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= 037049
(731 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WHW|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain
From Hypothetical Protein Bab23448
Length = 99
Score = 89.7 bits (221), Expect = 6e-18, Method: Compositional matrix adjust.
Identities = 39/84 (46%), Positives = 59/84 (70%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
RLFVRNL YT++E++L + FS +G +SE+H +D TK+ KG A+V + PE A +A
Sbjct: 10 RLFVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAE 69
Query: 360 LDNSIFQGRLLHVMPARHKKSSDK 383
+D +FQGR+LHV+P+ KK + +
Sbjct: 70 VDGQVFQGRMLHVLPSTIKKEASQ 93
Score = 37.4 bits (85), Expect = 0.030, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 44/90 (48%), Gaps = 11/90 (12%)
Query: 498 LVKNLPYDSSEGELAKMFGKFGSLDKVILP------STKTLALVVFLEPVEAAAAFKGLA 551
V+NL Y SSE +L K+F +G L ++ P K A V F+ P A A+ +
Sbjct: 12 FVRNLSYTSSEEDLEKLFSAYGPLSELHYPIDSLTKKPKGFAFVTFMFPEHAVKAYAEVD 71
Query: 552 YKRYKGVPLYLEWAPSDV---LSQSSTSKG 578
+ ++G L++ PS + SQS S G
Sbjct: 72 GQVFQGRMLHV--LPSTIKKEASQSGPSSG 99
Score = 31.6 bits (70), Expect = 1.5, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 35/77 (45%), Gaps = 9/77 (11%)
Query: 618 LFVKNLNFKTCDENLRKHFGEHIKEGRI--LSVKVKKHLKNGKNVSMGFGFIEFDSVETA 675
LFV+NL++ + +E+L K F + G + L + K K GF F+ F E A
Sbjct: 11 LFVRNLSYTSSEEDLEKLFSAY---GPLSELHYPIDSLTKKPK----GFAFVTFMFPEHA 63
Query: 676 TNVCRDLQGTILDGHAL 692
++ G + G L
Sbjct: 64 VKAYAEVDGQVFQGRML 80
>pdb|1WHX|A Chain A, Solution Structure Of The Second Rna Binding Domain From
Hypothetical Protein Bab23448
Length = 111
Score = 83.2 bits (204), Expect = 5e-16, Method: Composition-based stats.
Identities = 40/85 (47%), Positives = 53/85 (62%)
Query: 496 VFLVKNLPYDSSEGELAKMFGKFGSLDKVILPSTKTLALVVFLEPVEAAAAFKGLAYKRY 555
V L KNLP + E+ + F +FGSL +V+LP A+V FLEP+EA AF+ LAY ++
Sbjct: 12 VILAKNLPAGTLAAEIQETFSRFGSLGRVLLPEGGITAIVEFLEPLEARKAFRHLAYSKF 71
Query: 556 KGVPLYLEWAPSDVLSQSSTSKGNQ 580
VPLYLEWAP V + K +Q
Sbjct: 72 HHVPLYLEWAPIGVFGAAPQKKDSQ 96
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 66.6 bits (161), Expect = 4e-11, Method: Compositional matrix adjust.
Identities = 35/80 (43%), Positives = 51/80 (63%), Gaps = 1/80 (1%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
++V NL Y+AT ++++E FS+FG V V ++ D++TK+ KG +V ES S AI L
Sbjct: 4 IYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKGFGFVEMQ-EESVSEAIAKL 62
Query: 361 DNSIFQGRLLHVMPARHKKS 380
DN+ F GR + V A KKS
Sbjct: 63 DNTDFMGRTIRVTEANPKKS 82
>pdb|2E5H|A Chain A, Solution Structure Of Rna Binding Domain In Zinc Finger
Cchc-Type And Rna Binding Motif 1
Length = 94
Score = 62.0 bits (149), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 27/70 (38%), Positives = 47/70 (67%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
++V NLP++ T ++L FSK+G V +V I+ DKDT++SKG+A++L+ +SA +
Sbjct: 19 VYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTRAI 78
Query: 361 DNSIFQGRLL 370
+N GR++
Sbjct: 79 NNKQLFGRVI 88
Score = 36.2 bits (82), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 25/77 (32%), Positives = 37/77 (48%), Gaps = 1/77 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDG-KSRQFAFIGFRTEQEAEEAIK 59
S + V NLP +T + L FS+ G++ +M+ KD KS+ AFI F + A+ +
Sbjct: 17 STVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLDKDSAQNCTR 76
Query: 60 YFNKSYLDTCRISCEIA 76
N L I IA
Sbjct: 77 AINNKQLFGRVIKASIA 93
Score = 30.0 bits (66), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/56 (28%), Positives = 29/56 (51%), Gaps = 6/56 (10%)
Query: 490 LKRSNHVFLVKNLPYDSSEGELAKMFGKFGSLDKVILP------STKTLALVVFLE 539
L S V NLP+ + +L ++F K+G + KV + +K +A ++FL+
Sbjct: 12 LAPSKSTVYVSNLPFSLTNNDLYRIFSKYGKVVKVTIMKDKDTRKSKGVAFILFLD 67
>pdb|2CPF|A Chain A, Solution Structure Of The Penultimate Rna Recognition
Motif Of Hypothetical Rna-Binding Protein Rbm19
Length = 98
Score = 60.8 bits (146), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 36/83 (43%), Positives = 48/83 (57%), Gaps = 4/83 (4%)
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKV-KKHLKNGKNVSMGFGFIEFDSVE 673
S LF+KNLNF T +E L+ F K G I S + KK K G +SMGFGF+E+ E
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFS---KVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPE 61
Query: 674 TATNVCRDLQGTILDGHALILQL 696
A + LQG +DGH L +++
Sbjct: 62 QAQKALKQLQGHTVDGHKLEVRI 84
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 38/78 (48%), Gaps = 3/78 (3%)
Query: 298 SGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKR---SKGIAYVLYAIPESAS 354
S LF++NL ++ TE+ L+ FSK G + I K+ S G +V Y PE A
Sbjct: 5 SSGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQ 64
Query: 355 RAIEVLDNSIFQGRLLHV 372
+A++ L G L V
Sbjct: 65 KALKQLQGHTVDGHKLEV 82
Score = 36.2 bits (82), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 21/86 (24%), Positives = 42/86 (48%), Gaps = 4/86 (4%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK----SRQFAFIGFRTEQEAEE 56
S + +KNL TE+ L+ FS+ G I + + K+ S F F+ ++ ++A++
Sbjct: 6 SGLFIKNLNFSTTEETLKGVFSKVGAIKSCTISKKKNKAGVLLSMGFGFVEYKKPEQAQK 65
Query: 57 AIKYFNKSYLDTCRISCEIARKVGDP 82
A+K +D ++ I+ + P
Sbjct: 66 ALKQLQGHTVDGHKLEVRISERATKP 91
>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 = 59.7 bits (143), Expect = 5e-09, Method: Composition-based stats.
Identities = 31/84 (36%), Positives = 46/84 (54%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V NL Y + D LR F K+G V +V+I D+ TK S+G A+V + A A++ +
Sbjct: 50 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 109
Query: 361 DNSIFQGRLLHVMPARHKKSSDKQ 384
D ++ GR L V AR+ + D
Sbjct: 110 DGAVLDGRELRVQMARYGRPPDSH 133
Score = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKYFNK 63
V NL + D LR F + G + D + R + K SR FAF+ F +++AE+A+ +
Sbjct: 52 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 111
Query: 64 SYLDTCRISCEIAR 77
+ LD + ++AR
Sbjct: 112 AVLDGRELRVQMAR 125
Score = 38.9 bits (89), Expect = 0.009, Method: Composition-based stats.
Identities = 33/111 (29%), Positives = 48/111 (43%), Gaps = 6/111 (5%)
Query: 587 GEHDAKRALLEQQLEGVTDADIDPDRVES-RSLFVKNLNFKTCDENLRKHFGEHIKEGRI 645
G H A +Q G P VE SL V NL ++T + LR+ F K GR+
Sbjct: 18 GSHMASMTGGQQMGRGSMSYGRPPPDVEGMTSLKVDNLTYRTSPDTLRRVFE---KYGRV 74
Query: 646 LSVKVKKHLKNGKNVSMGFGFIEFDSVETATNVCRDLQGTILDGHALILQL 696
V + + + S GF F+ F A + + G +LDG L +Q+
Sbjct: 75 GDVYIPRDRYTKE--SRGFAFVRFHDKRDAEDAMDAMDGAVLDGRELRVQM 123
>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 = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 30/76 (39%), Positives = 47/76 (61%), Gaps = 1/76 (1%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
++V N+ Y AT +EL HF G+V+ V I+ DK + KG AY+ ++ ES ++ L
Sbjct: 8 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 66
Query: 361 DNSIFQGRLLHVMPAR 376
D S+F+GR + V+P R
Sbjct: 67 DESLFRGRQIKVIPKR 82
>pdb|1B7F|A Chain A, Sxl-Lethal ProteinRNA COMPLEX
pdb|1B7F|B Chain B, Sxl-Lethal ProteinRNA COMPLEX
Length = 168
Score = 58.5 bits (140), Expect = 1e-08, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 46/74 (62%)
Query: 294 EVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESA 353
E ++ L+V NLP T T+D+L F K+G++ + +I+ DK T R +G+A+V Y E A
Sbjct: 85 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 144
Query: 354 SRAIEVLDNSIFQG 367
AI L+N I +G
Sbjct: 145 QEAISALNNVIPEG 158
Score = 45.8 bits (107), Expect = 8e-05, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIK 59
+ + V NLP+ +T+D+L F + G I ++R K G+ R AF+ + +EA+EAI
Sbjct: 90 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 149
Query: 60 YFN 62
N
Sbjct: 150 ALN 152
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 28/96 (29%), Positives = 45/96 (46%), Gaps = 10/96 (10%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRT-KDGKSRQFAFIGFRTEQEAEEAIK 59
+ + V LP+ +T+ L F G I ++MR K G S +AF+ F +E +++ AIK
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 60 YFNKSYLDTCRISCEIARKVGDP---------NMPR 86
N + R+ AR G+ N+PR
Sbjct: 64 VLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPR 99
Score = 37.0 bits (84), Expect = 0.042, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 36/76 (47%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V LP T+ EL F G ++ I+ D T S G A+V + + RAI+VL
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 361 DNSIFQGRLLHVMPAR 376
+ + + L V AR
Sbjct: 66 NGITVRNKRLKVSYAR 81
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 33/86 (38%), Positives = 51/86 (59%), Gaps = 2/86 (2%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
+FV N+PY ATE++L++ FS+ G V +V D++T + KG + Y E+A A+ L
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 361 DNSIFQGRLLHVMPARHKKSSDKQEL 386
+ F GR L V A +K +K+EL
Sbjct: 71 NGREFSGRALRVDNAASEK--NKEEL 94
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 28/92 (30%), Positives = 50/92 (54%), Gaps = 5/92 (5%)
Query: 616 RSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETA 675
RS+FV N+ ++ +E L+ F E G ++S ++ + GK G+GF E+ ETA
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEV---GPVVSFRLVYDRETGK--PKGYGFCEYQDQETA 63
Query: 676 TNVCRDLQGTILDGHALILQLCHAKKDEQVVK 707
+ R+L G G AL + ++K+++ +K
Sbjct: 64 LSAMRNLNGREFSGRALRVDNAASEKNKEELK 95
Score = 37.4 bits (85), Expect = 0.028, Method: Compositional matrix adjust.
Identities = 17/61 (27%), Positives = 36/61 (59%), Gaps = 1/61 (1%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKD-GKSRQFAFIGFRTEQEAEEAIKYF 61
+ V N+P TE++L+D FS+ G + +L+ ++ GK + + F ++ ++ A A++
Sbjct: 11 VFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAMRNL 70
Query: 62 N 62
N
Sbjct: 71 N 71
>pdb|1X5S|A Chain A, Solution Structure Of Rrm Domain In A18 Hnrnp
Length = 102
Score = 58.2 bits (139), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 31/88 (35%), Positives = 50/88 (56%), Gaps = 2/88 (2%)
Query: 297 ESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRA 356
+ G+LFV L + E L + FSK+G +SEV +V D++T+RS+G +V + + A A
Sbjct: 11 DEGKLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDA 70
Query: 357 IEVLDNSIFQGRLLHVMPARHKKSSDKQ 384
+ ++ GR + V A KSSD +
Sbjct: 71 MMAMNGKSVDGRQIRVDQA--GKSSDNR 96
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 42/75 (56%), Gaps = 5/75 (6%)
Query: 618 LFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETATN 677
LFV L+F T +++L + F ++ G+I V V K + + S GFGF+ F++++ A +
Sbjct: 15 LFVGGLSFDTNEQSLEQVFSKY---GQISEVVVVKDRETQR--SRGFGFVTFENIDDAKD 69
Query: 678 VCRDLQGTILDGHAL 692
+ G +DG +
Sbjct: 70 AMMAMNGKSVDGRQI 84
Score = 33.1 bits (74), Expect = 0.56, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 44/89 (49%), Gaps = 2/89 (2%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDG-KSRQFAFIGFRTEQEAEEAIKY 60
++ V L E L FS+ G+I++ +++ ++ +SR F F+ F +A++A+
Sbjct: 14 KLFVGGLSFDTNEQSLEQVFSKYGQISEVVVVKDRETQRSRGFGFVTFENIDDAKDAMMA 73
Query: 61 FNKSYLDTCRISCEIARKVGDPNMPRPWS 89
N +D +I + A K D N P S
Sbjct: 74 MNGKSVDGRQIRVDQAGKSSD-NRSGPSS 101
>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 = 57.4 bits (137), Expect = 2e-08, Method: Composition-based stats.
Identities = 30/79 (37%), Positives = 48/79 (60%), Gaps = 1/79 (1%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
++V N+ Y AT +EL HF G+V+ V I+ DK + KG AY+ ++ ES ++ L
Sbjct: 9 IYVGNVDYGATAEELEAHFHGCGSVNRVTILCDKFSGHPKGFAYIEFSDKESVRTSL-AL 67
Query: 361 DNSIFQGRLLHVMPARHKK 379
D S+F+GR + V+P R +
Sbjct: 68 DESLFRGRQIKVIPKRTNR 86
>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 = 57.4 bits (137), Expect = 3e-08, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 46/74 (62%)
Query: 294 EVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESA 353
E ++ L+V NLP T T+D+L F K+G++ + +I+ DK T R +G+A+V Y E A
Sbjct: 96 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 155
Query: 354 SRAIEVLDNSIFQG 367
AI L+N I +G
Sbjct: 156 QEAISALNNVIPEG 169
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIK 59
+ + V NLP+ +T+D+L F + G I ++R K G+ R AF+ + +EA+EAI
Sbjct: 101 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 160
Query: 60 YFN 62
N
Sbjct: 161 ALN 163
Score = 37.4 bits (85), Expect = 0.033, Method: Composition-based stats.
Identities = 27/96 (28%), Positives = 43/96 (44%), Gaps = 10/96 (10%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRT-KDGKSRQFAFIGFRTEQEAEEAIK 59
+ + V LP+ T+ L F G I ++ R K G S +AF+ F +E +++ AIK
Sbjct: 15 TNLIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
Query: 60 YFNKSYLDTCRISCEIARKVGDP---------NMPR 86
N + R+ AR G+ N+PR
Sbjct: 75 VLNGITVRNKRLKVSYARPGGESIKDTNLYVTNLPR 110
Score = 35.8 bits (81), Expect = 0.087, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 35/76 (46%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V LP T+ EL F G ++ I D T S G A+V + + RAI+VL
Sbjct: 17 LIVNYLPQDXTDRELYALFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIKVL 76
Query: 361 DNSIFQGRLLHVMPAR 376
+ + + L V AR
Sbjct: 77 NGITVRNKRLKVSYAR 92
>pdb|2KN4|A Chain A, The Structure Of The Rrm Domain Of Sc35
Length = 158
Score = 57.4 bits (137), Expect = 3e-08, Method: Composition-based stats.
Identities = 31/84 (36%), Positives = 46/84 (54%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V NL Y + D LR F K+G V +V+I D+ TK S+G A+V + A A++ +
Sbjct: 73 LKVDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAM 132
Query: 361 DNSIFQGRLLHVMPARHKKSSDKQ 384
D ++ GR L V AR+ + D
Sbjct: 133 DGAVLDGRELRVQMARYGRPPDSH 156
Score = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 40/74 (54%), Gaps = 1/74 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKYFNK 63
V NL + D LR F + G + D + R + K SR FAF+ F +++AE+A+ +
Sbjct: 75 VDNLTYRTSPDTLRRVFEKYGRVGDVYIPRDRYTKESRGFAFVRFHDKRDAEDAMDAMDG 134
Query: 64 SYLDTCRISCEIAR 77
+ LD + ++AR
Sbjct: 135 AVLDGRELRVQMAR 148
Score = 35.8 bits (81), Expect = 0.088, Method: Composition-based stats.
Identities = 24/80 (30%), Positives = 40/80 (50%), Gaps = 5/80 (6%)
Query: 617 SLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETAT 676
SL V NL ++T + LR+ F ++ GR+ V + + + S GF F+ F A
Sbjct: 72 SLKVDNLTYRTSPDTLRRVFEKY---GRVGDVYIPRDRYTKE--SRGFAFVRFHDKRDAE 126
Query: 677 NVCRDLQGTILDGHALILQL 696
+ + G +LDG L +Q+
Sbjct: 127 DAMDAMDGAVLDGRELRVQM 146
>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 = 57.0 bits (136), Expect = 4e-08, Method: Composition-based stats.
Identities = 30/74 (40%), Positives = 46/74 (62%)
Query: 294 EVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESA 353
E ++ L+V NLP T T+D+L F K+G++ + +I+ DK T R +G+A+V Y E A
Sbjct: 9 ESIKDTNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEA 68
Query: 354 SRAIEVLDNSIFQG 367
AI L+N I +G
Sbjct: 69 QEAISALNNVIPEG 82
Score = 44.7 bits (104), Expect = 2e-04, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 36/63 (57%), Gaps = 1/63 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIK 59
+ + V NLP+ +T+D+L F + G I ++R K G+ R AF+ + +EA+EAI
Sbjct: 14 TNLYVTNLPRTITDDQLDTIFGKYGSIVQKNILRDKLTGRPRGVAFVRYNKREEAQEAIS 73
Query: 60 YFN 62
N
Sbjct: 74 ALN 76
>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 = 56.6 bits (135), Expect = 5e-08, Method: Composition-based stats.
Identities = 30/95 (31%), Positives = 55/95 (57%), Gaps = 2/95 (2%)
Query: 282 GNPSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKG 341
G P S + ++E+ + ++V N+ Y +T +L HFS G+++ + I+ DK + KG
Sbjct: 21 GPPQPLSAEEKKEI-DKRSVYVGNVDYGSTAQDLEAHFSSCGSINRITILCDKFSGHPKG 79
Query: 342 IAYVLYAIPESASRAIEVLDNSIFQGRLLHVMPAR 376
AY+ +A S A+ +D ++F+GR + V+P R
Sbjct: 80 YAYIEFAERNSVDAAV-AMDETVFRGRTIKVLPKR 113
>pdb|2JRS|A Chain A, Solution Nmr Structure Of Caper Rrm2 Domain. Northeast
Structural Genomics Target Hr4730a
Length = 108
Score = 54.7 bits (130), Expect = 2e-07, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 43/73 (58%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
RL+V +L + TED LR F FG + + +++D +T RSKG ++ ++ E A +A+E
Sbjct: 28 RLYVGSLHFNITEDMLRGIFEPFGRIESIQLMMDSETGRSKGYGFITFSDSECAKKALEQ 87
Query: 360 LDNSIFQGRLLHV 372
L+ GR + V
Sbjct: 88 LNGFELAGRPMKV 100
>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 = 54.3 bits (129), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 27/87 (31%), Positives = 47/87 (54%), Gaps = 2/87 (2%)
Query: 297 ESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRA 356
ES ++F+ L + TED LRE+F K+G V+++ I+ D T RS+G ++ + P S
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEV 61
Query: 357 IEVLDNSIFQGRLLHVMPARHKKSSDK 383
++ I G+++ A + DK
Sbjct: 62 VKT--QHILDGKVIDPKRAIPRDEQDK 86
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 32/117 (27%), Positives = 60/117 (51%), Gaps = 16/117 (13%)
Query: 614 ESRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
ES +F+ LN+ T ++NLR++FG++ G + +K+ K G+ S GFGF+ F+
Sbjct: 2 ESCKMFIGGLNWDTTEDNLREYFGKY---GTVTDLKIMKDPATGR--SRGFGFLSFEKPS 56
Query: 674 TATNVCRDLQGTILDGHALILQLCHAKKDEQVVKKAEKDKSSTKLLVRNVAFEAQRK 730
+ V + ILDG + ++ + + E+DK+ K+ V + + + K
Sbjct: 57 SVDEVVKTQH--ILDGKVI--------DPKRAIPRDEQDKTG-KIFVGGIGPDVRPK 102
Score = 45.1 bits (105), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/84 (26%), Positives = 46/84 (54%), Gaps = 5/84 (5%)
Query: 275 NGEIVDPGNPSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDK 334
+G+++DP + +D Q + +G++FV + E E FS++G + + +++DK
Sbjct: 69 DGKVIDP--KRAIPRDEQDK---TGKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDK 123
Query: 335 DTKRSKGIAYVLYAIPESASRAIE 358
DT +S+G +V Y ++ R +
Sbjct: 124 DTGQSRGFGFVTYDSADAVDRVCQ 147
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 1/59 (1%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMR-TKDGKSRQFAFIGFRTEQEAEEAIK 59
++ + L TED LR++F + G +TD K+M+ G+SR F F+ F +E +K
Sbjct: 5 KMFIGGLNWDTTEDNLREYFGKYGTVTDLKIMKDPATGRSRGFGFLSFEKPSSVDEVVK 63
Score = 36.2 bits (82), Expect = 0.074, Method: Compositional matrix adjust.
Identities = 20/49 (40%), Positives = 27/49 (55%), Gaps = 1/49 (2%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKD-GKSRQFAFIGF 48
+I V + V +FFSQ G I DA+LM KD G+SR F F+ +
Sbjct: 88 GKIFVGGIGPDVRPKEFEEFFSQWGTIIDAQLMLDKDTGQSRGFGFVTY 136
>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 = 53.9 bits (128), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 44/73 (60%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
R++V ++ Y ED +R+ F+ FG + + + D T + KG A+V Y +PE+A A+E
Sbjct: 15 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 74
Query: 360 LDNSIFQGRLLHV 372
+++ + GR + V
Sbjct: 75 MNSVMLGGRNIKV 87
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of Rna
Binding Motif Protein 23
Length = 95
Score = 53.5 bits (127), Expect = 4e-07, Method: Composition-based stats.
Identities = 28/75 (37%), Positives = 42/75 (56%)
Query: 298 SGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAI 357
S L+V +L + TED LR F FG + + ++ D DT RSKG ++ ++ E A RA+
Sbjct: 5 SSGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRAL 64
Query: 358 EVLDNSIFQGRLLHV 372
E L+ GR + V
Sbjct: 65 EQLNGFELAGRPMRV 79
Score = 37.0 bits (84), Expect = 0.041, Method: Composition-based stats.
Identities = 22/63 (34%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKD-GKSRQFAFIGFRTEQEAEEAIK 59
S + V +L +TED LR F G+I + LM+ D G+S+ + FI F + A A++
Sbjct: 6 SGLYVGSLHFNITEDMLRGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALE 65
Query: 60 YFN 62
N
Sbjct: 66 QLN 68
>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 = 53.1 bits (126), Expect = 6e-07, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIK 59
+ + V LP+ +T+D LR FS GE+ AKL+R K G S + F+ + T ++AE AI
Sbjct: 5 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 64
Query: 60 YFNKSYLDTCRISCEIAR 77
N L + I AR
Sbjct: 65 TLNGLRLQSKTIKVSYAR 82
Score = 48.1 bits (113), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 36/76 (47%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V LP T+DELR FS G V ++ DK S G +V Y + A RAI L
Sbjct: 7 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 66
Query: 361 DNSIFQGRLLHVMPAR 376
+ Q + + V AR
Sbjct: 67 NGLRLQSKTIKVSYAR 82
>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 = 52.8 bits (125), Expect = 7e-07, Method: Compositional matrix adjust.
