V FL P A +A++HL
Sbjct: 13 ILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGIT------AIVEFLEPLEARKAFRHL 66
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 75.5 bits (184), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 36/85 (42%), Positives = 58/85 (68%), Gaps = 2/85 (2%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
+ L+IKNLNF++TE++++ F K G I S T+++KK+ G LSMG+GFV++ E
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNK--AGVLLSMGFGFVEYKKPEQ 62
Query: 640 LNQALKVLQNSSLDEHQIELKRSNR 664
+ALK LQ ++D H++E++ S R
Sbjct: 63 AQKALKQLQGHTVDGHKLEVRISER 87
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 7/80 (8%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDK-----TKGFALVTFLMPEH 390
S +F++NL+++ TE+ L +F K G + I K+ +K + GF V + PE
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCT--ISKKKNKAGVLLSMGFGFVEYKKPEQ 62
Query: 391 ATQAYQHLDGTVFLGRMLHL 410
A +A + L G G L +
Sbjct: 63 AQKALKQLQGHTVDGHKLEV 82
Score = 39.3 bits (90), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 45/84 (53%), Gaps = 3/84 (3%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSG--LHRGFGFVEFITKNEAKR 743
S + ++N+ F + ++ +F G +K + KK +G L GFGFVE+ +A++
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 744 AMKALCQSTHLYGRRLVLEWAEEA 767
A+K L Q + G +L + +E A
Sbjct: 66 ALKQL-QGHTVDGHKLEVRISERA 88
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 62.8 bits (151), Expect = 6e-10, Method: Composition-based stats.
Identities = 53/201 (26%), Positives = 88/201 (43%), Gaps = 58/201 (28%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ NL+ TED ++++F+ GPIA++ + K+ K ++ Y FV+++ N
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNK------NVNYAFVEYHQSHDANI 56
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEV 702
AL+ L KQ + I+ N FQ++QS
Sbjct: 57 ALQTLN--------------------------------GKQIENNIVKINWAFQSQQSSS 84
Query: 703 EELFKAF-GELK-----------FVRLPKKMVG-------SGLHRGFGFVEFITKNEAKR 743
++ F F G+L F P + G +G RG+GFV F ++++A+
Sbjct: 85 DDTFNLFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQN 144
Query: 744 AMKALCQSTHLYGRRLVLEWA 764
AM ++ Q L GR L + WA
Sbjct: 145 AMDSM-QGQDLNGRPLRINWA 164
Score = 38.1 bits (87), Expect = 0.017, Method: Composition-based stats.
Identities = 22/62 (35%), Positives = 34/62 (54%), Gaps = 1/62 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL +TED L + F+ GP+A + + IDK +K +A V + A A Q L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDK-NNKNVNYAFVEYHQSHDANIALQTL 61
Query: 399 DG 400
+G
Sbjct: 62 NG 63
Score = 33.9 bits (76), Expect = 0.38, Method: Composition-based stats.
Identities = 16/62 (25%), Positives = 32/62 (51%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
IT++ LK F+ G + ++++ K +AF+ YH+ A AL N + ++ +
Sbjct: 12 ITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLNGKQIENNIV 71
Query: 89 KV 90
K+
Sbjct: 72 KI 73
Score = 31.6 bits (70), Expect = 2.0, Method: Composition-based stats.
Identities = 44/186 (23%), Positives = 76/186 (40%), Gaps = 29/186 (15%)
Query: 227 IVVKNLPAGVKKKDLKAYFK-PLPLASVRTTFLGMAYIGFKDEKNCNKALNKNKSFWKGK 285
+ V NL + + LK YF+ P+A+++ K+ KN N A +
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMI-------DKNNKNVNYAFVE-------- 47
Query: 286 QLNIYKYSKDNSAKYSGAADDNNNASMENIKAK-HWKSQEDSVQFAEDIAESGRIFVRNL 344
Y S D + A N +EN K +W Q S Q + D ++ +FV +L
Sbjct: 48 ----YHQSHDANI----ALQTLNGKQIENNIVKINWAFQ--SQQSSSD--DTFNLFVGDL 95
Query: 345 SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFL 404
+ V ++ L F+ + + D +T ++G+ V+F + A A + G
Sbjct: 96 NVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSMQGQDLN 155
Query: 405 GRMLHL 410
GR L +
Sbjct: 156 GRPLRI 161
>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 = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L+F +T++S+R HF++ G + V R DP + S G+GFV + T E ++
Sbjct: 9 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMR--DPNTK---RSRGFGFVTYATVEEVDA 63
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNV--AKQTGSKILVRNIPFQAKQS 700
A+ + +D +E KR+ V R+ S A T KI V I ++
Sbjct: 64 AMNA-RPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEH 112
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
+ + F+ +G+++ + + GSG RGF FV F
Sbjct: 113 HLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 146
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH---ATQA 394
++F+ LS+ T++ L FE++G L + ++ D T +++GF VT+ E A A
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 395 YQH-LDGTV 402
H +DG V
Sbjct: 68 RPHKVDGRV 76
Score = 36.2 bits (82), Expect = 0.069, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV + E L FE+YG + + + D+ + K +GFA VTF
Sbjct: 99 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 146
Score = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
++ T E L++ FE+ GT+TD V ++ + R F F+ Y ++ AA++
Sbjct: 16 FETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 66
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L+F +T++S+R HF++ G + V R DP + S G+GFV + T E ++
Sbjct: 14 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMR--DPNTK---RSRGFGFVTYATVEEVDA 68
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNV--AKQTGSKILVRNIPFQAKQS 700
A+ + +D +E KR+ V R+ S A T KI V I ++
Sbjct: 69 AMNA-RPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEH 117
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
+ + F+ +G+++ + + GSG RGF FV F
Sbjct: 118 HLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 151
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH---ATQA 394
++F+ LS+ T++ L FE++G L + ++ D T +++GF VT+ E A A
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 395 YQH-LDGTV 402
H +DG V
Sbjct: 73 RPHKVDGRV 81
Score = 36.2 bits (82), Expect = 0.075, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV + E L FE+YG + + + D+ + K +GFA VTF
Sbjct: 104 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 151
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
++ T E L++ FE+ GT+TD V ++ + R F F+ Y ++ AA++
Sbjct: 21 FETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 71
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 61.2 bits (147), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L+F +T++S+R HF++ G + V R DP + S G+GFV + T E ++
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMR--DPNTK---RSRGFGFVTYATVEEVDA 70
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNV--AKQTGSKILVRNIPFQAKQS 700
A+ + +D +E KR+ V R+ S A T KI V I ++
Sbjct: 71 AMNA-RPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
+ + F+ +G+++ + + GSG RGF FV F
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 153
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH---ATQA 394
++F+ LS+ T++ L FE++G L + ++ D T +++GF VT+ E A A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 395 YQH-LDGTV 402
H +DG V
Sbjct: 75 RPHKVDGRV 83
Score = 36.2 bits (82), Expect = 0.072, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV + E L FE+YG + + + D+ + K +GFA VTF
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
++ T E L++ FE+ GT+TD V ++ + R F F+ Y ++ AA++
Sbjct: 23 FETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
>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 = 60.8 bits (146), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L+F +T++S+R HF++ G + V R DP + S G+GFV + T E ++
Sbjct: 16 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMR--DPNTK---RSRGFGFVTYATVEEVDA 70
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNV--AKQTGSKILVRNIPFQAKQS 700
A+ + +D +E KR+ V R+ S A T KI V I ++
Sbjct: 71 AMNA-RPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEH 119
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
+ + F+ +G+++ + + GSG RGF FV F
Sbjct: 120 HLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 153
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH---ATQA 394
++F+ LS+ T++ L FE++G L + ++ D T +++GF VT+ E A A
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 395 YQH-LDGTV 402
H +DG V
Sbjct: 75 RPHKVDGRV 83
Score = 36.6 bits (83), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV + E L FE+YG + + + D+ + K +GFA VTF
Sbjct: 106 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 153
Score = 31.2 bits (69), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
++ T E L++ FE+ GT+TD V ++ + R F F+ Y ++ AA++
Sbjct: 23 FETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 73
>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 = 60.8 bits (146), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L+F +T++S+R HF++ G + V R DP + S G+GFV + T E ++
Sbjct: 15 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMR--DPNTK---RSRGFGFVTYATVEEVDA 69
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNV--AKQTGSKILVRNIPFQAKQS 700
A+ + +D +E KR+ V R+ S A T KI V I ++
Sbjct: 70 AMNA-RPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEH 118
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
+ + F+ +G+++ + + GSG RGF FV F
Sbjct: 119 HLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 152
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH---ATQA 394
++F+ LS+ T++ L FE++G L + ++ D T +++GF VT+ E A A
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 395 YQH-LDGTV 402
H +DG V
Sbjct: 74 RPHKVDGRV 82
Score = 36.6 bits (83), Expect = 0.054, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV + E L FE+YG + + + D+ + K +GFA VTF
Sbjct: 105 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 152
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
++ T E L++ FE+ GT+TD V ++ + R F F+ Y ++ AA++
Sbjct: 22 FETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 72
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 60.8 bits (146), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 46/155 (29%), Positives = 77/155 (49%), Gaps = 19/155 (12%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L+F +T++S+R HF++ G + V R DP + S G+GFV + T E ++
Sbjct: 17 LFIGGLSFETTDESLRSHFEQWGTLTDCVVMR--DPNTK---RSRGFGFVTYATVEEVDA 71
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNV--AKQTGSKILVRNIPFQAKQS 700
A+ + +D +E KR+ V R+ S A T KI V I ++
Sbjct: 72 AMNA-RPHKVDGRVVEPKRA----------VSREDSQRPGAHLTVKKIFVGGIKEDTEEH 120
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
+ + F+ +G+++ + + GSG RGF FV F
Sbjct: 121 HLRDYFEQYGKIEVIEIMTDR-GSGKKRGFAFVTF 154
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH---ATQA 394
++F+ LS+ T++ L FE++G L + ++ D T +++GF VT+ E A A
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 75
Query: 395 YQH-LDGTV 402
H +DG V
Sbjct: 76 RPHKVDGRV 84
Score = 36.6 bits (83), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 17/48 (35%), Positives = 26/48 (54%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV + E L FE+YG + + + D+ + K +GFA VTF
Sbjct: 107 KIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTF 154
Score = 31.2 bits (69), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 16/51 (31%), Positives = 30/51 (58%), Gaps = 1/51 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTD-VQLKYTTEGKFRRFAFIGYHREDQAQAALD 76
++ T E L++ FE+ GT+TD V ++ + R F F+ Y ++ AA++
Sbjct: 24 FETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN 74
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 58.9 bits (141), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 45/168 (26%), Positives = 74/168 (44%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T+D +R F G + S + R K S+GYGFV + T +
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGH-----SLGYGFVNYVTAKDA 57
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
+A+ L L I++ + R SS V K + + + +P Q
Sbjct: 58 ERAINTLNGLRLQSKTIKV------------SYARPSSEVIKD--ANLYISGLPRTMTQK 103
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+VE++F FG + R+ +GL RG F+ F ++EA+ A+ +
Sbjct: 104 DVEDMFSRFGRIINSRVLVDQT-TGLSRGVAFIRFDKRSEAEEAITSF 150
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/71 (19%), Positives = 36/71 (50%)
Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
+ ++ + +++ L T+T+ D+ +F ++G + + +D+ T ++G A + F
Sbjct: 82 SSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRS 141
Query: 390 HATQAYQHLDG 400
A +A +G
Sbjct: 142 EAEEAITSFNG 152
>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 = 58.9 bits (141), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 45/168 (26%), Positives = 74/168 (44%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T+D +R F G + S + R K S+GYGFV + T +
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGH-----SLGYGFVNYVTAKDA 57
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
+A+ L L I++ + R SS V K + + + +P Q
Sbjct: 58 ERAINTLNGLRLQSKTIKV------------SYARPSSEVIKD--ANLYISGLPRTMTQK 103
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+VE++F FG + R+ +GL RG F+ F ++EA+ A+ +
Sbjct: 104 DVEDMFSRFGRIINSRVLVDQT-TGLSRGVAFIRFDKRSEAEEAITSF 150
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 14/71 (19%), Positives = 36/71 (50%)
Query: 330 AEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
+ ++ + +++ L T+T+ D+ +F ++G + + +D+ T ++G A + F
Sbjct: 82 SSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRS 141
Query: 390 HATQAYQHLDG 400
A +A +G
Sbjct: 142 EAEEAITSFNG 152
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 57.4 bits (137), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 46/80 (57%), Gaps = 1/80 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
I+V NL Y+ T + + +LF ++G + V L D+ET K KGF V + E ++A L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVE-MQEESVSEAIAKL 62
Query: 399 DGTVFLGRMLHLIPGKPKEN 418
D T F+GR + + PK++
Sbjct: 63 DNTDFMGRTIRVTEANPKKS 82
Score = 37.0 bits (84), Expect = 0.042, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 43/81 (53%), Gaps = 6/81 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+Y+ NL +++T + ++ F + G + +V + ++ K P G+GFV+ ES+++
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPK-----GFGFVEM-QEESVSE 57
Query: 643 ALKVLQNSSLDEHQIELKRSN 663
A+ L N+ I + +N
Sbjct: 58 AIAKLDNTDFMGRTIRVTEAN 78
Score = 29.6 bits (65), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 13/77 (16%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRL-----PKKMVGSGLHRGFGFVEFITKNEAK 742
I V N+ + A +V+ELF FG++ V+L KK +GFGFVE + E+
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKK------PKGFGFVEM--QEESV 55
Query: 743 RAMKALCQSTHLYGRRL 759
A +T GR +
Sbjct: 56 SEAIAKLDNTDFMGRTI 72
>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 = 57.0 bits (136), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 49/168 (29%), Positives = 75/168 (44%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T++ R F G I S + R K GQ S+GYGFV + +
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDK---ITGQ--SLGYGFVNYIDPKDA 57
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
+A+ L L I++ + R SS A + + V +P Q
Sbjct: 58 EKAINTLNGLRLQTKTIKV------------SYARPSS--ASIRDANLYVSGLPKTMTQK 103
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
E+E+LF +G + R+ V +G+ RG GF+ F + EA+ A+K L
Sbjct: 104 ELEQLFSQYGRIITSRILVDQV-TGVSRGVGFIRFDKRIEAEEAIKGL 150
Score = 35.0 bits (79), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 17/62 (27%), Positives = 34/62 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L T+T+ +L +LF +YG + + +D+ T ++G + F A +A + L
Sbjct: 91 LYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIKGL 150
Query: 399 DG 400
+G
Sbjct: 151 NG 152
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With The
Au-Rich Element
Length = 174
Score = 57.0 bits (136), Expect = 4e-08, Method: Compositional matrix adjust.
Identities = 48/168 (28%), Positives = 74/168 (44%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T+D + F G I S + R K GQ S+GYGFV +
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDK---ITGQ--SLGYGFVNYSDPNDA 59
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
++A+ L L I++ + R SS A + + V +P Q
Sbjct: 60 DKAINTLNGLKLQTKTIKV------------SYARPSS--ASIRDANLYVSGLPKTMSQK 105
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
E+E+LF +G + R+ +G+ RG GF+ F + EA+ A+K L
Sbjct: 106 EMEQLFSQYGRIITSRILLDQA-TGVSRGVGFIRFDKRIEAEEAIKGL 152
Score = 33.9 bits (76), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 36/67 (53%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L T+++ ++ +LF +YG + + +D+ T ++G + F A +A + L
Sbjct: 93 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 152
Query: 399 DGTVFLG 405
+G LG
Sbjct: 153 NGQKPLG 159
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 56.6 bits (135), Expect = 5e-08, Method: Composition-based stats.
Identities = 29/86 (33%), Positives = 50/86 (58%), Gaps = 1/86 (1%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
++ G++FV LS+ E L ++F KYG ++EV++ D+ET +++GF VTF + A
Sbjct: 10 SDEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKD 69
Query: 394 AYQHLDGTVFLGRMLHL-IPGKPKEN 418
A ++G GR + + GK +N
Sbjct: 70 AMMAMNGKSVDGRQIRVDQAGKSSDN 95
Score = 43.1 bits (100), Expect = 6e-04, Method: Composition-based stats.
Identities = 22/88 (25%), Positives = 47/88 (53%), Gaps = 5/88 (5%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ L+F++ E S+ + F K G I+ V V + ++ + S G+GFV F +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQR-----SRGFGFVTFENIDDAKD 69
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEA 670
A+ + S+D QI + ++ ++ ++ +
Sbjct: 70 AMMAMNGKSVDGRQIRVDQAGKSSDNRS 97
Score = 36.2 bits (82), Expect = 0.070, Method: Composition-based stats.
Identities = 25/84 (29%), Positives = 46/84 (54%), Gaps = 3/84 (3%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V + F + +E++F +G++ V + K + RGFGFV F ++AK AM
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDR-ETQRSRGFGFVTFENIDDAKDAMM 72
Query: 747 ALCQSTHLYGRRLVLEWA-EEADN 769
A+ + GR++ ++ A + +DN
Sbjct: 73 AM-NGKSVDGRQIRVDQAGKSSDN 95
>pdb|2LEA|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm
pdb|2LEB|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uccagu-3'
pdb|2LEC|A Chain A, Solution Structure Of Human Srsf2 (Sc35) Rrm In Complex
With 5'- Uggagu-3'
Length = 135
Score = 56.6 bits (135), Expect = 5e-08, Method: Composition-based stats.
Identities = 28/70 (40%), Positives = 41/70 (58%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V NL+Y + D L ++FEKYG + +V +P D+ T +++GFA V F A A +DG
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 401 TVFLGRMLHL 410
V GR L +
Sbjct: 112 AVLDGRELRV 121
Score = 45.8 bits (107), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 48/90 (53%), Gaps = 7/90 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T+L + NL + ++ D++RR F+K G + V + R + K S G+ FV+F+ +
Sbjct: 48 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE-----SRGFAFVRFHDKRDA 102
Query: 641 NQALKVLQNSSLD--EHQIELKRSNRNLES 668
A+ + + LD E ++++ R R +S
Sbjct: 103 EDAMDAMDGAVLDGRELRVQMARYGRPPDS 132
Score = 35.4 bits (80), Expect = 0.12, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
Y+ + + L+ FE+ G V DV + +YT E R FAF+ +H + A+ A+D + +
Sbjct: 57 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKES--RGFAFVRFHDKRDAEDAMDAMDGAVL 114
Query: 84 FSSRIKVE 91
++V+
Sbjct: 115 DGRELRVQ 122
Score = 34.3 bits (77), Expect = 0.28, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
V NL YRT P L+ +FE +G +G V +P T V F K A+ A +++
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 55.8 bits (133), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 43/177 (24%), Positives = 85/177 (48%), Gaps = 21/177 (11%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ + +E +R F++ G + + V R + P S G FV FYTR++ +
Sbjct: 18 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ---SKGCCFVTFYTRKAALE 74
Query: 643 ALKVLQNSSL---DEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
A L N + H I++K ++ K++ V + K+ + I + +
Sbjct: 75 AQNALHNMKVLPGMHHPIQMKPAD----------SEKNNAVEDR---KLFIGMISKKCTE 121
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG 756
+++ +F +FG+++ R+ + GL RG FV F T+ A+ A+KA+ Q+ + G
Sbjct: 122 NDIRVMFSSFGQIEECRILRG--PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEG 176
Score = 53.1 bits (126), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 46/191 (24%), Positives = 83/191 (43%), Gaps = 31/191 (16%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD--KTKGFALVTFLMPEHATQAY 395
++FV + T +E DL +LFE+YG + E+ + D+ + ++KG VTF + A +A
Sbjct: 17 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 76
Query: 396 QHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNL 455
L L M H I KP ++E N A R + + +
Sbjct: 77 NALHNMKVLPGMHHPIQMKPADSEKN---------------------NAVEDRKLFIGMI 115
Query: 456 PYRTLPTDLKALFEPFGDL--GRVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYTKFKE 510
+ D++ +F FG + R+L P G++ V F + A+ A ++ + E
Sbjct: 116 SKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTME 175
Query: 511 ---VPLYLEWA 518
P+ +++A
Sbjct: 176 GCSSPMVVKFA 186
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 31/75 (41%), Gaps = 6/75 (8%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
D L+I ++ TE+ IR F G I + R D LS G FV F TR
Sbjct: 107 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDG------LSRGCAFVTFTTRAM 160
Query: 640 LNQALKVLQNSSLDE 654
A+K + + E
Sbjct: 161 AQTAIKAMHQAQTME 175
>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 = 55.8 bits (133), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 38/137 (27%), Positives = 69/137 (50%), Gaps = 14/137 (10%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R++V ++ Y + ED + + F +GP+ + + D T K KGFA V + +PE A A +
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 398 LDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPY 457
++ + GR + + G+P N G ++ +D + EAR+ I V ++
Sbjct: 75 MNSVMLGGRNIKV--GRPS-NIGQ---------AQPIIDQLAE--EARAFNRIYVASVHQ 120
Query: 458 RTLPTDLKALFEPFGDL 474
D+K++FE FG +
Sbjct: 121 DLSDDDIKSVFEAFGKI 137
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 36/169 (21%), Positives = 85/169 (50%), Gaps = 15/169 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSM---GYGFVQFYTRES 639
+Y+ ++ + ED+IR+ F GPI S+ ++ ++M G+ FV++ E+
Sbjct: 16 VYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDS--------VTMKHKGFAFVEYEVPEA 67
Query: 640 LNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
AL+ + + L I++ R + N+ + + + + ++I V ++
Sbjct: 68 AQLALEQMNSVMLGGRNIKVGRPS-NIGQAQPIIDQLAEEA--RAFNRIYVASVHQDLSD 124
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+++ +F+AFG++K L + +G H+G+GF+E+ ++ A+ ++
Sbjct: 125 DDIKSVFEAFGKIKSCTLARDPT-TGKHKGYGFIEYEKAQSSQDAVSSM 172
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/108 (23%), Positives = 53/108 (49%), Gaps = 3/108 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKY-TTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y++ ++ ++ F G + + + + + K + FAF+ Y + AQ AL+ N+ +
Sbjct: 23 YELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGG 82
Query: 86 SRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTK 133
IKV + SN+G + A ++ A+ +++ + QDL + K
Sbjct: 83 RNIKVGRPSNIGQAQ--PIIDQLAEEARAFNRIYVASVHQDLSDDDIK 128
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 328 QFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
Q AE+ RI+V ++ +++DD+ +FE +G + L D T K KG+ + +
Sbjct: 102 QLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEY 159
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 55.5 bits (132), Expect = 1e-07, Method: Composition-based stats.
