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= 001755
(1017 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3Q90|A Chain A, Crystal Structure Of The Ntf2 Domain Of Ras
Gtpase-Activating Protein- Binding Protein 1
pdb|3Q90|B Chain B, Crystal Structure Of The Ntf2 Domain Of Ras
Gtpase-Activating Protein- Binding Protein 1
Length = 140
Score = 77.0 bits (188), Expect = 5e-14, Method: Composition-based stats.
Identities = 47/127 (37%), Positives = 70/127 (55%), Gaps = 10/127 (7%)
Query: 571 VGSYFVGQYYQVLQQQPDLVHQFYSDASSMIR----VDGDSTESASSMLDIHSLVISLNF 626
VG FV QYY +L Q PD++H+FY SS + +G ++ +IH V+S NF
Sbjct: 12 VGREFVRQYYTLLNQAPDMLHRFYGKNSSYVHGGLDSNGKPADAVYGQKEIHRKVMSQNF 71
Query: 627 TA--IEIKTINSLGSWNGGVLVMVSGSVKTKEFCRRRKFVQTFFLAPQ---EKGYFVLND 681
T +I+ +++ + N GV+V V G + RR F+QTF LAP+ ++V ND
Sbjct: 72 TNCHTKIRHVDAHATLNDGVVVQVMGLLSNNNQALRR-FMQTFVLAPEGSVANKFYVHND 130
Query: 682 IFHFLDE 688
IF + DE
Sbjct: 131 IFRYQDE 137
>pdb|3UJM|A Chain A, Crystal Structure Of The Ntf2-Like Domain Of The
Drosophila Melanogaster Rasputin Protein
pdb|3UJM|B Chain B, Crystal Structure Of The Ntf2-Like Domain Of The
Drosophila Melanogaster Rasputin Protein
Length = 120
Score = 64.3 bits (155), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 43/118 (36%), Positives = 67/118 (56%), Gaps = 7/118 (5%)
Query: 571 VGSYFVGQYYQVLQQQPDLVHQFYSDASSMIRVDGDSTESASSMLDIHSLVISLNFT--A 628
VG FV QYY +L + P+ +H+FY+ SS I G+S + +IH+ + LNF
Sbjct: 6 VGREFVRQYYTLLNKAPNHLHRFYNHNSSYIH--GES-KLVVGQREIHNRIQQLNFNDCH 62
Query: 629 IEIKTINSLGSWNGGVLVMVSGSVKTKEFCRRRKFVQTFFLAPQE-KGYFVLNDIFHF 685
+I +++ + GV+V V+G + + + R+F QTF LA Q K Y+V NDIF +
Sbjct: 63 AKISQVDAQATLGNGVVVQVTGEL-SNDGQPMRRFTQTFVLAAQSPKKYYVHNDIFRY 119
>pdb|1ZO2|A Chain A, Structure Of Nuclear Transport Factor 2 (Ntf2) From
Cryptosporidium Parvum
pdb|1ZO2|B Chain B, Structure Of Nuclear Transport Factor 2 (Ntf2) From
Cryptosporidium Parvum
Length = 129
Score = 43.9 bits (102), Expect = 5e-04, Method: Composition-based stats.