Identities = 40/133 (30%), Positives = 66/133 (49%), Gaps = 15/133 (11%)
Query: 258 DSIIKDSIHSGVGEEDANGEIVDPGNPSSSSKDVQQEVLESGRLFVRNLPYTATEDELRE 317
DS +++IHS + + + ++PG P S +E LFV ++ A EDE++E
Sbjct: 41 DSNTREAIHSYERVRNEDDDELEPG-PQRS--------VEGWILFVTSIHEEAQEDEIQE 91
Query: 318 HFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVLDNSIFQGRLLHV----- 372
F +G + +H+ +D+ T SKG A V Y + A A E L+ + G+ + V
Sbjct: 92 KFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQALAAKEALNGAEIMGQTIQVDWCFV 151
Query: 373 -MPARHKKSSDKQ 384
P R KKS ++
Sbjct: 152 KGPKRVKKSEKRR 164
>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 = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIK 59
+ + V LP+ +T+D LR FS GE+ AKL+R K G S + F+ + T ++AE AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 60 YFNKSYLDTCRISCEIAR 77
N L + I AR
Sbjct: 63 TLNGLRLQSKTIKVSYAR 80
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 36/76 (47%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V LP T+DELR FS G V ++ DK S G +V Y + A RAI L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 361 DNSIFQGRLLHVMPAR 376
+ Q + + V AR
Sbjct: 65 NGLRLQSKTIKVSYAR 80
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 38/64 (59%)
Query: 294 EVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESA 353
EV++ L++ LP T T+ ++ + FS+FG + ++VD+ T S+G+A++ + A
Sbjct: 84 EVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEA 143
Query: 354 SRAI 357
AI
Sbjct: 144 EEAI 147
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAK-LMRTKDGKSRQFAFIGFRTEQEAEEAIKYF 61
+ + LP+ +T+ + D FS+ G I +++ L+ G SR AFI F EAEEAI F
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 62 N 62
N
Sbjct: 151 N 151
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs
Of Human Antigen R
Length = 177
Score = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIK 59
+ + V LP+ +T+D LR FS GE+ AKL+R K G S + F+ + T ++AE AI
Sbjct: 3 TNLIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 62
Query: 60 YFNKSYLDTCRISCEIAR 77
N L + I AR
Sbjct: 63 TLNGLRLQSKTIKVSYAR 80
Score = 48.1 bits (113), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 36/76 (47%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V LP T+DELR FS G V ++ DK S G +V Y + A RAI L
Sbjct: 5 LIVNYLPQNMTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 64
Query: 361 DNSIFQGRLLHVMPAR 376
+ Q + + V AR
Sbjct: 65 NGLRLQSKTIKVSYAR 80
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 38/64 (59%)
Query: 294 EVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESA 353
EV++ L++ LP T T+ ++ + FS+FG + ++VD+ T S+G+A++ + A
Sbjct: 84 EVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEA 143
Query: 354 SRAI 357
AI
Sbjct: 144 EEAI 147
Score = 44.3 bits (103), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/61 (39%), Positives = 35/61 (57%), Gaps = 1/61 (1%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAK-LMRTKDGKSRQFAFIGFRTEQEAEEAIKYF 61
+ + LP+ +T+ + D FS+ G I +++ L+ G SR AFI F EAEEAI F
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAITSF 150
Query: 62 N 62
N
Sbjct: 151 N 151
>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 = 52.0 bits (123), Expect = 1e-06, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 44/73 (60%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
R++V ++ Y ED +R+ F+ FG + + + D T + KG A+V Y +PE+A A+E
Sbjct: 30 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDMSWDSVTMKHKGFAFVEYEVPEAAQLALEQ 89
Query: 360 LDNSIFQGRLLHV 372
+++ + GR + V
Sbjct: 90 MNSVMLGGRNIKV 102
>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 = 52.0 bits (123), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 41/78 (52%), Gaps = 1/78 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIK 59
+ + V LP+ T+D LR FS GE+ AKL+R K G S + F+ + T ++AE AI
Sbjct: 20 TNLIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAIN 79
Query: 60 YFNKSYLDTCRISCEIAR 77
N L + I AR
Sbjct: 80 TLNGLRLQSKTIKVSYAR 97
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 28/76 (36%), Positives = 36/76 (47%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V LP T+DELR FS G V ++ DK S G +V Y + A RAI L
Sbjct: 22 LIVNYLPQNXTQDELRSLFSSIGEVESAKLIRDKVAGHSLGYGFVNYVTAKDAERAINTL 81
Query: 361 DNSIFQGRLLHVMPAR 376
+ Q + + V AR
Sbjct: 82 NGLRLQSKTIKVSYAR 97
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 35/102 (34%), Positives = 50/102 (49%), Gaps = 8/102 (7%)
Query: 285 SSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNV--------SEVHIVVDKDT 336
SS S E ++ ++V+ L + T D+L + F + G V +HI +DK+T
Sbjct: 2 SSGSSGDPDEDSDNSAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKET 61
Query: 337 KRSKGIAYVLYAIPESASRAIEVLDNSIFQGRLLHVMPARHK 378
+ KG A V Y P +A A+E D FQG L V AR K
Sbjct: 62 GKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKK 103
Score = 32.3 bits (72), Expect = 0.99, Method: Compositional matrix adjust.
Identities = 23/87 (26%), Positives = 38/87 (43%), Gaps = 9/87 (10%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAK---------LMRTKDGKSRQFAFIGFRTE 51
S I V+ L VT D L DFF Q G + K + + GK + A + +
Sbjct: 16 SAIYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSYEDP 75
Query: 52 QEAEEAIKYFNKSYLDTCRISCEIARK 78
A+ A+++F+ ++ +ARK
Sbjct: 76 PTAKAAVEWFDGKDFQGSKLKVSLARK 102
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 32/103 (31%), Positives = 54/103 (52%), Gaps = 7/103 (6%)
Query: 282 GNPSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKG 341
G+ S S K+ +Q +LF+ L + T++ LR HF ++G +++ ++ D +TKRS+G
Sbjct: 2 GSKSESPKEPEQ----LRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRG 57
Query: 342 IAYVLYAIPESASRAIEVLDNSIFQGRLLHVMPARHKKSSDKQ 384
+V YA E A+ + + GR+ V P R D Q
Sbjct: 58 FGFVTYATVEEVDAAMNARPHKV-DGRV--VEPKRAVSREDSQ 97
Score = 37.0 bits (84), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 616 RSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
R LF+ L+F+T DE+LR HF ++ L+ V N K S GFGF+ + +VE
Sbjct: 15 RKLFIGGLSFETTDESLRSHF----EQWGTLTDCVVMRDPNTKR-SRGFGFVTYATVE 67
Score = 36.2 bits (82), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 275 NGEIVDPGNPSSSSKDVQQEV--LESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVV 332
+G +V+P + S +D Q+ L ++FV + E LR++F ++G + + I+
Sbjct: 81 DGRVVEP-KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMT 139
Query: 333 DKDTKRSKGIAYVLY 347
D+ + + +G A+V +
Sbjct: 140 DRGSGKKRGFAFVTF 154
Score = 35.8 bits (81), Expect = 0.086, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 47/95 (49%), Gaps = 4/95 (4%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKY 60
++ + L T++ LR F Q G +TD +MR + K SR F F+ + T +E + A+
Sbjct: 16 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 74
Query: 61 FNKSYLDTCRISCEIARKVGDPNMPRPWSRYSLKK 95
+ + R+ E R V + RP + ++KK
Sbjct: 75 -ARPHKVDGRV-VEPKRAVSREDSQRPGAHLTVKK 107
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 51.2 bits (121), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 20/58 (34%), Positives = 37/58 (63%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAI 357
++FV +P+ E ELRE+F KFG V+EV ++ D + +R +G ++ + +S +A+
Sbjct: 12 KIFVGGIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAV 69
>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 = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 3/85 (3%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LF+ L + T++ LR HF ++G +++ ++ D +TKRS+G +V YA E A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 360 LDNSIFQGRLLHVMPARHKKSSDKQ 384
+ + GR+ V P R D Q
Sbjct: 75 RPHKV-DGRV--VEPKRAVSREDSQ 96
Score = 37.4 bits (85), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 616 RSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
R LF+ L+F+T DE+LR HF ++ L+ V N K S GFGF+ + +VE
Sbjct: 14 RKLFIGGLSFETTDESLRSHF----EQWGTLTDCVVMRDPNTKR-SRGFGFVTYATVE 66
Score = 36.2 bits (82), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 275 NGEIVDPGNPSSSSKDVQQEV--LESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVV 332
+G +V+P + S +D Q+ L ++FV + E LR++F ++G + + I+
Sbjct: 80 DGRVVEPKR-AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMT 138
Query: 333 DKDTKRSKGIAYVLY 347
D+ + + +G A+V +
Sbjct: 139 DRGSGKKRGFAFVTF 153
Score = 35.8 bits (81), Expect = 0.093, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 47/95 (49%), Gaps = 4/95 (4%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKY 60
++ + L T++ LR F Q G +TD +MR + K SR F F+ + T +E + A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 73
Query: 61 FNKSYLDTCRISCEIARKVGDPNMPRPWSRYSLKK 95
+ + R+ E R V + RP + ++KK
Sbjct: 74 -ARPHKVDGRV-VEPKRAVSREDSQRPGAHLTVKK 106
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 50.8 bits (120), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 32/96 (33%), Positives = 48/96 (50%), Gaps = 8/96 (8%)
Query: 491 KRSNHVFLVKNLPYDSSEGELAKMFGKFGSLDKVILPSTKT-------LALVVFLEPVEA 543
K++ LV+N+P+ +++ E+ ++F FG L V LP T V F+ +A
Sbjct: 12 KQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDA 71
Query: 544 AAAFKGLAYKRY-KGVPLYLEWAPSDVLSQSSTSKG 578
AF L + + G L LEWA S+V QS S G
Sbjct: 72 KKAFNALCHSTHLYGRRLVLEWADSEVTVQSGPSSG 107
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 21/60 (35%), Positives = 35/60 (58%), Gaps = 2/60 (3%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMR--TKDGKSRQFAFIGFRTEQEAEEAI 58
S+I V+N+P + +R+ FS GE+ +L + T G R F F+ F T+Q+A++A
Sbjct: 16 SKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAKKAF 75
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 28/88 (31%), Positives = 44/88 (50%), Gaps = 3/88 (3%)
Query: 285 SSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVD-KDTKRSKGIA 343
S SS V ++ S ++ VRN+P+ A + E+RE FS FG + V + T +G
Sbjct: 3 SGSSGQVPKKQTTS-KILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFG 61
Query: 344 YVLYAIPESASRAIEVLDNSI-FQGRLL 370
+V + + A +A L +S GR L
Sbjct: 62 FVDFITKQDAKKAFNALCHSTHLYGRRL 89
>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 = 50.8 bits (120), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 3/85 (3%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LF+ L + T++ LR HF ++G +++ ++ D +TKRS+G +V YA E A+
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 73
Query: 360 LDNSIFQGRLLHVMPARHKKSSDKQ 384
+ + GR+ V P R D Q
Sbjct: 74 RPHKV-DGRV--VEPKRAVSREDSQ 95
Score = 37.0 bits (84), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 616 RSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
R LF+ L+F+T DE+LR HF ++ L+ V N K S GFGF+ + +VE
Sbjct: 13 RKLFIGGLSFETTDESLRSHF----EQWGTLTDCVVMRDPNTKR-SRGFGFVTYATVE 65
Score = 36.2 bits (82), Expect = 0.068, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 41/75 (54%), Gaps = 3/75 (4%)
Query: 275 NGEIVDPGNPSSSSKDVQQEV--LESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVV 332
+G +V+P + S +D Q+ L ++FV + E LR++F ++G + + I+
Sbjct: 79 DGRVVEPKR-AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIMT 137
Query: 333 DKDTKRSKGIAYVLY 347
D+ + + +G A+V +
Sbjct: 138 DRGSGKKRGFAFVTF 152
Score = 35.8 bits (81), Expect = 0.096, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 47/95 (49%), Gaps = 4/95 (4%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKY 60
++ + L T++ LR F Q G +TD +MR + K SR F F+ + T +E + A+
Sbjct: 14 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 72
Query: 61 FNKSYLDTCRISCEIARKVGDPNMPRPWSRYSLKK 95
+ + R+ E R V + RP + ++KK
Sbjct: 73 -ARPHKVDGRV-VEPKRAVSREDSQRPGAHLTVKK 105
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 50.8 bits (120), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 3/85 (3%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LF+ L + T++ LR HF ++G +++ ++ D +TKRS+G +V YA E A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 74
Query: 360 LDNSIFQGRLLHVMPARHKKSSDKQ 384
+ + GR+ V P R D Q
Sbjct: 75 RPHKV-DGRV--VEPKRAVSREDSQ 96
Score = 37.0 bits (84), Expect = 0.043, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 616 RSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
R LF+ L+F+T DE+LR HF ++ L+ V N K S GFGF+ + +VE
Sbjct: 14 RKLFIGGLSFETTDESLRSHF----EQWGTLTDCVVMRDPNTKR-SRGFGFVTYATVE 66
Score = 36.2 bits (82), Expect = 0.059, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 45/86 (52%), Gaps = 3/86 (3%)
Query: 274 ANGEIVDPGNPSSSSKDVQQE--VLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIV 331
+G +V+P + S +D Q+ L ++FV + E LR++F ++G + + I+
Sbjct: 79 VDGRVVEPKR-AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 137
Query: 332 VDKDTKRSKGIAYVLYAIPESASRAI 357
D+ + + +G A+V + +S + +
Sbjct: 138 TDRGSGKKRGFAFVTFDDHDSVDKIV 163
Score = 35.8 bits (81), Expect = 0.097, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 47/95 (49%), Gaps = 4/95 (4%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKY 60
++ + L T++ LR F Q G +TD +MR + K SR F F+ + T +E + A+
Sbjct: 15 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 73
Query: 61 FNKSYLDTCRISCEIARKVGDPNMPRPWSRYSLKK 95
+ + R+ E R V + RP + ++KK
Sbjct: 74 -ARPHKVDGRV-VEPKRAVSREDSQRPGAHLTVKK 106
>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 = 50.8 bits (120), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 3/85 (3%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LF+ L + T++ LR HF ++G +++ ++ D +TKRS+G +V YA E A+
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 67
Query: 360 LDNSIFQGRLLHVMPARHKKSSDKQ 384
+ + GR+ V P R D Q
Sbjct: 68 RPHKV-DGRV--VEPKRAVSREDSQ 89
Score = 37.0 bits (84), Expect = 0.041, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 616 RSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
R LF+ L+F+T DE+LR HF ++ L+ V N K S GFGF+ + +VE
Sbjct: 7 RKLFIGGLSFETTDESLRSHF----EQWGTLTDCVVMRDPNTKR-SRGFGFVTYATVE 59
Score = 36.2 bits (82), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 45/86 (52%), Gaps = 3/86 (3%)
Query: 274 ANGEIVDPGNPSSSSKDVQQE--VLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIV 331
+G +V+P + S +D Q+ L ++FV + E LR++F ++G + + I+
Sbjct: 72 VDGRVVEP-KRAVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 130
Query: 332 VDKDTKRSKGIAYVLYAIPESASRAI 357
D+ + + +G A+V + +S + +
Sbjct: 131 TDRGSGKKRGFAFVTFDDHDSVDKIV 156
Score = 35.8 bits (81), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 47/95 (49%), Gaps = 4/95 (4%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKY 60
++ + L T++ LR F Q G +TD +MR + K SR F F+ + T +E + A+
Sbjct: 8 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 66
Query: 61 FNKSYLDTCRISCEIARKVGDPNMPRPWSRYSLKK 95
+ + R+ E R V + RP + ++KK
Sbjct: 67 -ARPHKVDGRV-VEPKRAVSREDSQRPGAHLTVKK 99
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 50.8 bits (120), Expect = 3e-06, Method: Compositional matrix adjust.
Identities = 27/85 (31%), Positives = 46/85 (54%), Gaps = 3/85 (3%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LF+ L + T++ LR HF ++G +++ ++ D +TKRS+G +V YA E A+
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMNA 72
Query: 360 LDNSIFQGRLLHVMPARHKKSSDKQ 384
+ + GR+ V P R D Q
Sbjct: 73 RPHKV-DGRV--VEPKRAVSREDSQ 94
Score = 37.0 bits (84), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 23/58 (39%), Positives = 33/58 (56%), Gaps = 5/58 (8%)
Query: 616 RSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
R LF+ L+F+T DE+LR HF ++ L+ V N K S GFGF+ + +VE
Sbjct: 12 RKLFIGGLSFETTDESLRSHF----EQWGTLTDCVVMRDPNTKR-SRGFGFVTYATVE 64
Score = 36.2 bits (82), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 20/86 (23%), Positives = 45/86 (52%), Gaps = 3/86 (3%)
Query: 274 ANGEIVDPGNPSSSSKDVQQE--VLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIV 331
+G +V+P + S +D Q+ L ++FV + E LR++F ++G + + I+
Sbjct: 77 VDGRVVEPKR-AVSREDSQRPGAHLTVKKIFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM 135
Query: 332 VDKDTKRSKGIAYVLYAIPESASRAI 357
D+ + + +G A+V + +S + +
Sbjct: 136 TDRGSGKKRGFAFVTFDDHDSVDKIV 161
Score = 35.4 bits (80), Expect = 0.11, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 47/95 (49%), Gaps = 4/95 (4%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKY 60
++ + L T++ LR F Q G +TD +MR + K SR F F+ + T +E + A+
Sbjct: 13 KLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVTYATVEEVDAAMN- 71
Query: 61 FNKSYLDTCRISCEIARKVGDPNMPRPWSRYSLKK 95
+ + R+ E R V + RP + ++KK
Sbjct: 72 -ARPHKVDGRV-VEPKRAVSREDSQRPGAHLTVKK 104
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 50.4 bits (119), Expect = 3e-06, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
++FV LPY T+ LR++F FG++ E ++ D+ T +S+G +V A +A RA +
Sbjct: 19 KIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACKD 78
Query: 360 LDNSIFQGRLLHV 372
N I GR +V
Sbjct: 79 -PNPIIDGRKANV 90
Score = 36.2 bits (82), Expect = 0.069, Method: Composition-based stats.
Identities = 20/60 (33%), Positives = 32/60 (53%), Gaps = 1/60 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKD-GKSRQFAFIGFRTEQEAEEAIK 59
++I V LP + T+ LR +F G+I +A ++ + GKSR + F+ AE A K
Sbjct: 18 TKIFVGGLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERACK 77
Score = 31.2 bits (69), Expect = 2.0, Method: Composition-based stats.
Identities = 25/81 (30%), Positives = 36/81 (44%), Gaps = 6/81 (7%)
Query: 618 LFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETATN 677
+FV L + T D +LRK+F G I V + GK S G+GF+ A
Sbjct: 20 IFVGGLPYHTTDASLRKYFEGF---GDIEEAVVITDRQTGK--SRGYGFVTMADRAAAER 74
Query: 678 VCRDLQGTILDGHALILQLCH 698
C+D I+DG + L +
Sbjct: 75 ACKD-PNPIIDGRKANVNLAY 94
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 50.1 bits (118), Expect = 5e-06, Method: Compositional matrix adjust.
Identities = 31/98 (31%), Positives = 47/98 (47%), Gaps = 2/98 (2%)
Query: 285 SSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAY 344
SS S V++ V ++ L V LP+ TE +L+E+FS FG V V + D T SKG +
Sbjct: 2 SSGSSGVKRAVQKTSDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGF 61
Query: 345 VLYAIPESASRAIEVLDNSIFQGRLLHVMPARHKKSSD 382
V + E+ + + + GR K+S D
Sbjct: 62 VRFTEYETQVKVMS--QRHMIDGRWCDCKLPNSKQSQD 97
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 30/86 (34%), Positives = 47/86 (54%), Gaps = 7/86 (8%)
Query: 618 LFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETATN 677
L V L +KT +++L+++F G +L V+VKK LK G S GFGF+ F ET
Sbjct: 18 LIVLGLPWKTTEQDLKEYFSTF---GEVLMVQVKKDLKTGH--SKGFGFVRFTEYETQVK 72
Query: 678 VCRDLQGTILDGHALILQLCHAKKDE 703
V Q ++DG +L ++K+ +
Sbjct: 73 VMS--QRHMIDGRWCDCKLPNSKQSQ 96
Score = 32.3 bits (72), Expect = 0.89, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 31/56 (55%), Gaps = 2/56 (3%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMR-TKDGKSRQFAFIGFRTEQEAE 55
S + V LP TE L+++FS GE+ ++ + K G S+ F F+ F TE E +
Sbjct: 16 SDLIVLGLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRF-TEYETQ 70
>pdb|2D9P|A Chain A, Solution Structure Of Rna Binding Domain 4 In
Polyadenylation Binding Protein 3
Length = 103
Score = 49.7 bits (117), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 47/79 (59%), Gaps = 2/79 (2%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L+V+NL ++ LR+ FS FG ++ ++++ RSKG +V ++ PE A++A+ +
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVMMEGG--RSKGFGFVCFSSPEEATKAVTEM 75
Query: 361 DNSIFQGRLLHVMPARHKK 379
+ I + L+V A+ K+
Sbjct: 76 NGRIVATKPLYVALAQRKE 94
Score = 48.5 bits (114), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 34/93 (36%), Positives = 48/93 (51%), Gaps = 7/93 (7%)
Query: 612 RVESRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDS 671
R + +L+VKNL+ DE LRK F G I S KV ++ G+ S GFGF+ F S
Sbjct: 12 RYQVVNLYVKNLDDGIDDERLRKAFSPF---GTITSAKV--MMEGGR--SKGFGFVCFSS 64
Query: 672 VETATNVCRDLQGTILDGHALILQLCHAKKDEQ 704
E AT ++ G I+ L + L K++ Q
Sbjct: 65 PEEATKAVTEMNGRIVATKPLYVALAQRKEERQ 97
Score = 46.2 bits (108), Expect = 6e-05, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYFN 62
+ VKNL + ++RLR FS G IT AK+M + G+S+ F F+ F + +EA +A+ N
Sbjct: 18 LYVKNLDDGIDDERLRKAFSPFGTITSAKVM-MEGGRSKGFGFVCFSSPEEATKAVTEMN 76
Query: 63 KSYLDTCRISCEIARK 78
+ T + +A++
Sbjct: 77 GRIVATKPLYVALAQR 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 = 49.3 bits (116), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 52/106 (49%), Gaps = 7/106 (6%)
Query: 283 NPSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGI 342
NPS+ S + L+V +L TE L E FS G + + + D T+RS G
Sbjct: 7 NPSAPSYPMAS-------LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGY 59
Query: 343 AYVLYAIPESASRAIEVLDNSIFQGRLLHVMPARHKKSSDKQELHN 388
AYV + P A RA++ ++ + +G+ + +M ++ S K + N
Sbjct: 60 AYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 105
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 299 GRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIE 358
G +F++NL + L + FS FGN+ +V D++ SKG +V + E+A RAIE
Sbjct: 104 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 161
Query: 359 VL------DNSIFQGRL 369
+ D +F GR
Sbjct: 162 KMNGMLLNDRKVFVGRF 178
>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 = 48.9 bits (115), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 31/106 (29%), Positives = 52/106 (49%), Gaps = 7/106 (6%)
Query: 283 NPSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGI 342
NPS+ S + L+V +L TE L E FS G + + + D T+RS G
Sbjct: 2 NPSAPSYPMAS-------LYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGY 54
Query: 343 AYVLYAIPESASRAIEVLDNSIFQGRLLHVMPARHKKSSDKQELHN 388
AYV + P A RA++ ++ + +G+ + +M ++ S K + N
Sbjct: 55 AYVNFQQPADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGN 100
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 40/77 (51%), Gaps = 8/77 (10%)
Query: 299 GRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIE 358
G +F++NL + L + FS FGN+ +V D++ SKG +V + E+A RAIE
Sbjct: 99 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 156
Query: 359 VL------DNSIFQGRL 369
+ D +F GR
Sbjct: 157 KMNGMLLNDRKVFVGRF 173
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 48.9 bits (115), Expect = 1e-05, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 41/72 (56%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V L TE +LRE FSK+G +++V IV D+ ++RS+G A+V + + A A E
Sbjct: 49 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 108
Query: 361 DNSIFQGRLLHV 372
+ GR + V
Sbjct: 109 NGMELDGRRIRV 120
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKYFNK 63
V L Y TE LR+ FS+ G I D ++ + + SR FAF+ F +A+EA + N
Sbjct: 51 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 110
Query: 64 SYLDTCRISCEIA 76
LD RI + +
Sbjct: 111 MELDGRRIRVDFS 123
>pdb|1OO0|B Chain B, Crystal Structure Of The Drosophila Mago Nashi-Y14 Complex
Length = 110
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/80 (33%), Positives = 43/80 (53%)
Query: 293 QEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPES 352
Q +E LFV ++ A EDE++E F +G + +H+ +D+ T SKG A V Y +
Sbjct: 21 QRSVEGWILFVTSIHEEAQEDEIQEKFCDYGEIKNIHLNLDRRTGFSKGYALVEYETHKQ 80
Query: 353 ASRAIEVLDNSIFQGRLLHV 372
A A E L+ + G+ + V
Sbjct: 81 ALAAKEALNGAEIMGQTIQV 100
>pdb|4F25|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
At Ph 6.0
pdb|4F26|A Chain A, Crystal Structure Of The Second Rrm Domain Of Human Pabpc1
A Ph 9.0
Length = 115
Score = 48.9 bits (115), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/84 (32%), Positives = 45/84 (53%), Gaps = 2/84 (2%)
Query: 296 LESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASR 355
L SG +F++NL + L + FS FGN+ +V D++ SKG +V + E+A R
Sbjct: 3 LGSGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAER 60
Query: 356 AIEVLDNSIFQGRLLHVMPARHKK 379
AIE ++ + R + V + +K
Sbjct: 61 AIEKMNGMLLNDRKVFVGRFKSRK 84
>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 = 48.9 bits (115), Expect = 1e-05, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 41/73 (56%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
R++V ++ Y ED +R+ F+ FG + + D T + KG A+V Y +PE+A A+E
Sbjct: 14 RVYVGSIYYELGEDTIRQAFAPFGPIKSIDXSWDSVTXKHKGFAFVEYEVPEAAQLALEQ 73
Query: 360 LDNSIFQGRLLHV 372
++ GR + V
Sbjct: 74 XNSVXLGGRNIKV 86
>pdb|2DNM|A Chain A, Solution Structure Of Rna Binding Domain In Srp46 Splicing
Factor
Length = 103
Score = 48.5 bits (114), Expect = 1e-05, Method: Composition-based stats.