Identities = 29/79 (36%), Positives = 44/79 (55%)
Query: 332 DIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
D+ + V NL+Y + D L ++FEKYG + +V +P D+ T +++GFA V F A
Sbjct: 66 DVEGMTSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDA 125
Query: 392 TQAYQHLDGTVFLGRMLHL 410
A +DG V GR L +
Sbjct: 126 EDAMDAMDGAVLDGRELRV 144
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 25/90 (27%), Positives = 48/90 (53%), Gaps = 7/90 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T+L + NL + ++ D++RR F+K G + V + R + K S G+ FV+F+ +
Sbjct: 71 TSLKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKE-----SRGFAFVRFHDKRDA 125
Query: 641 NQALKVLQNSSLD--EHQIELKRSNRNLES 668
A+ + + LD E ++++ R R +S
Sbjct: 126 EDAMDAMDGAVLDGRELRVQMARYGRPPDS 155
Score = 34.7 bits (78), Expect = 0.23, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 37/68 (54%), Gaps = 5/68 (7%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQL---KYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYV 83
Y+ + + L+ FE+ G V DV + +YT E R FAF+ +H + A+ A+D + +
Sbjct: 80 YRTSPDTLRRVFEKYGRVGDVYIPRDRYTKES--RGFAFVRFHDKRDAEDAMDAMDGAVL 137
Query: 84 FSSRIKVE 91
++V+
Sbjct: 138 DGRELRVQ 145
Score = 33.5 bits (75), Expect = 0.50, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 29/58 (50%), Gaps = 6/58 (10%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
V NL YRT P L+ +FE +G +G V +P T V F K A+ A +++
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 55.1 bits (131), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 43/177 (24%), Positives = 85/177 (48%), Gaps = 21/177 (11%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ + +E +R F++ G + + V R + P S G FV FYTR++ +
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ---SKGCCFVTFYTRKAALE 62
Query: 643 ALKVLQNSSL---DEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
A L N + H I++K ++ K++ V + K+ + I + +
Sbjct: 63 AQNALHNMKVLPGMHHPIQMKPAD----------SEKNNAVEDR---KLFIGMISKKCTE 109
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG 756
+++ +F +FG+++ R+ + GL RG FV F T+ A+ A+KA+ Q+ + G
Sbjct: 110 NDIRVMFSSFGQIEECRILRG--PDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTMEG 164
Score = 53.9 bits (128), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 46/191 (24%), Positives = 83/191 (43%), Gaps = 31/191 (16%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD--KTKGFALVTFLMPEHATQAY 395
++FV + T +E DL +LFE+YG + E+ + D+ + ++KG VTF + A +A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 396 QHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNL 455
L L M H I KP ++E N A R + + +
Sbjct: 65 NALHNMKVLPGMHHPIQMKPADSEKN---------------------NAVEDRKLFIGMI 103
Query: 456 PYRTLPTDLKALFEPFGDL--GRVLVPPYGIT---GLVEFLQKNQAKAAFNSLAYTKFKE 510
+ D++ +F FG + R+L P G++ V F + A+ A ++ + E
Sbjct: 104 SKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQAQTME 163
Query: 511 ---VPLYLEWA 518
P+ +++A
Sbjct: 164 GCSSPMVVKFA 174
Score = 34.7 bits (78), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 31/75 (41%), Gaps = 6/75 (8%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
D L+I ++ TE+ IR F G I + R D LS G FV F TR
Sbjct: 95 DRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDG------LSRGCAFVTFTTRAM 148
Query: 640 LNQALKVLQNSSLDE 654
A+K + + E
Sbjct: 149 AQTAIKAMHQAQTME 163
>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 = 54.7 bits (130), Expect = 2e-07, Method: Composition-based stats.
Identities = 44/177 (24%), Positives = 84/177 (47%), Gaps = 20/177 (11%)
Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
+A R++V ++ Y + ED + + F +GP+ + + D T K KGFA V + +PE A
Sbjct: 25 LAIMSRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQ 84
Query: 393 QAYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILV 452
A + ++ + GR + + G+P N G ++ +D + EAR+ I V
Sbjct: 85 LALEQMNSVMLGGRNIKV--GRP-SNIGQ---------AQPIIDQLAE--EARAFNRIYV 130
Query: 453 KNLPYRTLPTDLKALFEPFGDLGRVLVPPYGIT------GLVEFLQKNQAKAAFNSL 503
++ D+K++FE FG + + T G +E+ + ++ A +S+
Sbjct: 131 ASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEKAQSSQDAVSSM 187
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 35/168 (20%), Positives = 83/168 (49%), Gaps = 9/168 (5%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+ +Y+ ++ + ED+IR+ F GPI S+ ++ G+ FV++ E+
Sbjct: 29 SRVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMK-----HKGFAFVEYEVPEAA 83
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
AL+ + + L I++ R + N+ + + + + ++I V ++
Sbjct: 84 QLALEQMNSVMLGGRNIKVGRPS-NIGQAQPIIDQLAEEA--RAFNRIYVASVHQDLSDD 140
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+++ +F+AFG++K L + +G H+G+GF+E+ ++ A+ ++
Sbjct: 141 DIKSVFEAFGKIKSATLARDPT-TGKHKGYGFIEYEKAQSSQDAVSSM 187
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 25/108 (23%), Positives = 53/108 (49%), Gaps = 3/108 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKY-TTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y++ ++ ++ F G + + + + + K + FAF+ Y + AQ AL+ N+ +
Sbjct: 38 YELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQMNSVMLGG 97
Query: 86 SRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTK 133
IKV + SN+G + A ++ A+ +++ + QDL + K
Sbjct: 98 RNIKVGRPSNIGQAQ--PIIDQLAEEARAFNRIYVASVHQDLSDDDIK 143
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 18/72 (25%), Positives = 36/72 (50%)
Query: 328 QFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLM 387
Q AE+ RI+V ++ +++DD+ +FE +G + L D T K KG+ + +
Sbjct: 117 QLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSATLARDPTTGKHKGYGFIEYEK 176
Query: 388 PEHATQAYQHLD 399
+ + A ++
Sbjct: 177 AQSSQDAVSSMN 188
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 54.3 bits (129), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 43/70 (61%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL +++T +DL ++F KYG + +V + DK+T K+KG A + FL + A + +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 399 DGTVFLGRML 408
+ GR++
Sbjct: 79 NNKQLFGRVI 88
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 36/72 (50%), Gaps = 5/72 (6%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+T+Y+ NL F+ T + + R F K G + VT+ + KD + S G F+ F ++S
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRK-----SKGVAFILFLDKDSA 71
Query: 641 NQALKVLQNSSL 652
+ + N L
Sbjct: 72 QNCTRAINNKQL 83
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 54.3 bits (129), Expect = 3e-07, Method: Composition-based stats.
Identities = 25/69 (36%), Positives = 42/69 (60%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R++V +L + +TED L +FE +G + + L +D ET ++KG+ +TF E A +A +
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 398 LDGTVFLGR 406
L+G GR
Sbjct: 88 LNGFELAGR 96
Score = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 35/70 (50%), Gaps = 5/70 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ +L+FN TED +R F+ G I S+ + + S GYGF+ F E +
Sbjct: 29 LYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGR-----SKGYGFITFSDSECAKK 83
Query: 643 ALKVLQNSSL 652
AL+ L L
Sbjct: 84 ALEQLNGFEL 93
Score = 32.7 bits (73), Expect = 0.79, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 34/65 (52%), Gaps = 1/65 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
+ IT++ L+ FE G + +QL +E G+ + + FI + + A+ AL+ N +
Sbjct: 36 FNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQLNGFELAG 95
Query: 86 SRIKV 90
+KV
Sbjct: 96 RPMKV 100
Score = 30.0 bits (66), Expect = 5.1, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 9/72 (12%)
Query: 683 QTGS----KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGS--GLHRGFGFVEFI 736
Q GS ++ V ++ F + + +F+ FG ++ ++L M+ S G +G+GF+ F
Sbjct: 20 QKGSAGPMRLYVGSLHFNITEDMLRGIFEPFGRIESIQL---MMDSETGRSKGYGFITFS 76
Query: 737 TKNEAKRAMKAL 748
AK+A++ L
Sbjct: 77 DSECAKKALEQL 88
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 39/72 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV N+ Y TE+ L +F + GP+ L D+ET K KG+ + E A A ++L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 399 DGTVFLGRMLHL 410
+G F GR L +
Sbjct: 71 NGREFSGRALRV 82
Score = 37.7 bits (86), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 24/87 (27%), Positives = 45/87 (51%), Gaps = 2/87 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V NIP++A + +++++F G + RL +G +G+GF E+ + A AM+
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRE-TGKPKGYGFCEYQDQETALSAMRN 69
Query: 748 LCQSTHLYGRRLVLEWAEEADNVEDIR 774
L GR L ++ A N E+++
Sbjct: 70 L-NGREFSGRALRVDNAASEKNKEELK 95
Score = 37.4 bits (85), Expect = 0.029, Method: Compositional matrix adjust.
Identities = 25/85 (29%), Positives = 41/85 (48%), Gaps = 1/85 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y+ T+EQLK F E G V +L Y E GK + + F Y ++ A +A+ N
Sbjct: 18 YEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNLNGREFSG 77
Query: 86 SRIKVEKCSNLGDTTKPKSWSKYAP 110
++V+ ++ + + KS AP
Sbjct: 78 RALRVDNAASEKNKEELKSLGTGAP 102
Score = 35.4 bits (80), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 15/66 (22%), Positives = 36/66 (54%), Gaps = 5/66 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
++++ N+ + +TE+ ++ F + GP+ S + ++ P GYGF ++ +E+
Sbjct: 10 SVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKP-----KGYGFCEYQDQETAL 64
Query: 642 QALKVL 647
A++ L
Sbjct: 65 SAMRNL 70
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 53.5 bits (127), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 43/74 (58%), Gaps = 1/74 (1%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
G++F+ L+ E L +F K+GP++EV+L I T K++GFA +TF P A A +
Sbjct: 8 GKLFIGGLNRETNEKMLKAVFGKHGPISEVLL-IKDRTSKSRGFAFITFENPADAKNAAK 66
Query: 397 HLDGTVFLGRMLHL 410
++G G+ + +
Sbjct: 67 DMNGKSLHGKAIKV 80
Score = 32.7 bits (73), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 23/73 (31%), Positives = 33/73 (45%), Gaps = 4/73 (5%)
Query: 25 FIYKITQE----QLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
FI + +E LKA F + G +++V L K R FAFI + A+ A N
Sbjct: 11 FIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDMNG 70
Query: 81 TYVFSSRIKVEKC 93
+ IKVE+
Sbjct: 71 KSLHGKAIKVEQA 83
Score = 32.7 bits (73), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 21/82 (25%), Positives = 38/82 (46%), Gaps = 6/82 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I LN + E ++ F K GPI+ V + + + K S G+ F+ F
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSK------SRGFAFITFENPADAKN 63
Query: 643 ALKVLQNSSLDEHQIELKRSNR 664
A K + SL I+++++ +
Sbjct: 64 AAKDMNGKSLHGKAIKVEQAKK 85
>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 = 53.5 bits (127), Expect = 4e-07, Method: Composition-based stats.
Identities = 49/169 (28%), Positives = 77/169 (45%), Gaps = 26/169 (15%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++I LN+++TED++R +F K G TV K K P S G+GF+ F S+++
Sbjct: 6 MFIGGLNWDTTEDNLREYFGKYG-----TVTDLKIMKDPATGRSRGFGFLSFEKPSSVDE 60
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEV 702
+K LD I+ KR+ E + T KI V I + E
Sbjct: 61 VVKT--QHILDGKVIDPKRAIPRDEQDKT--------------GKIFVGGIGPDVRPKEF 104
Query: 703 EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQS 751
EE F +G + +L +G RGFGFV + ++ A+ +CQ+
Sbjct: 105 EEFFSQWGTIIDAQLMLDK-DTGQSRGFGFVTY----DSADAVDRVCQN 148
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 24/71 (33%), Positives = 41/71 (57%), Gaps = 3/71 (4%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
ES ++F+ L++ TED+L + F KYG + ++ + D T +++GF ++F P +
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 395 Y--QH-LDGTV 402
QH LDG V
Sbjct: 62 VKTQHILDGKV 72
Score = 36.6 bits (83), Expect = 0.054, Method: Composition-based stats.
Identities = 15/51 (29%), Positives = 31/51 (60%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
++G+IFV + V + + F ++G + + L +DK+T +++GF VT+
Sbjct: 86 KTGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
>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 = 53.1 bits (126), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 38/137 (27%), Positives = 66/137 (48%), Gaps = 14/137 (10%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R++V ++ Y + ED + + F +GP+ + D T K KGFA V + +PE A A +
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 398 LDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPY 457
+ GR + + G+P N G ++ +D + EAR+ I V ++
Sbjct: 74 XNSVXLGGRNIKV--GRPS-NIGQ---------AQPIIDQLAE--EARAFNRIYVASVHQ 119
Query: 458 RTLPTDLKALFEPFGDL 474
D+K++FE FG +
Sbjct: 120 DLSDDDIKSVFEAFGKI 136
Score = 49.3 bits (116), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 35/165 (21%), Positives = 79/165 (47%), Gaps = 9/165 (5%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+Y+ ++ + ED+IR+ F GPI S+ + G+ FV++ E+
Sbjct: 15 VYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXK-----HKGFAFVEYEVPEAAQL 69
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEV 702
AL+ + L I++ R + N+ + + + + ++I V ++ ++
Sbjct: 70 ALEQXNSVXLGGRNIKVGRPS-NIGQAQPIIDQLAEEA--RAFNRIYVASVHQDLSDDDI 126
Query: 703 EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ +F+AFG++K L + +G H+G+GF+E+ ++ A+ +
Sbjct: 127 KSVFEAFGKIKSCTLARDPT-TGKHKGYGFIEYEKAQSSQDAVSS 170
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 17/58 (29%), Positives = 31/58 (53%)
Query: 328 QFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
Q AE+ RI+V ++ +++DD+ +FE +G + L D T K KG+ + +
Sbjct: 101 QLAEEARAFNRIYVASVHQDLSDDDIKSVFEAFGKIKSCTLARDPTTGKHKGYGFIEY 158
Score = 38.1 bits (87), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 25/108 (23%), Positives = 52/108 (48%), Gaps = 3/108 (2%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKY-TTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y++ ++ ++ F G + + + + K + FAF+ Y + AQ AL+ N+ +
Sbjct: 22 YELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQXNSVXLGG 81
Query: 86 SRIKVEKCSNLGDTTKPKSWSKYAPDSSAYQKLHNIAPKQDLKPEHTK 133
IKV + SN+G + A ++ A+ +++ + QDL + K
Sbjct: 82 RNIKVGRPSNIGQAQ--PIIDQLAEEARAFNRIYVASVHQDLSDDDIK 127
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 52.4 bits (124), Expect = 1e-06, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 44/75 (58%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
S ++V +L + +TED L +FE +G + ++L D +T ++KG+ +TF E A +A
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 396 QHLDGTVFLGRMLHL 410
+ L+G GR + +
Sbjct: 65 EQLNGFELAGRPMRV 79
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 36/70 (51%), Gaps = 5/70 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ +L+FN TED +R F+ G I ++ + + D S GYGF+ F E +
Sbjct: 8 LYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGR-----SKGYGFITFSDSECARR 62
Query: 643 ALKVLQNSSL 652
AL+ L L
Sbjct: 63 ALEQLNGFEL 72
Score = 31.2 bits (69), Expect = 2.3, Method: Composition-based stats.
Identities = 17/63 (26%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
S + V ++ F + + +F+ FG++ + L K +G +G+GF+ F A+RA+
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDS-DTGRSKGYGFITFSDSECARRAL 64
Query: 746 KAL 748
+ L
Sbjct: 65 EQL 67
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 30/90 (33%), Positives = 47/90 (52%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++ I V NLS E DL +LF +G ++ + L DK T ++KGFA ++F E A +A
Sbjct: 14 DNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARA 73
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVDG 424
+ G + +L++ KP N G G
Sbjct: 74 IAGVSGFGYDHLILNVEWAKPSTNSGPSSG 103
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 46/86 (53%), Gaps = 6/86 (6%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ I V N+ ++++++ELF+ FG + + L K +G +GF F+ F + +A RA+
Sbjct: 16 ATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKT-TGQSKGFAFISFHRREDAARAI 74
Query: 746 KALC--QSTHLYGRRLVLEWAEEADN 769
+ HL L +EWA+ + N
Sbjct: 75 AGVSGFGYDHLI---LNVEWAKPSTN 97
Score = 37.0 bits (84), Expect = 0.046, Method: Composition-based stats.
Identities = 23/75 (30%), Positives = 35/75 (46%), Gaps = 6/75 (8%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSL 503
I V NL T TDL+ LF PFG + R+ + TG + F ++ A A +
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAIAGV 77
Query: 504 AYTKFKEVPLYLEWA 518
+ + + L +EWA
Sbjct: 78 SGFGYDHLILNVEWA 92
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 39/168 (23%), Positives = 72/168 (42%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+LY+ +L+ + TE + F GPI S+ V R + S+GY +V F
Sbjct: 16 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRR-----SLGYAYVNFQQPADA 70
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
+AL + + + + S R+ ++ K I ++N+
Sbjct: 71 ERALDTMNFDVIKGKPVRIMWSQRD------------PSLRKSGVGNIFIKNLDKSIDNK 118
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+ + F AFG + ++ GS +G+GFV F T+ A+RA++ +
Sbjct: 119 ALYDTFSAFGNILSCKVVCDENGS---KGYGFVHFETQEAAERAIEKM 163
Score = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 52/216 (24%), Positives = 81/216 (37%), Gaps = 61/216 (28%)
Query: 206 PSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTT-------F 257
PS PS P S + V +L V + L F P P+ S+R
Sbjct: 8 PSAPSYPMAS-----------LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRS 56
Query: 258 LGMAYIGFKDEKNCNKALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIK 316
LG AY+ F+ + +AL+ N KGK + I +D S + SG
Sbjct: 57 LGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGV------------- 103
Query: 317 AKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDK 376
G IF++NL ++ L F +G + + D+ +
Sbjct: 104 --------------------GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NG 141
Query: 377 TKGFALVTFLMPEHATQAYQHLDGT------VFLGR 406
+KG+ V F E A +A + ++G VF+GR
Sbjct: 142 SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 177
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 5/89 (5%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V +L VTE L + F GP+ + + D T ++ G+A V F P A +A +
Sbjct: 18 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 77
Query: 399 DGTVFLGRMLHLI-----PGKPKENEGNV 422
+ V G+ + ++ P K GN+
Sbjct: 78 NFDVIKGKPVRIMWSQRDPSLRKSGVGNI 106
Score = 34.7 bits (78), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 7/93 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++IKNL+ + ++ F G I S V ++ S GYGFV F T+E+ +
Sbjct: 106 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-------SKGYGFVHFETQEAAER 158
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKR 675
A++ + L++ ++ + R E EA R
Sbjct: 159 AIEKMNGMLLNDRKVFVGRFKSRKEREAELGAR 191
>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 = 50.4 bits (119), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 43/167 (25%), Positives = 77/167 (46%), Gaps = 21/167 (12%)
Query: 593 TEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVLQNSSL 652
+E +R F++ G + + V R + P S G FV FYTR++ +A L N +
Sbjct: 16 SEKDLRELFEQYGAVYEINVLRDRSQNPP---QSKGCCFVTFYTRKAALEAQNALHNXKV 72
Query: 653 ---DEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAF 709
H I+ K ++ K++ V + K+ + I + ++++ F +F
Sbjct: 73 LPGXHHPIQXKPAD----------SEKNNAVEDR---KLFIGXISKKCTENDIRVXFSSF 119
Query: 710 GELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYG 756
G+++ R+ + GL RG FV F T+ A+ A+KA Q+ G
Sbjct: 120 GQIEECRILRGP--DGLSRGCAFVTFTTRAXAQTAIKAXHQAQTXEG 164
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 42/172 (24%), Positives = 71/172 (41%), Gaps = 28/172 (16%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD--KTKGFALVTFLMPEHATQAY 395
+ FV + T +E DL +LFE+YG + E+ + D+ + ++KG VTF + A +A
Sbjct: 5 KXFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 396 QHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNL 455
L L H I KP ++E N A R + + +
Sbjct: 65 NALHNXKVLPGXHHPIQXKPADSEKN---------------------NAVEDRKLFIGXI 103
Query: 456 PYRTLPTDLKALFEPFGDL--GRVLVPPYGIT---GLVEFLQKNQAKAAFNS 502
+ D++ F FG + R+L P G++ V F + A+ A +
Sbjct: 104 SKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIKA 155
Score = 34.7 bits (78), Expect = 0.22, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 30/75 (40%), Gaps = 6/75 (8%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
D L+I ++ TE+ IR F G I + R D LS G FV F TR
Sbjct: 95 DRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPDG------LSRGCAFVTFTTRAX 148
Query: 640 LNQALKVLQNSSLDE 654
A+K + E
Sbjct: 149 AQTAIKAXHQAQTXE 163
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V LS TE DL ++F KYGP+A+V + D+++ +++GFA V F + A +A + +G
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 401 TVFLGRMLHL 410
GR + +
Sbjct: 111 MELDGRRIRV 120
Score = 33.1 bits (74), Expect = 0.61, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRR-FAFIGYHREDQAQAALDYFNNTYVFSSRI 88
T+ L+ F + G + DV + Y + + R FAF+ + D A+ A + N + RI
Sbjct: 59 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 118
Query: 89 KVE 91
+V+
Sbjct: 119 RVD 121
Score = 32.7 bits (73), Expect = 0.76, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 588 LNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL 647
L+ +TE +R F K GPIA V++ + + S G+ FV F + +A +
Sbjct: 54 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRR-----SRGFAFVYFENVDDAKEAKERA 108
Query: 648 QNSSLDEHQIELKRS 662
LD +I + S
Sbjct: 109 NGMELDGRRIRVDFS 123
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 50.1 bits (118), Expect = 5e-06, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V LS TE DL ++F KYGP+A+V + D+++ +++GFA V F + A +A + +G
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 401 TVFLGRMLHL 410
GR + +
Sbjct: 80 MELDGRRIRV 89
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 33/72 (45%), Gaps = 5/72 (6%)
Query: 588 LNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL 647
L+ +TE +R F K GPIA V++ + + S G+ FV F + +A +
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRR-----SRGFAFVYFENVDDAKEAKERA 77
Query: 648 QNSSLDEHQIEL 659
LD +I +
Sbjct: 78 NGMELDGRRIRV 89
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 1/62 (1%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRR-FAFIGYHREDQAQAALDYFNNTYVFSSRI 88
T+ L+ F + G + DV + Y + + R FAF+ + D A+ A + N + RI
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 89 KV 90
+V
Sbjct: 88 RV 89
>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 = 50.1 bits (118), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 39/168 (23%), Positives = 72/168 (42%), Gaps = 20/168 (11%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+LY+ +L+ + TE + F GPI S+ V R + S+GY +V F
Sbjct: 11 ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRR-----SLGYAYVNFQQPADA 65
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQS 700
+AL + + + + S R+ ++ K I ++N+
Sbjct: 66 ERALDTMNFDVIKGKPVRIMWSQRD------------PSLRKSGVGNIFIKNLDKSIDNK 113
Query: 701 EVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+ + F AFG + ++ GS +G+GFV F T+ A+RA++ +
Sbjct: 114 ALYDTFSAFGNILSCKVVCDENGS---KGYGFVHFETQEAAERAIEKM 158
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 52/216 (24%), Positives = 81/216 (37%), Gaps = 61/216 (28%)
Query: 206 PSDPSVPPVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFKPL-PLASVRTT-------F 257
PS PS P S + V +L V + L F P P+ S+R
Sbjct: 3 PSAPSYPMAS-----------LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRS 51
Query: 258 LGMAYIGFKDEKNCNKALNK-NKSFWKGKQLNIYKYSKDNSAKYSGAADDNNNASMENIK 316
LG AY+ F+ + +AL+ N KGK + I +D S + SG
Sbjct: 52 LGYAYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGV------------- 98
Query: 317 AKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDK 376
G IF++NL ++ L F +G + + D+ +
Sbjct: 99 --------------------GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NG 136
Query: 377 TKGFALVTFLMPEHATQAYQHLDGT------VFLGR 406
+KG+ V F E A +A + ++G VF+GR
Sbjct: 137 SKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGR 172
Score = 35.8 bits (81), Expect = 0.095, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 42/89 (47%), Gaps = 5/89 (5%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V +L VTE L + F GP+ + + D T ++ G+A V F P A +A +
Sbjct: 13 LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALDTM 72
Query: 399 DGTVFLGRMLHLI-----PGKPKENEGNV 422
+ V G+ + ++ P K GN+
Sbjct: 73 NFDVIKGKPVRIMWSQRDPSLRKSGVGNI 101
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 7/93 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++IKNL+ + ++ F G I S V ++ S GYGFV F T+E+ +
Sbjct: 101 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-------SKGYGFVHFETQEAAER 153
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKR 675
A++ + L++ ++ + R E EA R
Sbjct: 154 AIEKMNGMLLNDRKVFVGRFKSRKEREAELGAR 186
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 49.7 bits (117), Expect = 6e-06, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V LS TE DL ++F KYGP+A+V + D+++ +++GFA V F + A +A + +G
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 401 TVFLGRMLHL 410
GR + +
Sbjct: 77 MELDGRRIRV 86
Score = 32.3 bits (72), Expect = 0.95, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRR-FAFIGYHREDQAQAALDYFNNTYVFSSRI 88
T+ L+ F + G + DV + Y + + R FAF+ + D A+ A + N + RI
Sbjct: 25 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 84
Query: 89 KVE 91
+V+
Sbjct: 85 RVD 87
Score = 32.3 bits (72), Expect = 1.2, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 588 LNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL 647
L+ +TE +R F K GPIA V++ + + S G+ FV F + +A +
Sbjct: 20 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRR-----SRGFAFVYFENVDDAKEAKERA 74
Query: 648 QNSSLDEHQIELKRS 662
LD +I + S
Sbjct: 75 NGMELDGRRIRVDFS 89
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 49.7 bits (117), Expect = 6e-06, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 42/70 (60%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V LS TE DL ++F KYGP+A+V + D+++ +++GFA V F + A +A + +G
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 401 TVFLGRMLHL 410
GR + +
Sbjct: 80 MELDGRRIRV 89
Score = 32.3 bits (72), Expect = 0.99, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 30 TQEQLKAKFEEKGTVTDVQLKYTTEGKFRR-FAFIGYHREDQAQAALDYFNNTYVFSSRI 88
T+ L+ F + G + DV + Y + + R FAF+ + D A+ A + N + RI
Sbjct: 28 TERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANGMELDGRRI 87
Query: 89 KVE 91
+V+
Sbjct: 88 RVD 90
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 21/75 (28%), Positives = 34/75 (45%), Gaps = 5/75 (6%)
Query: 588 LNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQALKVL 647
L+ +TE +R F K GPIA V++ + + S G+ FV F + +A +
Sbjct: 23 LSLYTTERDLREVFSKYGPIADVSIVYDQQSRR-----SRGFAFVYFENVDDAKEAKERA 77
Query: 648 QNSSLDEHQIELKRS 662
LD +I + S
Sbjct: 78 NGMELDGRRIRVDFS 92
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 49.3 bits (116), Expect = 9e-06, Method: Composition-based stats.