Identities = 36/119 (30%), Positives = 52/119 (43%), Gaps = 8/119 (6%)
Query: 570 QVGSYFVGQYYQVLQQQPDLVHQFYSDASSMIRVDGDSTESASSMLDIHSLVISLNFTAI 629
Q+G FV YYQ Q + Y S + D A +I + SLNF +
Sbjct: 13 QIGKQFVQHYYQTFQTNRPALGGLYGPQSMLTWEDTQFQGQA----NIVNKFNSLNFQRV 68
Query: 630 --EIKTINSLGSWNGGVLVMVSGSVKTKEFCRRRKFVQTFFLAPQ-EKGYFVLNDIFHF 685
EI ++ S N G +V V+G V+ + + KF Q F L P G+ + ND+F
Sbjct: 69 QFEITRVDCQPSPNNGSIVFVTGDVRIDD-GQPLKFSQVFNLMPSGNGGFMIFNDLFRL 126
>pdb|1GY7|A Chain A, N77y Point Mutant Of S.Cerevisiae Ntf2
pdb|1GY7|B Chain B, N77y Point Mutant Of S.Cerevisiae Ntf2
pdb|1GY7|C Chain C, N77y Point Mutant Of S.Cerevisiae Ntf2
pdb|1GY7|D Chain D, N77y Point Mutant Of S.Cerevisiae Ntf2
pdb|1GYB|A Chain A, N77y Point Mutant Of Yntf2 Bound To Fxfg Nucleoporin
Repeat
pdb|1GYB|B Chain B, N77y Point Mutant Of Yntf2 Bound To Fxfg Nucleoporin
Repeat
pdb|1GYB|C Chain C, N77y Point Mutant Of Yntf2 Bound To Fxfg Nucleoporin
Repeat
pdb|1GYB|D Chain D, N77y Point Mutant Of Yntf2 Bound To Fxfg Nucleoporin
Repeat
Length = 125
Score = 42.4 bits (98), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 26/71 (36%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 616 DIHSLVISLNFTAIE--IKTINSL-GSWNGGVLVMVSGSVKTKEFCRRRKFVQTFFLAPQ 672
DI ++SL F ++ I T+++ S G VLVM++G + E ++F Q F L P
Sbjct: 49 DIVEKLVSLPFQKVQHRITTLDAQPASPYGDVLVMITGDLLIDEEQNPQRFSQVFHLIPD 108
Query: 673 EKGYFVLNDIF 683
Y+V NDIF
Sbjct: 109 GNSYYVFNDIF 119
>pdb|1X4A|A Chain A, Solution Structure Of Rrm Domain In Splicing Factor Sf2
Length = 109
Score = 38.5 bits (88), Expect = 0.018, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 35/58 (60%), Gaps = 4/58 (6%)
Query: 884 VYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFEDISGVQNAI 941
+YV NLP + +IE+ F +G I+ + ++NR+ G +AFVEFED ++A+
Sbjct: 25 IYVGNLPPDIRTKDIEDVFYKYGAIR--DIDLKNRRG--GPPFAFVEFEDPRDAEDAV 78
>pdb|2DK2|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein R (Hnrnp R)
Length = 97
Score = 38.5 bits (88), Expect = 0.021, Method: Composition-based stats.
Identities = 23/55 (41%), Positives = 33/55 (60%), Gaps = 9/55 (16%)
Query: 879 GEVKSVYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFED 933
+VK ++VRNL +TVT +E+ F FG+++ V+ KD YAFV FED
Sbjct: 13 AKVKVLFVRNLATTVTEEILEKSFSEFGKLER----VKKLKD-----YAFVHFED 58
>pdb|2DGU|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein Q
Length = 103
Score = 37.0 bits (84), Expect = 0.055, Method: Compositional matrix adjust.
Identities = 22/63 (34%), Positives = 37/63 (58%), Gaps = 9/63 (14%)
Query: 880 EVKSVYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFEDISGVQN 939
+VK ++VRNL +TVT +E+ F FG+++ V+ KD YAF+ F++ G
Sbjct: 10 KVKVLFVRNLANTVTEEILEKAFSQFGKLER----VKKLKD-----YAFIHFDERDGAVK 60
Query: 940 AIQ 942
A++
Sbjct: 61 AME 63
>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 = 35.0 bits (79), Expect = 0.19, Method: Composition-based stats.