Identities = 33/98 (33%), Positives = 47/98 (47%), Gaps = 4/98 (4%)
Query: 282 GNPSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKG 341
G+ SS DV + L V NL Y + D LR F K+G V +V+I + TK +G
Sbjct: 1 GSSGSSGPDVDGMI----TLKVDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRG 56
Query: 342 IAYVLYAIPESASRAIEVLDNSIFQGRLLHVMPARHKK 379
A+V + A A +D + GR L V AR+ +
Sbjct: 57 FAFVRFHDRRDAQDAEAAMDGAELDGRELRVQVARYGR 94
Score = 36.2 bits (82), Expect = 0.066, Method: Composition-based stats.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 1/74 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKS-RQFAFIGFRTEQEAEEAIKYFNK 63
V NL + D LR F + G + D + R K+ R FAF+ F ++A++A +
Sbjct: 18 VDNLTYRTSPDSLRRVFEKYGRVGDVYIPREPHTKAPRGFAFVRFHDRRDAQDAEAAMDG 77
Query: 64 SYLDTCRISCEIAR 77
+ LD + ++AR
Sbjct: 78 AELDGRELRVQVAR 91
Score = 32.0 bits (71), Expect = 1.4, Method: Composition-based stats.
Identities = 26/89 (29%), Positives = 43/89 (48%), Gaps = 9/89 (10%)
Query: 610 PDRVESRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKK--HLKNGKNVSMGFGFI 667
PD +L V NL ++T ++LR+ F ++ GR+ V + + H K + GF F+
Sbjct: 8 PDVDGMITLKVDNLTYRTSPDSLRRVFEKY---GRVGDVYIPREPHTKAPR----GFAFV 60
Query: 668 EFDSVETATNVCRDLQGTILDGHALILQL 696
F A + + G LDG L +Q+
Sbjct: 61 RFHDRRDAQDAEAAMDGAELDGRELRVQV 89
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 48.5 bits (114), Expect = 1e-05, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 41/72 (56%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V L TE +LRE FSK+G +++V IV D+ ++RS+G A+V + + A A E
Sbjct: 15 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 74
Query: 361 DNSIFQGRLLHV 372
+ GR + V
Sbjct: 75 NGMELDGRRIRV 86
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKYFNK 63
V L Y TE LR+ FS+ G I D ++ + + SR FAF+ F +A+EA + N
Sbjct: 17 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 76
Query: 64 SYLDTCRISCEIA 76
LD RI + +
Sbjct: 77 MELDGRRIRVDFS 89
>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 = 48.1 bits (113), Expect = 2e-05, Method: Composition-based stats.
Identities = 30/90 (33%), Positives = 43/90 (47%)
Query: 292 QQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPE 351
Q+E E LF+ +LP + +L + F FGNV + +DK T SK +V Y P
Sbjct: 19 QKEGPEGANLFIYHLPQEFGDQDLLQMFMPFGNVVSAKVFIDKQTNLSKCFGFVSYDNPV 78
Query: 352 SASRAIEVLDNSIFQGRLLHVMPARHKKSS 381
SA AI+ ++ + L V R K S
Sbjct: 79 SAQAAIQSMNGFQIGMKRLKVQLKRSKNDS 108
Score = 31.2 bits (69), Expect = 2.2, Method: Composition-based stats.
Identities = 24/91 (26%), Positives = 46/91 (50%), Gaps = 5/91 (5%)
Query: 614 ESRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
E +LF+ +L + D++L + F + G ++S KV + N+S FGF+ +D+
Sbjct: 24 EGANLFIYHLPQEFGDQDLLQMF---MPFGNVVSAKV--FIDKQTNLSKCFGFVSYDNPV 78
Query: 674 TATNVCRDLQGTILDGHALILQLCHAKKDEQ 704
+A + + G + L +QL +K D +
Sbjct: 79 SAQAAIQSMNGFQIGMKRLKVQLKRSKNDSK 109
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 48.1 bits (113), Expect = 2e-05, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 41/72 (56%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V L TE +LRE FSK+G +++V IV D+ ++RS+G A+V + + A A E
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 361 DNSIFQGRLLHV 372
+ GR + V
Sbjct: 78 NGMELDGRRIRV 89
Score = 40.0 bits (92), Expect = 0.005, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 36/68 (52%), Gaps = 1/68 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKYFNK 63
V L Y TE LR+ FS+ G I D ++ + + SR FAF+ F +A+EA + N
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 64 SYLDTCRI 71
LD RI
Sbjct: 80 MELDGRRI 87
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 47.8 bits (112), Expect = 2e-05, Method: Composition-based stats.
Identities = 27/72 (37%), Positives = 41/72 (56%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V L TE +LRE FSK+G +++V IV D+ ++RS+G A+V + + A A E
Sbjct: 18 LGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERA 77
Query: 361 DNSIFQGRLLHV 372
+ GR + V
Sbjct: 78 NGMELDGRRIRV 89
Score = 40.0 bits (92), Expect = 0.004, Method: Composition-based stats.
Identities = 26/73 (35%), Positives = 38/73 (52%), Gaps = 1/73 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKYFNK 63
V L Y TE LR+ FS+ G I D ++ + + SR FAF+ F +A+EA + N
Sbjct: 20 VFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEAKERANG 79
Query: 64 SYLDTCRISCEIA 76
LD RI + +
Sbjct: 80 MELDGRRIRVDFS 92
>pdb|1X4H|A Chain A, Solution Structure Of Rrm Domain In Rna-Binding Protein 28
Length = 111
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 38/64 (59%)
Query: 294 EVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESA 353
+V E +F+RNL + + E+ L E +FG++ V +V+ DT+ SKG A+ + E+A
Sbjct: 11 DVTEGKTVFIRNLSFDSEEEALGEVLQQFGDLKYVRVVLHPDTEHSKGCAFAQFMTQEAA 70
Query: 354 SRAI 357
+ +
Sbjct: 71 QKCL 74
>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 = 2e-05, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 41/70 (58%), Gaps = 1/70 (1%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V +P T E +LR+ F ++G + V IV D++T++S+G +V + SA +AI L
Sbjct: 45 LMVNYIPTTVDEVQLRQLFERYGPIESVKIVCDRETRQSRGYGFVKFQSGSSAQQAIAGL 104
Query: 361 DN-SIFQGRL 369
+ +I RL
Sbjct: 105 NGFNILNKRL 114
>pdb|2CQ3|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 9
Length = 103
Score = 47.8 bits (112), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 2/73 (2%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
RL V N+P+ + +LR+ F +FG + +V I+ ++ + SKG +V + A RA E
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREK 74
Query: 360 LDNSIFQGRLLHV 372
L ++ +GR + V
Sbjct: 75 LHGTVVEGRKIEV 87
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 41/75 (54%), Gaps = 7/75 (9%)
Query: 618 LFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETATN 677
L V N+ F+ D +LR+ FG+ G+IL V++ + + K GFGF+ F++ A
Sbjct: 18 LHVSNIPFRFRDPDLRQMFGQF---GKILDVEIIFNERGSK----GFGFVTFENSADADR 70
Query: 678 VCRDLQGTILDGHAL 692
L GT+++G +
Sbjct: 71 AREKLHGTVVEGRKI 85
Score = 34.3 bits (77), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEA 57
R+ V N+P + LR F Q G+I D +++ + G S+ F F+ F +A+ A
Sbjct: 17 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRA 71
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 24/84 (28%), Positives = 40/84 (47%), Gaps = 4/84 (4%)
Query: 499 VKNLPYDSSEGELAKMFGKFGS-LDKVIL---PSTKTLALVVFLEPVEAAAAFKGLAYKR 554
V N+P+ + +L +MFG+FG LD I+ +K V F +A A + L
Sbjct: 20 VSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERGSKGFGFVTFENSADADRAREKLHGTV 79
Query: 555 YKGVPLYLEWAPSDVLSQSSTSKG 578
+G + + A + V++ S S G
Sbjct: 80 VEGRKIEVNNATARVMTNSGPSSG 103
>pdb|2DH8|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Daz-Associated Protein 1
Length = 105
Score = 47.4 bits (111), Expect = 3e-05, Method: Composition-based stats.
Identities = 21/54 (38%), Positives = 35/54 (64%)
Query: 297 ESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIP 350
E G+LFV L ++ T++ LR +FS++G V + I+ DK T +S+G +V + P
Sbjct: 15 EIGKLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFKDP 68
Score = 37.4 bits (85), Expect = 0.027, Method: Composition-based stats.
Identities = 18/49 (36%), Positives = 29/49 (59%), Gaps = 1/49 (2%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFR 49
++ V L T++ LR +FSQ GE+ D +M+ K +SR F F+ F+
Sbjct: 18 KLFVGGLDWSTTQETLRSYFSQYGEVVDCVIMKDKTTNQSRGFGFVKFK 66
>pdb|2K8G|A Chain A, Solution Structure Of Rrm2 Domain Of Pabp1
Length = 95
Score = 47.0 bits (110), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 43/81 (53%), Gaps = 2/81 (2%)
Query: 299 GRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIE 358
G +F++NL + L + FS FGN+ +V D++ SKG +V + E+A RAIE
Sbjct: 12 GNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENG--SKGYGFVHFETQEAAERAIE 69
Query: 359 VLDNSIFQGRLLHVMPARHKK 379
++ + R + V + +K
Sbjct: 70 KMNGMLLNDRKVFVGRFKSRK 90
>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 = 46.6 bits (109), Expect = 4e-05, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 36/58 (62%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIE 358
+F+ L + T+ +L+++FSKFG V + + +D T RS+G +VL+ ES + ++
Sbjct: 2 MFIGGLSWDTTKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVMD 59
Score = 32.3 bits (72), Expect = 0.98, Method: Compositional matrix adjust.
Identities = 15/47 (31%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 13 TEDRLRDFFSQKGEITDAKL-MRTKDGKSRQFAFIGFRTEQEAEEAI 58
T+ L+D+FS+ GE+ D L + G+SR F F+ F+ + ++ +
Sbjct: 12 TKKDLKDYFSKFGEVVDCTLKLDPITGRSRGFGFVLFKESESVDKVM 58
>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 = 46.6 bits (109), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 38/62 (61%)
Query: 297 ESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRA 356
++G+ FV L + ++ +L+++F+KFG V + I D +T RS+G ++L+ S +
Sbjct: 10 DAGKXFVGGLSWDTSKKDLKDYFTKFGEVVDCTIKXDPNTGRSRGFGFILFKDAASVEKV 69
Query: 357 IE 358
++
Sbjct: 70 LD 71
>pdb|2ERR|A Chain A, Nmr Structure Of The Rna Binding Domain Of Human Fox-1 In
Complex With Ugcaugu
Length = 109
Score = 46.2 bits (108), Expect = 6e-05, Method: Composition-based stats.
Identities = 24/73 (32%), Positives = 42/73 (57%), Gaps = 2/73 (2%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
RL V N+P+ + +LR+ F +FG + +V I+ ++ + SKG +V + A RA E
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNE--RGSKGFGFVTFENSADADRAREK 88
Query: 360 LDNSIFQGRLLHV 372
L ++ +GR + V
Sbjct: 89 LHGTVVEGRKIEV 101
Score = 40.8 bits (94), Expect = 0.003, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 45/82 (54%), Gaps = 7/82 (8%)
Query: 611 DRVESRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFD 670
++ + + L V N+ F+ D +LR+ FG+ G+IL V++ + + K GFGF+ F+
Sbjct: 25 NKSQPKRLHVSNIPFRFRDPDLRQMFGQF---GKILDVEIIFNERGSK----GFGFVTFE 77
Query: 671 SVETATNVCRDLQGTILDGHAL 692
+ A L GT+++G +
Sbjct: 78 NSADADRAREKLHGTVVEGRKI 99
Score = 33.5 bits (75), Expect = 0.41, Method: Composition-based stats.
Identities = 18/56 (32%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEA 57
R+ V N+P + LR F Q G+I D +++ + G S+ F F+ F +A+ A
Sbjct: 31 RLHVSNIPFRFRDPDLRQMFGQFGKILDVEIIFNERG-SKGFGFVTFENSADADRA 85
>pdb|2DGT|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Rna- Binding Protein 30
Length = 92
Score = 46.2 bits (108), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 38/75 (50%), Gaps = 8/75 (10%)
Query: 298 SGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAI 357
S +L V N+ T T ELR F ++G V E IV D A+V E A AI
Sbjct: 10 STKLHVGNISPTCTNQELRAKFEEYGPVIECDIVKD--------YAFVHMERAEDAVEAI 61
Query: 358 EVLDNSIFQGRLLHV 372
LDN+ FQG+ +HV
Sbjct: 62 RGLDNTEFQGKRMHV 76
>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 = 46.2 bits (108), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 46/86 (53%), Gaps = 1/86 (1%)
Query: 296 LESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASR 355
LE +LF+ LP++ T++EL E G V ++ +V ++ K KG+AYV Y AS+
Sbjct: 15 LEKHKLFISGLPFSCTKEELEEICKAHGTVKDLRLVTNRAGK-PKGLAYVEYENESQASQ 73
Query: 356 AIEVLDNSIFQGRLLHVMPARHKKSS 381
A+ +D + ++ V + SS
Sbjct: 74 AVMKMDGMTIKENIIKVAISNSGPSS 99
>pdb|2JVO|A Chain A, Segmental Isotope Labeling Of Npl3
Length = 108
Score = 46.2 bits (108), Expect = 7e-05, Method: Composition-based stats.
Identities = 32/92 (34%), Positives = 45/92 (48%), Gaps = 12/92 (13%)
Query: 292 QQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPE 351
Q+ L + RLFVR P E EL E F FG + EV I+ G A+V + E
Sbjct: 25 QEGELSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAE 76
Query: 352 SASRAIEVLDNSIFQGRLLHV----MPARHKK 379
SA++AIE + F + L V +PA+ +
Sbjct: 77 SAAKAIEEVHGKSFANQPLEVVYSKLPAKRYR 108
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 493 SNHVFLVKNLPYDSSEGELAKMFGKFGSLDKVILPSTKTLALVVFLEPVEAAAAFKGLAY 552
SN V+ P D E EL ++FG FG + +V + A V F E AA A + +
Sbjct: 30 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKAIEEVHG 87
Query: 553 KRYKGVPL 560
K + PL
Sbjct: 88 KSFANQPL 95
>pdb|2DHS|A Chain A, Solution Structure Of Nucleic Acid Binding Protein
Cugbp1ab And Its Binding Study With Dna And Rna
Length = 187
Score = 45.8 bits (107), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 26/87 (29%), Positives = 48/87 (55%), Gaps = 9/87 (10%)
Query: 293 QEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDK--DTKRSKGIAYVLYAIP 350
Q L++ ++FV +P T +E +LRE F ++G V E++++ D+ + +SKG +V +
Sbjct: 10 QPDLDAIKMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTR 69
Query: 351 ESASRAIEVLDNSIFQGRLLHVMPARH 377
++A A L N + V+P H
Sbjct: 70 KAALEAQNALHN-------MKVLPGMH 89
Score = 43.9 bits (102), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 37/63 (58%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYF 61
++ + + K TE+ +R FS G+I + +++R DG SR AF+ F T A+ AIK
Sbjct: 109 KLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAM 168
Query: 62 NKS 64
+++
Sbjct: 169 HQA 171
Score = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 23/77 (29%), Positives = 39/77 (50%), Gaps = 4/77 (5%)
Query: 284 PSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIA 343
P+ S K+ +E +LF+ + TE+++R FS FG + E I+ D S+G A
Sbjct: 96 PADSEKN---NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCA 151
Query: 344 YVLYAIPESASRAIEVL 360
+V + A AI+ +
Sbjct: 152 FVTFTTRAMAQTAIKAM 168
>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 = 9e-05, Method: Compositional matrix adjust.
Identities = 28/108 (25%), Positives = 50/108 (46%)
Query: 285 SSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAY 344
SS S +++ +FV +L T ++++ F+ FG +S+ +V D T +SKG +
Sbjct: 2 SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGF 61
Query: 345 VLYAIPESASRAIEVLDNSIFQGRLLHVMPARHKKSSDKQELHNSTSQ 392
V + A AI+ + GR + A K + K ++T Q
Sbjct: 62 VSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRKPPAPKSTYESNTKQ 109
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 22/85 (25%), Positives = 44/85 (51%), Gaps = 3/85 (3%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAKLMR-TKDGKSRQFAFIGFRTEQEAEEAIKYF 61
+ V +L +T + ++ F+ G I+DA++++ GKS+ + F+ F + +AE AI+
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQM 77
Query: 62 NKSYLDTCRISCEIARKVGDPNMPR 86
+L +I A + P P+
Sbjct: 78 GGQWLGGRQIRTNWATR--KPPAPK 100
Score = 33.9 bits (76), Expect = 0.33, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 37/75 (49%), Gaps = 5/75 (6%)
Query: 618 LFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETATN 677
+FV +L+ + E+++ F GRI +V K + GK+ G+GF+ F + A N
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPF---GRISDARVVKDMATGKS--KGYGFVSFFNKWDAEN 72
Query: 678 VCRDLQGTILDGHAL 692
+ + G L G +
Sbjct: 73 AIQQMGGQWLGGRQI 87
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 45.4 bits (106), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/73 (34%), Positives = 41/73 (56%)
Query: 285 SSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAY 344
SS S + ++ + V NL E +L+E F FG++S +++ DK T +SKG A+
Sbjct: 2 SSGSSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAF 61
Query: 345 VLYAIPESASRAI 357
+ + E A+RAI
Sbjct: 62 ISFHRREDAARAI 74
Score = 32.3 bits (72), Expect = 0.97, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 30/57 (52%), Gaps = 1/57 (1%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKD-GKSRQFAFIGFRTEQEAEEAI 58
I V NL + E L++ F G I+ L + K G+S+ FAFI F ++A AI
Sbjct: 18 IRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISFHRREDAARAI 74
>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 = 45.4 bits (106), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 1/78 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIK 59
+ + V LP+ +T++ R F GEI KL+R K G+S + F+ + ++AE+AI
Sbjct: 3 TNLIVNYLPQNMTQEEFRSLFGSIGEIESCKLVRDKITGQSLGYGFVNYIDPKDAEKAIN 62
Query: 60 YFNKSYLDTCRISCEIAR 77
N L T I AR
Sbjct: 63 TLNGLRLQTKTIKVSYAR 80
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 43/83 (51%), Gaps = 7/83 (8%)
Query: 279 VDPGNPSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKR 338
V PSS+S + L+V LP T T+ EL + FS++G + I+VD+ T
Sbjct: 76 VSYARPSSAS-------IRDANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGV 128
Query: 339 SKGIAYVLYAIPESASRAIEVLD 361
S+G+ ++ + A AI+ L+
Sbjct: 129 SRGVGFIRFDKRIEAEEAIKGLN 151
Score = 42.7 bits (99), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 25/63 (39%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIK 59
+ + V LPK +T+ L FSQ G I ++++ + G SR FI F EAEEAIK
Sbjct: 89 ANLYVSGLPKTMTQKELEQLFSQYGRIITSRILVDQVTGVSRGVGFIRFDKRIEAEEAIK 148
Query: 60 YFN 62
N
Sbjct: 149 GLN 151
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 45.1 bits (105), Expect = 1e-04, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 40/71 (56%), Gaps = 4/71 (5%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYFN 62
+ KNLP VT+D L++ F EI + +KDGKS+ A+I F+TE +AE+ +
Sbjct: 96 LLAKNLPYKVTQDELKEVFEDAAEIR----LVSKDGKSKGIAYIEFKTEADAEKTFEEKQ 151
Query: 63 KSYLDTCRISC 73
+ +D IS
Sbjct: 152 GTEIDGRSISL 162
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/72 (36%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L +NLPY T+DEL+E F + +E+ + V KD K SKGIAY+ + A + E
Sbjct: 96 LLAKNLPYKVTQDELKEVFE---DAAEIRL-VSKDGK-SKGIAYIEFKTEADAEKTFEEK 150
Query: 361 DNSIFQGRLLHV 372
+ GR + +
Sbjct: 151 QGTEIDGRSISL 162
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 29/90 (32%), Positives = 45/90 (50%), Gaps = 10/90 (11%)
Query: 614 ESRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
++R+L KNL +K + L++ F E E R++S K+GK S G +IEF +
Sbjct: 92 DARTLLAKNLPYKVTQDELKEVF-EDAAEIRLVS-------KDGK--SKGIAYIEFKTEA 141
Query: 674 TATNVCRDLQGTILDGHALILQLCHAKKDE 703
A + QGT +DG ++ L K E
Sbjct: 142 DAEKTFEEKQGTEIDGRSISLYYTGEPKGE 171
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 45.1 bits (105), Expect = 1e-04, Method: Composition-based stats.