Identities = 26/70 (37%), Positives = 37/70 (52%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
V NL+Y + D L ++FEKYG + +V +P + T +GFA V F A A +DG
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 401 TVFLGRMLHL 410
GR L +
Sbjct: 78 AELDGRELRV 87
Score = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 26/85 (30%), Positives = 45/85 (52%), Gaps = 7/85 (8%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL + NL + ++ DS+RR F+K G + V + R+ K+P G+ FV+F+ R
Sbjct: 15 TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAP-----RGFAFVRFHDRRDAQ 69
Query: 642 QALKVLQNSSLD--EHQIELKRSNR 664
A + + LD E ++++ R R
Sbjct: 70 DAEAAMDGAELDGRELRVQVARYGR 94
Score = 33.5 bits (75), Expect = 0.44, Method: Composition-based stats.
Identities = 14/29 (48%), Positives = 19/29 (65%)
Query: 452 VKNLPYRTLPTDLKALFEPFGDLGRVLVP 480
V NL YRT P L+ +FE +G +G V +P
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIP 46
>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 = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 46/194 (23%), Positives = 86/194 (44%), Gaps = 21/194 (10%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMG----YGFVQFYTRE 638
LY+ N+ F TE+++ F + +T A P +P + + + F++F + +
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQA----PGNPVLAVQINQDKNFAFLEFRSVD 62
Query: 639 SLNQALK----VLQNSSLDEHQIELKRSNRNL----ESEATTVKRKSSNVAKQTGSKILV 690
QA+ + Q SL +I + L E+ + V S V + K+ +
Sbjct: 63 ETTQAMAFDGIIFQGQSL---KIRRPHDYQPLPGMSENPSVYVPGVVSTVVPDSAHKLFI 119
Query: 691 RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQ 750
+P +V+EL +FG LK L K +GL +G+ F E++ N +A+ L
Sbjct: 120 GGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA-TGLSKGYAFCEYVDINVTDQAIAGL-N 177
Query: 751 STHLYGRRLVLEWA 764
L ++L+++ A
Sbjct: 178 GMQLGDKKLLVQRA 191
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 30/63 (47%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++F+ L + +D + +L +GPL L D T +KG+A ++ QA
Sbjct: 116 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 175
Query: 398 LDG 400
L+G
Sbjct: 176 LNG 178
>pdb|1U6F|A Chain A, Nmr Solution Structure Of Tcubp1, A Single Rbd-Unit From
Trypanosoma Cruzi
Length = 139
Score = 47.8 bits (112), Expect = 3e-05, Method: Composition-based stats.
Identities = 25/72 (34%), Positives = 39/72 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ V + TV E L +LFE+YGP+ V + D+ET +++G+ V F A QA L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 399 DGTVFLGRMLHL 410
+G L + L +
Sbjct: 105 NGFNILNKRLKV 116
Score = 34.3 bits (77), Expect = 0.25, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 29/51 (56%), Gaps = 5/51 (9%)
Query: 594 EDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQAL 644
E +R+ F++ GPI SV + ++ + S GYGFV+F + S QA+
Sbjct: 56 EVQLRQLFERYGPIESVKIVCDRETRQ-----SRGYGFVKFQSGSSAQQAI 101
Score = 31.2 bits (69), Expect = 2.2, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
++V IP + ++ +LF+ +G ++ V++ + RG+GFV+F + + A++A+
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDR-ETRQSRGYGFVKFQSGSSAQQAIAG 103
Query: 748 L 748
L
Sbjct: 104 L 104
>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 = 47.4 bits (111), Expect = 3e-05, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV ++Y TE L + FE YGP+ + + K + K +G+A + + AY+H
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 399 DGTVFLGRML 408
DG GR +
Sbjct: 165 DGKKIDGRRV 174
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++ +N+++TE +RR F+ GPI + + K P GY F+++ ++
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKP-----RGYAFIEYEHERDMH 158
Query: 642 QALKVLQNSSLDEHQI 657
A K +D ++
Sbjct: 159 SAYKHADGKKIDGRRV 174
Score = 34.7 bits (78), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y T+ +L+ +FE G + + + Y+ GK R +AFI Y E +A + + +
Sbjct: 112 YDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 171
Query: 86 SRIKVE 91
R+ V+
Sbjct: 172 RRVLVD 177
>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 = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 22/70 (31%), Positives = 36/70 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV ++Y TE L + FE YGP+ + + K + K +G+A + + AY+H
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 399 DGTVFLGRML 408
DG GR +
Sbjct: 165 DGKKIDGRRV 174
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 19/76 (25%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++ +N+++TE +RR F+ GPI + + K P GY F+++ ++
Sbjct: 104 TLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKP-----RGYAFIEYEHERDMH 158
Query: 642 QALKVLQNSSLDEHQI 657
A K +D ++
Sbjct: 159 SAYKHADGKKIDGRRV 174
Score = 33.9 bits (76), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 33/66 (50%), Gaps = 1/66 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTE-GKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
Y T+ +L+ +FE G + + + Y+ GK R +AFI Y E +A + + +
Sbjct: 112 YDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDG 171
Query: 86 SRIKVE 91
R+ V+
Sbjct: 172 RRVLVD 177
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 46.6 bits (109), Expect = 6e-05, Method: Composition-based stats.
Identities = 23/77 (29%), Positives = 42/77 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L+ V + L F +G + ++ +P+D ET+K +GFA V F + E A A ++
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 399 DGTVFLGRMLHLIPGKP 415
+ + GR + + KP
Sbjct: 75 NESELFGRTIRVNLAKP 91
Score = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 28/87 (32%), Positives = 42/87 (48%), Gaps = 10/87 (11%)
Query: 28 KITQEQLKAKFEEKGTVTDVQ--LKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
++ + L A F G +TD+Q L Y TE K R FAF+ + + A AA+D N + +F
Sbjct: 23 EVDDKVLHAAFIPFGDITDIQIPLDYETE-KHRGFAFVEFELAEDAAAAIDNMNESELFG 81
Query: 86 SRIKVEKCSNLGDTTKPKSWSKYAPDS 112
I+V + KP + P S
Sbjct: 82 RTIRV-------NLAKPMRIKESGPSS 101
Score = 30.8 bits (68), Expect = 3.0, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 706 FKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE 765
F FG++ +++P + HRGF FVEF +A A+ + +S L+GR + + A+
Sbjct: 33 FIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVNLAK 90
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 46.6 bits (109), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 38/73 (52%), Gaps = 6/73 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+FV NL +TE+D +LFE+YG +EV + ++ +GF + A A
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 398 LDGTVFLGRMLHL 410
LDGT+ R L +
Sbjct: 78 LDGTILKSRPLRI 90
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 30/73 (41%)
Query: 450 ILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLAYTKFK 509
+ V NLP D K LFE +G+ V + G + + A+ A L T K
Sbjct: 25 LFVGNLPTDITEEDFKRLFERYGEPSEVFINRDRGFGFIRLESRTLAEIAKAELDGTILK 84
Query: 510 EVPLYLEWAPEGV 522
PL + +A G
Sbjct: 85 SRPLRIRFATHGA 97
Score = 30.8 bits (68), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 40/85 (47%), Gaps = 2/85 (2%)
Query: 341 VRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL-D 399
V+NLS V+ + L + F ++GP+ + ++ +D + + G V F A +A + D
Sbjct: 101 VKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERCGD 159
Query: 400 GTVFLGRMLHLIPGKPKENEGNVDG 424
G L + +P E + DG
Sbjct: 160 GAFLLTTTPRPVIVEPMEQFDDEDG 184
>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 = 45.8 bits (107), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV +LS +T +D+ F +G +++ + D T K+KG+ V+F A A Q +
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 399 DGTVFLGRML 408
G GR +
Sbjct: 78 GGQWLGGRQI 87
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V ++ + +++ F FG + R+ K M +G +G+GFV F K +A+ A++
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMA-TGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 748 LCQSTHLYGRRLVLEWA 764
+ L GR++ WA
Sbjct: 77 MG-GQWLGGRQIRTNWA 92
Score = 30.0 bits (66), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 22/103 (21%), Positives = 44/103 (42%), Gaps = 5/103 (4%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ +L+ T + I+ F P ++ AR + G+ S GYGFV F+ +
Sbjct: 18 VFVGDLSPEITTEDIKAAFA---PFGRISDARVVKDMATGK--SKGYGFVSFFNKWDAEN 72
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTG 685
A++ + L QI + R + +T + + +G
Sbjct: 73 AIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQSGPSSG 115
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 35/103 (33%), Positives = 49/103 (47%), Gaps = 14/103 (13%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYG----------PLAEVILPIDKETDKTKGFALV 383
+++ I+V+ L+ +VT DDL F++ G P+ + L DKET K KG A V
Sbjct: 13 SDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYL--DKETGKPKGDATV 70
Query: 384 TFLMPEHATQAYQHLDGTVFLGRML--HLIPGKPKENEGNVDG 424
++ P A A + DG F G L L KP N G G
Sbjct: 71 SYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSGPSSG 113
>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 = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 41/76 (53%), Gaps = 5/76 (6%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TLY+ NL+F +TE+ I F K G I + + K K+ + G+ FV++Y+R
Sbjct: 41 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKT-----ACGFCFVEYYSRADAE 95
Query: 642 QALKVLQNSSLDEHQI 657
A++ + + LD+ I
Sbjct: 96 NAMRYINGTRLDDRII 111
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 42/76 (55%)
Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
+ +S ++V NLS+ TE+ + +LF K G + ++I+ +DK GF V + A
Sbjct: 36 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAE 95
Query: 393 QAYQHLDGTVFLGRML 408
A ++++GT R++
Sbjct: 96 NAMRYINGTRLDDRII 111
Score = 32.0 bits (71), Expect = 1.3, Method: Composition-based stats.
Identities = 22/77 (28%), Positives = 41/77 (53%), Gaps = 4/77 (5%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLP-KKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+ V N+ F + ++ ELF G++K + + KM + GF FVE+ ++ +A+ AM+
Sbjct: 42 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTAC--GFCFVEYYSRADAENAMR 99
Query: 747 ALCQSTHLYGRRLVLEW 763
+ T L R + +W
Sbjct: 100 YI-NGTRLDDRIIRTDW 115
>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 = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 38/64 (59%), Gaps = 1/64 (1%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G+ ++V +P Q E+ LF + GE++ +L + V +G G+GFV ++T +A+RA
Sbjct: 19 GTNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVTAKDAERA 77
Query: 745 MKAL 748
+ L
Sbjct: 78 INTL 81
Score = 36.6 bits (83), Expect = 0.061, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T+D +R F G + S + R K S+GYGFV + T +
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGH-----SLGYGFVNYVTAKDA 74
Query: 641 NQALKVLQNSSLDEHQIEL 659
+A+ L L I++
Sbjct: 75 ERAINTLNGLRLQSKTIKV 93
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 47/180 (26%), Positives = 68/180 (37%), Gaps = 44/180 (24%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+ R+FV NL +TE+++ KLFEKYG EV + K KGF + A A
Sbjct: 21 QRSRLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIA 74
Query: 395 YQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKN 454
LD G+ L + + C + + V+N
Sbjct: 75 KVELDNMPLRGKQLRV--------------RFACHSAS-----------------LTVRN 103
Query: 455 LPYRTLPTDLKALFEPFGDLGRVLV------PPYGITGLVEFLQKNQAKAAFNSLAYTKF 508
LP L+ F FG + R +V P G G+VEF K A+ A + + F
Sbjct: 104 LPQYVSNELLEEAFSVFGQVERAVVIVDDRGRPSG-KGIVEFSGKPAARKALDRCSEGSF 162
Score = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 47/197 (23%), Positives = 87/197 (44%), Gaps = 38/197 (19%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
+ L++ NL + TE+ +R+ F+K G V + + K G+GF++ TR +L
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-----------GFGFIRLETR-TL 70
Query: 641 NQALKV-LQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
+ KV L N L Q+ ++ + + + + VRN+P
Sbjct: 71 AEIAKVELDNMPLRGKQLRVRFACHS--------------------ASLTVRNLPQYVSN 110
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHL---YG 756
+EE F FG+++ R + G G G VEF K A++A+ + + L +
Sbjct: 111 ELLEEAFSVFGQVE--RAVVIVDDRGRPSGKGIVEFSGKPAARKALDRCSEGSFLLTTFP 168
Query: 757 RRLVLEWAEEADNVEDI 773
R + +E ++ D+ E +
Sbjct: 169 RPVTVEPMDQLDDEEGL 185
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 45.1 bits (105), Expect = 2e-04, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L+ V + L F +G + ++ +P+D ET+K +GFA V F + E A A ++
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 399 DGTVFLGRMLHL 410
+ + GR + +
Sbjct: 126 NESELFGRTIRV 137
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 28 KITQEQLKAKFEEKGTVTDVQ--LKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
++ + L A F G +TD+Q L Y TE K R FAF+ + + A AA+D N + +F
Sbjct: 74 EVDDKVLHAAFIPFGDITDIQIPLDYETE-KHRGFAFVEFELAEDAAAAIDNMNESELFG 132
Query: 86 SRIKV 90
I+V
Sbjct: 133 RTIRV 137
Score = 31.6 bits (70), Expect = 2.0, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 706 FKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
F FG++ +++P + HRGF FVEF +A A+ + +S L+GR + + A
Sbjct: 84 FIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVNLA 140
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 41/185 (22%), Positives = 86/185 (46%), Gaps = 28/185 (15%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ NLNFN + ++ + V + ++ +G+V F + E L +
Sbjct: 10 LFVGNLNFNKSAPELKTGISDVFAKNDLAVVDVRIG------MTRKFGYVDFESAEDLEK 63
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSK-ILVRNIPFQAKQSE 701
AL+ L + ++I+L+ K K + K+ ++ +L +N+P++ Q E
Sbjct: 64 ALE-LTGLKVFGNEIKLE-------------KPKGKDSKKERDARTLLAKNLPYKVTQDE 109
Query: 702 VEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVL 761
++E+F+ E++ V G +G ++EF T+ +A++ + Q T + GR + L
Sbjct: 110 LKEVFEDAAEIRLVS------KDGKSKGIAYIEFKTEADAEKTFEE-KQGTEIDGRSISL 162
Query: 762 EWAEE 766
+ E
Sbjct: 163 YYTGE 167
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 33/111 (29%), Positives = 52/111 (46%), Gaps = 16/111 (14%)
Query: 307 NNNASMENIKAKHWKSQEDSVQFAEDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEV 366
N +E K K K + D+ + +NL Y VT+D+L ++FE AE+
Sbjct: 74 GNEIKLEKPKGKDSKKERDART----------LLAKNLPYKVTQDELKEVFE---DAAEI 120
Query: 367 ILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRMLHL-IPGKPK 416
L + K+ K+KG A + F A + ++ GT GR + L G+PK
Sbjct: 121 RL-VSKDG-KSKGIAYIEFKTEADAEKTFEEKQGTEIDGRSISLYYTGEPK 169
Score = 35.4 bits (80), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 25/82 (30%), Positives = 39/82 (47%), Gaps = 4/82 (4%)
Query: 213 PVSKAPVHKRQYHTIVVKNLPAGVKKKDLKAYFK---PLPLASVRTTFLGMAYIGFKDEK 269
P K +R T++ KNLP V + +LK F+ + L S G+AYI FK E
Sbjct: 82 PKGKDSKKERDARTLLAKNLPYKVTQDELKEVFEDAAEIRLVSKDGKSKGIAYIEFKTEA 141
Query: 270 NCNKAL-NKNKSFWKGKQLNIY 290
+ K K + G+ +++Y
Sbjct: 142 DAEKTFEEKQGTEIDGRSISLY 163
Score = 32.7 bits (73), Expect = 0.81, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 39/81 (48%), Gaps = 5/81 (6%)
Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGL--VEFLQKNQAKAAFNS 502
R R +L KNLPY+ +LK +FE ++ R++ G+ +EF + A+ F
Sbjct: 91 RDARTLLAKNLPYKVTQDELKEVFEDAAEI-RLVSKDGKSKGIAYIEFKTEADAEKTFEE 149
Query: 503 LAYTKF--KEVPLYLEWAPEG 521
T+ + + LY P+G
Sbjct: 150 KQGTEIDGRSISLYYTGEPKG 170
Score = 30.0 bits (66), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 21/78 (26%), Positives = 34/78 (43%), Gaps = 10/78 (12%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL KNL + T+D ++ F+ I V+ KD KS G +++F T
Sbjct: 95 TLLAKNLPYKVTQDELKEVFEDAAEIRLVS----KDGKSK------GIAYIEFKTEADAE 144
Query: 642 QALKVLQNSSLDEHQIEL 659
+ + Q + +D I L
Sbjct: 145 KTFEEKQGTEIDGRSISL 162
>pdb|3NNH|A Chain A, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|C Chain C, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|B Chain B, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
pdb|3NNH|D Chain D, Crystal Structure Of The Cugbp1 Rrm1 With Guuguuuuguuu Rna
Length = 88
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 48/88 (54%), Gaps = 2/88 (2%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETD--KTKGFALVTFLMPEHA 391
+++ ++FV + T +E DL +LFE+YG + E+ + D+ + ++KG VTF + A
Sbjct: 1 SDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAA 60
Query: 392 TQAYQHLDGTVFLGRMLHLIPGKPKENE 419
+A L L M H I KP ++E
Sbjct: 61 LEAQNALHNMKVLPGMHHPIQMKPADSE 88
Score = 32.7 bits (73), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 40/84 (47%), Gaps = 6/84 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
+++ + +E +R F++ G + + V R + P S G FV FYTR++ +
Sbjct: 6 MFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQ---SKGCCFVTFYTRKAALE 62
Query: 643 ALKVLQNSSL---DEHQIELKRSN 663
A L N + H I++K ++
Sbjct: 63 AQNALHNMKVLPGMHHPIQMKPAD 86
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 38/75 (50%), Gaps = 8/75 (10%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
S ++ V N+S T T +L FE+YGP+ E D K +A V E A +A
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIEC--------DIVKDYAFVHMERAEDAVEAI 61
Query: 396 QHLDGTVFLGRMLHL 410
+ LD T F G+ +H+
Sbjct: 62 RGLDNTEFQGKRMHV 76
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 36/77 (46%), Gaps = 8/77 (10%)
Query: 29 ITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSSRI 88
T ++L+AKFEE G V + + + +AF+ R + A A+ +NT R+
Sbjct: 22 CTNQELRAKFEEYGPVIECDI-------VKDYAFVHMERAEDAVEAIRGLDNTEFQGKRM 74
Query: 89 KVE-KCSNLGDTTKPKS 104
V+ S L + P S
Sbjct: 75 HVQLSTSRLRTASGPSS 91
>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 = 44.3 bits (103), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 39/169 (23%), Positives = 74/169 (43%), Gaps = 20/169 (11%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
+T L + L + T+ + F+ GPI + + R D K+ S GY FV F +
Sbjct: 14 NTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXR--DYKTG---YSFGYAFVDFTSEXD 68
Query: 640 LNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
+A+KVL ++ ++++ + ES T + V N+P
Sbjct: 69 SQRAIKVLNGITVRNKRLKVSYARPGGESIKDT--------------NLYVTNLPRTITD 114
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+++ +F +G + + + + +G RG FV + + EA+ A+ AL
Sbjct: 115 DQLDTIFGKYGSIVQKNILRDKL-TGRPRGVAFVRYNKREEAQEAISAL 162
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 35/64 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL T+T+D L +F KYG + + + DK T + +G A V + E A +A L
Sbjct: 103 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 162
Query: 399 DGTV 402
+ +
Sbjct: 163 NNVI 166
Score = 36.6 bits (83), Expect = 0.052, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
DT LY+ NL T+D + F K G I + R K P G FV++ RE
Sbjct: 100 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP-----RGVAFVRYNKREE 154
Query: 640 LNQALKVLQN 649
+A+ L N
Sbjct: 155 AQEAISALNN 164
Score = 31.6 bits (70), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQ-LKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT 81
IT +QL F + G++ L+ G+ R AF+ Y++ ++AQ A+ NN
Sbjct: 112 ITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNV 165
Score = 30.8 bits (68), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 36/82 (43%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
A + + V L T+ +L LF GP+ + D +T + G+A V F + +
Sbjct: 12 ASNTNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQR 71
Query: 394 AYQHLDGTVFLGRMLHLIPGKP 415
A + L+G + L + +P
Sbjct: 72 AIKVLNGITVRNKRLKVSYARP 93
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 36/70 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV +LS +T +D+ F +G +++ + D T K+KG+ V+F A A H+
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVHM 77
Query: 399 DGTVFLGRML 408
G GR +
Sbjct: 78 GGQWLGGRQI 87
Score = 38.1 bits (87), Expect = 0.017, Method: Compositional matrix adjust.