Identities = 25/93 (26%), Positives = 41/93 (44%), Gaps = 19/93 (20%)
Query: 878 EGEVKSVYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVC---------YAF 928
E + +S+YV N+ TA E+E F G + NR V +C +A+
Sbjct: 3 EADARSIYVGNVDYGATAEELEAHFHGCGSV--------NR--VTILCDKFSGHPKGFAY 52
Query: 929 VEFEDISGVQNAIQASPIQLAGRQVYIEERRPN 961
+EF D V+ ++ GRQ+ + +R N
Sbjct: 53 IEFSDKESVRTSLALDESLFRGRQIKVIPKRTN 85
>pdb|3LQV|A Chain A, Branch Recognition By Sf3b14
pdb|3LQV|B Chain B, Branch Recognition By Sf3b14
Length = 115
Score = 35.0 bits (79), Expect = 0.21, Method: Composition-based stats.
Identities = 21/58 (36%), Positives = 34/58 (58%), Gaps = 4/58 (6%)
Query: 884 VYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFEDISGVQNAI 941
+Y+RNLP +TA E+ + F +G I+ + V N + G A+V +EDI +NA+
Sbjct: 11 LYIRNLPYKITAEEMYDIFGKYGPIRQ--IRVGNTPETRGT--AYVVYEDIFDAKNAV 64
>pdb|2FHO|B Chain B, Nmr Solution Structure Of The Human Spliceosomal Protein
Complex P14-Sf3b155
Length = 87
Score = 35.0 bits (79), Expect = 0.21, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 884 VYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFEDISGVQNA 940
+Y+RNLP +TA E+ + F +G I+ + V N + G A+V +EDI +NA
Sbjct: 15 LYIRNLPYKITAEEMYDIFGKYGPIRQ--IRVGNTPETRGT--AYVVYEDIFDAKNA 67
>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 = 34.7 bits (78), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 41/93 (44%), Gaps = 19/93 (20%)
Query: 878 EGEVKSVYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVC---------YAF 928
E + +S+YV N+ TA E+E F G + NR V +C +A+
Sbjct: 2 EADARSIYVGNVDYGATAEELEAHFHGCGSV--------NR--VTILCDKFSGHPKGFAY 51
Query: 929 VEFEDISGVQNAIQASPIQLAGRQVYIEERRPN 961
+EF D V+ ++ GRQ+ + +R N
Sbjct: 52 IEFSDKESVRTSLALDESLFRGRQIKVIPKRTN 84
>pdb|3R27|A Chain A, Crystal Structure Of The First Rrm Domain Of Heterogeneous
Nuclear Ribonucleoprotein L (Hnrnp L)
pdb|3R27|B Chain B, Crystal Structure Of The First Rrm Domain Of Heterogeneous
Nuclear Ribonucleoprotein L (Hnrnp L)
Length = 100
Score = 34.3 bits (77), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 24/72 (33%), Positives = 34/72 (47%), Gaps = 11/72 (15%)
Query: 884 VYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFEDISGVQNAIQA 943
V++R L V ++ E Q FG I V + R+ A VEFED+ G NA+
Sbjct: 24 VHIRGLIDGVVEADLVEALQEFGPISYVVVMPKKRQ-------ALVEFEDVLGACNAVNY 76
Query: 944 SPIQLAGRQVYI 955
+ A Q+YI
Sbjct: 77 A----ADNQIYI 84
>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 = 34.3 bits (77), Expect = 0.34, Method: Composition-based stats.
Identities = 21/57 (36%), Positives = 33/57 (57%), Gaps = 4/57 (7%)
Query: 884 VYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFEDISGVQNA 940
+Y+RNLP +TA E+ + F +G I+ + V N + G A+V +EDI +NA
Sbjct: 21 LYIRNLPYKITAEEMYDIFGKYGPIRQ--IRVGNTPETRGT--AYVVYEDIFDAKNA 73
>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 = 33.5 bits (75), Expect = 0.69, Method: Composition-based stats.