Identities = 25/70 (35%), Positives = 37/70 (52%)
Query: 292 QQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPE 351
Q E E LF+ +LP T+ +L F FGNV + +DK T SK +V + P+
Sbjct: 34 QIEGPEGCNLFIYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPD 93
Query: 352 SASRAIEVLD 361
SA AI+ ++
Sbjct: 94 SAQVAIKAMN 103
Score = 30.4 bits (67), Expect = 3.4, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 34/74 (45%), Gaps = 1/74 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAIKYFNK 63
+ +LP+ T+ L F G + AK+ K S+ F F+ F A+ AIK N
Sbjct: 45 IYHLPQEFTDTDLASTFLPFGNVISAKVFIDKQTSLSKCFGFVSFDNPDSAQVAIKAMNG 104
Query: 64 SYLDTCRISCEIAR 77
+ T R+ ++ +
Sbjct: 105 FQVGTKRLKVQLKK 118
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
RLFV NLP TE+E+R+ F K+G EV I D KG ++ A A
Sbjct: 24 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 77
Query: 360 LDNSIFQGRLLHVMPARHKKS 380
LDN +G+ L V A H S
Sbjct: 78 LDNMPLRGKQLRVRFACHSAS 98
Score = 37.0 bits (84), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 26/77 (33%), Positives = 36/77 (46%), Gaps = 4/77 (5%)
Query: 298 SGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAI 357
S L VRNLP + + L E FS FG V ++VD D R G V ++ +A +A+
Sbjct: 96 SASLTVRNLPQYVSNELLEEAFSVFGQVERAVVIVD-DRGRPSGKGIVEFSGKPAARKAL 154
Query: 358 EVLDNSIFQGRLLHVMP 374
+ F LL P
Sbjct: 155 DRCSEGSF---LLTTFP 168
Score = 30.0 bits (66), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEA 57
SR+ V NLP +TE+ +R F + G+ + + + K F FI T AE A
Sbjct: 23 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKDKG-----FGFIRLETRTLAEIA 74
>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 = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 39/81 (48%), Gaps = 6/81 (7%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
RLFV NLP TE+E+R+ F K+G EV I D KG ++ A A
Sbjct: 17 RLFVGNLPPDITEEEMRKLFEKYGKAGEVFIHKD------KGFGFIRLETRTLAEIAKVE 70
Query: 360 LDNSIFQGRLLHVMPARHKKS 380
LDN +G+ L V A H S
Sbjct: 71 LDNMPLRGKQLRVRFACHSAS 91
Score = 30.4 bits (67), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 19/57 (33%), Positives = 28/57 (49%), Gaps = 5/57 (8%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEA 57
SR+ V NLP +TE+ +R F + G+ + + K + F FI T AE A
Sbjct: 16 SRLFVGNLPPDITEEEMRKLFEKYGKAGEVFIH-----KDKGFGFIRLETRTLAEIA 67
>pdb|2OSQ|A Chain A, Nmr Structure Of Rrm-1 Of Yeast Npl3 Protein
Length = 74
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 29/78 (37%), Positives = 39/78 (50%), Gaps = 8/78 (10%)
Query: 296 LESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASR 355
L + RLFVR P E EL E F FG + EV I+ G A+V + ESA++
Sbjct: 2 LSNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKIL--------NGFAFVEFEEAESAAK 53
Query: 356 AIEVLDNSIFQGRLLHVM 373
AIE + F + L V+
Sbjct: 54 AIEEVHGKSFANQPLEVV 71
Score = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 2/68 (2%)
Query: 493 SNHVFLVKNLPYDSSEGELAKMFGKFGSLDKVILPSTKTLALVVFLEPVEAAAAFKGLAY 552
SN V+ P D E EL ++FG FG + +V + A V F E AA A + +
Sbjct: 3 SNTRLFVRPFPLDVQESELNEIFGPFGPMKEVKI--LNGFAFVEFEEAESAAKAIEEVHG 60
Query: 553 KRYKGVPL 560
K + PL
Sbjct: 61 KSFANQPL 68
>pdb|3NNC|A Chain A, Crystal Structure Of Cugbp1 Rrm12-Rna Complex
Length = 175
Score = 44.7 bits (104), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 9/80 (11%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDK--DTKRSKGIAYVLYAIPESASRAI 357
++FV +P T +E +LRE F ++G V E++++ D+ + +SKG +V + ++A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 358 EVLDNSIFQGRLLHVMPARH 377
L N + V+P H
Sbjct: 65 NALHN-------MKVLPGMH 77
Score = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 21/57 (36%), Positives = 34/57 (59%)
Query: 8 LPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYFNKS 64
+ K TE+ +R FS G+I + +++R DG SR AF+ F T A+ AIK +++
Sbjct: 103 ISKKCTENDIRVMFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAMAQTAIKAMHQA 159
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 40/80 (50%), Gaps = 4/80 (5%)
Query: 284 PSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIA 343
P+ S K+ +E +LF+ + TE+++R FS FG + E I+ D S+G A
Sbjct: 84 PADSEKN---NAVEDRKLFIGMISKKCTENDIRVMFSSFGQIEECRILRGPD-GLSRGCA 139
Query: 344 YVLYAIPESASRAIEVLDNS 363
+V + A AI+ + +
Sbjct: 140 FVTFTTRAMAQTAIKAMHQA 159
>pdb|2RS2|A Chain A, 1h, 13c, And 15n Chemical Shift Assignments For Musashi1
Rbd1:r(Guagu) Complex
Length = 109
Score = 44.3 bits (103), Expect = 3e-04, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 31/48 (64%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLY 347
++F+ L + T++ LRE+F +FG V E ++ D TKRS+G +V +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 74
Score = 32.0 bits (71), Expect = 1.4, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIKY 60
++ + L T++ LR++F Q GE+ + +MR +SR F F+ F +Q + +
Sbjct: 27 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF-MDQAGVDKVLA 85
Query: 61 FNKSYLDTCRISCEIA 76
++ LD+ I ++A
Sbjct: 86 QSRHELDSKTIDPKVA 101
Score = 31.2 bits (69), Expect = 2.2, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 9/54 (16%)
Query: 618 LFVKNLNFKTCDENLRKHFGE--HIKEGRILSVKVKKHLKNGKNVSMGFGFIEF 669
+F+ L+++T E LR++FG+ +KE ++ + K S GFGF+ F
Sbjct: 28 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKR-------SRGFGFVTF 74
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 28/99 (28%), Positives = 49/99 (49%), Gaps = 4/99 (4%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L++RNLPY T +E+ + F K+G + ++ + +T ++G AYV+Y A A++ L
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 361 DNSIFQGRLLHVMPARHKKSSDKQELHNSTSQGTKTLKQ 399
R L V+ ++ K + Q K LK+
Sbjct: 68 SGFNVSNRYLVVLYYNANRAFQKMDTKKKEEQ-LKLLKE 105
Score = 35.4 bits (80), Expect = 0.10, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 34/61 (55%), Gaps = 3/61 (4%)
Query: 494 NHVFLVKNLPYDSSEGELAKMFGKFGSLDKVIL---PSTKTLALVVFLEPVEAAAAFKGL 550
N + ++NLPY + E+ +FGK+G + ++ + P T+ A VV+ + +A A L
Sbjct: 8 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNAVDHL 67
Query: 551 A 551
+
Sbjct: 68 S 68
>pdb|2CQB|A Chain A, Solution Structure Of The Rna Recognition Motif In
Peptidyl- Prolyl Cis-Trans Isomerase E
Length = 102
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 25/84 (29%), Positives = 46/84 (54%), Gaps = 3/84 (3%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L+V L + L F FG+++++ I +D +T++ +G A+V + + E A+ AI+ +
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 361 DNSIFQGRLLHV---MPARHKKSS 381
+ S GR + V P R K+S
Sbjct: 75 NESELFGRTIRVNLAKPMRIKESG 98
Score = 30.8 bits (68), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 38/78 (48%), Gaps = 1/78 (1%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAKL-MRTKDGKSRQFAFIGFRTEQEAEEAIKYF 61
+ V L + V + L F G+ITD ++ + + K R FAF+ F ++A AI
Sbjct: 15 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 74
Query: 62 NKSYLDTCRISCEIARKV 79
N+S L I +A+ +
Sbjct: 75 NESELFGRTIRVNLAKPM 92
>pdb|1UAW|A Chain A, Solution Structure Of The N-Terminal Rna-Binding Domain Of
Mouse Musashi1
Length = 77
Score = 43.9 bits (102), Expect = 3e-04, Method: Composition-based stats.
Identities = 18/48 (37%), Positives = 31/48 (64%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLY 347
++F+ L + T++ LRE+F +FG V E ++ D TKRS+G +V +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF 49
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 20/76 (26%), Positives = 40/76 (52%), Gaps = 2/76 (2%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIKY 60
++ + L T++ LR++F Q GE+ + +MR +SR F F+ F +Q + +
Sbjct: 2 KMFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKRSRGFGFVTF-MDQAGVDKVLA 60
Query: 61 FNKSYLDTCRISCEIA 76
++ LD+ I ++A
Sbjct: 61 QSRHELDSKTIDPKVA 76
Score = 30.8 bits (68), Expect = 2.7, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 30/54 (55%), Gaps = 9/54 (16%)
Query: 618 LFVKNLNFKTCDENLRKHFGE--HIKEGRILSVKVKKHLKNGKNVSMGFGFIEF 669
+F+ L+++T E LR++FG+ +KE ++ + K S GFGF+ F
Sbjct: 3 MFIGGLSWQTTQEGLREYFGQFGEVKECLVMRDPLTKR-------SRGFGFVTF 49
>pdb|1FNX|H Chain H, Solution Structure Of The Huc Rbd1-Rbd2 Complexed With
The Au-Rich Element
Length = 174
Score = 43.9 bits (102), Expect = 3e-04, Method: Compositional matrix adjust.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIK 59
+ + V LP+ +T+D + F G+I KL+R K G+S + F+ + +A++AI
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 60 YFNKSYLDTCRISCEIAR 77
N L T I AR
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 24/63 (38%), Positives = 33/63 (52%), Gaps = 1/63 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAK-LMRTKDGKSRQFAFIGFRTEQEAEEAIK 59
+ + V LPK +++ + FSQ G I ++ L+ G SR FI F EAEEAIK
Sbjct: 91 ANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIK 150
Query: 60 YFN 62
N
Sbjct: 151 GLN 153
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 42/78 (53%), Gaps = 7/78 (8%)
Query: 284 PSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIA 343
PSS+S + L+V LP T ++ E+ + FS++G + I++D+ T S+G+
Sbjct: 83 PSSAS-------IRDANLYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVG 135
Query: 344 YVLYAIPESASRAIEVLD 361
++ + A AI+ L+
Sbjct: 136 FIRFDKRIEAEEAIKGLN 153
>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 = 43.5 bits (101), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 24/80 (30%), Positives = 44/80 (55%), Gaps = 9/80 (11%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDK--DTKRSKGIAYVLYAIPESASRAI 357
++FV +P T +E +LRE F ++G V E++++ D+ + +SKG +V + ++A A
Sbjct: 5 KMFVGQVPRTWSEKDLRELFEQYGAVYEINVLRDRSQNPPQSKGCCFVTFYTRKAALEAQ 64
Query: 358 EVLDNSIFQGRLLHVMPARH 377
L N + V+P H
Sbjct: 65 NALHN-------MKVLPGMH 77
>pdb|2DO0|A Chain A, Solution Structure Of The Rna Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein M
Length = 114
Score = 43.1 bits (100), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 30/81 (37%), Positives = 42/81 (51%), Gaps = 5/81 (6%)
Query: 296 LESGRL----FVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPE 351
L++GRL FV NL Y +L+E FS G V I+ DKD K S+GI V +
Sbjct: 9 LQAGRLGSTVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGK-SRGIGTVTFEQSI 67
Query: 352 SASRAIEVLDNSIFQGRLLHV 372
A +AI + + + R +HV
Sbjct: 68 EAVQAISMFNGQLLFDRPMHV 88
Score = 43.1 bits (100), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 24/66 (36%), Positives = 33/66 (50%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKY 60
S + V NL V +L++ FS G + A ++ KDGKSR + F EA +AI
Sbjct: 16 STVFVANLDYKVGWKKLKEVFSMAGVVVRADILEDKDGKSRGIGTVTFEQSIEAVQAISM 75
Query: 61 FNKSYL 66
FN L
Sbjct: 76 FNGQLL 81
>pdb|2HYI|B Chain B, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
pdb|2HYI|H Chain H, Structure Of The Human Exon Junction Complex With A
Trapped Dead-Box Helicase Bound To Rna
Length = 91
Score = 43.1 bits (100), Expect = 5e-04, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 42/80 (52%)
Query: 293 QEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPES 352
Q +E LFV + ATE+++ + F+++G + +H+ +D+ T KG V Y +
Sbjct: 4 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 63
Query: 353 ASRAIEVLDNSIFQGRLLHV 372
A A+E L+ G+ + V
Sbjct: 64 AQAAMEGLNGQDLMGQPISV 83
>pdb|2XB2|D Chain D, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
pdb|2XB2|Z Chain Z, Crystal Structure Of The Core Mago-Y14-Eif4aiii-Barentsz-
Upf3b Assembly Shows How The Ejc Is Bridged To The Nmd
Machinery
Length = 90
Score = 43.1 bits (100), Expect = 6e-04, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 42/80 (52%)
Query: 293 QEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPES 352
Q +E LFV + ATE+++ + F+++G + +H+ +D+ T KG V Y +
Sbjct: 2 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 353 ASRAIEVLDNSIFQGRLLHV 372
A A+E L+ G+ + V
Sbjct: 62 AQAAMEGLNGQDLMGQPISV 81
>pdb|2J0S|D Chain D, The Crystal Structure Of The Exon Junction Complex At 2.2
A Resolution
Length = 89
Score = 43.1 bits (100), Expect = 6e-04, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 42/80 (52%)
Query: 293 QEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPES 352
Q +E LFV + ATE+++ + F+++G + +H+ +D+ T KG V Y +
Sbjct: 2 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 353 ASRAIEVLDNSIFQGRLLHV 372
A A+E L+ G+ + V
Sbjct: 62 AQAAMEGLNGQDLMGQPISV 81
>pdb|2J0Q|D Chain D, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
pdb|2J0Q|G Chain G, The Crystal Structure Of The Exon Junction Complex At 3.2
A Resolution
Length = 109
Score = 42.7 bits (99), Expect = 6e-04, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 42/80 (52%)
Query: 293 QEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPES 352
Q +E LFV + ATE+++ + F+++G + +H+ +D+ T KG V Y +
Sbjct: 2 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 61
Query: 353 ASRAIEVLDNSIFQGRLLHV 372
A A+E L+ G+ + V
Sbjct: 62 AQAAMEGLNGQDLMGQPISV 81
>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 = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/55 (38%), Positives = 32/55 (58%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIK 59
+ + K TE+ +R FS G+I + +++R DG SR AF+ F T A+ AIK
Sbjct: 100 IGXISKKCTENDIRVXFSSFGQIEECRILRGPDGLSRGCAFVTFTTRAXAQTAIK 154
Score = 37.7 bits (86), Expect = 0.023, Method: Compositional matrix adjust.
Identities = 23/75 (30%), Positives = 38/75 (50%), Gaps = 4/75 (5%)
Query: 284 PSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIA 343
P+ S K+ +E +LF+ + TE+++R FS FG + E I+ D S+G A
Sbjct: 84 PADSEKN---NAVEDRKLFIGXISKKCTENDIRVXFSSFGQIEECRILRGPD-GLSRGCA 139
Query: 344 YVLYAIPESASRAIE 358
+V + A AI+
Sbjct: 140 FVTFTTRAXAQTAIK 154
>pdb|2KU7|A Chain A, Solution Structure Of Mll1 Phd3-Cyp33 Rrm Chimeric Protein
Length = 140
Score = 42.7 bits (99), Expect = 7e-04, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 41/72 (56%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L+V L + L F FG+++++ I +D +T++ +G A+V + + E A+ AI+ +
Sbjct: 66 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 125
Query: 361 DNSIFQGRLLHV 372
+ S GR + V
Sbjct: 126 NESELFGRTIRV 137
Score = 30.0 bits (66), Expect = 4.3, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKL-MRTKDGKSRQFAFIGFRTEQEAEEAIKYFNK 63
V L + V + L F G+ITD ++ + + K R FAF+ F ++A AI N+
Sbjct: 68 VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 127
Query: 64 SYL 66
S L
Sbjct: 128 SEL 130
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 42.7 bits (99), Expect = 7e-04, Method: Composition-based stats.
Identities = 17/47 (36%), Positives = 31/47 (65%), Gaps = 3/47 (6%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLY 347
L++RNLPY T +E+ + F K+G + ++ + +T ++G AYV+Y
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVY 58
Score = 36.2 bits (82), Expect = 0.061, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 494 NHVFLVKNLPYDSSEGELAKMFGKFGSLDKVIL---PSTKTLALVVFLEPVEAAAA 546
N + ++NLPY + E+ +FGK+G + ++ + P T+ A VV+ + +A A
Sbjct: 12 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 67
>pdb|2FY1|A Chain A, A Dual Mode Of Rna Recognition By The Rbmy Protein
Length = 116
Score = 42.7 bits (99), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 23/79 (29%), Positives = 40/79 (50%), Gaps = 1/79 (1%)
Query: 294 EVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESA 353
E G+LF+ L E L+ F K G +SEV ++ D+ T +S+G A++ + P A
Sbjct: 3 EADHPGKLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDR-TSKSRGFAFITFENPADA 61
Query: 354 SRAIEVLDNSIFQGRLLHV 372
A + ++ G+ + V
Sbjct: 62 KNAAKDMNGKSLHGKAIKV 80
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/77 (31%), Positives = 38/77 (49%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYF 61
++ + L + E L+ F + G I++ L++ + KSR FAFI F +A+ A K
Sbjct: 9 KLFIGGLNRETNEKMLKAVFGKHGPISEVLLIKDRTSKSRGFAFITFENPADAKNAAKDM 68
Query: 62 NKSYLDTCRISCEIARK 78
N L I E A+K
Sbjct: 69 NGKSLHGKAIKVEQAKK 85
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 618 LFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETATN 677
LF+ LN +T ++ L+ FG+H G I V + +K+ + S GF FI F++ A N
Sbjct: 10 LFIGGLNRETNEKMLKAVFGKH---GPISEVLL---IKDRTSKSRGFAFITFENPADAKN 63
Query: 678 VCRDLQGTILDGHAL 692
+D+ G L G A+
Sbjct: 64 AAKDMNGKSLHGKAI 78
>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 = 42.7 bits (99), Expect = 8e-04, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 43/76 (56%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L+V L + L F FG+++++ I +D +T++ +G A+V + + E A+ AI+ +
Sbjct: 10 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 69
Query: 361 DNSIFQGRLLHVMPAR 376
+ S GR + V A+
Sbjct: 70 NESELFGRTIRVNLAK 85
Score = 29.6 bits (65), Expect = 6.7, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKL-MRTKDGKSRQFAFIGFRTEQEAEEAIKYFNK 63
V L + V + L F G+ITD ++ + + K R FAF+ F ++A AI N+
Sbjct: 12 VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 71
Query: 64 SYLDTCRISCEIAR 77
S L I +A+
Sbjct: 72 SELFGRTIRVNLAK 85
>pdb|2KYX|A Chain A, Solution Structure Of The Rrm Domain Of Cyp33
Length = 83
Score = 42.4 bits (98), Expect = 9e-04, Method: Composition-based stats.
Identities = 22/76 (28%), Positives = 43/76 (56%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L+V L + L F FG+++++ I +D +T++ +G A+V + + E A+ AI+ +
Sbjct: 8 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 67
Query: 361 DNSIFQGRLLHVMPAR 376
+ S GR + V A+
Sbjct: 68 NESELFGRTIRVNLAK 83
Score = 29.3 bits (64), Expect = 7.1, Method: Composition-based stats.
Identities = 23/74 (31%), Positives = 36/74 (48%), Gaps = 1/74 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKL-MRTKDGKSRQFAFIGFRTEQEAEEAIKYFNK 63
V L + V + L F G+ITD ++ + + K R FAF+ F ++A AI N+
Sbjct: 10 VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 69
Query: 64 SYLDTCRISCEIAR 77
S L I +A+
Sbjct: 70 SELFGRTIRVNLAK 83
>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 = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 42/80 (52%)
Query: 293 QEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPES 352
Q +E LFV + ATE+++ + F+++G + +H+ +D+ T KG V Y +
Sbjct: 18 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 77
Query: 353 ASRAIEVLDNSIFQGRLLHV 372
A A+E L+ G+ + V
Sbjct: 78 AQAAMEGLNGQDLMGQPISV 97
>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 = 42.4 bits (98), Expect = 0.001, Method: Composition-based stats.
Identities = 21/72 (29%), Positives = 41/72 (56%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L+V L + L F FG+++++ I +D +T++ +G A+V + + E A+ AI+ +
Sbjct: 5 LYVGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNM 64
Query: 361 DNSIFQGRLLHV 372
+ S GR + V
Sbjct: 65 NESELFGRTIRV 76
Score = 29.6 bits (65), Expect = 6.7, Method: Composition-based stats.
Identities = 21/63 (33%), Positives = 32/63 (50%), Gaps = 1/63 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKL-MRTKDGKSRQFAFIGFRTEQEAEEAIKYFNK 63
V L + V + L F G+ITD ++ + + K R FAF+ F ++A AI N+
Sbjct: 7 VGGLAEEVDDKVLHAAFIPFGDITDIQIPLDYETEKHRGFAFVEFELAEDAAAAIDNMNE 66
Query: 64 SYL 66
S L
Sbjct: 67 SEL 69
>pdb|2SXL|A Chain A, Sex-Lethal Rbd1, Nmr, Minimized Average Structure
Length = 88
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 25/82 (30%), Positives = 41/82 (50%), Gaps = 1/82 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRT-KDGKSRQFAFIGFRTEQEAEEAIK 59
+ + V LP+ +T+ L F G I ++MR K G S +AF+ F +E +++ AIK
Sbjct: 4 TNLIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIK 63
Query: 60 YFNKSYLDTCRISCEIARKVGD 81
N + R+ AR G+
Sbjct: 64 VLNGITVRNKRLKVSYARPGGE 85
Score = 37.4 bits (85), Expect = 0.032, Method: Composition-based stats.
Identities = 25/76 (32%), Positives = 36/76 (47%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V LP T+ EL F G ++ I+ D T S G A+V + + RAI+VL
Sbjct: 6 LIVNYLPQDMTDRELYALFRAIGPINTCRIMRDYKTGYSYGYAFVDFTSEMDSQRAIKVL 65
Query: 361 DNSIFQGRLLHVMPAR 376
+ + + L V AR
Sbjct: 66 NGITVRNKRLKVSYAR 81
>pdb|1X4B|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleaoproteins A2B1
Length = 116
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 19/72 (26%), Positives = 41/72 (56%), Gaps = 1/72 (1%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LF+ L + TE+ LR ++ ++G +++ ++ D +KRS+G +V ++ A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAMAA 88
Query: 360 LDNSIFQGRLLH 371
+SI GR++
Sbjct: 89 RPHSI-DGRVVE 99
Score = 37.0 bits (84), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 19/58 (32%), Positives = 33/58 (56%), Gaps = 1/58 (1%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGK-SRQFAFIGFRTEQEAEEAI 58
++ + L TE+ LR+++ Q G++TD +MR K SR F F+ F + E + A+
Sbjct: 29 KLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSMAEVDAAM 86
Score = 35.0 bits (79), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 22/77 (28%), Positives = 42/77 (54%), Gaps = 5/77 (6%)
Query: 596 LEQQLEGVTDADIDPDRVESRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLK 655
+E+ LE V ++ + R LF+ L+F+T +E+LR ++ + G++ V +
Sbjct: 8 MEKTLETVPLERKKREKEQFRKLFIGGLSFETTEESLRNYYEQW---GKLTDCVVMRDPA 64
Query: 656 NGKNVSMGFGFIEFDSV 672
+ + S GFGF+ F S+
Sbjct: 65 SKR--SRGFGFVTFSSM 79
>pdb|2DH7|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Nucleolysin Tiar
Length = 105
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 24/86 (27%), Positives = 46/86 (53%), Gaps = 2/86 (2%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMR-TKDGKSRQFAFIGFRTEQEAEEAIKY 60
+ V +L +T + ++ F+ G+I+DA++++ GKS+ + F+ F + +AE AI +
Sbjct: 17 HVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGFVSFYNKLDAENAIVH 76
Query: 61 FNKSYLDTCRISCEIA-RKVGDPNMP 85
+L +I A RK P+ P
Sbjct: 77 MGGQWLGGRQIRTNWATRKPPAPSGP 102
Score = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/86 (26%), Positives = 41/86 (47%)
Query: 285 SSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAY 344
SS S +++ +FV +L T ++++ F+ FG +S+ +V D T +SKG +
Sbjct: 2 SSGSSGQKKDTSNHFHVFVGDLSPEITTEDIKSAFAPFGKISDARVVKDMATGKSKGYGF 61
Query: 345 VLYAIPESASRAIEVLDNSIFQGRLL 370
V + A AI + GR +
Sbjct: 62 VSFYNKLDAENAIVHMGGQWLGGRQI 87
>pdb|3EX7|B Chain B, The Crystal Structure Of Ejc In Its Transition State
pdb|3EX7|G Chain G, The Crystal Structure Of Ejc In Its Transition State
Length = 126
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 42/80 (52%)
Query: 293 QEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPES 352
Q +E LFV + ATE+++ + F+++G + +H+ +D+ T KG V Y +
Sbjct: 17 QRSVEGWILFVTGVHEEATEEDIHDKFAEYGEIKNIHLNLDRRTGYLKGYTLVEYETYKE 76
Query: 353 ASRAIEVLDNSIFQGRLLHV 372
A A+E L+ G+ + V
Sbjct: 77 AQAAMEGLNGQDLMGQPISV 96
>pdb|2DNK|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 4
Rna Binding Protein
Length = 105
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 25/64 (39%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LFV L +ED++R F FGN+ E I+ D SKG A+V Y+ A AI
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGN-SKGCAFVKYSSHAEAQAAINA 75
Query: 360 LDNS 363
L S
Sbjct: 76 LHGS 79
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 33/63 (52%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYF 61
++ V L K +ED +R F G I + ++R DG S+ AF+ + + EA+ AI
Sbjct: 17 KLFVGMLNKQQSEDDVRRLFEAFGNIEECTILRGPDGNSKGCAFVKYSSHAEAQAAINAL 76
Query: 62 NKS 64
+ S
Sbjct: 77 HGS 79
>pdb|2DGP|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 4 Rna-Binding Protein
Length = 106
Score = 42.0 bits (97), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 20/61 (32%), Positives = 34/61 (55%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LF+ +P E +L+ F +FG + E+ ++ D+ T KG A++ Y ESA +A
Sbjct: 15 KLFIGQIPRNLDEKDLKPLFEEFGKIYELTVLKDRFTGMHKGCAFLTYCERESALKAQSA 74
Query: 360 L 360
L
Sbjct: 75 L 75
>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 = 41.6 bits (96), Expect = 0.002, Method: Composition-based stats.