Identities = 21/77 (27%), Positives = 40/77 (51%), Gaps = 2/77 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V ++ + +++ F FG++ R+ K M +G +G+GFV F K +A+ A+
Sbjct: 18 VFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMA-TGKSKGYGFVSFYNKLDAENAIVH 76
Query: 748 LCQSTHLYGRRLVLEWA 764
+ L GR++ WA
Sbjct: 77 MG-GQWLGGRQIRTNWA 92
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 44.3 bits (103), Expect = 3e-04, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV NL V E+ L +LF + GPL +V + D+E K K F V F PE + A L
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDRE-GKPKSFGFVCFKHPESVSYAIALL 77
Query: 399 DGTVFLGRMLHL 410
+G GR +++
Sbjct: 78 NGIRLYGRPINV 89
Score = 34.7 bits (78), Expect = 0.22, Method: Composition-based stats.
Identities = 22/75 (29%), Positives = 38/75 (50%), Gaps = 10/75 (13%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKD--PKSPGQFLSMGYGFVQFYTR 637
D T+++ NL E+ + F + GP+ VT+ + ++ PKS +GFV F
Sbjct: 16 DRTVFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKS--------FGFVCFKHP 67
Query: 638 ESLNQALKVLQNSSL 652
ES++ A+ +L L
Sbjct: 68 ESVSYAIALLNGIRL 82
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FVRNL+ TVTE+ L K F ++G L V K K +A + F + A +A + +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERDGAVKAMEEM 65
Query: 399 DGTVFLGRMLHLIPGKP 415
+G G + ++ KP
Sbjct: 66 NGKDLEGENIEIVFAKP 82
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 44.3 bits (103), Expect = 3e-04, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 33/54 (61%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMP 388
E G++FV L ++ T++ L F +YG + + ++ DK T++++GF V F P
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68
>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 = 44.3 bits (103), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L+ V + L F +G + ++ +P+D ET+K +GFA V F + E A A ++
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 399 DGTVFLGRMLHL 410
+ + GR + +
Sbjct: 65 NESELFGRTIRV 76
Score = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 28 KITQEQLKAKFEEKGTVTDVQ--LKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
++ + L A F G +TD+Q L Y TE K R FAF+ + + A AA+D N + +F
Sbjct: 13 EVDDKVLHAAFIPFGDITDIQIPLDYETE-KHRGFAFVEFELAEDAAAAIDNMNESELFG 71
Query: 86 SRIKV 90
I+V
Sbjct: 72 RTIRV 76
Score = 30.8 bits (68), Expect = 3.2, Method: Composition-based stats.
Identities = 19/59 (32%), Positives = 32/59 (54%), Gaps = 2/59 (3%)
Query: 706 FKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
F FG++ +++P + HRGF FVEF +A A+ + +S L+GR + + A
Sbjct: 23 FIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVNLA 79
>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 = 44.3 bits (103), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L+ V + L F +G + ++ +P+D ET+K +GFA V F + E A A ++
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 399 DGTVFLGRMLHL 410
+ + GR + +
Sbjct: 70 NESELFGRTIRV 81
Score = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 28 KITQEQLKAKFEEKGTVTDVQ--LKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
++ + L A F G +TD+Q L Y TE K R FAF+ + + A AA+D N + +F
Sbjct: 18 EVDDKVLHAAFIPFGDITDIQIPLDYETE-KHRGFAFVEFELAEDAAAAIDNMNESELFG 76
Query: 86 SRIKV 90
I+V
Sbjct: 77 RTIRV 81
Score = 31.2 bits (69), Expect = 2.6, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 706 FKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE 765
F FG++ +++P + HRGF FVEF +A A+ + +S L+GR + + A+
Sbjct: 28 FIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVNLAK 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L+ V + L F +G + ++ +P+D ET+K +GFA V F + E A A ++
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 399 DGTVFLGRMLHL 410
+ + GR + +
Sbjct: 68 NESELFGRTIRV 79
Score = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 24/65 (36%), Positives = 36/65 (55%), Gaps = 3/65 (4%)
Query: 28 KITQEQLKAKFEEKGTVTDVQ--LKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFS 85
++ + L A F G +TD+Q L Y TE K R FAF+ + + A AA+D N + +F
Sbjct: 16 EVDDKVLHAAFIPFGDITDIQIPLDYETE-KHRGFAFVEFELAEDAAAAIDNMNESELFG 74
Query: 86 SRIKV 90
I+V
Sbjct: 75 RTIRV 79
Score = 30.8 bits (68), Expect = 3.0, Method: Composition-based stats.
Identities = 19/60 (31%), Positives = 33/60 (55%), Gaps = 2/60 (3%)
Query: 706 FKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAE 765
F FG++ +++P + HRGF FVEF +A A+ + +S L+GR + + A+
Sbjct: 26 FIPFGDITDIQIPLDY-ETEKHRGFAFVEFELAEDAAAAIDNMNES-ELFGRTIRVNLAK 83
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 43.5 bits (101), Expect = 4e-04, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 39/64 (60%), Gaps = 1/64 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDK-ETDKTKGFALVTFLMPEHATQAYQ 396
++ + L+ VT+D + ++F YG + + +P+++ +KG+A V F P+ A +A +
Sbjct: 6 KVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALK 65
Query: 397 HLDG 400
H+DG
Sbjct: 66 HMDG 69
Score = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 36/60 (60%), Gaps = 4/60 (6%)
Query: 689 LVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
L RN+ + + E+F +G++K + +P + + L +G+ +VEF +EA++A+K +
Sbjct: 12 LTRNV----TKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKALKHM 67
Score = 30.8 bits (68), Expect = 3.1, Method: Composition-based stats.
Identities = 22/78 (28%), Positives = 35/78 (44%), Gaps = 6/78 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTV-ARKKDPKSPGQFLSMGYGFVQFYTRES 639
T ++I L N T+D I F G I + + + P LS GY +V+F +
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPH-----LSKGYAYVEFENPDE 59
Query: 640 LNQALKVLQNSSLDEHQI 657
+ALK + +D +I
Sbjct: 60 AEKALKHMDGGQIDGQEI 77
>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 = 43.5 bits (101), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 8/85 (9%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
++Y+ N+++ +T + + HF CG + VT+ K P G+ +++F +ES+
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHP-----KGFAYIEFSDKESVR 61
Query: 642 QALKVLQNSSLDEHQIEL--KRSNR 664
+L L S QI++ KR+NR
Sbjct: 62 TSL-ALDESLFRGRQIKVIPKRTNR 85
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 1/79 (1%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
A++ I+V N+ Y T ++L F G + V + DK + KGFA + F E + +
Sbjct: 3 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE-SVR 61
Query: 394 AYQHLDGTVFLGRMLHLIP 412
LD ++F GR + +IP
Sbjct: 62 TSLALDESLFRGRQIKVIP 80
Score = 34.3 bits (77), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 10/73 (13%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL---------GMAYIGFKDEKNCNKALN 276
+I V N+ G ++L+A+F + R T L G AYI F D+++ +L
Sbjct: 7 SIYVGNVDYGATAEELEAHFHGCGSVN-RVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 65
Query: 277 KNKSFWKGKQLNI 289
++S ++G+Q+ +
Sbjct: 66 LDESLFRGRQIKV 78
>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 = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 38/182 (20%), Positives = 76/182 (41%), Gaps = 17/182 (9%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ N+ F TE+++ F + +T A P +P + + ++
Sbjct: 9 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQA----PGNP-----------VLAVQINQDK 53
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEV 702
L+ S+DE + + ++ ++R K+ + +P +V
Sbjct: 54 NFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQV 113
Query: 703 EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE 762
+EL +FG LK L K +GL +G+ F E++ N +A+ L L ++L+++
Sbjct: 114 KELLTSFGPLKAFNLVKDSA-TGLSKGYAFCEYVDINVTDQAIAGL-NGMQLGDKKLLVQ 171
Query: 763 WA 764
A
Sbjct: 172 RA 173
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 30/63 (47%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++F+ L + +D + +L +GPL L D T +KG+A ++ QA
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 398 LDG 400
L+G
Sbjct: 158 LNG 160
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 29/90 (32%), Positives = 50/90 (55%), Gaps = 9/90 (10%)
Query: 668 SEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLH 727
S ++ VKR A Q S ++V +P++ + +++E F FGE+ V++ KK + +G
Sbjct: 3 SGSSGVKR-----AVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQV-KKDLKTGHS 56
Query: 728 RGFGFVEFITKNEAKRAMKALCQSTHLYGR 757
+GFGFV F E + +K + Q + GR
Sbjct: 57 KGFGFVRF---TEYETQVKVMSQRHMIDGR 83
Score = 32.7 bits (73), Expect = 0.70, Method: Composition-based stats.
Identities = 19/61 (31%), Positives = 31/61 (50%), Gaps = 2/61 (3%)
Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
+ ++ + V L + TE DL + F +G + V + D +T +KGF V F E+ T
Sbjct: 12 VQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF--TEYET 69
Query: 393 Q 393
Q
Sbjct: 70 Q 70
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV ++ ED++ + F YG + + L +D+ T +KG+ALV + + A A + L
Sbjct: 29 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 88
Query: 399 DGTVFLGRMLHL 410
+G +G+ + +
Sbjct: 89 NGAEIMGQTIQV 100
Score = 38.1 bits (87), Expect = 0.021, Method: Compositional matrix adjust.
Identities = 22/80 (27%), Positives = 43/80 (53%), Gaps = 2/80 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G + V +I +A++ E++E F +GE+K + L +G +G+ VE+ T +A A
Sbjct: 26 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRR-TGFSKGYALVEYETHKQALAA 84
Query: 745 MKALCQSTHLYGRRLVLEWA 764
+AL + G+ + ++W
Sbjct: 85 KEAL-NGAEIMGQTIQVDWC 103
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 38/182 (20%), Positives = 76/182 (41%), Gaps = 17/182 (9%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+ N+ F TE+++ F + +T A P +P + + ++
Sbjct: 7 LYVGNIPFGITEEAMMDFFNAQMRLGGLTQA----PGNP-----------VLAVQINQDK 51
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEV 702
L+ S+DE + + ++ ++R K+ + +P +V
Sbjct: 52 NFAFLEFRSVDETTQAMAFDGIIFQGQSLKIRRPHDYQPLPGAHKLFIGGLPNYLNDDQV 111
Query: 703 EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLE 762
+EL +FG LK L K +GL +G+ F E++ N +A+ L L ++L+++
Sbjct: 112 KELLTSFGPLKAFNLVKDSA-TGLSKGYAFCEYVDINVTDQAIAGL-NGMQLGDKKLLVQ 169
Query: 763 WA 764
A
Sbjct: 170 RA 171
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 30/63 (47%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++F+ L + +D + +L +GPL L D T +KG+A ++ QA
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 398 LDG 400
L+G
Sbjct: 156 LNG 158
>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 = 9e-04, Method: Composition-based stats.
Identities = 23/76 (30%), Positives = 39/76 (51%), Gaps = 6/76 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TLY+ NL+F +TE+ I F K G I + + K + G+ FV++Y+R
Sbjct: 20 TLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK------MKTACGFCFVEYYSRADAE 73
Query: 642 QALKVLQNSSLDEHQI 657
A++ + + LD+ I
Sbjct: 74 NAMRYINGTRLDDRII 89
Score = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 42/76 (55%), Gaps = 1/76 (1%)
Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHAT 392
+ +S ++V NLS+ TE+ + +LF K G + ++I+ +DK GF V + A
Sbjct: 15 LKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYYSRADAE 73
Query: 393 QAYQHLDGTVFLGRML 408
A ++++GT R++
Sbjct: 74 NAMRYINGTRLDDRII 89
Score = 32.3 bits (72), Expect = 0.95, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 3/76 (3%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V N+ F + ++ ELF G++K + + + + GF FVE+ ++ +A+ AM+
Sbjct: 21 LYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTAC--GFCFVEYYSRADAENAMRY 78
Query: 748 LCQSTHLYGRRLVLEW 763
+ T L R + +W
Sbjct: 79 I-NGTRLDDRIIRTDW 93
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 42.7 bits (99), Expect = 9e-04, Method: Composition-based stats.
Identities = 39/169 (23%), Positives = 74/169 (43%), Gaps = 20/169 (11%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
+T L + L + T+ + F+ GPI + + R D K+ S GY FV F +
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMR--DYKTG---YSYGYAFVDFTSEMD 57
Query: 640 LNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQ 699
+A+KVL ++ ++++ + ES T + V N+P
Sbjct: 58 SQRAIKVLNGITVRNKRLKVSYARPGGESIKDT--------------NLYVTNLPRTITD 103
Query: 700 SEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
+++ +F +G + + + + +G RG FV + + EA+ A+ AL
Sbjct: 104 DQLDTIFGKYGSIVQKNILRDKL-TGRPRGVAFVRYNKREEAQEAISAL 151
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 35/64 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL T+T+D L +F KYG + + + DK T + +G A V + E A +A L
Sbjct: 92 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 151
Query: 399 DGTV 402
+ +
Sbjct: 152 NNVI 155
Score = 37.0 bits (84), Expect = 0.039, Method: Composition-based stats.
Identities = 23/70 (32%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
DT LY+ NL T+D + F K G I + R K P G FV++ RE
Sbjct: 89 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP-----RGVAFVRYNKREE 143
Query: 640 LNQALKVLQN 649
+A+ L N
Sbjct: 144 AQEAISALNN 153
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 17/53 (32%), Positives = 29/53 (54%), Gaps = 1/53 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQ-LKYTTEGKFRRFAFIGYHREDQAQAALDYFNN 80
IT +QL F + G++ L+ G+ R AF+ Y++ ++AQ A+ NN
Sbjct: 101 ITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNN 153
Score = 30.4 bits (67), Expect = 3.6, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 37/82 (45%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
A + + V L +T+ +L LF GP+ + D +T + G+A V F + +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 394 AYQHLDGTVFLGRMLHLIPGKP 415
A + L+G + L + +P
Sbjct: 61 AIKVLNGITVRNKRLKVSYARP 82
>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 = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 45/85 (52%), Gaps = 8/85 (9%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
++Y+ N+++ +T + + HF CG + VT+ K P G+ +++F +ES+
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHP-----KGFAYIEFSDKESVR 62
Query: 642 QALKVLQNSSLDEHQIEL--KRSNR 664
+L L S QI++ KR+NR
Sbjct: 63 TSL-ALDESLFRGRQIKVIPKRTNR 86
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 42/81 (51%), Gaps = 1/81 (1%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
A++ I+V N+ Y T ++L F G + V + DK + KGFA + F E + +
Sbjct: 4 ADARSIYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKE-SVR 62
Query: 394 AYQHLDGTVFLGRMLHLIPGK 414
LD ++F GR + +IP +
Sbjct: 63 TSLALDESLFRGRQIKVIPKR 83
Score = 31.2 bits (69), Expect = 2.1, Method: Composition-based stats.
Identities = 20/73 (27%), Positives = 38/73 (52%), Gaps = 10/73 (13%)
Query: 226 TIVVKNLPAGVKKKDLKAYFKPLPLASVRTTFL---------GMAYIGFKDEKNCNKALN 276
+I V N+ G ++L+A+F + R T L G AYI F D+++ +L
Sbjct: 8 SIYVGNVDYGATAEELEAHFHGCGSVN-RVTILCDKFSGHPKGFAYIEFSDKESVRTSLA 66
Query: 277 KNKSFWKGKQLNI 289
++S ++G+Q+ +
Sbjct: 67 LDESLFRGRQIKV 79
>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 = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 37/63 (58%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ ++V +P Q E+ LF + GE++ +L + V +G G+GFV ++T +A+RA+
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKV-AGHSLGYGFVNYVTAKDAERAI 63
Query: 746 KAL 748
L
Sbjct: 64 NTL 66
Score = 36.2 bits (82), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T+D +R F G + S + R K S+GYGFV + T +
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGH-----SLGYGFVNYVTAKDA 59
Query: 641 NQALKVLQNSSLDEHQIEL 659
+A+ L L I++
Sbjct: 60 ERAINTLNGLRLQSKTIKV 78
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 23/72 (31%), Positives = 35/72 (48%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
S +++R L T+ DL KL + YG + +DK T+K KG+ V F P A +A
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 396 QHLDGTVFLGRM 407
L + +M
Sbjct: 65 TALKASGVQAQM 76
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 19/47 (40%), Positives = 29/47 (61%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
IFV LS T +D+ FE++G + + +L DK T++ +GF VTF
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTF 48
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 36/62 (58%)
Query: 332 DIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHA 391
D+ E +F+RNLS+ E+ L ++ +++G L V + + +T+ +KG A F+ E A
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 392 TQ 393
+
Sbjct: 71 QK 72
Score = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 25/95 (26%), Positives = 47/95 (49%), Gaps = 18/95 (18%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLH------RGFGFVEFITK 738
G + +RN+ F +++ + E+ + FG+LK+VR+ LH +G F +F+T+
Sbjct: 15 GKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVV-------LHPDTEHSKGCAFAQFMTQ 67
Query: 739 NEAKRAMKALCQSTH-----LYGRRLVLEWAEEAD 768
A++ + A L GR+L ++ A D
Sbjct: 68 EAAQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRD 102
Score = 37.7 bits (86), Expect = 0.024, Method: Composition-based stats.
Identities = 27/98 (27%), Positives = 50/98 (51%), Gaps = 8/98 (8%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T++I+NL+F+S E+++ ++ G + V V D + S G F QF T+E+
Sbjct: 17 TVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEH-----SKGCAFAQFMTQEA-- 69
Query: 642 QALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSN 679
A K L +SL+ LK R L+ + + ++++
Sbjct: 70 -AQKCLAAASLEAEGGGLKLDGRQLKVDLAVTRDEAAS 106
>pdb|1SXL|A Chain A, Resonance Assignments And Solution Structure Of The Second
Rna-Binding Domain Of Sex-Lethal Determined By
Multidimensional Heteronuclear Magnetic Resonance
Spectroscopy
Length = 97
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 35/64 (54%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V NL T+T+D L +F KYG + + + DK T + +G A V + E A +A L
Sbjct: 16 LYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISAL 75
Query: 399 DGTV 402
+ +
Sbjct: 76 NNVI 79
Score = 37.0 bits (84), Expect = 0.038, Method: Compositional matrix adjust.