Identities = 25/71 (35%), Positives = 35/71 (49%), Gaps = 2/71 (2%)
Query: 884 VYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFEDISGVQNAIQA 943
V+V +L +T +I+ F FGRI D V++ Y FV F + +NAIQ
Sbjct: 18 VFVGDLSPEITTEDIKAAFAPFGRIS-DARVVKDMATGKSKGYGFVSFFNKWDAENAIQQ 76
Query: 944 SPIQ-LAGRQV 953
Q L GRQ+
Sbjct: 77 MGGQWLGGRQI 87
>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 = 33.1 bits (74), Expect = 0.73, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 883 SVYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFEDISGVQNAIQ 942
++Y+ LP T+T ++E+ F FGRI V V ++ + AF+ F+ S + AI
Sbjct: 90 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV-DQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 943 A 943
+
Sbjct: 149 S 149
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 33.1 bits (74), Expect = 0.78, Method: Compositional matrix adjust.
Identities = 19/61 (31%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 883 SVYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFEDISGVQNAIQ 942
++Y+ LP T+T ++E+ F FGRI V V ++ + AF+ F+ S + AI
Sbjct: 90 NLYISGLPRTMTQKDVEDMFSRFGRIINSRVLV-DQTTGLSRGVAFIRFDKRSEAEEAIT 148
Query: 943 A 943
+
Sbjct: 149 S 149
>pdb|2KHC|A Chain A, Bruno Rrm3+
Length = 118
Score = 32.7 bits (73), Expect = 0.98, Method: Composition-based stats.
Identities = 16/61 (26%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 883 SVYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFEDISGVQNAIQ 942
++++ +LP T ++ F FG + VF+ +++ + C+ FV F++ Q AI+
Sbjct: 42 NLFIYHLPQEFTDTDLASTFLPFGNVISAKVFI-DKQTSLSKCFGFVSFDNPDSAQVAIK 100
Query: 943 A 943
A
Sbjct: 101 A 101
>pdb|3QNK|A Chain A, Crystal Structure Of A Hypothetical Susd-Like Protein
(Bf3747) From Bacteroides Fragilis Nctc 9343 At 2.70 A
Resolution
pdb|3QNK|B Chain B, Crystal Structure Of A Hypothetical Susd-Like Protein
(Bf3747) From Bacteroides Fragilis Nctc 9343 At 2.70 A
Resolution
pdb|3QNK|C Chain C, Crystal Structure Of A Hypothetical Susd-Like Protein
(Bf3747) From Bacteroides Fragilis Nctc 9343 At 2.70 A
Resolution
pdb|3QNK|D Chain D, Crystal Structure Of A Hypothetical Susd-Like Protein
(Bf3747) From Bacteroides Fragilis Nctc 9343 At 2.70 A
Resolution
Length = 517
Score = 32.0 bits (71), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 11/66 (16%)
Query: 264 ATHVFVKRLPEIHLFAARFKEQNGDIDGARAAYQLVH--------TETSPGLLEAIIKHA 315
+T+ + R EI+L A + + GD++GAR A + TE+ P L +I+
Sbjct: 383 STNWIILRYAEIYLNDAEARLETGDVEGARKAVNXIRQRVGLPDLTESDPEKLRELIRK- 441
Query: 316 NMERRL 321
ERR+
Sbjct: 442 --ERRI 445
>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 = 31.6 bits (70), Expect = 2.5, Method: Composition-based stats.
Identities = 20/55 (36%), Positives = 31/55 (56%), Gaps = 4/55 (7%)
Query: 886 VRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFEDISGVQNA 940
+RNLP +TA E+ + F +G I+ + V N + G A+V +EDI +NA
Sbjct: 23 IRNLPYKITAEEMYDIFGKYGPIRQ--IRVGNTPETRGT--AYVVYEDIFDAKNA 73
>pdb|1W3B|A Chain A, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha.