Identities = 28/99 (28%), Positives = 48/99 (48%), Gaps = 4/99 (4%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L++RNLPY T +E+ + F K+G + ++ + +T ++G AYV+Y A A + L
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 361 DNSIFQGRLLHVMPARHKKSSDKQELHNSTSQGTKTLKQ 399
R L V+ ++ K + Q K LK+
Sbjct: 78 SGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQ-LKLLKE 115
Score = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 494 NHVFLVKNLPYDSSEGELAKMFGKFGSLDKVIL---PSTKTLALVVFLEPVEAAAA 546
N + ++NLPY + E+ +FGK+G + ++ + P T+ A VV+ + +A A
Sbjct: 18 NRILYIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 73
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 41.6 bits (96), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 37/78 (47%), Gaps = 6/78 (7%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
RLFV NLP TE++ + F ++G SEV I R +G ++ A A
Sbjct: 24 RLFVGNLPTDITEEDFKRLFERYGEPSEVFI------NRDRGFGFIRLESRTLAEIAKAE 77
Query: 360 LDNSIFQGRLLHVMPARH 377
LD +I + R L + A H
Sbjct: 78 LDGTILKSRPLRIRFATH 95
Score = 37.4 bits (85), Expect = 0.034, Method: Compositional matrix adjust.
Identities = 25/74 (33%), Positives = 38/74 (51%), Gaps = 4/74 (5%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V+NL + + L + FS+FG V + +VVD D R+ G +V +A A +A+E
Sbjct: 99 LTVKNLSPVVSNELLEQAFSQFGPVEKAVVVVD-DRGRATGKGFVEFAAKPPARKALERC 157
Query: 361 DNSIFQGRLLHVMP 374
+ F LL P
Sbjct: 158 GDGAF---LLTTTP 168
>pdb|1D8Z|A Chain A, Solution Structure Of The First Rna-Binding Domain
(Rbd1) Of Hu Antigen C (Huc)
Length = 89
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 39/78 (50%), Gaps = 1/78 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIK 59
+ + V LP+ +T+D + F G+I KL+R K G+S + F+ + +A++AI
Sbjct: 5 TNLIVNYLPQNMTQDEFKSLFGSIGDIESCKLVRDKITGQSLGYGFVNYSDPNDADKAIN 64
Query: 60 YFNKSYLDTCRISCEIAR 77
N L T I AR
Sbjct: 65 TLNGLKLQTKTIKVSYAR 82
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 24/78 (30%), Positives = 43/78 (55%), Gaps = 2/78 (2%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
++FVRNLP+ T L++ F++ G+V ++ + + +SKG V + PE A RA +
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERACRM 67
Query: 360 LDNSIFQGRLLHVMPARH 377
++ GR + V R+
Sbjct: 68 MNGMKLSGREIDVRIDRN 85
Score = 37.7 bits (86), Expect = 0.024, Method: Composition-based stats.
Identities = 26/79 (32%), Positives = 42/79 (53%), Gaps = 7/79 (8%)
Query: 618 LFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETATN 677
+FV+NL F + L+ F E G +L +K ++NGK S G G ++F+S E A
Sbjct: 11 IFVRNLPFDFTWKMLKDKFNEC---GHVLYADIK--MENGK--SKGCGVVKFESPEVAER 63
Query: 678 VCRDLQGTILDGHALILQL 696
CR + G L G + +++
Sbjct: 64 ACRMMNGMKLSGREIDVRI 82
Score = 36.6 bits (83), Expect = 0.050, Method: Composition-based stats.
Identities = 24/82 (29%), Positives = 40/82 (48%), Gaps = 1/82 (1%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYF 61
+I V+NLP T L+D F++ G + A + + ++GKS+ + F + + AE A +
Sbjct: 10 QIFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCGVVKFESPEVAERACRMM 68
Query: 62 NKSYLDTCRISCEIARKVGDPN 83
N L I I R P+
Sbjct: 69 NGMKLSGREIDVRIDRNASGPS 90
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 43/80 (53%), Gaps = 2/80 (2%)
Query: 298 SGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAI 357
S +FVRNLP+ T L++ F++ G+V ++ + + +SKG V + PE A RA
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNECGHV--LYADIKMENGKSKGCGVVKFESPEVAERAC 62
Query: 358 EVLDNSIFQGRLLHVMPARH 377
+++ GR + V R+
Sbjct: 63 RMMNGMKLSGREIDVRIDRN 82
Score = 38.5 bits (88), Expect = 0.013, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 43/82 (52%), Gaps = 7/82 (8%)
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVET 674
S +FV+NL F + L+ F E G +L +K ++NGK S G G ++F+S E
Sbjct: 5 SSGIFVRNLPFDFTWKMLKDKFNEC---GHVLYADIK--MENGK--SKGCGVVKFESPEV 57
Query: 675 ATNVCRDLQGTILDGHALILQL 696
A CR + G L G + +++
Sbjct: 58 AERACRMMNGMKLSGREIDVRI 79
Score = 36.6 bits (83), Expect = 0.049, Method: Composition-based stats.
Identities = 25/83 (30%), Positives = 40/83 (48%), Gaps = 1/83 (1%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKY 60
S I V+NLP T L+D F++ G + A + + ++GKS+ + F + + AE A +
Sbjct: 6 SGIFVRNLPFDFTWKMLKDKFNECGHVLYADI-KMENGKSKGCGVVKFESPEVAERACRM 64
Query: 61 FNKSYLDTCRISCEIARKVGDPN 83
N L I I R P+
Sbjct: 65 MNGMKLSGREIDVRIDRNASGPS 87
>pdb|3MD3|A Chain A, Crystal Structure Of The First Two Rrm Domains Of Yeast
Poly Binding Protein (Pub1)
Length = 166
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 20/58 (34%), Positives = 33/58 (56%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYFN 62
V NL K +TED L+ +F G I + K+M K+ K+ +AF+ + +A A++ N
Sbjct: 5 VGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNKNVNYAFVEYHQSHDANIALQTLN 62
Score = 38.1 bits (87), Expect = 0.019, Method: Composition-based stats.
Identities = 27/79 (34%), Positives = 39/79 (49%), Gaps = 5/79 (6%)
Query: 614 ESRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
++ +LFV +LN DE LR F + LS V ++ G S G+GF+ F S +
Sbjct: 86 DTFNLFVGDLNVNVDDETLRNAFKDF---PSYLSGHVMWDMQTGS--SRGYGFVSFTSQD 140
Query: 674 TATNVCRDLQGTILDGHAL 692
A N +QG L+G L
Sbjct: 141 DAQNAMDSMQGQDLNGRPL 159
Score = 37.4 bits (85), Expect = 0.032, Method: Composition-based stats.
Identities = 23/88 (26%), Positives = 45/88 (51%), Gaps = 1/88 (1%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L+V NL TED L+++F G ++ + I++DK+ K + A+V Y A+ A++ L
Sbjct: 3 LYVGNLDKAITEDILKQYFQVGGPIANIKIMIDKNNK-NVNYAFVEYHQSHDANIALQTL 61
Query: 361 DNSIFQGRLLHVMPARHKKSSDKQELHN 388
+ + ++ + A + S + N
Sbjct: 62 NGKQIENNIVKINWAFQSQQSSSDDTFN 89
Score = 34.7 bits (78), Expect = 0.19, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 33/72 (45%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
LFV +L ++ LR F F + H++ D T S+G +V + + A A++ +
Sbjct: 90 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 149
Query: 361 DNSIFQGRLLHV 372
GR L +
Sbjct: 150 QGQDLNGRPLRI 161
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 41.2 bits (95), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 25/81 (30%), Positives = 45/81 (55%), Gaps = 3/81 (3%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYFN 62
+ + NL TE+ L++ F + T K+ + ++GKS+ +AFI F + ++A+EA+ N
Sbjct: 18 LVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 63 KSYLDTCRISCEIARKVGDPN 83
K ++ I E+ G PN
Sbjct: 75 KREIEGRAIRLELQGPRGSPN 95
Score = 37.0 bits (84), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 26/83 (31%), Positives = 44/83 (53%), Gaps = 9/83 (10%)
Query: 614 ESRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
ES++L + NL++ +E L++ F + +KV ++ +NGK S G+ FIEF S E
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVF------EKATFIKVPQN-QNGK--SKGYAFIEFASFE 64
Query: 674 TATNVCRDLQGTILDGHALILQL 696
A ++G A+ L+L
Sbjct: 65 DAKEALNSCNKREIEGRAIRLEL 87
Score = 36.6 bits (83), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 24/76 (31%), Positives = 42/76 (55%), Gaps = 4/76 (5%)
Query: 297 ESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRA 356
ES L + NL Y+ATE+ L+E F K + + + +++ K SKG A++ +A E A A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEK---ATFIKVPQNQNGK-SKGYAFIEFASFEDAKEA 69
Query: 357 IEVLDNSIFQGRLLHV 372
+ + +GR + +
Sbjct: 70 LNSCNKREIEGRAIRL 85
>pdb|2DGQ|A Chain A, Solution Structure Of The N-Terminal Rna Binding Domain In
Bruno-Like 6 Rna-Binding Protein
Length = 108
Score = 41.2 bits (95), Expect = 0.002, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 41/76 (53%)
Query: 285 SSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAY 344
SS S V + ++ +LFV +P E +L+ F +FG + E+ ++ D+ T KG A+
Sbjct: 2 SSGSSGVPMKDHDAIKLFVGQIPRGLDEQDLKPLFEEFGRIYELTVLKDRLTGLHKGCAF 61
Query: 345 VLYAIPESASRAIEVL 360
+ Y +SA +A L
Sbjct: 62 LTYCARDSALKAQSAL 77
>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 = 40.8 bits (94), Expect = 0.002, Method: Composition-based stats.
Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 6/89 (6%)
Query: 280 DPGNPSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRS 339
DP N ++ D + LFV + Y TE +LR F +G + +H+V K + +
Sbjct: 90 DPHNDPNAQGDAFKT------LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKP 143
Query: 340 KGIAYVLYAIPESASRAIEVLDNSIFQGR 368
+G A++ Y A + D GR
Sbjct: 144 RGYAFIEYEHERDMHSAYKHADGKKIDGR 172
Score = 33.9 bits (76), Expect = 0.31, Method: Composition-based stats.
Identities = 20/66 (30%), Positives = 34/66 (51%), Gaps = 1/66 (1%)
Query: 13 TEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIKYFNKSYLDTCRI 71
TE +LR F G I ++ +K GK R +AFI + E++ A K+ + +D R+
Sbjct: 115 TESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRRV 174
Query: 72 SCEIAR 77
++ R
Sbjct: 175 LVDVER 180
Score = 30.8 bits (68), Expect = 2.6, Method: Composition-based stats.
Identities = 21/81 (25%), Positives = 40/81 (49%), Gaps = 5/81 (6%)
Query: 616 RSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETA 675
++LFV +N+ T + LR+ F + RI V K ++GK G+ FIE++
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSK---RSGK--PRGYAFIEYEHERDM 157
Query: 676 TNVCRDLQGTILDGHALILQL 696
+ + G +DG +++ +
Sbjct: 158 HSAYKHADGKKIDGRRVLVDV 178
>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 = 40.4 bits (93), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 21/72 (29%), Positives = 34/72 (47%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
LFV + Y TE +LR F +G + +H+V K + + +G A++ Y A +
Sbjct: 105 LFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHA 164
Query: 361 DNSIFQGRLLHV 372
D GR + V
Sbjct: 165 DGKKIDGRRVLV 176
Score = 34.7 bits (78), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 20/67 (29%), Positives = 34/67 (50%), Gaps = 1/67 (1%)
Query: 12 VTEDRLRDFFSQKGEITDAKLMRTK-DGKSRQFAFIGFRTEQEAEEAIKYFNKSYLDTCR 70
TE +LR F G I ++ +K GK R +AFI + E++ A K+ + +D R
Sbjct: 114 TTESKLRREFEVYGPIKRIHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHADGKKIDGRR 173
Query: 71 ISCEIAR 77
+ ++ R
Sbjct: 174 VLVDVER 180
Score = 33.5 bits (75), Expect = 0.42, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 38/81 (46%), Gaps = 5/81 (6%)
Query: 616 RSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETA 675
++LFV +N+ T + LR+ F + RI V K+ K G+ FIE++
Sbjct: 103 KTLFVARVNYDTTESKLRREFEVYGPIKRIHMVYSKRSGK-----PRGYAFIEYEHERDM 157
Query: 676 TNVCRDLQGTILDGHALILQL 696
+ + G +DG +++ +
Sbjct: 158 HSAYKHADGKKIDGRRVLVDV 178
>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 = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 28/99 (28%), Positives = 47/99 (47%), Gaps = 4/99 (4%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L +RNLPY T +E+ + F K+G + ++ + +T ++G AYV+Y A A + L
Sbjct: 21 LMIRNLPYKITAEEMYDIFGKYGPIRQIRV---GNTPETRGTAYVVYEDIFDAKNACDHL 77
Query: 361 DNSIFQGRLLHVMPARHKKSSDKQELHNSTSQGTKTLKQ 399
R L V+ ++ K + Q K LK+
Sbjct: 78 SGFNVCNRYLVVLYYNANRAFQKMDTKKKEEQ-LKLLKE 115
Score = 36.6 bits (83), Expect = 0.058, Method: Composition-based stats.
Identities = 17/56 (30%), Positives = 33/56 (58%), Gaps = 3/56 (5%)
Query: 494 NHVFLVKNLPYDSSEGELAKMFGKFGSLDKVIL---PSTKTLALVVFLEPVEAAAA 546
N + +++NLPY + E+ +FGK+G + ++ + P T+ A VV+ + +A A
Sbjct: 18 NRILMIRNLPYKITAEEMYDIFGKYGPIRQIRVGNTPETRGTAYVVYEDIFDAKNA 73
>pdb|1D9A|A Chain A, Solution Structure Of The Second Rna-Binding Domain
(Rbd2) Of Hu Antigen C (Huc)
Length = 85
Score = 40.4 bits (93), Expect = 0.004, Method: Composition-based stats.
Identities = 24/59 (40%), Positives = 31/59 (52%), Gaps = 1/59 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAK-LMRTKDGKSRQFAFIGFRTEQEAEEAIKYFN 62
V LPK +++ + FSQ G I ++ L+ G SR FI F EAEEAIK N
Sbjct: 6 VSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGLN 64
Score = 38.1 bits (87), Expect = 0.020, Method: Composition-based stats.
Identities = 18/61 (29%), Positives = 36/61 (59%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L+V LP T ++ E+ + FS++G + I++D+ T S+G+ ++ + A AI+ L
Sbjct: 4 LYVSGLPKTMSQKEMEQLFSQYGRIITSRILLDQATGVSRGVGFIRFDKRIEAEEAIKGL 63
Query: 361 D 361
+
Sbjct: 64 N 64
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 40.0 bits (92), Expect = 0.004, Method: Compositional matrix adjust.
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 3/78 (3%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
LFV+ L TE+ L+E F G+V IV D++T SKG +V + E A A E +
Sbjct: 18 LFVKGLSEDTTEETLKESFD--GSV-RARIVTDRETGSSKGFGFVDFNSEEDAKAAKEAM 74
Query: 361 DNSIFQGRLLHVMPARHK 378
++ G + + A+ K
Sbjct: 75 EDGEIDGNKVTLDWAKPK 92
Score = 40.0 bits (92), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 25/86 (29%), Positives = 44/86 (51%), Gaps = 8/86 (9%)
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVET 674
S++LFVK L+ T +E L++ F ++ RI++ + S GFGF++F+S E
Sbjct: 15 SKTLFVKGLSEDTTEETLKESFDGSVR-ARIVTDRET-------GSSKGFGFVDFNSEED 66
Query: 675 ATNVCRDLQGTILDGHALILQLCHAK 700
A ++ +DG+ + L K
Sbjct: 67 AKAAKEAMEDGEIDGNKVTLDWAKPK 92
>pdb|3PGW|A Chain A, Crystal Structure Of Human U1 Snrnp
pdb|3PGW|P Chain P, Crystal Structure Of Human U1 Snrnp
Length = 282
Score = 39.7 bits (91), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 610 PDRVESRSLFVKNLNFKTCDENLRKHFGEHIKE-GRILSVKVKKHLKNGKNVSMGFGFIE 668
P+ + ++++ NLN K + L+K + G+IL + V + LK G F+
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK-----MRGQAFVI 58
Query: 669 FDSVETATNVCRDLQGTILDGHALILQLCHAKKDEQVVKK 708
F V +ATN R +QG + +Q +AK D ++ K
Sbjct: 59 FKEVSSATNALRSMQGFPFYDKPMRIQ--YAKTDSDIIAK 96
Score = 37.0 bits (84), Expect = 0.039, Method: Compositional matrix adjust.
Identities = 60/270 (22%), Positives = 105/270 (38%), Gaps = 45/270 (16%)
Query: 301 LFVRNLPYTATEDELREH----FSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRA 356
+++ NL +DEL++ FS+FG + + I+V + K +G A+V++ SA+ A
Sbjct: 12 IYINNLNEKIKKDELKKSLYAIFSQFGQI--LDILVSRSLK-MRGQAFVIFKEVSSATNA 68
Query: 357 IEVLDNSIFQGRLLHVMPARHKKSSD--------------KQELHNSTSQGTKTLKQXXX 402
+ + F + + + A K SD K+E SQ T K
Sbjct: 69 LRSMQGFPFYDKPMRIQYA--KTDSDIIAKMKGTFVERDRKREKRKPKSQETPATK---- 122
Query: 403 XXXKASEASGNTKAWNSL-----FMRPDTVVENIARKHGVSKSDLLDREANDLAVRIALG 457
KA + G T ++ M P T I H + + +A G
Sbjct: 123 ---KAVQGGGATPVVGAVQGPVPGMPPMTQAPRIMH-HMPGQPPYMPPPGMIPPPGLAPG 178
Query: 458 ETQVIAETKKALTNAGVNVSSLEEFSAGKTDGLKRSNHVFLVKNLPYDSSEGELAKMFGK 517
+ A + L + + NH+ + NLP +++E L+ +F +
Sbjct: 179 QIPPGAMPPQQLMPG--------QMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQ 230
Query: 518 FGSLDKV-ILPSTKTLALVVFLEPVEAAAA 546
F +V ++P +A V F V+A AA
Sbjct: 231 FPGFKEVRLVPGRHDIAFVEFDNEVQAGAA 260
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In
Trinucleotide Repeat Containing 4 Variant
Length = 102
Score = 39.7 bits (91), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYF 61
++ V L K T++ +R F G I + ++R DG S+ AF+ F+T EA+ AI
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGTSKGCAFVKFQTHAEAQAAINTL 73
Query: 62 NKS 64
+ S
Sbjct: 74 HSS 76
Score = 36.6 bits (83), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 21/64 (32%), Positives = 33/64 (51%), Gaps = 1/64 (1%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LFV L T++++R+ F FG + E ++ D SKG A+V + A AI
Sbjct: 14 KLFVGMLGKQQTDEDVRKMFEPFGTIDECTVLRGPDGT-SKGCAFVKFQTHAEAQAAINT 72
Query: 360 LDNS 363
L +S
Sbjct: 73 LHSS 76
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 39.7 bits (91), Expect = 0.006, Method: Composition-based stats.
Identities = 26/78 (33%), Positives = 40/78 (51%), Gaps = 5/78 (6%)
Query: 314 ELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVLDNSIFQGRLLHVM 373
+L + FS G V +V I+ D++++RSKGIAYV + +S AI + RLL V
Sbjct: 41 DLEDFFSAVGKVRDVRIISDRNSRRSKGIAYVEFCEIQSVPLAIGLTGQ-----RLLGVP 95
Query: 374 PARHKKSSDKQELHNSTS 391
++K L +S
Sbjct: 96 IIVQASQAEKNRLSGPSS 113
>pdb|1FHT|A Chain A, Rna-Binding Domain Of The U1a Spliceosomal Protein U1a117,
Nmr, 43 Structures
Length = 116
Score = 39.7 bits (91), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 610 PDRVESRSLFVKNLNFKTCDENLRKHFGEHIKE-GRILSVKVKKHLKNGKNVSMGFGFIE 668
P+ + ++++ NLN K + L+K + G+IL + V + LK G F+
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK-----MRGQAFVI 57
Query: 669 FDSVETATNVCRDLQGTILDGHALILQLCHAKKDEQVVKK 708
F V +ATN R +QG + +Q +AK D ++ K
Sbjct: 58 FKEVSSATNALRSMQGFPFYDKPMRIQ--YAKTDSDIIAK 95
>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 = 39.3 bits (90), Expect = 0.007, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 35/63 (55%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYFNKS 64
V NL Y TE+++ + FS+ G+I + K + F F+ + + +AE A++Y N +
Sbjct: 23 VGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKTACGFCFVEYYSRADAENAMRYINGT 82
Query: 65 YLD 67
LD
Sbjct: 83 RLD 85
Score = 35.8 bits (81), Expect = 0.083, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 3/81 (3%)
Query: 292 QQEVL--ESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAI 349
+QE L +S L+V NL + TE+++ E FSK G++ ++ + +DK K + G +V Y
Sbjct: 10 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDK-MKTACGFCFVEYYS 68
Query: 350 PESASRAIEVLDNSIFQGRLL 370
A A+ ++ + R++
Sbjct: 69 RADAENAMRYINGTRLDDRII 89
Score = 31.6 bits (70), Expect = 1.6, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 6/75 (8%)
Query: 614 ESRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
+S +L+V NL+F T +E + + F K G I K+ L K + GF F+E+ S
Sbjct: 17 KSCTLYVGNLSFYTTEEQIYELFS---KSGDI--KKIIMGLDKMKT-ACGFCFVEYYSRA 70
Query: 674 TATNVCRDLQGTILD 688
A N R + GT LD
Sbjct: 71 DAENAMRYINGTRLD 85
>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 = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 39/70 (55%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
+++ ++PY TE+++ + S G V + ++ D T RSKG A++ + ES++ A+ L
Sbjct: 7 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 66
Query: 361 DNSIFQGRLL 370
+ R L
Sbjct: 67 NGYQLGSRFL 76
Score = 35.8 bits (81), Expect = 0.078, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 7 NLPKYVTEDRLRDFFSQKGEITDAKLM-RTKDGKSRQFAFIGFRTEQEAEEAIKYFNKSY 65
++P TE+++ D S G + + K+M + G+S+ +AFI FR + + A++ N
Sbjct: 11 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 70
Query: 66 LDTCRISC 73
L + + C
Sbjct: 71 LGSRFLKC 78
>pdb|2X1A|A Chain A, Structure Of Rna15 Rrm With Rna Bound (G)
pdb|2X1B|A Chain A, Structure Of Rna15 Rrm
Length = 97
Score = 39.3 bits (90), Expect = 0.008, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 39/70 (55%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
+++ ++PY TE+++ + S G V + ++ D T RSKG A++ + ES++ A+ L
Sbjct: 6 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 65
Query: 361 DNSIFQGRLL 370
+ R L
Sbjct: 66 NGYQLGSRFL 75
Score = 35.8 bits (81), Expect = 0.078, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 7 NLPKYVTEDRLRDFFSQKGEITDAKLM-RTKDGKSRQFAFIGFRTEQEAEEAIKYFNKSY 65
++P TE+++ D S G + + K+M + G+S+ +AFI FR + + A++ N
Sbjct: 10 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 69
Query: 66 LDTCRISC 73
L + + C
Sbjct: 70 LGSRFLKC 77
>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 = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 45/81 (55%), Gaps = 2/81 (2%)
Query: 292 QQEVL--ESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAI 349
+QE L +S L+V NL + TE+++ E FSK G++ ++ + +DK K + G +V Y
Sbjct: 31 EQEKLLKKSCTLYVGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYS 90
Query: 350 PESASRAIEVLDNSIFQGRLL 370
A A+ ++ + R++
Sbjct: 91 RADAENAMRYINGTRLDDRII 111
Score = 37.7 bits (86), Expect = 0.025, Method: Composition-based stats.