Identities = 23/70 (32%), Positives = 31/70 (44%), Gaps = 5/70 (7%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
DT LY+ NL T+D + F K G I + R K P G FV++ RE
Sbjct: 13 DTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRP-----RGVAFVRYNKREE 67
Query: 640 LNQALKVLQN 649
+A+ L N
Sbjct: 68 AQEAISALNN 77
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 1/54 (1%)
Query: 29 ITQEQLKAKFEEKGTVTDVQ-LKYTTEGKFRRFAFIGYHREDQAQAALDYFNNT 81
IT +QL F + G++ L+ G+ R AF+ Y++ ++AQ A+ NN
Sbjct: 25 ITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAISALNNV 78
>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 = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 35/73 (47%), Gaps = 6/73 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+FV NL +TE+++ KLFEKYG EV + K KGF + A A
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFI------HKDKGFGFIRLETRTLAEIAKVE 70
Query: 398 LDGTVFLGRMLHL 410
LD G+ L +
Sbjct: 71 LDNMPLRGKQLRV 83
Score = 31.2 bits (69), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 13/79 (16%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ NL + TE+ +R+ F+K G V + + K G+GF++ TR +L +
Sbjct: 18 LFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDK-----------GFGFIRLETR-TLAE 65
Query: 643 ALKV-LQNSSLDEHQIELK 660
KV L N L Q+ ++
Sbjct: 66 IAKVELDNMPLRGKQLRVR 84
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 36/77 (46%), Gaps = 11/77 (14%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY++NL +++E+ I + F P A V + +D Y FV F RE +
Sbjct: 18 LYVRNLMLSTSEEMIEKEFNNIKPGAVERVKKIRD-----------YAFVHFSNREDAVE 66
Query: 643 ALKVLQNSSLDEHQIEL 659
A+K L LD IE+
Sbjct: 67 AMKALNGKVLDGSPIEV 83
Score = 33.9 bits (76), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 26/86 (30%), Positives = 40/86 (46%), Gaps = 7/86 (8%)
Query: 331 EDIAESGRI-FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPE 389
ED S +I +VRNL + +E+ + K F P A + K + +A V F E
Sbjct: 9 EDTMSSVKILYVRNLMLSTSEEMIEKEFNNIKPGAV------ERVKKIRDYAFVHFSNRE 62
Query: 390 HATQAYQHLDGTVFLGRMLHLIPGKP 415
A +A + L+G V G + + KP
Sbjct: 63 DAVEAMKALNGKVLDGSPIEVTLAKP 88
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 28/86 (32%), Positives = 47/86 (54%), Gaps = 6/86 (6%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L+I L+F +TE+S+R ++++ G + V R DP S S G+GFV F + ++
Sbjct: 30 LFIGGLSFETTEESLRNYYEQWGKLTDCVVMR--DPASK---RSRGFGFVTFSSMAEVDA 84
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLES 668
A+ + S+D +E KR+ ES
Sbjct: 85 AMAA-RPHSIDGRVVEPKRAVAREES 109
Score = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 15/48 (31%), Positives = 30/48 (62%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
++F+ LS+ TE+ L +E++G L + ++ D + +++GF VTF
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTF 76
Score = 30.4 bits (67), Expect = 4.3, Method: Composition-based stats.
Identities = 22/85 (25%), Positives = 37/85 (43%), Gaps = 7/85 (8%)
Query: 666 LESEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELK---FVRLPKKMV 722
+E TV + K+ K+ + + F+ + + ++ +G+L +R P
Sbjct: 8 MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDP---- 63
Query: 723 GSGLHRGFGFVEFITKNEAKRAMKA 747
S RGFGFV F + E AM A
Sbjct: 64 ASKRSRGFGFVTFSSMAEVDAAMAA 88
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 6/81 (7%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPL--AEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
++V+NL + ++ L K F +G + A+V++ E ++KGF V F PE AT+A
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMM----EGGRSKGFGFVCFSSPEEATKAVT 73
Query: 397 HLDGTVFLGRMLHLIPGKPKE 417
++G + + L++ + KE
Sbjct: 74 EMNGRIVATKPLYVALAQRKE 94
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 24/46 (52%)
Query: 703 EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
E L KAF + K M+ G +GFGFV F + EA +A+ +
Sbjct: 30 ERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAVTEM 75
Score = 29.3 bits (64), Expect = 8.3, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 30/62 (48%), Gaps = 7/62 (11%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
LY+KNL+ ++ +R+ F G I S V + S G+GFV F + E +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGGR-------SKGFGFVCFSSPEEATK 70
Query: 643 AL 644
A+
Sbjct: 71 AV 72
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 35/74 (47%), Gaps = 8/74 (10%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+FVR V E +L ++F +GP+ KE GFA V F E A +A +
Sbjct: 6 RLFVRPFPLDVQESELNEIFGPFGPM--------KEVKILNGFAFVEFEEAESAAKAIEE 57
Query: 398 LDGTVFLGRMLHLI 411
+ G F + L ++
Sbjct: 58 VHGKSFANQPLEVV 71
Score = 36.6 bits (83), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 22/65 (33%), Positives = 35/65 (53%), Gaps = 12/65 (18%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
+ +++ VR P ++SE+ E+F FG +K V+ + GF FVEF EA+
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK---------ILNGFAFVEF---EEAES 50
Query: 744 AMKAL 748
A KA+
Sbjct: 51 AAKAI 55
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 40.8 bits (94), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 25/76 (32%), Positives = 38/76 (50%), Gaps = 4/76 (5%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
ES + + NLSY+ TE+ L ++FEK A I + K+KG+A + F E A +A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEK----ATFIKVPQNQNGKSKGYAFIEFASFEDAKEA 69
Query: 395 YQHLDGTVFLGRMLHL 410
+ GR + L
Sbjct: 70 LNSCNKREIEGRAIRL 85
Score = 38.1 bits (87), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 45/78 (57%), Gaps = 7/78 (8%)
Query: 686 SKILV-RNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
SK LV N+ + A + ++E+F+ + F+++P+ +G +G+ F+EF + +AK A
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFE---KATFIKVPQNQ--NGKSKGYAFIEFASFEDAKEA 69
Query: 745 MKALCQSTHLYGRRLVLE 762
+ + C + GR + LE
Sbjct: 70 LNS-CNKREIEGRAIRLE 86
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 20/79 (25%), Positives = 41/79 (51%), Gaps = 9/79 (11%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL + NL++++TE++++ F+K + V + ++ K S GY F++F + E
Sbjct: 17 TLVLSNLSYSATEETLQEVFEKA---TFIKVPQNQNGK------SKGYAFIEFASFEDAK 67
Query: 642 QALKVLQNSSLDEHQIELK 660
+AL ++ I L+
Sbjct: 68 EALNSCNKREIEGRAIRLE 86
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 44/80 (55%), Gaps = 2/80 (2%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
E+ ++ R+ V N+ + + DL ++F ++G + +V + ++ +KGF VTF
Sbjct: 24 ENKSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSAD 81
Query: 391 ATQAYQHLDGTVFLGRMLHL 410
A +A + L GTV GR + +
Sbjct: 82 ADRAREKLHGTVVEGRKIEV 101
Score = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 25/78 (32%), Positives = 42/78 (53%), Gaps = 4/78 (5%)
Query: 682 KQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEA 741
K ++ V NIPF+ + ++ ++F FG++ V + GS +GFGFV F +A
Sbjct: 26 KSQPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFENSADA 82
Query: 742 KRAMKALCQSTHLYGRRL 759
RA + L T + GR++
Sbjct: 83 DRAREKL-HGTVVEGRKI 99
>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 = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 36/68 (52%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV + TE+D+ F +YG + + L +D+ T KG+ LV + + A A + L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 399 DGTVFLGR 406
+G +G+
Sbjct: 70 NGQDLMGQ 77
Score = 34.3 bits (77), Expect = 0.26, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G + V + +A + ++ + F +GE+K + L +G +G+ VE+ T EA+ A
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAA 65
Query: 745 MKALCQSTHLYGRRLVLEW 763
M+ L L G+ + ++W
Sbjct: 66 MEGL-NGQDLMGQPISVDW 83
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 25/78 (32%), Positives = 41/78 (52%), Gaps = 4/78 (5%)
Query: 335 ESGRI-FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
E RI ++RNL Y +T +++ +F KYGP+ ++ + T +T+G A V + A
Sbjct: 6 EVNRILYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKN 62
Query: 394 AYQHLDGTVFLGRMLHLI 411
A HL G R L ++
Sbjct: 63 AVDHLSGFNVSNRYLVVL 80
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 36/68 (52%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV + TE+D+ F +YG + + L +D+ T KG+ LV + + A A + L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 399 DGTVFLGR 406
+G +G+
Sbjct: 70 NGQDLMGQ 77
Score = 34.3 bits (77), Expect = 0.27, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G + V + +A + ++ + F +GE+K + L +G +G+ VE+ T EA+ A
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAA 65
Query: 745 MKALCQSTHLYGRRLVLEW 763
M+ L L G+ + ++W
Sbjct: 66 MEGL-NGQDLMGQPISVDW 83
>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 = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 36/68 (52%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV + TE+D+ F +YG + + L +D+ T KG+ LV + + A A + L
Sbjct: 12 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 71
Query: 399 DGTVFLGR 406
+G +G+
Sbjct: 72 NGQDLMGQ 79
Score = 34.3 bits (77), Expect = 0.27, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G + V + +A + ++ + F +GE+K + L +G +G+ VE+ T EA+ A
Sbjct: 9 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAA 67
Query: 745 MKALCQSTHLYGRRLVLEW 763
M+ L L G+ + ++W
Sbjct: 68 MEGL-NGQDLMGQPISVDW 85
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 8/74 (10%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+FVR V E +L ++F +GP+ EV + GFA V F E A +A +
Sbjct: 33 RLFVRPFPLDVQESELNEIFGPFGPMKEVKI--------LNGFAFVEFEEAESAAKAIEE 84
Query: 398 LDGTVFLGRMLHLI 411
+ G F + L ++
Sbjct: 85 VHGKSFANQPLEVV 98
Score = 37.0 bits (84), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 40/80 (50%), Gaps = 16/80 (20%)
Query: 673 VKRKSSNVAKQTG----SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHR 728
V R S +Q G +++ VR P ++SE+ E+F FG +K V+ +
Sbjct: 15 VPRGSHMHHRQEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVK---------ILN 65
Query: 729 GFGFVEFITKNEAKRAMKAL 748
GF FVEF EA+ A KA+
Sbjct: 66 GFAFVEF---EEAESAAKAI 82
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+++RNL Y +T +++ +F KYGP+ ++ + T +T+G A V + A A HL
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNACDHL 71
Query: 399 DGTVFLGRML 408
G R L
Sbjct: 72 SGFNVCNRYL 81
>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 = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 36/68 (52%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV + TE+D+ F +YG + + L +D+ T KG+ LV + + A A + L
Sbjct: 10 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 69
Query: 399 DGTVFLGR 406
+G +G+
Sbjct: 70 NGQDLMGQ 77
Score = 34.3 bits (77), Expect = 0.30, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G + V + +A + ++ + F +GE+K + L +G +G+ VE+ T EA+ A
Sbjct: 7 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAA 65
Query: 745 MKALCQSTHLYGRRLVLEW 763
M+ L L G+ + ++W
Sbjct: 66 MEGL-NGQDLMGQPISVDW 83
>pdb|1HL6|A Chain A, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1HL6|C Chain C, A Novel Mode Of Rbd-Protein Recognition In The Y14-Mago
Complex
pdb|1RK8|A Chain A, Structure Of The Cytosolic Protein Pym Bound To The Mago-
Y14 Core Of The Exon Junction Complex
pdb|2X1G|A Chain A, Crystal Structure Of Importin13 - Mago-Y14 Complex
pdb|2X1G|C Chain C, Crystal Structure Of Importin13 - Mago-Y14 Complex
Length = 165
Score = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 20/72 (27%), Positives = 40/72 (55%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV ++ ED++ + F YG + + L +D+ T +KG+ALV + + A A + L
Sbjct: 75 LFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEAL 134
Query: 399 DGTVFLGRMLHL 410
+G +G+ + +
Sbjct: 135 NGAEIMGQTIQV 146
Score = 35.0 bits (79), Expect = 0.17, Method: Composition-based stats.
Identities = 22/79 (27%), Positives = 43/79 (54%), Gaps = 2/79 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G + V +I +A++ E++E F +GE+K + L +G +G+ VE+ T +A A
Sbjct: 72 GWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDR-RTGFSKGYALVEYETHKQALAA 130
Query: 745 MKALCQSTHLYGRRLVLEW 763
+AL + G+ + ++W
Sbjct: 131 KEAL-NGAEIMGQTIQVDW 148
>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 = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 36/68 (52%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV + TE+D+ F +YG + + L +D+ T KG+ LV + + A A + L
Sbjct: 26 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 85
Query: 399 DGTVFLGR 406
+G +G+
Sbjct: 86 NGQDLMGQ 93
Score = 33.9 bits (76), Expect = 0.36, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G + V + +A + ++ + F +GE+K + L +G +G+ VE+ T EA+ A
Sbjct: 23 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAA 81
Query: 745 MKALCQSTHLYGRRLVLEW 763
M+ L L G+ + ++W
Sbjct: 82 MEGL-NGQDLMGQPISVDW 99
>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 = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 36/68 (52%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV + TE+D+ F +YG + + L +D+ T KG+ LV + + A A + L
Sbjct: 25 LFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKEAQAAMEGL 84
Query: 399 DGTVFLGR 406
+G +G+
Sbjct: 85 NGQDLMGQ 92
Score = 33.9 bits (76), Expect = 0.36, Method: Composition-based stats.
Identities = 21/79 (26%), Positives = 41/79 (51%), Gaps = 2/79 (2%)
Query: 685 GSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRA 744
G + V + +A + ++ + F +GE+K + L +G +G+ VE+ T EA+ A
Sbjct: 22 GWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDR-RTGYLKGYTLVEYETYKEAQAA 80
Query: 745 MKALCQSTHLYGRRLVLEW 763
M+ L L G+ + ++W
Sbjct: 81 MEGL-NGQDLMGQPISVDW 98
>pdb|2CPX|A Chain A, Solution Structure Of Rna Binding Domain In Hypothetical
Protein Flj11016
Length = 115
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 29/83 (34%), Positives = 44/83 (53%), Gaps = 8/83 (9%)
Query: 339 IFVRNLSYTVTEDDLTKLF----EKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
++++NLS VTE DL LF EK GP + + T + +G A +TF E A QA
Sbjct: 28 LYLKNLSPRVTERDLVSLFARFQEKKGPPIQFRM----MTGRMRGQAFITFPNKEIAWQA 83
Query: 395 YQHLDGTVFLGRMLHLIPGKPKE 417
++G G++L + GK K+
Sbjct: 84 LHLVNGYKLYGKILVIEFGKNKK 106
>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 = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 36/72 (50%), Gaps = 4/72 (5%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF----LMPEH 390
++G+ FV LS+ ++ DL F K+G + + + D T +++GF + F + +
Sbjct: 10 DAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKV 69
Query: 391 ATQAYQHLDGTV 402
Q LDG V
Sbjct: 70 LDQKEHRLDGRV 81
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
+TG+K+LV N+ F ++++ELF FG LK + G L G V F + +A
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL--GTADVHFERRADAL 90
Query: 743 RAMK 746
+AMK
Sbjct: 91 KAMK 94
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
+TG+K+LV N+ F ++++ELF FG LK + G L G V F + +A
Sbjct: 33 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL--GTADVHFERRADAL 90
Query: 743 RAMK 746
+AMK
Sbjct: 91 KAMK 94
>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 = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 57/140 (40%), Gaps = 26/140 (18%)
Query: 628 GYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSK 687
G FV E A+ S L E ++ ++ + T +
Sbjct: 56 GTAFVTLLNGEQAEAAINAFHQSRLRERELSVQ--------------------LQPTDAL 95
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ V N+P Q + EEL + FG L+ F+ ++ +G +G+GF E++ K+ A RA
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER---TGQSKGYGFAEYMKKDSAARAK 152
Query: 746 KALCQSTHLYGRRLVLEWAE 765
L L R L + W +
Sbjct: 153 SDLL-GKPLGPRTLYVHWTD 171
Score = 32.3 bits (72), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 45/190 (23%), Positives = 65/190 (34%), Gaps = 44/190 (23%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+I +R L VT ++ L Y E+ DK KG A VT L E A
Sbjct: 22 KILIRGLPGDVTNQEVHDLLSDY----ELKYCF---VDKYKGTAFVTLLNGEQA------ 68
Query: 398 LDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPY 457
E ++ + ER+L Q +A ++ V NLP
Sbjct: 69 ---------------------EAAINAFHQSRLRERELSVQLQPTDA----LLCVANLPP 103
Query: 458 RTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSLAYTKFKEV 511
+ L PFG L R + TG E+++K+ A A + L
Sbjct: 104 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 163
Query: 512 PLYLEWAPEG 521
LY+ W G
Sbjct: 164 TLYVHWTDAG 173
>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 = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 18/63 (28%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
++Y+ N+++ ST + HF CG I +T+ K P GY +++F R S++
Sbjct: 38 SVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHP-----KGYAYIEFAERNSVD 92
Query: 642 QAL 644
A+
Sbjct: 93 AAV 95
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 57/140 (40%), Gaps = 26/140 (18%)
Query: 628 GYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSK 687
G FV E A+ S L E ++ ++ + T +
Sbjct: 58 GTAFVTLLNGEQAEAAINAFHQSRLRERELSVQ--------------------LQPTDAL 97
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ V N+P Q + EEL + FG L+ F+ ++ +G +G+GF E++ K+ A RA
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER---TGQSKGYGFAEYMKKDSAARAK 154
Query: 746 KALCQSTHLYGRRLVLEWAE 765
L L R L + W +
Sbjct: 155 SDLL-GKPLGPRTLYVHWTD 173
Score = 32.7 bits (73), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 45/190 (23%), Positives = 65/190 (34%), Gaps = 44/190 (23%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+I +R L VT ++ L Y E+ DK KG A VT L E A
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDY----ELKYCF---VDKYKGTAFVTLLNGEQA------ 70
Query: 398 LDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPY 457
E ++ + ER+L Q +A ++ V NLP
Sbjct: 71 ---------------------EAAINAFHQSRLRERELSVQLQPTDA----LLCVANLPP 105
Query: 458 RTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSLAYTKFKEV 511
+ L PFG L R + TG E+++K+ A A + L
Sbjct: 106 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 165
Query: 512 PLYLEWAPEG 521
LY+ W G
Sbjct: 166 TLYVHWTDAG 175
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 34/140 (24%), Positives = 57/140 (40%), Gaps = 26/140 (18%)
Query: 628 GYGFVQFYTRESLNQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSNVAKQTGSK 687
G FV E A+ S L E ++ ++ + T +
Sbjct: 58 GTAFVTLLNGEQAEAAINAFHQSRLRERELSVQ--------------------LQPTDAL 97
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELK--FVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ V N+P Q + EEL + FG L+ F+ ++ +G +G+GF E++ K+ A RA
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSER---TGQSKGYGFAEYMKKDSAARAK 154
Query: 746 KALCQSTHLYGRRLVLEWAE 765
L L R L + W +
Sbjct: 155 SDLL-GKPLGPRTLYVHWTD 173
Score = 32.7 bits (73), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 45/190 (23%), Positives = 65/190 (34%), Gaps = 44/190 (23%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+I +R L VT ++ L Y E+ DK KG A VT L E A
Sbjct: 24 KILIRGLPGDVTNQEVHDLLSDY----ELKYCF---VDKYKGTAFVTLLNGEQA------ 70
Query: 398 LDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCISERKLDAFNQVVEARSKRIILVKNLPY 457
E ++ + ER+L Q +A ++ V NLP
Sbjct: 71 ---------------------EAAINAFHQSRLRERELSVQLQPTDA----LLCVANLPP 105
Query: 458 RTLPTDLKALFEPFGDLGRVLVPPYGITG------LVEFLQKNQAKAAFNSLAYTKFKEV 511
+ L PFG L R + TG E+++K+ A A + L
Sbjct: 106 SLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDLLGKPLGPR 165
Query: 512 PLYLEWAPEG 521
LY+ W G
Sbjct: 166 TLYVHWTDAG 175
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 32/57 (56%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+IFV + + E +L + F+K+G + EV++ D E + +GF +TF + QA
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQA 68
Score = 30.4 bits (67), Expect = 4.3, Method: Composition-based stats.
Identities = 24/87 (27%), Positives = 42/87 (48%), Gaps = 9/87 (10%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFG---ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
+KI V IP ++E+ E FK FG E+ + +K RGFGF+ F +
Sbjct: 11 NKIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQ----RPRGFGFITFEDEQSVD 66
Query: 743 RAMKALCQSTHLYGRRLVLEWAEEADN 769
+A+ + G+++ ++ AE D+
Sbjct: 67 QAVNM--HFHDIMGKKVEVKRAEPRDS 91
>pdb|1X5U|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor 3b
Length = 105
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 21/56 (37%), Positives = 34/56 (60%), Gaps = 2/56 (3%)
Query: 704 ELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRL 759
ELF G + +PK V +G H+G+GFVEF+++ +A A+K + LYG+ +
Sbjct: 34 ELFLQAGPVVNTHMPKDRV-TGQHQGYGFVEFLSEEDADYAIK-IMDMIKLYGKPI 87
Score = 39.3 bits (90), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 37/72 (51%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L V+E L +LF + GP+ +P D+ T + +G+ V FL E A A + +
Sbjct: 18 VYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDRVTGQHQGYGFVEFLSEEDADYAIKIM 77
Query: 399 DGTVFLGRMLHL 410
D G+ + +
Sbjct: 78 DMIKLYGKPIRV 89
Score = 37.7 bits (86), Expect = 0.022, Method: Compositional matrix adjust.
Identities = 24/95 (25%), Positives = 47/95 (49%), Gaps = 8/95 (8%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
D T+Y+ L+ +E + F + GP+ + + + + GQ GYGFV+F + E
Sbjct: 15 DATVYVGGLDEKVSEPLLWELFLQAGPVVNTHMPKDR---VTGQH--QGYGFVEFLSEED 69
Query: 640 LNQALKVLQNSSLDEHQIELKRS---NRNLESEAT 671
+ A+K++ L I + ++ N+NL ++
Sbjct: 70 ADYAIKIMDMIKLYGKPIRVNKASAHNKNLSGPSS 104
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 39.7 bits (91), Expect = 0.007, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 42/76 (55%), Gaps = 4/76 (5%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
T ++ V NIPF+ + ++ ++F FG++ V + GS +GFGFV F +A R
Sbjct: 14 TPKRLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGS---KGFGFVTFENSADADR 70
Query: 744 AMKALCQSTHLYGRRL 759
A + L T + GR++
Sbjct: 71 AREKL-HGTVVEGRKI 85
Score = 38.9 bits (89), Expect = 0.012, Method: Composition-based stats.