pdb|1W3B|B Chain B, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha
Length = 388
Score = 31.6 bits (70), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 33/136 (24%), Positives = 55/136 (40%), Gaps = 4/136 (2%)
Query: 220 FNKVVKLYERCLIACANYPEYWIRYVLCMEASGSMDLAHNALARATHVFVKRLPEIHLFA 279
F++ V Y R L N+ G +DLA + RA + P+ +
Sbjct: 219 FDRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIEL-QPHFPDAYCNL 277
Query: 280 ARFKEQNGDIDGARAAYQLVHTETSPGLLEAIIKHANMERRLGNLEDAFSLYEQAIAI-- 337
A ++ G + A Y P +++ AN++R GN+E+A LY +A+ +
Sbjct: 278 ANALKEKGSVAEAEDCYNTA-LRLCPTHADSLNNLANIKREQGNIEEAVRLYRKALEVFP 336
Query: 338 EKGKEHSQTLPMLYAQ 353
E HS +L Q
Sbjct: 337 EFAAAHSNLASVLQQQ 352
>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 = 31.6 bits (70), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 18/77 (23%), Positives = 36/77 (46%), Gaps = 1/77 (1%)
Query: 880 EVKSVYVRNLPSTVTAFEI-EEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEFEDISGVQ 938
E + + +RNL + + + E F+ FG I+ + ++ C AF FE+ +
Sbjct: 209 EGREIXIRNLSTELLDENLLRESFEGFGSIEKINIPAGQKEHSFNNCCAFXVFENKDSAE 268
Query: 939 NAIQASPIQLAGRQVYI 955
A+Q + L R++ +
Sbjct: 269 RALQXNRSLLGNREISV 285
>pdb|2CPD|A Chain A, Solution Structure Of The Rna Recognition Motif Of Human
Apobec-1 Complementation Factor, Acf
Length = 99
Score = 31.2 bits (69), Expect = 2.7, Method: Composition-based stats.
Identities = 25/64 (39%), Positives = 34/64 (53%), Gaps = 9/64 (14%)
Query: 881 VKSVYVRNLPSTVTAFEIEEEFQNFGRIKPDGV-FVRNRKDVVGVCYAFVEFEDISGVQN 939
VK +YVRNL + + IE+EF N IKP V V+ +D YAFV F +
Sbjct: 15 VKILYVRNLMLSTSEEMIEKEFNN---IKPGAVERVKKIRD-----YAFVHFSNREDAVE 66
Query: 940 AIQA 943
A++A
Sbjct: 67 AMKA 70
>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 = 31.2 bits (69), Expect = 2.8, Method: Composition-based stats.
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 5/63 (7%)
Query: 883 SVYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVC--YAFVEFEDISGVQNA 940
++YV LP T+T E+E+ F +GRI + V V GV F+ F+ + A
Sbjct: 90 NLYVSGLPKTMTQKELEQLFSQYGRIITSRILV---DQVTGVSRGVGFIRFDKRIEAEEA 146
Query: 941 IQA 943
I+
Sbjct: 147 IKG 149
>pdb|3H4C|A Chain A, Structure Of The C-Terminal Domain Of Transcription Factor
Iib From Trypanosoma Brucei
Length = 260
Score = 30.8 bits (68), Expect = 3.7, Method: Composition-based stats.
Identities = 17/50 (34%), Positives = 23/50 (46%)
Query: 331 YEQAIAIEKGKEHSQTLPMLYAQYSRFLHLVSRNAEKARQILVDSLDHVQ 380
+EQ I KGKE + +YA +S HL K + VD L +Q
Sbjct: 175 WEQGTHISKGKECDLGMEAIYANFSSKAHLEVTKVNKIMHLAVDVLPLIQ 224
>pdb|2FO7|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
(Trigonal Crystal Form)
pdb|2HYZ|A Chain A, Crystal Structure Of An 8 Repeat Consensus Tpr Superhelix
(Orthorombic Crystal Form)
Length = 136
Score = 30.8 bits (68), Expect = 4.1, Method: Composition-based stats.