Identities = 21/64 (32%), Positives = 36/64 (56%), Gaps = 1/64 (1%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSR-QFAFIGFRTEQEAEEAIKYFNK 63
V NL Y TE+++ + FS+ G+I + K K+ F F+ + + +AE A++Y N
Sbjct: 44 VGNLSFYTTEEQIYELFSKSGDIKKIIMGLDKMKKTACGFCFVEYYSRADAENAMRYING 103
Query: 64 SYLD 67
+ LD
Sbjct: 104 TRLD 107
Score = 35.8 bits (81), Expect = 0.084, Method: Composition-based stats.
Identities = 27/75 (36%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 614 ESRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVE 673
+S +L+V NL+F T +E + + F K G I K+ L K + GF F+E+ S
Sbjct: 38 KSCTLYVGNLSFYTTEEQIYELFS---KSGDI--KKIIMGLDKMKKTACGFCFVEYYSRA 92
Query: 674 TATNVCRDLQGTILD 688
A N R + GT LD
Sbjct: 93 DAENAMRYINGTRLD 107
>pdb|2X1F|A Chain A, Structure Of Rna15 Rrm With Bound Rna (Gu)
Length = 96
Score = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 20/70 (28%), Positives = 39/70 (55%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
+++ ++PY TE+++ + S G V + ++ D T RSKG A++ + ES++ A+ L
Sbjct: 5 VYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNL 64
Query: 361 DNSIFQGRLL 370
+ R L
Sbjct: 65 NGYQLGSRFL 74
Score = 35.8 bits (81), Expect = 0.096, Method: Composition-based stats.
Identities = 19/68 (27%), Positives = 37/68 (54%), Gaps = 1/68 (1%)
Query: 7 NLPKYVTEDRLRDFFSQKGEITDAKLM-RTKDGKSRQFAFIGFRTEQEAEEAIKYFNKSY 65
++P TE+++ D S G + + K+M + G+S+ +AFI FR + + A++ N
Sbjct: 9 SIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSASAVRNLNGYQ 68
Query: 66 LDTCRISC 73
L + + C
Sbjct: 69 LGSRFLKC 76
>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 = 38.9 bits (89), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 35/72 (48%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V NLP + T+ + E FG++ +V + T +SKG + Y +SA+RA L
Sbjct: 96 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 155
Query: 361 DNSIFQGRLLHV 372
R L+V
Sbjct: 156 LGKPLGPRTLYV 167
>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 = 38.9 bits (89), Expect = 0.010, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
+FV + E E+R F+++G+V EV I+ D+ T SKG +V + + +E
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 361 DNSIFQGRLLHVMPARHKKS 380
N F G+ L + PA K++
Sbjct: 71 IN--FHGKKLKLGPAIRKQN 88
>pdb|3VF0|B Chain B, Raver1 In Complex With Metavinculin L954 Deletion Mutant
Length = 285
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 35/72 (48%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V NLP + T+ + E FG++ +V + T +SKG + Y +SA+RA L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 361 DNSIFQGRLLHV 372
R L+V
Sbjct: 158 LGKPLGPRTLYV 169
>pdb|3SMZ|A Chain A, Human Raver1 Rrm1-3 Domains (Residues 39-320)
Length = 284
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 35/72 (48%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L V NLP + T+ + E FG++ +V + T +SKG + Y +SA+RA L
Sbjct: 98 LCVANLPPSLTQQQFEELVRPFGSLERCFLVYSERTGQSKGYGFAEYMKKDSAARAKSDL 157
Query: 361 DNSIFQGRLLHV 372
R L+V
Sbjct: 158 LGKPLGPRTLYV 169
>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 = 38.5 bits (88), Expect = 0.012, Method: Composition-based stats.
Identities = 27/76 (35%), Positives = 37/76 (48%), Gaps = 5/76 (6%)
Query: 617 SLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETAT 676
+LFV +LN DE LR F + LS V ++ G S G+GF+ F S + A
Sbjct: 3 NLFVGDLNVNVDDETLRNAFKDF---PSYLSGHVMWDMQTGS--SRGYGFVSFTSQDDAQ 57
Query: 677 NVCRDLQGTILDGHAL 692
N +QG L+G L
Sbjct: 58 NAMDSMQGQDLNGRPL 73
Score = 35.4 bits (80), Expect = 0.13, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 33/72 (45%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
LFV +L ++ LR F F + H++ D T S+G +V + + A A++ +
Sbjct: 4 LFVGDLNVNVDDETLRNAFKDFPSYLSGHVMWDMQTGSSRGYGFVSFTSQDDAQNAMDSM 63
Query: 361 DNSIFQGRLLHV 372
GR L +
Sbjct: 64 QGQDLNGRPLRI 75
>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 = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 25/79 (31%), Positives = 41/79 (51%), Gaps = 3/79 (3%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
+FV + E E+R F+++G+V EV I+ D+ T SKG +V + + +E
Sbjct: 12 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 70
Query: 361 DNSIFQGRLLHVMPARHKK 379
N F G+ L + PA K+
Sbjct: 71 IN--FHGKKLKLGPAIRKQ 87
>pdb|1URN|A Chain A, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|B Chain B, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1URN|C Chain C, U1a MutantRNA COMPLEX + GLYCEROL
pdb|1NU4|A Chain A, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|1NU4|B Chain B, U1a Rna Binding Domain At 1.8 Angstrom Resolution Reveals
A Pre- Organized C-Terminal Helix
pdb|3HHN|B Chain B, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
pdb|3HHN|D Chain D, Crystal Structure Of Class I Ligase Ribozyme Self-Ligation
Product, In Complex With U1a Rbd
Length = 97
Score = 38.5 bits (88), Expect = 0.012, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 610 PDRVESRSLFVKNLNFKTCDENLRKHFGEHI-KEGRILSVKVKKHLKNGKNVSMGFGFIE 668
P+ + ++++ NLN K + L+K + G+IL + V + LK G F+
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK-----MRGQAFVI 57
Query: 669 FDSVETATNVCRDLQGTILDGHALILQLCHAKKDEQVVKK 708
F V +ATN R +QG + +Q +AK D ++ K
Sbjct: 58 FKEVSSATNALRSMQGFPFYDKPMRIQ--YAKTDSDIIAK 95
>pdb|2XSF|A Chain A, Crystal Structure Of The Rrm Domain Of Mouse Deleted In
Azoospermia-Like
Length = 89
Score = 38.5 bits (88), Expect = 0.012, Method: Composition-based stats.
Identities = 25/80 (31%), Positives = 42/80 (52%), Gaps = 3/80 (3%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
+FV + E E+R F+++G+V EV I+ D+ T SKG +V + + +E
Sbjct: 13 VFVGGIDVRMDETEIRSFFARYGSVKEVKIITDR-TGVSKGYGFVSFYNDVDVQKIVESQ 71
Query: 361 DNSIFQGRLLHVMPARHKKS 380
N F G+ L + PA K++
Sbjct: 72 IN--FHGKKLKLGPAIRKQN 89
>pdb|1M5K|C Chain C, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5K|F Chain F, Crystal Structure Of A Hairpin Ribozyme In The
Catalytically-Active Conformation
pdb|1M5O|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5O|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5P|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|C Chain C, Transition State Stabilization By A Catalytic Rna
pdb|1M5V|F Chain F, Transition State Stabilization By A Catalytic Rna
pdb|1SJ3|P Chain P, Hepatitis Delta Virus Gemonic Ribozyme Precursor, With
Mg2+ Bound
pdb|1SJ4|P Chain P, Crystal Structure Of A C75u Mutant Hepatitis Delta Virus
Ribozyme Precursor, In Cu2+ Solution
pdb|1SJF|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Cobalt
Hexammine Solution
pdb|1VBX|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Edta Solution
pdb|1VBY|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, And Mn2+ Bound
pdb|1VBZ|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Ba2+ Solution
pdb|1VC0|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Imidazole And
Sr2+ Solution
pdb|1VC5|A Chain A, Crystal Structure Of The Wild Type Hepatitis Delta Virus
Gemonic Ribozyme Precursor, In Edta Solution
pdb|1VC6|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Product With C75u Mutaion, Cleaved In Imidazole
And Mg2+ Solutions
pdb|1VC7|A Chain A, Crystal Structure Of The Hepatitis Delta Virus Gemonic
Ribozyme Precursor, With C75u Mutaion, In Sr2+ Solution
pdb|2OIH|A Chain A, Hepatitis Delta Virus Gemonic Ribozyme Precursor With C75u
Mutation And Bound To Monovalent Cation Tl+
pdb|2OJ3|A Chain A, Hepatitis Delta Virus Ribozyme Precursor Structure, With
C75u Mutation, Bound To Tl+ And Cobalt Hexammine
(Co(Nh3) 63+)
Length = 100
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 610 PDRVESRSLFVKNLNFKTCDENLRKHFGEHI-KEGRILSVKVKKHLKNGKNVSMGFGFIE 668
P+ + ++++ NLN K + L+K + G+IL + V + LK G F+
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK-----MRGQAFVI 58
Query: 669 FDSVETATNVCRDLQGTILDGHALILQLCHAKKDEQVVKK 708
F V +ATN R +QG + +Q +AK D ++ K
Sbjct: 59 FKEVSSATNALRSMQGFPFYDKPMRIQ--YAKTDSDIIAK 96
>pdb|1OIA|A Chain A, U1a Rnp Domain 1-95
pdb|1OIA|B Chain B, U1a Rnp Domain 1-95
Length = 95
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 27/98 (27%), Positives = 47/98 (47%), Gaps = 8/98 (8%)
Query: 610 PDRVESRSLFVKNLNFKTCDENLRKHFGEHIKE-GRILSVKVKKHLKNGKNVSMGFGFIE 668
P+ + ++++ NLN K + L+K + G+IL + V + LK G F+
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLYAIFSQFGQILDILVSRSLK-----MRGQAFVI 58
Query: 669 FDSVETATNVCRDLQGTILDGHALILQLCHAKKDEQVV 706
F V +ATN R +QG + +Q +AK D ++
Sbjct: 59 FKEVSSATNALRSMQGFPFYDKPMRIQ--YAKTDSDII 94
>pdb|3K0J|A Chain A, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|B Chain B, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|C Chain C, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
pdb|3K0J|D Chain D, Crystal Structure Of The E. Coli Thim Riboswitch In
Complex With Thiamine Pyrophosphate And The U1a
Crystallization Module
Length = 96
Score = 38.5 bits (88), Expect = 0.013, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 610 PDRVESRSLFVKNLNFKTCDENLRKHFGEHI-KEGRILSVKVKKHLKNGKNVSMGFGFIE 668
P+ + ++++ NLN K + L+K + G+IL + V + LK G F+
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK-----MRGQAFVI 57
Query: 669 FDSVETATNVCRDLQGTILDGHALILQLCHAKKDEQVVKK 708
F V +ATN R +QG + +Q +AK D ++ K
Sbjct: 58 FKEVSSATNALRSMQGFPFYDKPMRIQ--YAKTDSDIIAK 95
>pdb|1U6B|A Chain A, Crystal Structure Of A Self-Splicing Group I Intron With
Both Exons
pdb|1ZZN|A Chain A, Crystal Structure Of A Group I IntronTWO EXON COMPLEX THAT
Includes All Catalytic Metal Ion Ligands.
pdb|3G8S|A Chain A, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|B Chain B, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|C Chain C, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8S|D Chain D, Crystal Structure Of The Pre-Cleaved Bacillus Anthracis
Glms Ribozyme
pdb|3G8T|A Chain A, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|B Chain B, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|C Chain C, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G8T|D Chain D, Crystal Structure Of The G33a Mutant Bacillus Anthracis
Glms Ribozyme Bound To Glcn6p
pdb|3G96|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G96|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Man6p
pdb|3G9C|A Chain A, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|B Chain B, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|C Chain C, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3G9C|D Chain D, Crystal Structure Of The Product Bacillus Anthracis Glms
Ribozyme
pdb|3IRW|P Chain P, Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3MUM|P Chain P, Crystal Structure Of The G20a Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUR|P Chain P, Crystal Structure Of The C92u Mutant C-Di-Gmp Riboswith
Bound To C-Di- Gmp
pdb|3MUT|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Gmp
pdb|3MUV|P Chain P, Crystal Structure Of The G20aC92U MUTANT C-Di-Gmp
Riboswith Bound To C-Di-Amp
pdb|3MXH|P Chain P, Native Structure Of A C-Di-Gmp Riboswitch From V. Cholerae
pdb|3P49|B Chain B, Crystal Structure Of A Glycine Riboswitch From
Fusobacterium Nucleatum
pdb|3R1H|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1H|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Ca2+ Bound
pdb|3R1L|A Chain A, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3R1L|D Chain D, Crystal Structure Of The Class I Ligase Ribozyme-Substrate
Preligation Complex, C47u Mutant, Mg2+ Bound
pdb|3UCU|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Pgpg
pdb|3UCZ|P Chain P, The C-Di-Gmp-I Riboswitch Bound To Gpg
pdb|3UD3|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Pgpa
pdb|3UD4|P Chain P, The C92u Mutant C-Di-Gmp-I Riboswitch Bound To Gpa
Length = 98
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 610 PDRVESRSLFVKNLNFKTCDENLRKHFGEHI-KEGRILSVKVKKHLKNGKNVSMGFGFIE 668
P+ + ++++ NLN K + L+K + G+IL + V + LK G F+
Sbjct: 4 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK-----MRGQAFVI 58
Query: 669 FDSVETATNVCRDLQGTILDGHALILQLCHAKKDEQVVKK 708
F V +ATN R +QG + +Q +AK D ++ K
Sbjct: 59 FKEVSSATNALRSMQGFPFYDKPMRIQ--YAKTDSDIIAK 96
>pdb|3BO2|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO3|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3BO4|A Chain A, A Relaxed Active Site Following Exon Ligation By A Group I
Intron
pdb|3IIN|A Chain A, Plasticity Of The Kink Turn Structural Motif
Length = 95
Score = 38.5 bits (88), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 28/102 (27%), Positives = 49/102 (48%), Gaps = 8/102 (7%)
Query: 610 PDRVESRSLFVKNLNFKTCDENLRKHFGEHI-KEGRILSVKVKKHLKNGKNVSMGFGFIE 668
P+ + ++++ NLN K + L+K + G+IL + V + LK G F+
Sbjct: 1 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK-----MRGQAFVI 55
Query: 669 FDSVETATNVCRDLQGTILDGHALILQLCHAKKDEQVVKKAE 710
F V +ATN R +QG + +Q +AK D ++ K +
Sbjct: 56 FKEVSSATNALRSMQGFPFYDKPMRIQ--YAKTDSDIIAKMK 95
>pdb|2YWK|A Chain A, Crystal Structure Of Rrm-Domain Derived From Human
Putative Rna-Binding Protein 11
Length = 95
Score = 38.5 bits (88), Expect = 0.015, Method: Composition-based stats.
Identities = 18/60 (30%), Positives = 30/60 (50%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYFN 62
+ V NL V E+ L + F Q G +T + + ++GK + F F+ F+ + AI N
Sbjct: 19 VFVGNLEARVREEILYELFLQAGPLTKVTICKDREGKPKSFGFVCFKHPESVSYAIALLN 78
>pdb|1AUD|A Chain A, U1a-Utrrna, Nmr, 31 Structures
pdb|1DZ5|A Chain A, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
pdb|1DZ5|B Chain B, The Nmr Structure Of The 38kda U1a Protein-Pie Rna Complex
Reveals The Basis Of Cooperativity In Regulation Of
Polyadenylation By Human U1a Protein
Length = 101
Score = 38.1 bits (87), Expect = 0.016, Method: Compositional matrix adjust.
Identities = 28/100 (28%), Positives = 48/100 (48%), Gaps = 8/100 (8%)
Query: 610 PDRVESRSLFVKNLNFKTCDENLRKHFGEHI-KEGRILSVKVKKHLKNGKNVSMGFGFIE 668
P+ + ++++ NLN K + L+K + G+IL + V + LK G F+
Sbjct: 3 PETRPNHTIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK-----MRGQAFVI 57
Query: 669 FDSVETATNVCRDLQGTILDGHALILQLCHAKKDEQVVKK 708
F V +ATN R +QG + +Q +AK D ++ K
Sbjct: 58 FKEVSSATNALRSMQGFPFYDKPMRIQ--YAKTDSDIIAK 95
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 38.1 bits (87), Expect = 0.019, Method: Compositional matrix adjust.
Identities = 23/76 (30%), Positives = 41/76 (53%), Gaps = 8/76 (10%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
LFVRNL T TE+ L + FS+FG + V K+ K A++ + + A +A+E +
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERV--------KKLKDYAFIHFDERDGAVKAMEEM 65
Query: 361 DNSIFQGRLLHVMPAR 376
+ +G + ++ A+
Sbjct: 66 NGKDLEGENIEIVFAK 81
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 25/98 (25%), Positives = 43/98 (43%), Gaps = 13/98 (13%)
Query: 618 LFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETATN 677
LFV+NL +E L K F + K R+ K LK+ + FI FD + A
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFGKLERV------KKLKD-------YAFIHFDERDGAVK 60
Query: 678 VCRDLQGTILDGHALILQLCHAKKDEQVVKKAEKDKSS 715
++ G L+G + + ++ +KA++ +S
Sbjct: 61 AMEEMNGKDLEGENIEIVFAKPPDQKRKERKAQRQAAS 98
Score = 30.0 bits (66), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 36/75 (48%), Gaps = 7/75 (9%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYFN 62
+ V+NL VTE+ L FSQ G KL R K K + +AFI F A +A++ N
Sbjct: 14 LFVRNLANTVTEEILEKAFSQFG-----KLERVK--KLKDYAFIHFDERDGAVKAMEEMN 66
Query: 63 KSYLDTCRISCEIAR 77
L+ I A+
Sbjct: 67 GKDLEGENIEIVFAK 81
>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 = 37.4 bits (85), Expect = 0.026, Method: Compositional matrix adjust.
Identities = 22/71 (30%), Positives = 40/71 (56%), Gaps = 4/71 (5%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYFN 62
+ KNL +TED L++ F EI + ++DGKS+ A+I F++E +AE+ ++
Sbjct: 102 LLAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAEKNLEEKQ 157
Query: 63 KSYLDTCRISC 73
+ +D +S
Sbjct: 158 GAEIDGRSVSL 168
Score = 34.3 bits (77), Expect = 0.28, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L +NL + TEDEL+E F + E+ + V +D K SKGIAY+ + A + +E
Sbjct: 102 LLAKNLSFNITEDELKEVFE---DALEIRL-VSQDGK-SKGIAYIEFKSEADAEKNLEEK 156
Query: 361 DNSIFQGR 368
+ GR
Sbjct: 157 QGAEIDGR 164
Score = 33.9 bits (76), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 27/86 (31%), Positives = 43/86 (50%), Gaps = 10/86 (11%)
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVET 674
+R+L KNL+F ++ L++ F E E R++S ++GK S G +IEF S
Sbjct: 99 ARTLLAKNLSFNITEDELKEVF-EDALEIRLVS-------QDGK--SKGIAYIEFKSEAD 148
Query: 675 ATNVCRDLQGTILDGHALILQLCHAK 700
A + QG +DG ++ L K
Sbjct: 149 AEKNLEEKQGAEIDGRSVSLYYTGEK 174
>pdb|1X5T|A Chain A, Solution Structure Of The Second Rrm Domain In Splicing
Factor 3b
Length = 96
Score = 37.4 bits (85), Expect = 0.030, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 42/84 (50%), Gaps = 1/84 (1%)
Query: 298 SGRLFVRNLPYTATEDELREHFSKFGNVSEV-HIVVDKDTKRSKGIAYVLYAIPESASRA 356
S +F+ NL E L + FS FG + + I+ D DT SKG A++ +A +++ A
Sbjct: 5 SSGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAA 64
Query: 357 IEVLDNSIFQGRLLHVMPARHKKS 380
IE ++ R + V A K S
Sbjct: 65 IEAMNGQYLCNRPITVSYAFKKDS 88
Score = 37.0 bits (84), Expect = 0.040, Method: Composition-based stats.
Identities = 26/68 (38%), Positives = 35/68 (51%), Gaps = 2/68 (2%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDA-KLMRTKD-GKSRQFAFIGFRTEQEAEEAI 58
S I + NL + E L D FS G I K+MR D G S+ +AFI F + ++ AI
Sbjct: 6 SGIFIGNLDPEIDEKLLYDTFSAFGVILQTPKIMRDPDTGNSKGYAFINFASFDASDAAI 65
Query: 59 KYFNKSYL 66
+ N YL
Sbjct: 66 EAMNGQYL 73
>pdb|1X5O|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 1
Length = 114
Score = 37.4 bits (85), Expect = 0.031, Method: Composition-based stats.
Identities = 16/68 (23%), Positives = 32/68 (47%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKY 60
+ + + NLP + E L + G++ +++R G SR F + ++ E I +
Sbjct: 26 TNLYISNLPLSMDEQELENMLKPFGQVISTRILRDSSGTSRGVGFARMESTEKCEAVIGH 85
Query: 61 FNKSYLDT 68
FN ++ T
Sbjct: 86 FNGKFIKT 93
Score = 30.4 bits (67), Expect = 3.2, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 38/84 (45%), Gaps = 6/84 (7%)
Query: 292 QQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPE 351
+Q+ + L++ NLP + E EL FG V I+ D + S+G+ +A E
Sbjct: 19 KQQEQDPTNLYISNLPLSMDEQELENMLKPFGQVISTRILRDS-SGTSRGVG---FARME 74
Query: 352 SASRAIEVLDNSIFQGRLLHVMPA 375
S + V+ + F G+ + P
Sbjct: 75 STEKCEAVIGH--FNGKFIKTPPG 96
>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 = 0.031, Method: Composition-based stats.