Identities = 22/73 (30%), Positives = 40/73 (54%), Gaps = 2/73 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
R+ V N+ + + DL ++F ++G + +V + ++ +KGF VTF A +A +
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNER--GSKGFGFVTFENSADADRAREK 74
Query: 398 LDGTVFLGRMLHL 410
L GTV GR + +
Sbjct: 75 LHGTVVEGRKIEV 87
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 39.3 bits (90), Expect = 0.009, Method: Composition-based stats.
Identities = 23/64 (35%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 683 QTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
+TG+K+LV N+ F ++++ELF FG LK + G L G V F + +A
Sbjct: 86 ETGAKLLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSL--GTADVHFERRADAL 143
Query: 743 RAMK 746
+AMK
Sbjct: 144 KAMK 147
>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 = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 27/47 (57%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+F+ LS+ T+ DL F K+G + + L +D T +++GF V F
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLF 48
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 39/78 (50%), Gaps = 3/78 (3%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV+ LS TE+ L + F+ G + I+ D+ET +KGF V F E A A + +
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSVRARIV-TDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 399 DGTVFLGRMLHLIPGKPK 416
+ G + L KPK
Sbjct: 75 EDGEIDGNKVTLDWAKPK 92
Score = 36.6 bits (83), Expect = 0.049, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 28/41 (68%), Gaps = 1/41 (2%)
Query: 724 SGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
+G +GFGFV+F ++ +AK A +A+ + + G ++ L+WA
Sbjct: 50 TGSSKGFGFVDFNSEEDAKAAKEAM-EDGEIDGNKVTLDWA 89
Score = 36.6 bits (83), Expect = 0.058, Method: Compositional matrix adjust.
Identities = 19/78 (24%), Positives = 42/78 (53%), Gaps = 8/78 (10%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL++K L+ ++TE++++ F G + + V ++ S G+GFV F + E
Sbjct: 17 TLFVKGLSEDTTEETLKESFD--GSVRARIVTDRETGS------SKGFGFVDFNSEEDAK 68
Query: 642 QALKVLQNSSLDEHQIEL 659
A + +++ +D +++ L
Sbjct: 69 AAKEAMEDGEIDGNKVTL 86
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 38.5 bits (88), Expect = 0.015, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 41/83 (49%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++FV + + E DL LFE++G + E+ + D+ T KG A +T+ + A +A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAFLTYCARDSALKAQSA 76
Query: 398 LDGTVFLGRMLHLIPGKPKENEG 420
L L M I KP +EG
Sbjct: 77 LHEQKTLPGMNRPIQVKPAASEG 99
Score = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 38/70 (54%), Gaps = 1/70 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V IP + +++ LF+ FG + + + K + +GLH+G F+ + ++ A +A
Sbjct: 17 KLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRL-TGLHKGCAFLTYCARDSALKAQS 75
Query: 747 ALCQSTHLYG 756
AL + L G
Sbjct: 76 ALHEQKTLPG 85
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 38.5 bits (88), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 34/66 (51%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
E +F+ +L T+ DL F +G + + IDK+T +K F V+F P+ A A
Sbjct: 39 EGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVA 98
Query: 395 YQHLDG 400
+ ++G
Sbjct: 99 IKAMNG 104
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 5/72 (6%)
Query: 25 FIYKITQE----QLKAKFEEKGTVTDVQLKYTTEGKFRR-FAFIGYHREDQAQAALDYFN 79
FIY + QE L + F G V ++ + + F F+ + D AQ A+ N
Sbjct: 44 FIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMN 103
Query: 80 NTYVFSSRIKVE 91
V + R+KV+
Sbjct: 104 GFQVGTKRLKVQ 115
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 38.5 bits (88), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 22/79 (27%), Positives = 40/79 (50%), Gaps = 2/79 (2%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ + +P +V+EL +FG LK L K +GL +G+ F E++ N +A+
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSA-TGLSKGYAFCEYVDINVTDQAIA 61
Query: 747 ALCQSTHLYGRRLVLEWAE 765
L L ++L+++ A
Sbjct: 62 GL-NGMQLGDKKLLVQRAS 79
Score = 32.7 bits (73), Expect = 0.84, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 30/63 (47%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++F+ L + +D + +L +GPL L D T +KG+A ++ QA
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 398 LDG 400
L+G
Sbjct: 63 LNG 65
>pdb|2F9D|A Chain A, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
pdb|2F9D|B Chain B, 2.5 Angstrom Resolution Structure Of The Spliceosomal
Protein P14 Bound To Region Of Sf3b155
Length = 125
Score = 38.5 bits (88), Expect = 0.016, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 37/70 (52%), Gaps = 3/70 (4%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+++RNL Y +T +++ +F KYGP+ ++ + T +T+G A V + A A HL
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 399 DGTVFLGRML 408
G R L
Sbjct: 78 SGFNVCNRYL 87
>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 = 38.1 bits (87), Expect = 0.017, Method: Composition-based stats.
Identities = 23/78 (29%), Positives = 44/78 (56%), Gaps = 5/78 (6%)
Query: 668 SEATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLH 727
S ++ V R S+++ K K+ + +PF + E+EE+ KA G +K +RL G
Sbjct: 3 SGSSGVFRYSTSLEKH---KLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGKP-- 57
Query: 728 RGFGFVEFITKNEAKRAM 745
+G +VE+ +++A +A+
Sbjct: 58 KGLAYVEYENESQASQAV 75
Score = 33.5 bits (75), Expect = 0.47, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 1/74 (1%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
+ T+E+L+ + GTV D++L GK + A++ Y E QA A+ + + +
Sbjct: 27 FSCTKEELEEICKAHGTVKDLRLVTNRAGKPKGLAYVEYENESQASQAVMKMDGMTIKEN 86
Query: 87 RIKVEKCSNLGDTT 100
IKV SN G ++
Sbjct: 87 IIKV-AISNSGPSS 99
Score = 33.5 bits (75), Expect = 0.48, Method: Composition-based stats.
Identities = 17/66 (25%), Positives = 36/66 (54%), Gaps = 1/66 (1%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
E ++F+ L ++ T+++L ++ + +G + ++ L + K KG A V + A+QA
Sbjct: 16 EKHKLFISGLPFSCTKEELEEICKAHGTVKDLRL-VTNRAGKPKGLAYVEYENESQASQA 74
Query: 395 YQHLDG 400
+DG
Sbjct: 75 VMKMDG 80
>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 = 38.1 bits (87), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 8/78 (10%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
SG IF++NL ++ L F +G + + D+ + +KG+ V F E A +A
Sbjct: 5 SGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAI 62
Query: 396 QHLDGT------VFLGRM 407
+ ++G VF+GR
Sbjct: 63 EKMNGMLLNDRKVFVGRF 80
Score = 34.3 bits (77), Expect = 0.27, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 44/93 (47%), Gaps = 7/93 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++IKNL+ + ++ F G I S V ++ S GYGFV F T+E+ +
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-------SKGYGFVHFETQEAAER 60
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEATTVKR 675
A++ + L++ ++ + R E EA R
Sbjct: 61 AIEKMNGMLLNDRKVFVGRFKSRKEREAELGAR 93
Score = 29.6 bits (65), Expect = 7.2, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
I ++N+ + + F AFG + ++ GS +G+GFV F T+ A+RA++
Sbjct: 8 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS---KGYGFVHFETQEAAERAIEK 64
Query: 748 L 748
+
Sbjct: 65 M 65
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 38.1 bits (87), Expect = 0.019, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 37/70 (52%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+++ ++ Y TE+ + L GP+ + + D +T ++KG+A + F E + A ++L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 399 DGTVFLGRML 408
+G R L
Sbjct: 65 NGYQLGSRFL 74
>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 = 38.1 bits (87), Expect = 0.019, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 37/70 (52%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+++ ++ Y TE+ + L GP+ + + D +T ++KG+A + F E + A ++L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 399 DGTVFLGRML 408
+G R L
Sbjct: 66 NGYQLGSRFL 75
>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 = 38.1 bits (87), Expect = 0.019, Method: Composition-based stats.
Identities = 17/48 (35%), Positives = 29/48 (60%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+IFV LS E+ + + F +G + + LP+D +T+K +GF +TF
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 50
Score = 30.0 bits (66), Expect = 5.3, Method: Composition-based stats.
Identities = 17/60 (28%), Positives = 29/60 (48%), Gaps = 1/60 (1%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
KI V + + ++ E F FGE++ + LP + RGF F+ F + K+ M+
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDN-KTNKRRGFCFITFKEEEPVKKIME 61
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 38.1 bits (87), Expect = 0.021, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 31/49 (63%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFL 386
++F+ LS+ T++ L + F ++G + E ++ D T +++GF VTF+
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 50
Score = 32.3 bits (72), Expect = 0.97, Method: Composition-based stats.
Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 4/67 (5%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ + + +Q Q + E F FGE+K + + + + RGFGFV F+ + K
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL-TKRSRGFGFVTFMDQAGVD---K 57
Query: 747 ALCQSTH 753
L QS H
Sbjct: 58 VLAQSRH 64
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 38.1 bits (87), Expect = 0.021, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 31/49 (63%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFL 386
++F+ LS+ T++ L + F ++G + E ++ D T +++GF VTF+
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTFM 75
Score = 35.0 bits (79), Expect = 0.17, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 35/70 (50%), Gaps = 4/70 (5%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKR 743
+G K+ + + +Q Q + E F FGE+K + + + + RGFGFV F+ +
Sbjct: 24 SGCKMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPL-TKRSRGFGFVTFMDQAGVD- 81
Query: 744 AMKALCQSTH 753
K L QS H
Sbjct: 82 --KVLAQSRH 89
>pdb|1WF2|A Chain A, Solution Structure Of Rrm Domain In Hnrpc Protein
Length = 98
Score = 37.7 bits (86), Expect = 0.022, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 36/65 (55%), Gaps = 10/65 (15%)
Query: 682 KQTGSKILVRNI-PFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNE 740
+ S++ + N+ K+S+VE +F +G K+VG +H+GF FV+++ +
Sbjct: 12 RSMNSRVFIGNLNTLVVKKSDVEAIFSKYG---------KIVGCSVHKGFAFVQYVNERN 62
Query: 741 AKRAM 745
A+ A+
Sbjct: 63 ARAAV 67
Score = 34.3 bits (77), Expect = 0.28, Method: Composition-based stats.
Identities = 24/85 (28%), Positives = 42/85 (49%), Gaps = 10/85 (11%)
Query: 336 SGRIFVRNL-SYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
+ R+F+ NL + V + D+ +F KYG + + KGFA V ++ +A A
Sbjct: 15 NSRVFIGNLNTLVVKKSDVEAIFSKYGKIVGCSV--------HKGFAFVQYVNERNARAA 66
Query: 395 YQHLDGTVFLGRMLHL-IPGKPKEN 418
DG + G++L + + +PK N
Sbjct: 67 VAGEDGRMIAGQVLDINLAAEPKVN 91
>pdb|2CPZ|A Chain A, Solution Structure Of Rna Binding Domain 3 In Cug Triplet
Repeat Rna-Binding Protein 1
pdb|2RQ4|A Chain A, Refinement Of Rna Binding Domain 3 In Cug Triplet Repeat
Rna-Binding Protein 1
pdb|2RQC|A Chain A, Solution Structure Of Rna-Binding Domain 3 Of Cugbp1 In
Complex With Rna (Ug)3
Length = 115
Score = 37.7 bits (86), Expect = 0.022, Method: Composition-based stats.
Identities = 19/66 (28%), Positives = 35/66 (53%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQA 394
E +F+ +L + DL ++F +G + + IDK+T+ +K F V++ P A A
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPVSAQAA 83
Query: 395 YQHLDG 400
Q ++G
Sbjct: 84 IQSMNG 89
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain (Rbd1)
Of Hu Antigen C (Huc)
Length = 89
Score = 37.7 bits (86), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 17/63 (26%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ ++V +P Q E + LF + G+++ +L + + +G G+GFV + N+A +A+
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKI-TGQSLGYGFVNYSDPNDADKAI 63
Query: 746 KAL 748
L
Sbjct: 64 NTL 66
Score = 33.1 bits (74), Expect = 0.68, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 5/79 (6%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T L + L N T+D + F G I S + R K GQ S+GYGFV +
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDK---ITGQ--SLGYGFVNYSDPNDA 59
Query: 641 NQALKVLQNSSLDEHQIEL 659
++A+ L L I++
Sbjct: 60 DKAINTLNGLKLQTKTIKV 78
>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 = 0.024, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
+ + V +P Q E+E+LF +G + R+ +G+ RG GF+ F + EA+ A+
Sbjct: 2 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQA-TGVSRGVGFIRFDKRIEAEEAI 60
Query: 746 KAL 748
K L
Sbjct: 61 KGL 63
Score = 34.3 bits (77), Expect = 0.30, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 36/67 (53%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
++V L T+++ ++ +LF +YG + + +D+ T ++G + F A +A + L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 399 DGTVFLG 405
+G LG
Sbjct: 64 NGQKPLG 70
>pdb|1WF1|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein
Np_057951
Length = 110
Score = 37.7 bits (86), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 40/81 (49%), Gaps = 10/81 (12%)
Query: 338 RIFVRNLSYT-VTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
R+F+ NL+ V + D+ +F KYG +A + KG+A V + HA A
Sbjct: 29 RVFIGNLNTALVKKSDVETIFSKYGRVAGCSV--------HKGYAFVQYSNERHARAAVL 80
Query: 397 HLDGTVFLGRMLHL-IPGKPK 416
+G V G+ L + + G+PK
Sbjct: 81 GENGRVLAGQTLDINMAGEPK 101
Score = 33.1 bits (74), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 21/81 (25%), Positives = 42/81 (51%), Gaps = 12/81 (14%)
Query: 666 LESEATTVKRKSSNVAKQTGSKILVRNIPFQ-AKQSEVEELFKAFGELKFVRLPKKMVGS 724
L+ +A+ V K N K S++ + N+ K+S+VE +F +G ++ G
Sbjct: 10 LKLQASNVTNK--NDPKSINSRVFIGNLNTALVKKSDVETIFSKYG---------RVAGC 58
Query: 725 GLHRGFGFVEFITKNEAKRAM 745
+H+G+ FV++ + A+ A+
Sbjct: 59 SVHKGYAFVQYSNERHARAAV 79
>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 = 37.7 bits (86), Expect = 0.024, Method: Composition-based stats.
Identities = 18/70 (25%), Positives = 37/70 (52%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+++ ++ Y TE+ + L GP+ + + D +T ++KG+A + F E + A ++L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 399 DGTVFLGRML 408
+G R L
Sbjct: 67 NGYQLGSRFL 76
>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 = 37.7 bits (86), Expect = 0.025, Method: Composition-based stats.
Identities = 17/46 (36%), Positives = 30/46 (65%), Gaps = 1/46 (2%)
Query: 724 SGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
+G RG+GFV F ++++A+ AM ++ Q L GR L + WA + ++
Sbjct: 39 TGSSRGYGFVSFTSQDDAQNAMDSM-QGQDLNGRPLRINWAAKLEH 83
Score = 32.0 bits (71), Expect = 1.2, Method: Composition-based stats.
Identities = 20/71 (28%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ +LN N ++++R FK S V S S GYGFV F +++
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGS-----SRGYGFVSFTSQDDAQN 58
Query: 643 ALKVLQNSSLD 653
A+ +Q L+
Sbjct: 59 AMDSMQGQDLN 69
Score = 29.6 bits (65), Expect = 6.9, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 33/72 (45%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV +L+ V ++ L F+ + + D +T ++G+ V+F + A A +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 399 DGTVFLGRMLHL 410
G GR L +
Sbjct: 64 QGQDLNGRPLRI 75
>pdb|2HVZ|A Chain A, Solution Structure Of The Rrm Domain Of Sr Rich Factor 9g8
Length = 101
Score = 37.7 bits (86), Expect = 0.027, Method: Composition-based stats.
Identities = 26/83 (31%), Positives = 37/83 (44%), Gaps = 7/83 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+++V NL + +L + F YGPL V + GFA V F P A A +
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWI-----ARNPPGFAFVEFEDPRDAEDAVRG 56
Query: 398 LDGTVFLGR--MLHLIPGKPKEN 418
LDG V G + L G P+ +
Sbjct: 57 LDGKVICGSRVRVELSTGMPRRS 79
Score = 30.4 bits (67), Expect = 4.3, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 31/62 (50%), Gaps = 6/62 (9%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ V N+ A + E+E F +G L+ V + + GF FVEF +A+ A++
Sbjct: 2 KVYVGNLGTGAGKGELERAFSYYGPLRTVWIARN------PPGFAFVEFEDPRDAEDAVR 55
Query: 747 AL 748
L
Sbjct: 56 GL 57
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 37.4 bits (85), Expect = 0.029, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 28/47 (59%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
IFV LS E+ + + F +G + + LP+D +T+K +GF +TF
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITF 48
>pdb|2LXI|A Chain A, Nmr Structure Of The N-Terminal Rna Binding Domain 1
(Rrm1) Of The Protein Rbm10 From Homo Sapiens
Length = 91
Score = 37.4 bits (85), Expect = 0.030, Method: Composition-based stats.
Identities = 22/86 (25%), Positives = 47/86 (54%), Gaps = 2/86 (2%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFG-ELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+++R +P A + ++ ++ G + + VRL + SG RGF FVEF +A R M+
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNK-SSGQSRGFAFVEFSHLQDATRWME 62
Query: 747 ALCQSTHLYGRRLVLEWAEEADNVED 772
A S ++ G+++ + +++ + +
Sbjct: 63 ANQHSLNILGQKVSMHYSDPKPKINE 88
>pdb|2F9J|A Chain A, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
pdb|2F9J|B Chain B, 3.0 Angstrom Resolution Structure Of A Y22m Mutant Of The
Spliceosomal Protein P14 Bound To A Region Of Sf3b155
Length = 125
Score = 37.4 bits (85), Expect = 0.036, Method: Composition-based stats.
Identities = 22/70 (31%), Positives = 36/70 (51%), Gaps = 3/70 (4%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ +RNL Y +T +++ +F KYGP+ ++ + T +T+G A V + A A HL
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 399 DGTVFLGRML 408
G R L
Sbjct: 78 SGFNVCNRYL 87
>pdb|2LCW|A Chain A, Solution Structure Of FusTLS RRM DOMAIN
Length = 116
Score = 37.4 bits (85), Expect = 0.036, Method: Compositional matrix adjust.
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 8/88 (9%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKETDKTKGFAL 382
+D +++ IFV+ L VT + + F++ G + + L D+ET K KG A
Sbjct: 2 QDNSDNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEAT 61
Query: 383 VTFLMPEHATQAYQHLDGTVFLGRMLHL 410
V+F P A A DG F G + +
Sbjct: 62 VSFDDPPSAKAAIDWFDGKEFSGNPIKV 89
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 37.0 bits (84), Expect = 0.048, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 39/83 (46%), Gaps = 15/83 (18%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
TTLY+ L TE +R HF + G I ++TV +++ F+QF TR
Sbjct: 13 TTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQ-----------CAFIQFATR--- 58
Query: 641 NQALKVLQNSSLDEHQIELKRSN 663
QA +V S ++ + +R N
Sbjct: 59 -QAAEVAAEKSFNKLIVNGRRLN 80
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 36.2 bits (82), Expect = 0.079, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++F+ + + E DL LFE++G + E+ + D+ T KG A +T+ E A +A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 398 L 398
L
Sbjct: 75 L 75
Score = 34.7 bits (78), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 20/80 (25%), Positives = 40/80 (50%), Gaps = 1/80 (1%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
SS + K+ + IP + +++ LF+ FG++ + + K +G+H+G F+ +
Sbjct: 5 SSGMKDHDAIKLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRF-TGMHKGCAFLTYC 63
Query: 737 TKNEAKRAMKALCQSTHLYG 756
+ A +A AL + L G
Sbjct: 64 ERESALKAQSALHEQKTLPG 83
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 36.2 bits (82), Expect = 0.080, Method: Compositional matrix adjust.
Identities = 25/70 (35%), Positives = 36/70 (51%), Gaps = 8/70 (11%)
Query: 331 EDIAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEH 390
E +A+ +FVRNL+ TVTE+ L K F ++G L V K K +A V F
Sbjct: 10 EVMAKVKVLFVRNLATTVTEEILEKSFSEFGKLERV--------KKLKDYAFVHFEDRGA 61
Query: 391 ATQAYQHLDG 400
A +A ++G
Sbjct: 62 AVKAMDEMNG 71
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 35.8 bits (81), Expect = 0.091, Method: Composition-based stats.
Identities = 24/69 (34%), Positives = 35/69 (50%), Gaps = 2/69 (2%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+IFVRNL + T L F + G + + I E K+KG +V F PE A +A +
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERACRM 67
Query: 398 LDGTVFLGR 406
++G GR
Sbjct: 68 MNGMKLSGR 76
Score = 30.4 bits (67), Expect = 4.0, Method: Composition-based stats.
Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 8/83 (9%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++++NL F+ T ++ F +CG + + + S G G V+F + E +
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGK-------SKGCGVVKFESPEVAER 63
Query: 643 ALKVLQNSSLDEHQIELKRSNRN 665
A +++ L +I++ R +RN
Sbjct: 64 ACRMMNGMKLSGREIDV-RIDRN 85
Score = 29.3 bits (64), Expect = 8.7, Method: Composition-based stats.
Identities = 19/73 (26%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
+I VRN+PF +++ F G + + + + +G +G G V+F + A+RA +
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME---NGKSKGCGVVKFESPEVAERACR 66
Query: 747 ALCQSTHLYGRRL 759
+ L GR +
Sbjct: 67 MM-NGMKLSGREI 78
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 35.8 bits (81), Expect = 0.095, Method: Composition-based stats.
Identities = 26/88 (29%), Positives = 41/88 (46%), Gaps = 11/88 (12%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
S +FV + +TED+L + F +YG + +V +P + FA VTF Q
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFIP-----KPFRAFAFVTFA----DDQIA 55
Query: 396 QHLDGT--VFLGRMLHLIPGKPKENEGN 421
Q L G + G +H+ +PK N +
Sbjct: 56 QSLCGEDLIIKGISVHISNAEPKHNSNS 83
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 35.8 bits (81), Expect = 0.097, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 336 SGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAY 395
S IFVRNL + T L F + G + + I E K+KG +V F PE A +A
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERAC 62
Query: 396 QHLDGTVFLGR 406
+ ++G GR
Sbjct: 63 RMMNGMKLSGR 73
Score = 30.4 bits (67), Expect = 4.5, Method: Composition-based stats.