Identities = 29/134 (21%), Positives = 54/134 (40%), Gaps = 2/134 (1%)
Query: 205 ENWHNYLDFIERDGDFNKVVKLYERCLIACANYPEYWIRYVLCMEASGSMDLAHNALARA 264
E W+N + + GD+++ ++ Y++ L E W G D A +A
Sbjct: 2 EAWYNLGNAYYKQGDYDEAIEYYQKALELDPRSAEAWYNLGNAYYKQGDYDEAIEYYQKA 61
Query: 265 THVFVKRLPEIHLFAARFKEQNGDIDGARAAYQLVHTETSPGLLEAIIKHANMERRLGNL 324
+ + + + +Q GD D A YQ E P EA N + G+
Sbjct: 62 LELDPRSAEAWYNLGNAYYKQ-GDYDEAIEYYQKA-LELDPRSAEAWYNLGNAYYKQGDY 119
Query: 325 EDAFSLYEQAIAIE 338
++A Y++A+ ++
Sbjct: 120 DEAIEYYQKALELD 133
>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 = 30.4 bits (67), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 24/89 (26%), Positives = 39/89 (43%), Gaps = 19/89 (21%)
Query: 882 KSVYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVC---------YAFVEFE 932
+SVYV N+ TA ++E F + G I NR ++ C YA++EF
Sbjct: 37 RSVYVGNVDYGSTAQDLEAHFSSCGSI--------NRITIL--CDKFSGHPKGYAYIEFA 86
Query: 933 DISGVQNAIQASPIQLAGRQVYIEERRPN 961
+ + V A+ GR + + +R N
Sbjct: 87 ERNSVDAAVAMDETVFRGRTIKVLPKRTN 115
>pdb|2OND|A Chain A, Crystal Structure Of The Hat-C Domain Of Murine Cstf-77
pdb|2OND|B Chain B, Crystal Structure Of The Hat-C Domain Of Murine Cstf-77
Length = 308
Score = 30.0 bits (66), Expect = 6.1, Method: Compositional matrix adjust.
Identities = 55/286 (19%), Positives = 106/286 (37%), Gaps = 40/286 (13%)
Query: 198 PLSVTELENWHNYLDFIE----RDGDFNKVVK----LYERCLIACANYPEYWIRYVLCME 249
P +++ W Y+ + + R D + K YE+CL+ ++P+ W +E
Sbjct: 2 PQEAQQVDXWKKYIQWEKSNPLRTEDQTLITKRVXFAYEQCLLVLGHHPDIWYEAAQYLE 61
Query: 250 ASGSM--------------DLAHNALARATHVFVKRLPEIHLFAARFKEQNGDIDGARAA 295
S + D A N RA +K+ ++ A ++E + +
Sbjct: 62 QSSKLLAEKGDXNNAKLFSDEAANIYERAISTLLKKNXLLYFAYADYEESRXKYEKVHSI 121
Query: 296 YQ--LVHTETSPGLLEAIIKHANMERRLGNLEDAFSLYEQAIAIEKGKEHSQTLPMLYAQ 353
Y L + P L+ I++ RR ++ ++++A +E ++T +Y
Sbjct: 122 YNRLLAIEDIDPTLV--YIQYXKFARRAEGIKSGRXIFKKA------REDARTRHHVYVT 173
Query: 354 YSRFLHLVSRNAEKARQILVDSLDHVQLSKPLLEALIHFESIQSSPKQIDFLEQLVDKFL 413
+ + S++ A +I L + E ++ + S + + L ++ L
Sbjct: 174 AALXEYYCSKDKSVAFKIFELGLKKYG---DIPEYVLAYIDYLSHLNEDNNTRVLFERVL 230
Query: 414 MSNSDSPSTANAAEREELSCVFLEFLGLFGDAQLIKKAEDRHARLF 459
S S P + E+ FL F GD I K E R F
Sbjct: 231 TSGSLPPEKSG-----EIWARFLAFESNIGDLASILKVEKRRFTAF 271
>pdb|2ARH|A Chain A, Crystal Structure Of A Protein Of Unknown Function Aq1966
From Aquifex Aeolicus Vf5
pdb|2ARH|B Chain B, Crystal Structure Of A Protein Of Unknown Function Aq1966
From Aquifex Aeolicus Vf5
pdb|2ARH|C Chain C, Crystal Structure Of A Protein Of Unknown Function Aq1966
From Aquifex Aeolicus Vf5
Length = 203
Score = 29.6 bits (65), Expect = 7.9, Method: Composition-based stats.