Identities = 21/68 (30%), Positives = 39/68 (57%), Gaps = 1/68 (1%)
Query: 298 SGRLFVRNLPYTATEDELREHFSKFG-NVSEVHIVVDKDTKRSKGIAYVLYAIPESASRA 356
S + +R LP ATED++R G EV ++ +K + +S+G A+V ++ + A+R
Sbjct: 1 SNIVMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDATRW 60
Query: 357 IEVLDNSI 364
+E +S+
Sbjct: 61 MEANQHSL 68
Score = 33.9 bits (76), Expect = 0.29, Method: Composition-based stats.
Identities = 20/54 (37%), Positives = 31/54 (57%), Gaps = 2/54 (3%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKG-EITDAKLMRTKD-GKSRQFAFIGFRTEQEA 54
+ ++ LP+ TED +R G + + +LMR K G+SR FAF+ F Q+A
Sbjct: 4 VMLRMLPQAATEDDIRGQLQSHGVQAREVRLMRNKSSGQSRGFAFVEFSHLQDA 57
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 37.4 bits (85), Expect = 0.032, Method: Compositional matrix adjust.
Identities = 23/80 (28%), Positives = 37/80 (46%), Gaps = 11/80 (13%)
Query: 618 LFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETATN 677
L+V+NL T +E + K F +IK G + VK + + F+ F + E A
Sbjct: 18 LYVRNLMLSTSEEMIEKEF-NNIKPGAVERVKKIRD----------YAFVHFSNREDAVE 66
Query: 678 VCRDLQGTILDGHALILQLC 697
+ L G +LDG + + L
Sbjct: 67 AMKALNGKVLDGSPIEVTLA 86
>pdb|1X4E|A Chain A, Solution Structure Of Rrm Domain In Rna Binding Motif,
Single-Stranded Interacting Protein 2
Length = 85
Score = 37.0 bits (84), Expect = 0.035, Method: Composition-based stats.
Identities = 19/72 (26%), Positives = 36/72 (50%)
Query: 298 SGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAI 357
S L++R L T+ +L + +G + ++DK T + KG +V + P +A +A+
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPYGKIVSTKAILDKTTNKCKGYGFVDFDSPSAAQKAV 64
Query: 358 EVLDNSIFQGRL 369
L S Q ++
Sbjct: 65 TALKASGVQAQM 76
Score = 28.9 bits (63), Expect = 9.4, Method: Composition-based stats.
Identities = 21/71 (29%), Positives = 34/71 (47%), Gaps = 5/71 (7%)
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVET 674
S L+++ L T D++L K + G+I+S K L N G+GF++FDS
Sbjct: 5 SSGLYIRGLQPGTTDQDLVKLCQPY---GKIVSTKAI--LDKTTNKCKGYGFVDFDSPSA 59
Query: 675 ATNVCRDLQGT 685
A L+ +
Sbjct: 60 AQKAVTALKAS 70
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 37.0 bits (84), Expect = 0.040, Method: Composition-based stats.
Identities = 24/76 (31%), Positives = 35/76 (46%), Gaps = 2/76 (2%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYF 61
RI V NLP + + D F + G I D L + G FAF+ F ++AE+A+
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDLKNRRGGPP--FAFVEFEDPRDAEDAVYGR 81
Query: 62 NKSYLDTCRISCEIAR 77
+ D R+ E R
Sbjct: 82 DGYDYDGYRLRVEFPR 97
Score = 29.3 bits (64), Expect = 8.9, Method: Composition-based stats.
Identities = 18/73 (24%), Positives = 34/73 (46%), Gaps = 3/73 (4%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
R++V NLP ++ + F K+G + ++ + K+ + A+V + P A A+
Sbjct: 24 RIYVGNLPPDIRTKDIEDVFYKYGAIRDIDL---KNRRGGPPFAFVEFEDPRDAEDAVYG 80
Query: 360 LDNSIFQGRLLHV 372
D + G L V
Sbjct: 81 RDGYDYDGYRLRV 93
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 37.0 bits (84), Expect = 0.040, Method: Compositional matrix adjust.
Identities = 20/53 (37%), Positives = 32/53 (60%), Gaps = 4/53 (7%)
Query: 3 ICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAE 55
+ KNL +TED L++ F EI + ++DGKS+ A+I F++E +AE
Sbjct: 19 LLAKNLSFNITEDELKEVFEDALEIR----LVSQDGKSKGIAYIEFKSEADAE 67
Score = 34.7 bits (78), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 5/68 (7%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
L +NL + TEDEL+E F + E+ + V +D K SKGIAY+ + A + +E
Sbjct: 19 LLAKNLSFNITEDELKEVFE---DALEIRL-VSQDGK-SKGIAYIEFKSEADAEKNLEEK 73
Query: 361 DNSIFQGR 368
+ GR
Sbjct: 74 QGAEIDGR 81
Score = 33.9 bits (76), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 26/80 (32%), Positives = 42/80 (52%), Gaps = 10/80 (12%)
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVET 674
+R+L KNL+F ++ L++ F E E R++S ++GK S G +IEF S
Sbjct: 16 ARTLLAKNLSFNITEDELKEVF-EDALEIRLVS-------QDGK--SKGIAYIEFKSEAD 65
Query: 675 ATNVCRDLQGTILDGHALIL 694
A + QG +DG ++ L
Sbjct: 66 AEKNLEEKQGAEIDGRSVSL 85
>pdb|2MSS|A Chain A, Musashi1 Rbd2, Nmr
pdb|2MST|A Chain A, Musashi1 Rbd2, Nmr
Length = 75
Score = 37.0 bits (84), Expect = 0.044, Method: Composition-based stats.
Identities = 15/59 (25%), Positives = 31/59 (52%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+FV L T ++++ +F +FG V + ++ DK T R +G +V + + + E+
Sbjct: 2 IFVGGLSVNTTVEDVKHYFEQFGKVDDAMLMFDKTTNRHRGFGFVTFESEDIVEKVCEI 60
>pdb|4A8X|A Chain A, Structure Of The Core Asap Complex
Length = 88
Score = 36.6 bits (83), Expect = 0.048, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 2/74 (2%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEIT--DAKLMRTKDGKSRQFAFIGFRTEQEAEEAI 58
+++ + L + VT+D + + FS G+I D + R S+ +A++ F EAE+A+
Sbjct: 5 TKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAEKAL 64
Query: 59 KYFNKSYLDTCRIS 72
K+ + +D I+
Sbjct: 65 KHMDGGQIDGQEIT 78
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 19/74 (25%), Positives = 39/74 (52%), Gaps = 1/74 (1%)
Query: 296 LESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDK-DTKRSKGIAYVLYAIPESAS 354
++ ++ + L T+D + E FS +G + + + V++ SKG AYV + P+ A
Sbjct: 2 MKPTKVHIGRLTRNVTKDHIMEIFSTYGKIKMIDMPVERMHPHLSKGYAYVEFENPDEAE 61
Query: 355 RAIEVLDNSIFQGR 368
+A++ +D G+
Sbjct: 62 KALKHMDGGQIDGQ 75
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 36.6 bits (83), Expect = 0.053, Method: Compositional matrix adjust.
Identities = 28/98 (28%), Positives = 47/98 (47%), Gaps = 4/98 (4%)
Query: 282 GNPSSSSKDVQQEVLESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKG 341
G+ SS K++ E + +V NLP+ + ++ F ++ V +V DKDT + KG
Sbjct: 1 GSSGSSGKELPTEPPYTA--YVGNLPFNTVQGDIDAIFKDL-SIRSVRLVRDKDTDKFKG 57
Query: 342 IAYVLYAIPESASRAIEVLDNSIFQGRLLHVMPARHKK 379
YV + +S A+ D ++ R L V A +K
Sbjct: 58 FCYVEFDEVDSLKEAL-TYDGALLGDRSLRVDIAEGRK 94
>pdb|2NZ4|A Chain A, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|B Chain B, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|C Chain C, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
pdb|2NZ4|D Chain D, Structural Investigation Of The Glms Ribozyme Bound To Its
Catalytic Cofactor
Length = 94
Score = 36.6 bits (83), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 46/95 (48%), Gaps = 8/95 (8%)
Query: 617 SLFVKNLNFKTCDENLRKHFGEHI-KEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETA 675
++++ NLN K + L+K + G+IL + V + LK G F+ F V +A
Sbjct: 7 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK-----MRGQAFVIFKEVSSA 61
Query: 676 TNVCRDLQGTILDGHALILQLCHAKKDEQVVKKAE 710
TN R +QG + +Q +AK D ++ K +
Sbjct: 62 TNALRSMQGFPFYDKPMRIQ--YAKTDSDIIAKMK 94
>pdb|2LA4|A Chain A, Nmr Structure Of The C-Terminal Rrm Domain Of Poly(U)
Binding 1
Length = 101
Score = 36.6 bits (83), Expect = 0.056, Method: Composition-based stats.
Identities = 23/69 (33%), Positives = 33/69 (47%), Gaps = 6/69 (8%)
Query: 302 FVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVLD 361
++ N+P+ ATE +L F FG ++D KG ++ Y E A+ I L
Sbjct: 31 YIGNIPHFATEADLIPLFQNFG------FILDFKHYPEKGCCFIKYDTHEQAAVCIVALA 84
Query: 362 NSIFQGRLL 370
N FQGR L
Sbjct: 85 NFPFQGRNL 93
>pdb|3IWN|C Chain C, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
pdb|3IWN|D Chain D, Co-Crystal Structure Of A Bacterial C-Di-Gmp Riboswitch
Length = 91
Score = 36.6 bits (83), Expect = 0.056, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 8/93 (8%)
Query: 617 SLFVKNLNFKTCDENLRKHFGEHI-KEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETA 675
++++ NLN K + L+K + G+IL + V + LK G F+ F V +A
Sbjct: 6 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK-----MRGQAFVIFKEVSSA 60
Query: 676 TNVCRDLQGTILDGHALILQLCHAKKDEQVVKK 708
TN R +QG + +Q +AK D ++ K
Sbjct: 61 TNALRSMQGFPFYDKPMRIQ--YAKTDSDIIAK 91
>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 = 36.6 bits (83), Expect = 0.057, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 39/81 (48%), Gaps = 2/81 (2%)
Query: 283 NPSSSSKDVQQEVL--ESGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSK 340
NPS V V+ + +LF+ LP +D+++E + FG + ++V D T SK
Sbjct: 97 NPSVYVPGVVSTVVPDSAHKLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSK 156
Query: 341 GIAYVLYAIPESASRAIEVLD 361
G A+ Y +AI L+
Sbjct: 157 GYAFCEYVDINVTDQAIAGLN 177
Score = 35.4 bits (80), Expect = 0.11, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 6/65 (9%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQK---GEITDA---KLMRTKDGKSRQFAFIGFRTEQEAE 55
R+ V N+P +TE+ + DFF+ + G +T A ++ + + + FAF+ FR+ E
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 56 EAIKY 60
+A+ +
Sbjct: 66 QAMAF 70
Score = 33.1 bits (74), Expect = 0.53, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 35/84 (41%), Gaps = 1/84 (1%)
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVET 674
+R L+V N+ F +E + F ++ G + L N F F+EF SV+
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 675 ATNVCRDLQGTILDGHALILQLCH 698
T G I G +L ++ H
Sbjct: 64 TTQAMA-FDGIIFQGQSLKIRRPH 86
Score = 30.4 bits (67), Expect = 3.6, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 300 RLFVRNLPYTATEDELREHFS---KFGNVSEV--HIVVDKDTKRSKGIAYVLYAIPESAS 354
RL+V N+P+ TE+ + + F+ + G +++ + V+ + K A++ + + +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 355 RAIEVLDNSIFQGRLLHV 372
+A+ D IFQG+ L +
Sbjct: 66 QAM-AFDGIIFQGQSLKI 82
>pdb|1WTB|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D (Auf1) With Telomere Dna
pdb|1X0F|A Chain A, Complex Structure Of The C-Terminal Rna-Binding Domain Of
Hnrnp D(Auf1) With Telomeric Dna
Length = 79
Score = 36.2 bits (82), Expect = 0.058, Method: Composition-based stats.
Identities = 15/59 (25%), Positives = 31/59 (52%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIE 358
++FV L E+++RE+F FG V + + +D T + +G ++ + E + +E
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 61
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 24/75 (32%), Positives = 36/75 (48%), Gaps = 4/75 (5%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKL-MRTKDGKSRQFAFIGFRTEQEAEEAIKY 60
+I V L E+++R++F GE+ +L M K K R F FI F+ E+ + K
Sbjct: 3 KIFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVK---KI 59
Query: 61 FNKSYLDTCRISCEI 75
K Y + CEI
Sbjct: 60 MEKKYHNVGLSKCEI 74
>pdb|3L3C|A Chain A, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|B Chain B, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|C Chain C, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
pdb|3L3C|D Chain D, Crystal Structure Of The Bacillus Anthracis Glms Ribozyme
Bound To Glc6p
Length = 90
Score = 36.2 bits (82), Expect = 0.060, Method: Compositional matrix adjust.
Identities = 27/93 (29%), Positives = 45/93 (48%), Gaps = 8/93 (8%)
Query: 617 SLFVKNLNFKTCDENLRKHFGEHI-KEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETA 675
++++ NLN K + L+K + G+IL + V + LK G F+ F V +A
Sbjct: 5 TIYINNLNEKIKKDELKKSLHAIFSRFGQILDILVSRSLK-----MRGQAFVIFKEVSSA 59
Query: 676 TNVCRDLQGTILDGHALILQLCHAKKDEQVVKK 708
TN R +QG + +Q +AK D ++ K
Sbjct: 60 TNALRSMQGFPFYDKPMRIQ--YAKTDSDIIAK 90
>pdb|2DNQ|A Chain A, Solution Structure Of Rna Binding Domain 1 In
Rna-Binding Protein 30
Length = 90
Score = 36.2 bits (82), Expect = 0.062, Method: Compositional matrix adjust.
Identities = 17/76 (22%), Positives = 37/76 (48%), Gaps = 7/76 (9%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYF 61
++ + NLP+ TE +R F Q G++ + +++ + F+ + AE+AI+
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDIIKN-------YGFVHIEDKTAAEDAIRNL 62
Query: 62 NKSYLDTCRISCEIAR 77
+ L I+ E ++
Sbjct: 63 HHYKLHGVNINVEASK 78
Score = 35.8 bits (81), Expect = 0.090, Method: Compositional matrix adjust.
Identities = 15/32 (46%), Positives = 21/32 (65%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIV 331
+LF+ NLP ATE E+R F ++G V E I+
Sbjct: 10 KLFIGNLPREATEQEIRSLFEQYGKVLECDII 41
>pdb|3S8S|A Chain A, Crystal Structure Of The Rrm Domain Of Human Setd1a
Length = 110
Score = 36.2 bits (82), Expect = 0.068, Method: Composition-based stats.
Identities = 20/78 (25%), Positives = 39/78 (50%), Gaps = 5/78 (6%)
Query: 299 GRLFVRNLPYTATEDELREHF-----SKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESA 353
G++ ++ + + D +RE F K+G V EV I++ T++ G+A VL+ A
Sbjct: 2 GQIPLKEVTFARLNDNVRETFLKDMCRKYGEVEEVEILLHPRTRKHLGLARVLFTSTRGA 61
Query: 354 SRAIEVLDNSIFQGRLLH 371
++ L + G ++H
Sbjct: 62 KETVKNLHLTSVMGNIIH 79
>pdb|1IQT|A Chain A, Solution Structure Of The C-Terminal Rna-Binding Domain Of
Heterogeneous Nuclear Ribonucleoprotein D0 (Auf1)
Length = 75
Score = 35.8 bits (81), Expect = 0.079, Method: Composition-based stats.
Identities = 15/58 (25%), Positives = 30/58 (51%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIE 358
+FV L E+++RE+F FG V + + +D T + +G ++ + E + +E
Sbjct: 2 IFVGGLSPDTPEEKIREYFGGFGEVESIELPMDNKTNKRRGFCFITFKEEEPVKKIME 59
>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 = 35.8 bits (81), Expect = 0.085, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LF+ LP +D+++E + FG + ++V D T SKG A+ Y +AI
Sbjct: 98 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 157
Query: 360 LD 361
L+
Sbjct: 158 LN 159
Score = 35.8 bits (81), Expect = 0.093, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 6/65 (9%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQK---GEITDA---KLMRTKDGKSRQFAFIGFRTEQEAE 55
R+ V N+P +TE+ + DFF+ + G +T A ++ + + + FAF+ FR+ E
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 56 EAIKY 60
+A+ +
Sbjct: 68 QAMAF 72
Score = 33.5 bits (75), Expect = 0.43, Method: Composition-based stats.
Identities = 26/97 (26%), Positives = 40/97 (41%), Gaps = 4/97 (4%)
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVET 674
+R L+V N+ F +E + F ++ G + L N F F+EF SV+
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65
Query: 675 ATNVCRDLQGTILDGHALILQLCHAKKDEQVVKKAEK 711
T G I G +L ++ H D Q + A K
Sbjct: 66 TTQAMA-FDGIIFQGQSLKIRRPH---DYQPLPGAHK 98
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 22/92 (23%), Positives = 46/92 (50%), Gaps = 14/92 (15%)
Query: 300 RLFVRNLPYTATEDELREHFS---KFGNVSEV--HIVVDKDTKRSKGIAYVLYAIPESAS 354
RL+V N+P+ TE+ + + F+ + G +++ + V+ + K A++ + + +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 355 RAIEVLDNSIFQGRLLHV--------MPARHK 378
+A+ D IFQG+ L + +P HK
Sbjct: 68 QAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHK 98
>pdb|2CPI|A Chain A, Solution Structure Of The Rna Recognition Motif Of Cnot4
Length = 111
Score = 35.8 bits (81), Expect = 0.087, Method: Composition-based stats.
Identities = 27/82 (32%), Positives = 40/82 (48%), Gaps = 6/82 (7%)
Query: 295 VLESGRLFVRNLPYTATEDEL---REHFSKFGNVSEVHIVVDKDTKRSKG---IAYVLYA 348
V++ +FV L + E+ E+F KFG + +V I S+G AYV Y
Sbjct: 12 VVQKNLVFVVGLSQRLADPEVLKRPEYFGKFGKIHKVVINNSTSYAGSQGPSASAYVTYI 71
Query: 349 IPESASRAIEVLDNSIFQGRLL 370
E A RAI+ ++N + GR L
Sbjct: 72 RSEDALRAIQCVNNVVVDGRTL 93
>pdb|1U2F|A Chain A, Solution Structure Of The First Rna-Binding Domain Of
Hu2af65
Length = 90
Score = 35.8 bits (81), Expect = 0.088, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 6/65 (9%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQK---GEITDA---KLMRTKDGKSRQFAFIGFRTEQEAE 55
R+ V N+P +TE+ + DFF+ + G +T A ++ + + + FAF+ FR+ E
Sbjct: 3 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62
Query: 56 EAIKY 60
+A+ +
Sbjct: 63 QAMAF 67
Score = 33.5 bits (75), Expect = 0.47, Method: Composition-based stats.
Identities = 22/84 (26%), Positives = 35/84 (41%), Gaps = 1/84 (1%)
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVET 674
+R L+V N+ F +E + F ++ G + L N F F+EF SV+
Sbjct: 1 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 60
Query: 675 ATNVCRDLQGTILDGHALILQLCH 698
T G I G +L ++ H
Sbjct: 61 TTQAMA-FDGIIFQGQSLKIRRPH 83
Score = 30.8 bits (68), Expect = 2.8, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 300 RLFVRNLPYTATEDELREHFS---KFGNVSEV--HIVVDKDTKRSKGIAYVLYAIPESAS 354
RL+V N+P+ TE+ + + F+ + G +++ + V+ + K A++ + + +
Sbjct: 3 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 62
Query: 355 RAIEVLDNSIFQGRLLHV 372
+A+ D IFQG+ L +
Sbjct: 63 QAM-AFDGIIFQGQSLKI 79
>pdb|2HZC|A Chain A, Crystal Structure Of The N-terminal Rrm Of The U2af
Large Subunit
Length = 87
Score = 35.8 bits (81), Expect = 0.088, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 6/65 (9%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQK---GEITDA---KLMRTKDGKSRQFAFIGFRTEQEAE 55
R+ V N+P +TE+ + DFF+ + G +T A ++ + + + FAF+ FR+ E
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 56 EAIKY 60
+A+ +
Sbjct: 68 QAMAF 72
Score = 32.3 bits (72), Expect = 0.93, Method: Composition-based stats.
Identities = 21/78 (26%), Positives = 32/78 (41%), Gaps = 1/78 (1%)
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVET 674
+R L+V N+ F +E + F ++ G + L N F F+EF SV+
Sbjct: 6 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 65
Query: 675 ATNVCRDLQGTILDGHAL 692
T G I G +L
Sbjct: 66 TTQAMA-FDGIIFQGQSL 82
Score = 30.8 bits (68), Expect = 2.8, Method: Composition-based stats.
Identities = 19/78 (24%), Positives = 42/78 (53%), Gaps = 6/78 (7%)
Query: 300 RLFVRNLPYTATEDELREHFS---KFGNVSEV--HIVVDKDTKRSKGIAYVLYAIPESAS 354
RL+V N+P+ TE+ + + F+ + G +++ + V+ + K A++ + + +
Sbjct: 8 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 67
Query: 355 RAIEVLDNSIFQGRLLHV 372
+A+ D IFQG+ L +
Sbjct: 68 QAM-AFDGIIFQGQSLKI 84
>pdb|1WF0|A Chain A, Solution Structure Of Rrm Domain In Tar Dna-Binding
Protein- 43
Length = 88
Score = 35.8 bits (81), Expect = 0.090, Method: Composition-based stats.
Identities = 18/44 (40%), Positives = 27/44 (61%), Gaps = 4/44 (9%)
Query: 12 VTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAE 55
+TED LR+FFSQ G++ D + + R FAF+ F +Q A+
Sbjct: 17 MTEDELREFFSQYGDVMDVFIPK----PFRAFAFVTFADDQIAQ 56
Score = 35.0 bits (79), Expect = 0.17, Method: Composition-based stats.
Identities = 27/85 (31%), Positives = 43/85 (50%), Gaps = 7/85 (8%)
Query: 298 SGRLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAI 357
S +FV TEDELRE FS++G+V +V I K + A+V +A + A
Sbjct: 5 SSGVFVGRCTGDMTEDELREFFSQYGDVMDVFI-----PKPFRAFAFVTFADDQIAQSLC 59
Query: 358 EVLDNSIFQGRLLHVMPARHKKSSD 382
++ I +G +H+ A K +S+
Sbjct: 60 G--EDLIIKGISVHISNAEPKHNSN 82
>pdb|2G4B|A Chain A, Structure Of U2af65 Variant With Polyuridine Tract
Length = 172
Score = 35.8 bits (81), Expect = 0.092, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LF+ LP +D+++E + FG + ++V D T SKG A+ Y +AI
Sbjct: 96 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 155
Query: 360 LD 361
L+
Sbjct: 156 LN 157
Score = 35.4 bits (80), Expect = 0.10, Method: Composition-based stats.
Identities = 19/65 (29%), Positives = 37/65 (56%), Gaps = 6/65 (9%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQK---GEITDA---KLMRTKDGKSRQFAFIGFRTEQEAE 55
R+ V N+P +TE+ + DFF+ + G +T A ++ + + + FAF+ FR+ E
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 56 EAIKY 60
+A+ +
Sbjct: 66 QAMAF 70
Score = 33.5 bits (75), Expect = 0.48, Method: Composition-based stats.