Identities = 19/83 (22%), Positives = 40/83 (48%), Gaps = 8/83 (9%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++++NL F+ T ++ F +CG + + + S G G V+F + E +
Sbjct: 8 IFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGK-------SKGCGVVKFESPEVAER 60
Query: 643 ALKVLQNSSLDEHQIELKRSNRN 665
A +++ L +I++ R +RN
Sbjct: 61 ACRMMNGMKLSGREIDV-RIDRN 82
Score = 29.6 bits (65), Expect = 6.9, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 36/74 (48%), Gaps = 4/74 (5%)
Query: 686 SKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
S I VRN+PF +++ F G + + + + +G +G G V+F + A+RA
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKME---NGKSKGCGVVKFESPEVAERAC 62
Query: 746 KALCQSTHLYGRRL 759
+ + L GR +
Sbjct: 63 RMM-NGMKLSGREI 75
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 35.8 bits (81), Expect = 0.10, Method: Composition-based stats.
Identities = 22/72 (30%), Positives = 34/72 (47%), Gaps = 1/72 (1%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV NL Y V L ++F G + + DK+ K++G VTF A QA
Sbjct: 18 VFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKD-GKSRGIGTVTFEQSIEAVQAISMF 76
Query: 399 DGTVFLGRMLHL 410
+G + R +H+
Sbjct: 77 NGQLLFDRPMHV 88
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 22/89 (24%), Positives = 37/89 (41%), Gaps = 3/89 (3%)
Query: 27 YKITQEQLKAKFEEKGTVTDVQLKYTTEGKFRRFAFIGYHREDQAQAALDYFNNTYVFSS 86
YK+ ++LK F G V + +GK R + + + +A A+ FN +F
Sbjct: 25 YKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISMFNGQLLFDR 84
Query: 87 RIKV---EKCSNLGDTTKPKSWSKYAPDS 112
+ V E+ GD P+ + P S
Sbjct: 85 PMHVKMDERALPKGDFFPPERPQQSGPSS 113
>pdb|2I2Y|A Chain A, Solution Structure Of The Rrm Of Srp20 Bound To The Rna
Cauc
Length = 150
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+++V NL + +L + F YGPL V + GFA V F P A A +
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRE 129
Query: 398 LDGTVFLG 405
LDG G
Sbjct: 130 LDGRTLCG 137
Score = 33.9 bits (76), Expect = 0.37, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 10/84 (11%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
D +Y+ NL N + + R F GP+ SV VAR G+ FV+F
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP----------GFAFVEFEDPRD 122
Query: 640 LNQALKVLQNSSLDEHQIELKRSN 663
A++ L +L ++ ++ SN
Sbjct: 123 AADAVRELDGRTLCGCRVRVELSN 146
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 35.4 bits (80), Expect = 0.12, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 37/73 (50%)
Query: 669 EATTVKRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHR 728
+A+ V+ + + +Q + + + N+P + E+E + K FG++ R+ + G+
Sbjct: 9 KASGVQAQMAKQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGV 68
Query: 729 GFGFVEFITKNEA 741
GF +E K EA
Sbjct: 69 GFARMESTEKCEA 81
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 5/68 (7%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
+++V NL + +L + F YGPL V + GFA V F P A A +
Sbjct: 75 KVYVGNLGNNGNKTELERAFGYYGPLRSVWV-----ARNPPGFAFVEFEDPRDAADAVRD 129
Query: 398 LDGTVFLG 405
LDG G
Sbjct: 130 LDGRTLCG 137
Score = 33.5 bits (75), Expect = 0.44, Method: Composition-based stats.
Identities = 23/84 (27%), Positives = 37/84 (44%), Gaps = 10/84 (11%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
D +Y+ NL N + + R F GP+ SV VAR G+ FV+F
Sbjct: 73 DCKVYVGNLGNNGNKTELERAFGYYGPLRSVWVARNPP----------GFAFVEFEDPRD 122
Query: 640 LNQALKVLQNSSLDEHQIELKRSN 663
A++ L +L ++ ++ SN
Sbjct: 123 AADAVRDLDGRTLCGCRVRVELSN 146
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 35.0 bits (79), Expect = 0.17, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 31/60 (51%), Gaps = 2/60 (3%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+LV N+ F ++++ELF FG LK + G L G V F K +A +AMK
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSL--GTADVHFERKADALKAMK 87
>pdb|2LA6|A Chain A, Solution Nmr Structure Of Rrm Domain Of Rna-Binding
Protein Fus From Homo Sapiens, Northeast Structural
Genomics Consortium Target Hr6430a
Length = 99
Score = 34.7 bits (78), Expect = 0.18, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 38/84 (45%), Gaps = 8/84 (9%)
Query: 335 ESGRIFVRNLSYTVTEDDLTKLFEKYGPLAE--------VILPIDKETDKTKGFALVTFL 386
++ IFV+ L VT + + F++ G + + L D+ET K KG A V+F
Sbjct: 12 DNNTIFVQGLGENVTIESVADYFKQIGIIKTNKKTGQPMINLYTDRETGKLKGEATVSFD 71
Query: 387 MPEHATQAYQHLDGTVFLGRMLHL 410
P A A DG F G + +
Sbjct: 72 DPPSAKAAIDWFDGKEFSGNPIKV 95
>pdb|2DIS|A Chain A, Solution Structure Of The Rrm Domain Of Unnamed Protein
Product
Length = 109
Score = 34.7 bits (78), Expect = 0.19, Method: Composition-based stats.
Identities = 26/90 (28%), Positives = 44/90 (48%), Gaps = 3/90 (3%)
Query: 687 KILVRNIPFQAKQSEV-EELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAM 745
++ + IP K+ E+ EE+ K + V + +RGF FVE+ + A A
Sbjct: 10 RLFIGGIPKMKKREEILEEIAKVTEGVLDVIVYASAADKMKNRGFAFVEYESHRAAAMAR 69
Query: 746 KALCQS-THLYGRRLVLEWAE-EADNVEDI 773
+ L L+G ++ ++WAE E D ED+
Sbjct: 70 RKLMPGRIQLWGHQIAVDWAEPEIDVDEDV 99
>pdb|3NS5|A Chain A, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
pdb|3NS5|B Chain B, Crystal Structure Of The Rna Recognition Motif Of Yeast
Eif3b Residues 76-161
Length = 91
Score = 34.3 bits (77), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 26/51 (50%)
Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
I +G + + V + LT LF K G + + PID+ T KTKGF V
Sbjct: 9 IVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 34.3 bits (77), Expect = 0.26, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 34/64 (53%), Gaps = 3/64 (4%)
Query: 684 TGSKILVRNIPFQAKQSEVEELFKAFGEL-KFVRLPKKMVGSGLHRGFGFVEFITKNEAK 742
T +KI V +P+ + + + F+ FG++ + V + + G RG+GFV + A+
Sbjct: 16 TFTKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKS--RGYGFVTMADRAAAE 73
Query: 743 RAMK 746
RA K
Sbjct: 74 RACK 77
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 18/65 (27%), Positives = 32/65 (49%), Gaps = 5/65 (7%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
T +++ L +++T+ S+R++F+ G I V + S GYGFV R +
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGK-----SRGYGFVTMADRAAA 72
Query: 641 NQALK 645
+A K
Sbjct: 73 ERACK 77
>pdb|3BJ7|A Chain A, SpermineSPERMIDINE N1-Acetyltransferase From Mouse:
Crystal Structure Of A Ternary Complex Reveals
Solvent-Mediated Spermine Binding
pdb|3BJ7|B Chain B, SpermineSPERMIDINE N1-Acetyltransferase From Mouse:
Crystal Structure Of A Ternary Complex Reveals
Solvent-Mediated Spermine Binding
pdb|3BJ7|C Chain C, SpermineSPERMIDINE N1-Acetyltransferase From Mouse:
Crystal Structure Of A Ternary Complex Reveals
Solvent-Mediated Spermine Binding
pdb|3BJ7|D Chain D, SpermineSPERMIDINE N1-Acetyltransferase From Mouse:
Crystal Structure Of A Ternary Complex Reveals
Solvent-Mediated Spermine Binding
pdb|3BJ8|A Chain A, SpermineSPERMIDINE N1-Acetyltransferase From Mouse:
Crystal Structure Of A Ternary Complex Reveals
Solvent-Mediated Spermine Binding
pdb|3BJ8|B Chain B, SpermineSPERMIDINE N1-Acetyltransferase From Mouse:
Crystal Structure Of A Ternary Complex Reveals
Solvent-Mediated Spermine Binding
pdb|3BJ8|C Chain C, SpermineSPERMIDINE N1-Acetyltransferase From Mouse:
Crystal Structure Of A Ternary Complex Reveals
Solvent-Mediated Spermine Binding
pdb|3BJ8|D Chain D, SpermineSPERMIDINE N1-Acetyltransferase From Mouse:
Crystal Structure Of A Ternary Complex Reveals
Solvent-Mediated Spermine Binding
Length = 171
Score = 34.3 bits (77), Expect = 0.27, Method: Composition-based stats.
Identities = 19/43 (44%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 727 HRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
+RGFG I KN ++ AMK C S H LV EW E + N
Sbjct: 100 YRGFGIGSEILKNLSQVAMKCRCSSMHF----LVAEWNEPSIN 138
>pdb|2GO9|A Chain A, Rrm Domains 1 And 2 Of Prp24 From S. Cerevisiae
Length = 161
Score = 34.3 bits (77), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 37/172 (21%), Positives = 68/172 (39%), Gaps = 38/172 (22%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESL 640
TT+ +KNL + ++ + ++FK CGPI V VA +SL
Sbjct: 5 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA------------------------DSL 40
Query: 641 NQALKVLQNSSLDEHQIELKRSNRNLESEATTVKRKSSN---VAKQTGSKILVRNIPFQA 697
+ + +IE R + L + T K N V+ T + + N P
Sbjct: 41 KKNFRF--------ARIEFARYDGALAAITKTHKVVGQNEIIVSHLTECTLWMTNFPPSY 92
Query: 698 KQSEVEELFKAFGELKF-VRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKAL 748
Q + +L + + +RLP + R F +++ +K +A+ ++ L
Sbjct: 93 TQRNIRDLLQDINVVALSIRLPSLRFNTS--RRFAYIDVTSKEDARYCVEKL 142
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 33.9 bits (76), Expect = 0.33, Method: Composition-based stats.
Identities = 24/88 (27%), Positives = 43/88 (48%), Gaps = 7/88 (7%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
++IKNL+ + ++ F G I S V ++ S GYGFV F T+E+ +
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG-------SKGYGFVHFETQEAAER 66
Query: 643 ALKVLQNSSLDEHQIELKRSNRNLESEA 670
A++ + L++ ++ + R E EA
Sbjct: 67 AIEKMNGMLLNDRKVFVGRFKSRKEREA 94
Score = 32.3 bits (72), Expect = 0.94, Method: Composition-based stats.
Identities = 21/76 (27%), Positives = 37/76 (48%), Gaps = 8/76 (10%)
Query: 337 GRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQ 396
G IF++NL ++ L F +G + + D+ + +KG+ V F E A +A +
Sbjct: 12 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDE--NGSKGYGFVHFETQEAAERAIE 69
Query: 397 HLDG------TVFLGR 406
++G VF+GR
Sbjct: 70 KMNGMLLNDRKVFVGR 85
Score = 30.0 bits (66), Expect = 5.5, Method: Composition-based stats.
Identities = 17/61 (27%), Positives = 32/61 (52%), Gaps = 3/61 (4%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
I ++N+ + + F AFG + ++ GS +G+GFV F T+ A+RA++
Sbjct: 14 IFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS---KGYGFVHFETQEAAERAIEK 70
Query: 748 L 748
+
Sbjct: 71 M 71
>pdb|2KRB|A Chain A, Solution Structure Of Eif3b-Rrm Bound To Eif3j Peptide
Length = 81
Score = 33.9 bits (76), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 353 LTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
+ K+F K+G + P +E KTKG+ + + P HA A ++ DG
Sbjct: 24 IHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADG 69
>pdb|3NS6|A Chain A, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
pdb|3NS6|B Chain B, Crystal Structure Of Hte Rna Recognition Motif Of Yeast
Eif3b Residues 76-170
Length = 100
Score = 33.9 bits (76), Expect = 0.34, Method: Compositional matrix adjust.
Identities = 19/51 (37%), Positives = 26/51 (50%)
Query: 333 IAESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALV 383
I +G + + V + LT LF K G + + PID+ T KTKGF V
Sbjct: 9 IVVNGAPVIPSAKVPVLKKALTSLFSKAGKVVNMEFPIDEATGKTKGFLFV 59
>pdb|2NLW|A Chain A, Solution Structure Of The Rrm Domain Of Human Eukaryotic
Initiation Factor 3b
Length = 105
Score = 33.5 bits (75), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 16/48 (33%), Positives = 26/48 (54%), Gaps = 2/48 (4%)
Query: 353 LTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDG 400
+ K+F K+G + P +E KTKG+ + + P HA A ++ DG
Sbjct: 38 IHKIFSKFGKITNDFYP--EEDGKTKGYIFLEYASPAHAVDAVKNADG 83
>pdb|2JEV|A Chain A, Crystal Structure Of Human Spermine,Spermidine
Acetyltransferase In Complex With A Bisubstrate Analog
(N1- Acetylspermine-S-Coa).
pdb|2JEV|B Chain B, Crystal Structure Of Human Spermine,Spermidine
Acetyltransferase In Complex With A Bisubstrate Analog
(N1- Acetylspermine-S-Coa)
Length = 174
Score = 33.5 bits (75), Expect = 0.43, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 727 HRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
+RGFG I KN ++ AM+ C S H LV EW E + N
Sbjct: 103 YRGFGIGSEILKNLSQVAMRCRCSSMHF----LVAEWNEPSIN 141
>pdb|2F5I|A Chain A, X-Ray Structure Of SpermidineSPERMINE N1-Acetyltransferase
(Sat) From Homo Sapiens
pdb|2F5I|B Chain B, X-Ray Structure Of SpermidineSPERMINE N1-Acetyltransferase
(Sat) From Homo Sapiens
pdb|2G3T|A Chain A, Crsytal Structure Of Human SpermidineSPERMINE N1-
Acetyltransferase (Hssat)
pdb|2G3T|B Chain B, Crsytal Structure Of Human SpermidineSPERMINE N1-
Acetyltransferase (Hssat)
Length = 179
Score = 33.5 bits (75), Expect = 0.44, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 727 HRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
+RGFG I KN ++ AM+ C S H LV EW E + N
Sbjct: 100 YRGFGIGSEILKNLSQVAMRCRCSSMHF----LVAEWNEPSIN 138
>pdb|2FXF|A Chain A, Human SpermidineSPERMINE N1-Acetyltransferase
pdb|2FXF|B Chain B, Human SpermidineSPERMINE N1-Acetyltransferase
Length = 170
Score = 33.5 bits (75), Expect = 0.44, Method: Composition-based stats.
Identities = 18/43 (41%), Positives = 23/43 (53%), Gaps = 4/43 (9%)
Query: 727 HRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
+RGFG I KN ++ AM+ C S H LV EW E + N
Sbjct: 99 YRGFGIGSEILKNLSQVAMRCRCSSMHF----LVAEWNEPSIN 137
>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 = 33.1 bits (74), Expect = 0.55, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 709 FGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWA 764
FG + R+ K M +G +G+GFV F K +A+ A++ + L GR++ WA
Sbjct: 30 FGRISDARVVKDM-ATGKSKGYGFVSFFNKWDAENAIQQM-GGQWLGGRQIRTNWA 83
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 33.1 bits (74), Expect = 0.59, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 7/72 (9%)
Query: 225 HTIVVKNLPAGVKKKDLKAYFKPLPLASVRTT-------FLGMAYIGFKDEKNCNKALNK 277
+T V NLP + D+ A FK L + SVR F G Y+ F + + +AL
Sbjct: 16 YTAYVGNLPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY 75
Query: 278 NKSFWKGKQLNI 289
+ + + L +
Sbjct: 76 DGALLGDRSLRV 87
Score = 32.7 bits (73), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 340 FVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLD 399
+V NL + + D+ +F+ + V L DK+TDK KGF V F + +A + D
Sbjct: 19 YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTY-D 76
Query: 400 GTVFLGRMLHL 410
G + R L +
Sbjct: 77 GALLGDRSLRV 87
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 23/63 (36%), Positives = 33/63 (52%), Gaps = 6/63 (9%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
T Y+ NL FN+ + I FK I SV + R KD +F G+ +V+F +SL
Sbjct: 17 TAYVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTD---KF--KGFCYVEFDEVDSLK 70
Query: 642 QAL 644
+AL
Sbjct: 71 EAL 73
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 32.7 bits (73), Expect = 0.73, Method: Composition-based stats.
Identities = 20/68 (29%), Positives = 30/68 (44%), Gaps = 6/68 (8%)
Query: 583 LYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLNQ 642
L++ LN +ED +RR F+ G I T+ R D S G FV++ +
Sbjct: 18 LFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSK------GCAFVKYSSHAEAQA 71
Query: 643 ALKVLQNS 650
A+ L S
Sbjct: 72 AINALHGS 79
Score = 31.6 bits (70), Expect = 1.8, Method: Composition-based stats.
Identities = 30/96 (31%), Positives = 48/96 (50%), Gaps = 12/96 (12%)
Query: 677 SSNVAKQTGS--KILVRNIPFQAKQSEVEELFKAFG---ELKFVRLPKKMVGSGLHRGFG 731
SS +Q S K+ V + Q + +V LF+AFG E +R P G +G
Sbjct: 5 SSGCLRQPPSHRKLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGP-----DGNSKGCA 59
Query: 732 FVEFITKNEAKRAMKALCQSTHLYG--RRLVLEWAE 765
FV++ + EA+ A+ AL S + G LV+++A+
Sbjct: 60 FVKYSSHAEAQAAINALHGSQTMPGASSSLVVKFAD 95
Score = 30.4 bits (67), Expect = 3.7, Method: Composition-based stats.
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++FV L+ +EDD+ +LFE +G + E + + +KG A V + A A
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTI-LRGPDGNSKGCAFVKYSSHAEAQAAINA 75
Query: 398 LDGT 401
L G+
Sbjct: 76 LHGS 79
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 32.7 bits (73), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ +NLS+ +TED+L ++FE + + + + K+KG A + F A + +
Sbjct: 19 LLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 399 DGTVFLGRMLHL 410
G GR + L
Sbjct: 74 QGAEIDGRSVSL 85
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 222 RQYHTIVVKNLPAGVKKKDLKAYFK---PLPLASVRTTFLGMAYIGFKDEKNCNKAL-NK 277
R T++ KNL + + +LK F+ + L S G+AYI FK E + K L K
Sbjct: 14 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 73
Query: 278 NKSFWKGKQLNIY 290
+ G+ +++Y
Sbjct: 74 QGAEIDGRSVSLY 86
Score = 32.0 bits (71), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 10/78 (12%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL KNL+FN TED ++ F+ I V+ +D KS G +++F +
Sbjct: 18 TLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSK------GIAYIEFKSEADAE 67
Query: 642 QALKVLQNSSLDEHQIEL 659
+ L+ Q + +D + L
Sbjct: 68 KNLEEKQGAEIDGRSVSL 85
>pdb|2GHP|A Chain A, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|B Chain B, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|C Chain C, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|D Chain D, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|E Chain E, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|F Chain F, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|G Chain G, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
pdb|2GHP|H Chain H, Crystal Structure Of The N-Terminal 3 Rna Binding Domains
Of The Yeast Splicing Factor Prp24
Length = 292
Score = 32.7 bits (73), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 14/33 (42%), Positives = 22/33 (66%)
Query: 581 TTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVA 613
TT+ +KNL + ++ + ++FK CGPI V VA
Sbjct: 42 TTVLVKNLPKSYNQNKVYKYFKHCGPIIHVDVA 74
Score = 30.8 bits (68), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 18/74 (24%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 674 KRKSSNVAKQTGSKILVRNIPFQA-KQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGF 732
K K ++ A G +I +RN+ + ++ + E F+ FG ++ + +P + F
Sbjct: 199 KSKRTDSATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAF 258
Query: 733 VEFITKNEAKRAMK 746
F K+ A+RA++
Sbjct: 259 XVFENKDSAERALQ 272
>pdb|4IDP|A Chain A, Human Atlastin-1 1-446, N440t, Gppnhp
pdb|4IDP|B Chain B, Human Atlastin-1 1-446, N440t, Gppnhp
pdb|4IDP|C Chain C, Human Atlastin-1 1-446, N440t, Gppnhp
pdb|4IDP|D Chain D, Human Atlastin-1 1-446, N440t, Gppnhp
Length = 447
Score = 32.3 bits (72), Expect = 0.93, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 43/98 (43%), Gaps = 13/98 (13%)
Query: 339 IFVRNLSYTVTEDDLT--KLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ--- 393
I V NLS V EDDL +LF +YG LA E K F + FL+ + +
Sbjct: 174 IQVYNLSQNVQEDDLQHLQLFTEYGRLA-------XEETFLKPFQSLIFLVRDWSFPYEF 226
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCIS 431
+Y G FL + L + G E NV +H C +
Sbjct: 227 SYGADGGAKFLEKRLK-VSGNQHEELQNVRKHIHSCFT 263
>pdb|4II2|A Chain A, Crystal Structure Of Ubiquitin Activating Enzyme 1 (uba1)
In Complex With The Ub E2 Ubc4, Ubiquitin, And Atp/mg
pdb|4II3|A Chain A, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme
1 (uba1) In Complex With Ubiquitin And Atp/mg
pdb|4II3|C Chain C, Crystal Structure Of S. Pombe Ubiquitin Activating Enzyme
1 (uba1) In Complex With Ubiquitin And Atp/mg
Length = 1001
Score = 32.3 bits (72), Expect = 0.94, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 27/53 (50%)
Query: 735 FITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFGTAVGL 787
F TK A + + A+C ST + + LE + D + I + N +F A+GL
Sbjct: 831 FKTKFVAGKIVPAMCTSTAVVSGLVCLELVKLVDGKKKIEEYKNGFFNLAIGL 883
>pdb|3Q5D|A Chain A, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 1
Length = 447
Score = 32.3 bits (72), Expect = 0.96, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 43/98 (43%), Gaps = 13/98 (13%)
Query: 339 IFVRNLSYTVTEDDLT--KLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ--- 393
I V NLS V EDDL +LF +YG LA E K F + FL+ + +
Sbjct: 173 IQVYNLSQNVQEDDLQHLQLFTEYGRLA-------XEETFLKPFQSLIFLVRDWSFPYEF 225
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCIS 431
+Y G FL + L + G E NV +H C +
Sbjct: 226 SYGADGGAKFLEKRLK-VSGNQHEELQNVRKHIHSCFT 262
>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 = 32.3 bits (72), Expect = 1.00, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 35/72 (48%), Gaps = 5/72 (6%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+ +NLS+ +TED+L ++FE + + + + K+KG A + F A + +
Sbjct: 102 LLAKNLSFNITEDELKEVFEDA-----LEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 156
Query: 399 DGTVFLGRMLHL 410
G GR + L
Sbjct: 157 QGAEIDGRSVSL 168
Score = 32.0 bits (71), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 37/78 (47%), Gaps = 10/78 (12%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRESLN 641
TL KNL+FN TED ++ F+ I V+ +D KS G +++F +
Sbjct: 101 TLLAKNLSFNITEDELKEVFEDALEIRLVS----QDGKSK------GIAYIEFKSEADAE 150
Query: 642 QALKVLQNSSLDEHQIEL 659
+ L+ Q + +D + L
Sbjct: 151 KNLEEKQGAEIDGRSVSL 168
Score = 31.6 bits (70), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 22/73 (30%), Positives = 36/73 (49%), Gaps = 4/73 (5%)
Query: 222 RQYHTIVVKNLPAGVKKKDLKAYFK---PLPLASVRTTFLGMAYIGFKDEKNCNKAL-NK 277
R T++ KNL + + +LK F+ + L S G+AYI FK E + K L K
Sbjct: 97 RAARTLLAKNLSFNITEDELKEVFEDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEEK 156
Query: 278 NKSFWKGKQLNIY 290
+ G+ +++Y
Sbjct: 157 QGAEIDGRSVSLY 169
>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 = 32.3 bits (72), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+LV N+ F ++++ELF FG LK + G L G V F K +A +A K
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSL--GTADVHFERKADALKAXK 88
>pdb|2M2B|A Chain A, Nmr Structure Of The Rrm2 Domain Of The Protein Rbm10 From
Homo Sapiens
Length = 131
Score = 32.3 bits (72), Expect = 1.1, Method: Composition-based stats.
Identities = 23/69 (33%), Positives = 38/69 (55%), Gaps = 4/69 (5%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
+ T+ ++NLN +ST DSI ++S V KD ++ L+ G+ F+Q T E+
Sbjct: 23 NDTIILRNLNPHSTMDSILGALAPYAVLSSSNVRVIKDKQTQ---LNRGFAFIQLSTIEA 79
Query: 640 LNQALKVLQ 648
Q L++LQ
Sbjct: 80 A-QLLQILQ 87
>pdb|4IDN|A Chain A, Human Atlastin-1 1-446, C-his6, Gppnhp
pdb|4IDN|B Chain B, Human Atlastin-1 1-446, C-his6, Gppnhp
pdb|4IDO|A Chain A, Human Atlastin-1 1-446, C-his6, Gdpalf4-
pdb|4IDO|B Chain B, Human Atlastin-1 1-446, C-his6, Gdpalf4-
Length = 457
Score = 32.3 bits (72), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 43/98 (43%), Gaps = 13/98 (13%)
Query: 339 IFVRNLSYTVTEDDLT--KLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ--- 393
I V NLS V EDDL +LF +YG LA E K F + FL+ + +
Sbjct: 173 IQVYNLSQNVQEDDLQHLQLFTEYGRLA-------MEETFLKPFQSLIFLVRDWSFPYEF 225
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCIS 431
+Y G FL + L + G E NV +H C +
Sbjct: 226 SYGADGGAKFLEKRLK-VSGNQHEELQNVRKHIHSCFT 262
>pdb|3QNU|A Chain A, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Hexagonal Form
pdb|3QOF|A Chain A, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Orthorhombic Form
pdb|3QOF|B Chain B, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Orthorhombic Form
pdb|3QOF|C Chain C, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Orthorhombic Form
pdb|3QOF|D Chain D, Crystal Structure Of The Cytosolic Domain Of Human
Atlastin-1 In Complex With Gdp, Orthorhombic Form
Length = 459
Score = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 43/98 (43%), Gaps = 13/98 (13%)
Query: 339 IFVRNLSYTVTEDDLT--KLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ--- 393
I V NLS V EDDL +LF +YG LA E K F + FL+ + +
Sbjct: 185 IQVYNLSQNVQEDDLQHLQLFTEYGRLA-------MEETFLKPFQSLIFLVRDWSFPYEF 237
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCIS 431
+Y G FL + L + G E NV +H C +
Sbjct: 238 SYGADGGAKFLEKRLK-VSGNQHEELQNVRKHIHSCFT 274
>pdb|4IDQ|A Chain A, Human Atlastin-1 1-446, N440t, Gdpalf4-
pdb|4IDQ|B Chain B, Human Atlastin-1 1-446, N440t, Gdpalf4-
pdb|4IDQ|C Chain C, Human Atlastin-1 1-446, N440t, Gdpalf4-
pdb|4IDQ|D Chain D, Human Atlastin-1 1-446, N440t, Gdpalf4-
Length = 447
Score = 32.3 bits (72), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 43/98 (43%), Gaps = 13/98 (13%)
Query: 339 IFVRNLSYTVTEDDLT--KLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ--- 393
I V NLS V EDDL +LF +YG LA E K F + FL+ + +
Sbjct: 174 IQVYNLSQNVQEDDLQHLQLFTEYGRLA-------MEETFLKPFQSLIFLVRDWSFPYEF 226
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCIS 431
+Y G FL + L + G E NV +H C +
Sbjct: 227 SYGADGGAKFLEKRLK-VSGNQHEELQNVRKHIHSCFT 263
>pdb|3Q5E|A Chain A, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 2
pdb|3Q5E|C Chain C, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 2
pdb|3Q5E|E Chain E, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 2
pdb|3Q5E|G Chain G, Crystal Structure Of Human Atlastin-1 (Residues 1-447)
Bound To Gdp, Crystal Form 2
Length = 447
Score = 32.0 bits (71), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 32/98 (32%), Positives = 43/98 (43%), Gaps = 13/98 (13%)
Query: 339 IFVRNLSYTVTEDDLT--KLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ--- 393
I V NLS V EDDL +LF +YG LA E K F + FL+ + +
Sbjct: 173 IQVYNLSQNVQEDDLQHLQLFTEYGRLA-------MEETFLKPFQSLIFLVRDWSFPYEF 225
Query: 394 AYQHLDGTVFLGRMLHLIPGKPKENEGNVDGKVHCCIS 431
+Y G FL + L + G E NV +H C +
Sbjct: 226 SYGADGGAKFLEKRLK-VSGNQHEELQNVRKHIHSCFT 262
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 31.6 bits (70), Expect = 1.8, Method: Composition-based stats.
Identities = 24/86 (27%), Positives = 42/86 (48%), Gaps = 11/86 (12%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++FV + +T ++L + F +YG + +V +P + FA VTF + A Q
Sbjct: 13 KVFVGRCTEDMTAEELQQFFCQYGEVVDVFIP-----KPFRAFAFVTFADDKVA----QS 63
Query: 398 LDGT--VFLGRMLHLIPGKPKENEGN 421
L G + G +H+ +PK N+ N
Sbjct: 64 LCGEDLIIKGISVHISNAEPKHNKLN 89
>pdb|2IWA|A Chain A, Unbound Glutaminyl Cyclotransferase From Carica Papaya.
pdb|2FAW|A Chain A, Crystal Structure Of Papaya Glutaminyl Cyclase
pdb|2FAW|B Chain B, Crystal Structure Of Papaya Glutaminyl Cyclase
Length = 266
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 17/41 (41%), Positives = 23/41 (56%)
Query: 747 ALCQSTHLYGRRLVLEWAEEADNVEDIRKRTNRYFGTAVGL 787
L +ST LYGR V + A + VE+I K + YFG + L
Sbjct: 33 TLFESTGLYGRSSVRQVALQTGKVENIHKMDDSYFGEGLTL 73
>pdb|1WI8|A Chain A, Solution Structure Of The Rna Binding Domain Of Eukaryotic
Initiation Factor 4b
Length = 104
Score = 31.2 bits (69), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 692 NIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
N+P+ + ++E F+ + VRLP++ +GFG+ EF
Sbjct: 22 NLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEF 64
>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 = 31.2 bits (69), Expect = 2.4, Method: Compositional matrix adjust.
Identities = 18/83 (21%), Positives = 42/83 (50%), Gaps = 5/83 (6%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V I + ++E+ F +G +K V++ +G+ +G+GFV F + ++ +++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR--TGVSKGYGFVSFYNDVDVQKIVES 69
Query: 748 LCQSTHLYGRRLVLEWAEEADNV 770
+ +G++L L A N+
Sbjct: 70 ---QINFHGKKLKLGPAIRKQNL 89
Score = 30.0 bits (66), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+FV + + E ++ F +YG + EV + D+ T +KG+ V+F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
Score = 29.6 bits (65), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
T+++ ++ E IR F + G + V + + +S GYGFV FY
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG------VSKGYGFVSFY 58
>pdb|2B4D|B Chain B, Ssat+coa+sp- Sp Disordered
pdb|2B5G|B Chain B, Wild Type Ssat- 1.7a Structure
Length = 171
Score = 30.8 bits (68), Expect = 2.7, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 727 HRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
+RGFG I KN ++ A + C S H LV EW E + N
Sbjct: 100 YRGFGIGSEILKNLSQVAXRCRCSSXHF----LVAEWNEPSIN 138
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 30.8 bits (68), Expect = 2.8, Method: Composition-based stats.
Identities = 23/73 (31%), Positives = 32/73 (43%), Gaps = 3/73 (4%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
RI+V NL + D+ +F KYG + ++ L K FA V F P A A
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVYG 80
Query: 398 LDGTVFLGRMLHL 410
DG + G L +
Sbjct: 81 RDGYDYDGYRLRV 93
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 30.8 bits (68), Expect = 3.2, Method: Composition-based stats.
Identities = 20/82 (24%), Positives = 37/82 (45%)
Query: 334 AESGRIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQ 393
A + + V L +T+ +L LF GP+ + D +T + G+A V F + +
Sbjct: 1 ASNTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQR 60
Query: 394 AYQHLDGTVFLGRMLHLIPGKP 415
A + L+G + L + +P
Sbjct: 61 AIKVLNGITVRNKRLKVSYARP 82
Score = 30.0 bits (66), Expect = 5.7, Method: Composition-based stats.
Identities = 23/89 (25%), Positives = 42/89 (47%), Gaps = 5/89 (5%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
+T L + L + T+ + F+ GPI + + R D K+ S GY FV F +
Sbjct: 3 NTNLIVNYLPQDMTDRELYALFRAIGPINTCRIMR--DYKTG---YSYGYAFVDFTSEMD 57
Query: 640 LNQALKVLQNSSLDEHQIELKRSNRNLES 668
+A+KVL ++ ++++ + ES
Sbjct: 58 SQRAIKVLNGITVRNKRLKVSYARPGGES 86
>pdb|2CQH|A Chain A, Solution Structure Of The Rna Binding Domain Of Igf-Ii
Mrna- Binding Protein 2
Length = 93
Score = 30.8 bits (68), Expect = 3.2, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 38/74 (51%), Gaps = 7/74 (9%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQH 397
++++ NLS VT DDL +LF + LP+ + G+A V + A +A +
Sbjct: 10 KLYIGNLSPAVTADDLRQLF------GDRKLPLAGQVLLKSGYAFVDYPDQNWAIRAIET 63
Query: 398 LDGTVFL-GRMLHL 410
L G V L G+++ +
Sbjct: 64 LSGKVELHGKIMEV 77
>pdb|2B3U|A Chain A, Human Spermine Spermidine Acetyltransferase K26r Mutant
pdb|2B3U|B Chain B, Human Spermine Spermidine Acetyltransferase K26r Mutant
pdb|2B3V|A Chain A, Spermine Spermidine Acetyltransferase In Complex With
Acetylcoa, K26r Mutant
pdb|2B4B|A Chain A, Ssat+coa+be-3-3-3, K6r Mutant
pdb|2B4B|B Chain B, Ssat+coa+be-3-3-3, K6r Mutant
pdb|2B58|A Chain A, Ssat With Coa_sp, Spermine Disordered, K26r Mutant
Length = 171
Score = 30.8 bits (68), Expect = 3.2, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 727 HRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
+RGFG I KN ++ A + C S H LV EW E + N
Sbjct: 100 YRGFGIGSEILKNLSQVAXRCRCSSXHF----LVAEWNEPSIN 138
>pdb|2B4D|A Chain A, Ssat+coa+sp- Sp Disordered
pdb|2B5G|A Chain A, Wild Type Ssat- 1.7a Structure
Length = 171
Score = 30.8 bits (68), Expect = 3.3, Method: Composition-based stats.
Identities = 17/43 (39%), Positives = 22/43 (51%), Gaps = 4/43 (9%)
Query: 727 HRGFGFVEFITKNEAKRAMKALCQSTHLYGRRLVLEWAEEADN 769
+RGFG I KN ++ A + C S H LV EW E + N
Sbjct: 100 YRGFGIGSEILKNLSQVAXRCRCSSXHF----LVAEWNEPSIN 138
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 30.4 bits (67), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 27/89 (30%), Positives = 41/89 (46%), Gaps = 8/89 (8%)
Query: 674 KRKSSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMV--GSGLHRGFG 731
KR S + G + ++ +PF+A+ V + FK +L V + +G G G
Sbjct: 14 KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFK---KLDIVEDSIYIAYGPNGKATGEG 70
Query: 732 FVEFITKNEAKRAMKALCQSTHLYGRRLV 760
FVEF +NEA ALC+ G R +
Sbjct: 71 FVEF--RNEADYKA-ALCRHKQYMGNRFI 96
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 30.4 bits (67), Expect = 3.5, Method: Composition-based stats.
Identities = 13/44 (29%), Positives = 24/44 (54%), Gaps = 1/44 (2%)
Query: 692 NIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEF 735
N+P+ + ++E F+ + VRLP++ +GFG+ EF
Sbjct: 26 NLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEF 68
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 30.4 bits (67), Expect = 3.5, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 30/58 (51%), Gaps = 4/58 (6%)
Query: 351 DDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHLDGTVFLGRML 408
+DL K+G + +++L D+ D G A V+F PE A Q LDG F GR +
Sbjct: 41 EDLRVECSKFGQIRKLLL-FDRHPD---GVASVSFRDPEEADYCIQTLDGRWFGGRQI 94
>pdb|2CYB|A Chain A, Crystal Structure Of Tyrosyl-Trna Synthetase Complexed
With L-Tyrosine From Archaeoglobus Fulgidus
pdb|2CYB|B Chain B, Crystal Structure Of Tyrosyl-Trna Synthetase Complexed
With L-Tyrosine From Archaeoglobus Fulgidus
Length = 323
Score = 30.4 bits (67), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 33/74 (44%), Gaps = 14/74 (18%)
Query: 332 DIAESGRIFVRNLSYTVTEDDLTKLFEK---------YGPLAEV----ILPIDKETD-KT 377
DI E R+ RN VTE++L +L E Y P E+ ++ + K D +
Sbjct: 2 DITEKLRLITRNAEEVVTEEELRQLIETKEKPRAYVGYEPSGEIHLGHMMTVQKLMDLQE 61
Query: 378 KGFALVTFLMPEHA 391
GF ++ L HA
Sbjct: 62 AGFEIIVLLADIHA 75
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 30.4 bits (67), Expect = 4.2, Method: Composition-based stats.
Identities = 16/74 (21%), Positives = 39/74 (52%), Gaps = 5/74 (6%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V I + ++E+ F +G +K V++ +G+ +G+GFV F + ++ +++
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR--TGVSKGYGFVSFYNDVDVQKIVES 70
Query: 748 LCQSTHLYGRRLVL 761
+ +G++L L
Sbjct: 71 ---QINFHGKKLKL 81
Score = 29.6 bits (65), Expect = 6.5, Method: Composition-based stats.
Identities = 21/80 (26%), Positives = 37/80 (46%), Gaps = 3/80 (3%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTFLMPEHATQAYQHL 398
+FV + + E ++ F +YG + EV + D+ T +KG+ V+F + +
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVE-- 69
Query: 399 DGTVFLGRMLHLIPGKPKEN 418
F G+ L L P K+N
Sbjct: 70 SQINFHGKKLKLGPAIRKQN 89
>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 = 30.4 bits (67), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 16/74 (21%), Positives = 39/74 (52%), Gaps = 5/74 (6%)
Query: 688 ILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMKA 747
+ V I + ++E+ F +G +K V++ +G+ +G+GFV F + ++ +++
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR--TGVSKGYGFVSFYNDVDVQKIVES 69
Query: 748 LCQSTHLYGRRLVL 761
+ +G++L L
Sbjct: 70 ---QINFHGKKLKL 80
Score = 30.0 bits (66), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 26/47 (55%), Gaps = 1/47 (2%)
Query: 339 IFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDKTKGFALVTF 385
+FV + + E ++ F +YG + EV + D+ T +KG+ V+F
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSF 57
Score = 30.0 bits (66), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 6/54 (11%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
T+++ ++ E IR F + G + V + + +S GYGFV FY
Sbjct: 11 TVFVGGIDVRMDETEIRSFFARYGSVKEVKIITDRTG------VSKGYGFVSFY 58
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 30.0 bits (66), Expect = 5.2, Method: Composition-based stats.
Identities = 19/79 (24%), Positives = 35/79 (44%), Gaps = 11/79 (13%)
Query: 580 DTTLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFYTRES 639
+ T+Y + T+ +R+ F G I + V F GY FV+F T ES
Sbjct: 25 NCTVYCGGIASGLTDQLMRQTFSPFGQIMEIRV-----------FPEKGYSFVRFSTHES 73
Query: 640 LNQALKVLQNSSLDEHQIE 658
A+ + ++++ H ++
Sbjct: 74 AAHAIVSVNGTTIEGHVVK 92
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In Rna-Binding
Protein 30
Length = 90
Score = 30.0 bits (66), Expect = 5.8, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 32/62 (51%), Gaps = 9/62 (14%)
Query: 687 KILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFITKNEAKRAMK 746
K+ + N+P +A + E+ LF+ +G K++ + + +GFV K A+ A++
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYG---------KVLECDIIKNYGFVHIEDKTAAEDAIR 60
Query: 747 AL 748
L
Sbjct: 61 NL 62
>pdb|2CQI|A Chain A, Solution Structure Of The Rna Binding Domain Of
Nucleolysin Tiar
Length = 103
Score = 29.6 bits (65), Expect = 6.0, Method: Composition-based stats.
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 582 TLYIKNLNFNSTEDSIRRHFKKCGPIASVTVARKKDPKSPGQFLSMGYGFVQFY 635
TLY+ NL+ + TE I + F + GP S + + P Y FV+FY
Sbjct: 17 TLYVGNLSRDVTEVLILQLFSQIGPCKSCKMITEHTSNDP-------YCFVEFY 63
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 29.3 bits (64), Expect = 8.0, Method: Composition-based stats.
Identities = 23/81 (28%), Positives = 35/81 (43%), Gaps = 5/81 (6%)
Query: 677 SSNVAKQTGSKILVRNIPFQAKQSEVEELFKAFGELKFVRLPKKMVGSGLHRGFGFVEFI 736
SS + T + +R PF + V E LK V + G G+ FV+F
Sbjct: 2 SSGSSGTTCHTVKLRGAPFNVTEKNVMEFL---APLKPVAIRIVRNAHGNKTGYIFVDFS 58
Query: 737 TKNEAKRAMKALCQSTHLYGR 757
+ E K+A+K C ++ GR
Sbjct: 59 NEEEVKQALK--CNREYMGGR 77
>pdb|1WG4|A Chain A, Solution Structure Of Rrm Domain In Protein Bab31986
Length = 98
Score = 29.3 bits (64), Expect = 8.7, Method: Composition-based stats.
Identities = 23/65 (35%), Positives = 31/65 (47%), Gaps = 1/65 (1%)
Query: 445 RSKRIILVKNLPYRTLPTDLKALFEPFGDLGRVLVPPYGITGLVEFLQKNQAKAAFNSLA 504
RS +LV LP DLK GD+ V G+ G+VE+L+K + A L
Sbjct: 13 RSDFRVLVSGLPPSGSWQDLKDHMREAGDVCYADVQKDGM-GMVEYLRKEDMEYALRKLD 71
Query: 505 YTKFK 509
TKF+
Sbjct: 72 DTKFR 76
>pdb|2DNL|A Chain A, Solution Structure Of Rna Binding Domain In Cytoplasmic
Polyadenylation Element Binding Protein 3
Length = 114
Score = 29.3 bits (64), Expect = 8.9, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 338 RIFVRNLSYTVTEDDLTKLFEKYGPLAEVILPIDKETDK---TKGFALVTFLMPEHATQA 394
++FV L + ED++T F ++GPL V P E+ KG+A + F E + QA
Sbjct: 10 KVFVGGLPPDIDEDEITASFRRFGPLV-VDWPHKAESKSYFPPKGYAFLLF-QEESSVQA 67
Database: pdbaa
Posted date: Mar 3, 2013 10:34 PM
Number of letters in database: 14,973,337
Number of sequences in database: 62,578
Lambda K H
0.316 0.133 0.385
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 21,215,988
Number of Sequences: 62578
Number of extensions: 852865
Number of successful extensions: 2919
Number of sequences better than 100.0: 206
Number of HSP's better than 100.0 without gapping: 135
Number of HSP's successfully gapped in prelim test: 71
Number of HSP's that attempted gapping in prelim test: 2338
Number of HSP's gapped (non-prelim): 590
length of query: 787
length of database: 14,973,337
effective HSP length: 107
effective length of query: 680
effective length of database: 8,277,491
effective search space: 5628693880
effective search space used: 5628693880
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 55 (25.8 bits)