Identities = 26/97 (26%), Positives = 40/97 (41%), Gaps = 4/97 (4%)
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVET 674
+R L+V N+ F +E + F ++ G + L N F F+EF SV+
Sbjct: 4 ARRLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDE 63
Query: 675 ATNVCRDLQGTILDGHALILQLCHAKKDEQVVKKAEK 711
T G I G +L ++ H D Q + A K
Sbjct: 64 TTQAMA-FDGIIFQGQSLKIRRPH---DYQPLPGAHK 96
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 22/92 (23%), Positives = 46/92 (50%), Gaps = 14/92 (15%)
Query: 300 RLFVRNLPYTATEDELREHFS---KFGNVSEV--HIVVDKDTKRSKGIAYVLYAIPESAS 354
RL+V N+P+ TE+ + + F+ + G +++ + V+ + K A++ + + +
Sbjct: 6 RLYVGNIPFGITEEAMMDFFNAQMRLGGLTQAPGNPVLAVQINQDKNFAFLEFRSVDETT 65
Query: 355 RAIEVLDNSIFQGRLLHV--------MPARHK 378
+A+ D IFQG+ L + +P HK
Sbjct: 66 QAM-AFDGIIFQGQSLKIRRPHDYQPLPGAHK 96
>pdb|2U1A|A Chain A, Rna Binding Domain 2 Of Human U1a Protein, Nmr, 20
Structures
Length = 88
Score = 35.8 bits (81), Expect = 0.099, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 32/58 (55%), Gaps = 1/58 (1%)
Query: 494 NHVFLVKNLPYDSSEGELAKMFGKFGSLDKV-ILPSTKTLALVVFLEPVEAAAAFKGL 550
NH+ + NLP +++E L+ +F +F +V ++P +A V F V+A AA L
Sbjct: 13 NHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAFVEFDNEVQAGAARDAL 70
>pdb|2ADB|A Chain A, Solution Structure Of Polypyrimidine Tract Binding Protein
Rbd2 Complexed With Cucucu Rna
Length = 148
Score = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
R+ V NL Y T D L + FSKFG V ++ TK ++ A + YA P SA A
Sbjct: 35 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPVSAQHAKLS 90
Query: 360 LD 361
LD
Sbjct: 91 LD 92
>pdb|2U2F|A Chain A, Solution Structure Of The Second Rna-Binding Domain Of
Hu2af65
Length = 85
Score = 35.0 bits (79), Expect = 0.14, Method: Composition-based stats.
Identities = 19/62 (30%), Positives = 32/62 (51%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LF+ LP +D+++E + FG + ++V D T SKG A+ Y +AI
Sbjct: 3 KLFIGGLPNYLNDDQVKELLTSFGPLKAFNLVKDSATGLSKGYAFCEYVDINVTDQAIAG 62
Query: 360 LD 361
L+
Sbjct: 63 LN 64
>pdb|3ZZY|A Chain A, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZY|B Chain B, Crystal Structure Of A Raver1 Pri3 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|A Chain A, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
pdb|3ZZZ|B Chain B, Crystal Structure Of A Raver1 Pri4 Peptide In Complex With
Polypyrimidine Tract Binding Protein Rrm2
Length = 130
Score = 34.7 bits (78), Expect = 0.17, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
R+ V NL Y T D L + FSKFG V ++ TK ++ A + YA P SA A
Sbjct: 30 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPVSAQHAKLS 85
Query: 360 LD 361
LD
Sbjct: 86 LD 87
>pdb|1SJR|A Chain A, Nmr Structure Of Rrm2 From Human Polypyrimidine Tract
Binding Protein Isoform 1 (Ptb1)
Length = 164
Score = 34.7 bits (78), Expect = 0.18, Method: Composition-based stats.
Identities = 25/62 (40%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
R+ V NL Y T D L + FSKFG V ++ TK ++ A + YA P SA A
Sbjct: 48 RIIVENLFYPVTLDVLHQIFSKFGTVLKIITF----TKNNQFQALLQYADPVSAQHAKLS 103
Query: 360 LD 361
LD
Sbjct: 104 LD 105
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 34.7 bits (78), Expect = 0.20, Method: Compositional matrix adjust.
Identities = 19/63 (30%), Positives = 32/63 (50%)
Query: 2 RICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYF 61
++ V L K +E+ + F G I + ++R DG S+ AF+ F + EA+ AI
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGSSKGCAFVKFSSHTEAQAAIHAL 76
Query: 62 NKS 64
+ S
Sbjct: 77 HGS 79
Score = 31.2 bits (69), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 31/64 (48%), Gaps = 1/64 (1%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+LFV L +E+++ F FG + E ++ D SKG A+V ++ A AI
Sbjct: 17 KLFVGMLNKQQSEEDVLRLFQPFGVIDECTVLRGPDGS-SKGCAFVKFSSHTEAQAAIHA 75
Query: 360 LDNS 363
L S
Sbjct: 76 LHGS 79
>pdb|2YTC|A Chain A, Solution Structure Of Rna Binding Domain In Pre-Mrna-
Splicing Factor Rbm22
Length = 85
Score = 34.3 bits (77), Expect = 0.23, Method: Composition-based stats.
Identities = 27/74 (36%), Positives = 38/74 (51%), Gaps = 6/74 (8%)
Query: 5 VKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAI-KYFNK 63
V L +TE LR+ F Q GEI ++ + +Q AFI F T Q AE A K FNK
Sbjct: 17 VGGLGDTITETDLRNHFYQFGEIRTITVV-----QRQQCAFIQFATRQAAEVAAEKSFNK 71
Query: 64 SYLDTCRISCEIAR 77
++ R++ + R
Sbjct: 72 LIVNGRRLNVKWGR 85
Score = 34.3 bits (77), Expect = 0.24, Method: Composition-based stats.
Identities = 24/77 (31%), Positives = 39/77 (50%), Gaps = 7/77 (9%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIE-V 359
L+V L T TE +LR HF +FG + + +V + + A++ +A ++A A E
Sbjct: 15 LYVGGLGDTITETDLRNHFYQFGEIRTITVV------QRQQCAFIQFATRQAAEVAAEKS 68
Query: 360 LDNSIFQGRLLHVMPAR 376
+ I GR L+V R
Sbjct: 69 FNKLIVNGRRLNVKWGR 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 = 33.5 bits (75), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 23/78 (29%), Positives = 39/78 (50%), Gaps = 2/78 (2%)
Query: 283 NPSSSSKDVQQEVLESGRLFVRNLPYTAT-EDELREHFSKFGNVSEVHIVV-DKDTKRSK 340
NP SK LE + +RNL E+ LRE F FG++ +++I K+ +
Sbjct: 195 NPLEKSKRTDSATLEGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNN 254
Query: 341 GIAYVLYAIPESASRAIE 358
A+ ++ +SA RA++
Sbjct: 255 CCAFXVFENKDSAERALQ 272
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 33.1 bits (74), Expect = 0.53, Method: Compositional matrix adjust.
Identities = 21/62 (33%), Positives = 34/62 (54%), Gaps = 8/62 (12%)
Query: 301 LFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVL 360
LFVRNL T TE+ L + FS+FG + V K+ K A+V + +A +A++ +
Sbjct: 18 LFVRNLATTVTEEILEKSFSEFGKLERV--------KKLKDYAFVHFEDRGAAVKAMDEM 69
Query: 361 DN 362
+
Sbjct: 70 NG 71
>pdb|1WG1|A Chain A, Solution Structure Of Rna Binding Domain In
Bab13405(Homolog Exc-7)
Length = 88
Score = 33.1 bits (74), Expect = 0.58, Method: Composition-based stats.
Identities = 24/81 (29%), Positives = 36/81 (44%), Gaps = 1/81 (1%)
Query: 498 LVKNLPYDSSEGELAKMFGKFGSLDKVILPSTKTLALVVFLEPVEAAAAFKGLAYKRYKG 557
LVKNLP DS+ E+ + + L + K A V L +A A + ++G
Sbjct: 9 LVKNLPQDSNCQEVHDLLKDY-DLKYCYVDRNKRTAFVTLLNGEQAQNAIQMFHQYSFRG 67
Query: 558 VPLYLEWAPSDVLSQSSTSKG 578
L ++ P+D L S S G
Sbjct: 68 KDLIVQLQPTDALLCSGPSSG 88
>pdb|1A9N|B Chain B, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|D Chain D, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 96
Score = 32.7 bits (73), Expect = 0.69, Method: Composition-based stats.
Identities = 26/103 (25%), Positives = 48/103 (46%), Gaps = 12/103 (11%)
Query: 607 DIDPDRVESRSLFVKNLNFKTCDENLRKHFGEHIKE-GRILSVKVKKHLKNGKNVSMGFG 665
DI P+ ++++ N+N K E L++ + G ++ + K +K G
Sbjct: 2 DIRPNH----TIYINNMNDKIKKEELKRSLYALFSQFGHVVDIVALKTMK-----MRGQA 52
Query: 666 FIEFDSVETATNVCRDLQGTILDGHALILQLCHAKKDEQVVKK 708
F+ F + ++TN R LQG G + +Q +AK D ++ K
Sbjct: 53 FVIFKELGSSTNALRQLQGFPFYGKPMRIQ--YAKTDSDIISK 93
>pdb|1X4G|A Chain A, Solution Structure Of Rrm Domain In Nucleolysin Tiar
Length = 109
Score = 32.7 bits (73), Expect = 0.74, Method: Composition-based stats.
Identities = 16/60 (26%), Positives = 34/60 (56%), Gaps = 6/60 (10%)
Query: 311 TEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVLDNSIFQGRLL 370
T+ +R+ FS FG + E+ + +K G ++V ++ ESA+ AI ++ + +G ++
Sbjct: 38 TDQLMRQTFSPFGQIMEIRVFPEK------GYSFVRFSTHESAAHAIVSVNGTTIEGHVV 91
>pdb|2HGN|A Chain A, Nmr Structure Of The Third Qrrm Domain Of Human Hnrnp F
pdb|2KG1|A Chain A, Structure Of The Third Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 139
Score = 32.0 bits (71), Expect = 1.4, Method: Composition-based stats.
Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 303 VRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAI 357
+R LPY ATE+++ FS N VHI + D R G A V +A E A A+
Sbjct: 51 MRGLPYKATENDIYNFFSPL-NPVRVHIEIGPD-GRVTGEADVEFATHEEAVAAM 103
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 8/68 (11%)
Query: 497 FLVKNLPYDSSEGELAKMFGKFGSLDKVILP---STKTLALV-VFLEPVEAAAAFKGLAY 552
LV NL + S+ ++ ++F +FG+L K + S ++L V E A A K A
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFE--RRADALK--AM 93
Query: 553 KRYKGVPL 560
K+YKGVPL
Sbjct: 94 KQYKGVPL 101
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 31.6 bits (70), Expect = 1.5, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 8/68 (11%)
Query: 497 FLVKNLPYDSSEGELAKMFGKFGSLDKVILP---STKTLALV-VFLEPVEAAAAFKGLAY 552
LV NL + S+ ++ ++F +FG+L K + S ++L V E A A K A
Sbjct: 91 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFE--RRADALK--AM 146
Query: 553 KRYKGVPL 560
K+YKGVPL
Sbjct: 147 KQYKGVPL 154
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 31.6 bits (70), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/73 (24%), Positives = 40/73 (54%), Gaps = 1/73 (1%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+L V NL + ++ +++E F++FG + + + D+ + RS G A V + A +A++
Sbjct: 30 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAMKQ 88
Query: 360 LDNSIFQGRLLHV 372
+ GR +++
Sbjct: 89 YNGVPLDGRPMNI 101
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 25/68 (36%), Positives = 37/68 (54%), Gaps = 8/68 (11%)
Query: 497 FLVKNLPYDSSEGELAKMFGKFGSLDKVILP---STKTLALV-VFLEPVEAAAAFKGLAY 552
LV NL + S+ ++ ++F +FG+L K + S ++L V E A A K A
Sbjct: 38 LLVSNLDFGVSDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFE--RRADALK--AM 93
Query: 553 KRYKGVPL 560
K+YKGVPL
Sbjct: 94 KQYKGVPL 101
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein H'
Length = 102
Score = 31.6 bits (70), Expect = 1.7, Method: Composition-based stats.
Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 2/55 (3%)
Query: 303 VRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAI 357
+R LPY ATE+++ FS N VHI + D R G A V +A E A A+
Sbjct: 20 MRGLPYRATENDIYNFFSPL-NPMRVHIEIGPD-GRVTGEADVEFATHEDAVAAM 72
>pdb|2DIT|A Chain A, Solution Structure Of The Rrm_1 Domain Of Hiv Tat Specific
Factor 1 Variant
Length = 112
Score = 31.2 bits (69), Expect = 2.2, Method: Composition-based stats.
Identities = 19/56 (33%), Positives = 30/56 (53%), Gaps = 4/56 (7%)
Query: 313 DELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVLDNSIFQGR 368
++LR SKFG + ++ ++ D+ G+A V + PE A I+ LD F GR
Sbjct: 41 EDLRVECSKFGQIRKL-LLFDR---HPDGVASVSFRDPEEADYCIQTLDGRWFGGR 92
>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 = 16/47 (34%), Positives = 26/47 (55%), Gaps = 2/47 (4%)
Query: 302 FVRNLPYTATEDELREHFSKFGNVSEVHIVVDK-DTKRSKGIAYVLY 347
F+ NLPY TE+ ++E F N+S V + + + +R KG Y +
Sbjct: 19 FLGNLPYDVTEESIKEFFRGL-NISAVRLPREPSNPERLKGFGYAEF 64
>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 = 30.8 bits (68), Expect = 2.8, Method: Composition-based stats.
Identities = 14/43 (32%), Positives = 26/43 (60%), Gaps = 1/43 (2%)
Query: 25 GEITDAKLMR-TKDGKSRQFAFIGFRTEQEAEEAIKYFNKSYL 66
G I+DA++++ GKS+ + F+ F + +AE AI+ +L
Sbjct: 31 GRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWL 73
Score = 29.6 bits (65), Expect = 6.3, Method: Composition-based stats.
Identities = 17/57 (29%), Positives = 26/57 (45%)
Query: 322 FGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEVLDNSIFQGRLLHVMPARHK 378
FG +S+ +V D T +SKG +V + A AI+ + GR + A K
Sbjct: 30 FGRISDARVVKDMATGKSKGYGFVSFFNKWDAENAIQQMGGQWLGGRQIRTNWATRK 86
>pdb|2WTA|A Chain A, Acinetobacter Baumanii Nicotinamidase Pyrazinamidease
Length = 213
Score = 30.8 bits (68), Expect = 3.0, Method: Composition-based stats.
Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 11/86 (12%)
Query: 555 YKGVPLYLEWAPSDVLSQSSTSKGNQKNDAVVGEHDAKRALLEQQLEGVTDADIDPDRVE 614
++ V L +W P + +S ++ G Q + + ++ ++ + ++G DA+ PD
Sbjct: 44 FENVVLTQDWHPDNHISFAANHPGKQPFETIELDYGSQVLWPKHCIQGTHDAEFHPD--- 100
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHI 640
LN T +RK F HI
Sbjct: 101 --------LNIPTAQLIIRKGFHAHI 118
>pdb|2WT9|A Chain A, Acinetobacter Baumanii Nicotinamidase Pyrazinamidease
pdb|2WT9|B Chain B, Acinetobacter Baumanii Nicotinamidase Pyrazinamidease
Length = 235
Score = 30.8 bits (68), Expect = 3.0, Method: Composition-based stats.
Identities = 20/86 (23%), Positives = 38/86 (44%), Gaps = 11/86 (12%)
Query: 555 YKGVPLYLEWAPSDVLSQSSTSKGNQKNDAVVGEHDAKRALLEQQLEGVTDADIDPDRVE 614
++ V L +W P + +S ++ G Q + + ++ ++ + ++G DA+ PD
Sbjct: 67 FENVVLTQDWHPDNHISFAANHPGKQPFETIELDYGSQVLWPKHCIQGTHDAEFHPD--- 123
Query: 615 SRSLFVKNLNFKTCDENLRKHFGEHI 640
LN T +RK F HI
Sbjct: 124 --------LNIPTAQLIIRKGFHAHI 141
>pdb|2I38|A Chain A, Solution Structure Of The Rrm Of Srp20
Length = 150
Score = 30.4 bits (67), Expect = 4.2, Method: Composition-based stats.
Identities = 24/84 (28%), Positives = 39/84 (46%), Gaps = 10/84 (11%)
Query: 618 LFVKNLNFKTCDENLRKHFGEHIKEGRILSVKVKKHLKNGKNVSMGFGFIEFDSVETATN 677
++V NL L + FG + G + SV V ++ GF F+EF+ A +
Sbjct: 76 VYVGNLGNNGNKTELERAFGYY---GPLRSVWVARN-------PPGFAFVEFEDPRDAAD 125
Query: 678 VCRDLQGTILDGHALILQLCHAKK 701
RDL G L G + ++L + +K
Sbjct: 126 AVRDLDGRTLCGCRVRVELSNGEK 149
>pdb|2BZ2|A Chain A, Solution Structure Of Nelf E Rrm
pdb|2JX2|A Chain A, Solution Conformation Of Rna-Bound Nelf-E Rrm
Length = 121
Score = 30.0 bits (66), Expect = 4.6, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 12 VTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYFNKSYLDTCRI 71
+T LR FS G I D + R AF+ + + A++A+ N + +++ ++
Sbjct: 49 MTPTLLRGAFSPFGNIIDLSM-----DPPRNCAFVTYEKMESADQAVAELNGTQVESVQL 103
Query: 72 SCEIARK 78
IARK
Sbjct: 104 KVNIARK 110
>pdb|1X5P|A Chain A, Solution Structure Of Rrm Domain In Parp14
Length = 97
Score = 29.6 bits (65), Expect = 6.6, Method: Composition-based stats.
Identities = 18/67 (26%), Positives = 32/67 (47%), Gaps = 5/67 (7%)
Query: 12 VTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAEEAIKYFNKSYLDTCRI 71
+T LR FS G I D + R AF+ + + A++A+ N + +++ ++
Sbjct: 25 MTPTLLRGAFSPFGNIIDLSM-----DPPRNCAFVTYEKMESADQAVAELNGTQVESVQL 79
Query: 72 SCEIARK 78
IARK
Sbjct: 80 KVNIARK 86
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Hypothetical Protein Flj201171
Length = 123
Score = 29.6 bits (65), Expect = 6.7, Method: Composition-based stats.
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 303 VRNLPYTATEDELREHFSKFGNVS---EVHIVVDKDTKRSKGIAYVLYAIPESASRAI 357
+R LP+TAT +E+ F + ++ E + V R G A+VL+A E A A+
Sbjct: 28 MRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
>pdb|4PGM|A Chain A, Saccharomyces Cerevisiae Phosphoglycerate Mutase
pdb|4PGM|B Chain B, Saccharomyces Cerevisiae Phosphoglycerate Mutase
pdb|4PGM|C Chain C, Saccharomyces Cerevisiae Phosphoglycerate Mutase
pdb|4PGM|D Chain D, Saccharomyces Cerevisiae Phosphoglycerate Mutase
pdb|1BQ3|D Chain D, Saccharomyces Cerevisiae Phosphoglycerate Mutase In
Complex With Inositol Hexakisphosphate
pdb|1BQ3|C Chain C, Saccharomyces Cerevisiae Phosphoglycerate Mutase In
Complex With Inositol Hexakisphosphate
pdb|1BQ3|A Chain A, Saccharomyces Cerevisiae Phosphoglycerate Mutase In
Complex With Inositol Hexakisphosphate
pdb|1BQ3|B Chain B, Saccharomyces Cerevisiae Phosphoglycerate Mutase In
Complex With Inositol Hexakisphosphate
pdb|1BQ4|D Chain D, Saccharomyces Cerevisiae Phosphoglycerate Mutase In
Complex With Benzene Hexacarboxylate
pdb|1BQ4|C Chain C, Saccharomyces Cerevisiae Phosphoglycerate Mutase In
Complex With Benzene Hexacarboxylate
pdb|1BQ4|A Chain A, Saccharomyces Cerevisiae Phosphoglycerate Mutase In
Complex With Benzene Hexacarboxylate
pdb|1BQ4|B Chain B, Saccharomyces Cerevisiae Phosphoglycerate Mutase In
Complex With Benzene Hexacarboxylate
pdb|5PGM|D Chain D, Saccharomyces Cerevisiae Phosphoglycerate Mutase
pdb|5PGM|C Chain C, Saccharomyces Cerevisiae Phosphoglycerate Mutase
pdb|5PGM|A Chain A, Saccharomyces Cerevisiae Phosphoglycerate Mutase
pdb|5PGM|B Chain B, Saccharomyces Cerevisiae Phosphoglycerate Mutase
pdb|5PGM|F Chain F, Saccharomyces Cerevisiae Phosphoglycerate Mutase
pdb|5PGM|G Chain G, Saccharomyces Cerevisiae Phosphoglycerate Mutase
pdb|5PGM|H Chain H, Saccharomyces Cerevisiae Phosphoglycerate Mutase
pdb|5PGM|E Chain E, Saccharomyces Cerevisiae Phosphoglycerate Mutase
Length = 246
Score = 29.6 bits (65), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 32/131 (24%), Positives = 56/131 (42%), Gaps = 30/131 (22%)
Query: 478 SLEEFSAGKTDGLKRSNHVFLVKNLPYDSSEGELAKMFGKFGSLDKVILPSTKTLALVVF 537
+L++F K + +RS F V P D+S K ++ +D +LP T++LALV+
Sbjct: 100 TLKKFGEEKFNTYRRS---FDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVID 156
Query: 538 LEPVEAAAAFKGLAYKRYKGVPLYLEWAPSDVLSQSSTSKGNQKNDAVVGEHDAKRALLE 597
+ +P + + D+LS + ++ H L
Sbjct: 157 ------------------RLLPYWQDVIAKDLLSGKTV---------MIAAHGNSLRGLV 189
Query: 598 QQLEGVTDADI 608
+ LEG++DADI
Sbjct: 190 KHLEGISDADI 200
>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 = 29.3 bits (64), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 18/69 (26%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 300 RLFVRNLPYTATEDELREHFSKFGNVSEVHIVVDKDTKRSKGIAYVLYAIPESASRAIEV 359
+L V NL + ++ +++E F++FG + + + D+ + RS G A V + A +A +
Sbjct: 31 KLLVSNLDFGVSDADIQELFAEFGTLKKAAVHYDR-SGRSLGTADVHFERKADALKAXKQ 89
Query: 360 LDNSIFQGR 368
+ GR
Sbjct: 90 YNGVPLDGR 98
>pdb|3D2W|A Chain A, Crystal Structure Of Mouse Tdp-43 Rrm2 Domain In Complex
Wit
Length = 89
Score = 29.3 bits (64), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 29/55 (52%), Gaps = 4/55 (7%)
Query: 1 SRICVKNLPKYVTEDRLRDFFSQKGEITDAKLMRTKDGKSRQFAFIGFRTEQEAE 55
S++ V + +T + L+ FF Q GE+ D + + R FAF+ F ++ A+
Sbjct: 12 SKVFVGRCTEDMTAEELQQFFCQYGEVVDVFIPK----PFRAFAFVTFADDKVAQ 62
>pdb|1QHF|A Chain A, Yeast Phosphoglycerate Mutase-3pg Complex Structure To 1.7
A
pdb|1QHF|B Chain B, Yeast Phosphoglycerate Mutase-3pg Complex Structure To 1.7
A
Length = 240
Score = 29.3 bits (64), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 32/131 (24%), Positives = 56/131 (42%), Gaps = 30/131 (22%)
Query: 478 SLEEFSAGKTDGLKRSNHVFLVKNLPYDSSEGELAKMFGKFGSLDKVILPSTKTLALVVF 537
+L++F K + +RS F V P D+S K ++ +D +LP T++LALV+
Sbjct: 100 TLKKFGEEKFNTYRRS---FDVPPPPIDASSPFSQKGDERYKYVDPNVLPETESLALVID 156
Query: 538 LEPVEAAAAFKGLAYKRYKGVPLYLEWAPSDVLSQSSTSKGNQKNDAVVGEHDAKRALLE 597
+ +P + + D+LS + ++ H L
Sbjct: 157 ------------------RLLPYWQDVIAKDLLSGKTV---------MIAAHGNSLRGLV 189
Query: 598 QQLEGVTDADI 608
+ LEG++DADI
Sbjct: 190 KHLEGISDADI 200
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
0.313 0.129 0.358
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 19,300,509
Number of Sequences: 62578
Number of extensions: 773020
Number of successful extensions: 2276
Number of sequences better than 100.0: 209
Number of HSP's better than 100.0 without gapping: 141
Number of HSP's successfully gapped in prelim test: 68
Number of HSP's that attempted gapping in prelim test: 1754
Number of HSP's gapped (non-prelim): 513
length of query: 731
length of database: 14,973,337
effective HSP length: 106
effective length of query: 625
effective length of database: 8,340,069
effective search space: 5212543125
effective search space used: 5212543125
T: 11
A: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 55 (25.8 bits)