Identities = 20/52 (38%), Positives = 28/52 (53%), Gaps = 4/52 (7%)
Query: 417 SDSPSTANAAER--EELSCVFLEFLGLFGDAQLIKKAEDRHARLFLPHRSTS 466
++ P T A +R E L F EF+G D LIKK ++R+ FL H +S
Sbjct: 154 AEKPKTEEAKKRHLENLKKEFEEFIGKCEDEGLIKKVKERYN--FLEHEGSS 203
>pdb|2JQH|A Chain A, Vps4b Mit
pdb|2JQK|A Chain A, Vps4b Mit-Chmp2b Complex
Length = 89
Score = 29.6 bits (65), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 31/104 (29%), Positives = 46/104 (44%), Gaps = 24/104 (23%)
Query: 301 TETSPGLLEAI--IKHANMERRLGNLEDAFSLYEQAIAIEKGKEHSQTLPMLYAQYSRFL 358
+ TSP L +AI A E + GN E+A LY+ A+ QY FL
Sbjct: 5 SSTSPNLQKAIDLASKAAQEDKAGNYEEALQLYQHAV-----------------QY--FL 45
Query: 359 HLVSRNAE--KARQ-ILVDSLDHVQLSKPLLEALIHFESIQSSP 399
H+V A+ KA+Q I +++ ++ L E L + E P
Sbjct: 46 HVVKYEAQGDKAKQSIRAKCTEYLDRAEKLKEYLKNKEKKAQKP 89
>pdb|2CQ4|A Chain A, Solution Structure Of Rna Binding Domain In Rna Binding
Motif Protein 23
Length = 114
Score = 29.6 bits (65), Expect = 8.6, Method: Compositional matrix adjust.
Identities = 20/85 (23%), Positives = 43/85 (50%), Gaps = 1/85 (1%)
Query: 872 DSLGLDEGEVKSVYVRNLPSTVTAFEIEEEFQNFGRIKPDGVFVRNRKDVVGVCYAFVEF 931
D+L +E + ++V+ L + + ++E+ F G+++ D + +R A+VEF
Sbjct: 16 DNLSPEERDARTVFCMQLAARIRPRDLEDFFSAVGKVR-DVRIISDRNSRRSKGIAYVEF 74
Query: 932 EDISGVQNAIQASPIQLAGRQVYIE 956
+I V AI + +L G + ++
Sbjct: 75 CEIQSVPLAIGLTGQRLLGVPIIVQ 99
>pdb|2KI2|A Chain A, Solution Structure Of Ss-Dna Binding Protein 12rnp2
Precursor, Hp0827(O25501_helpy) Form Helicobacter Pylori
Length = 90
Score = 29.6 bits (65), Expect = 8.7, Method: Compositional matrix adjust.
Identities = 20/81 (24%), Positives = 40/81 (49%), Gaps = 3/81 (3%)
Query: 881 VKSVYVRNLPSTVTAFEIEEEFQNFGRI-KPDGVFVRNRKDVVGVCYAFVEFEDISGVQN 939
++++YV NL + T+ +++E F FG++ ++ R K G + FVE ++ S +
Sbjct: 1 MRNIYVGNLVYSATSEQVKELFSQFGKVFNVKLIYDRETKKPKG--FGFVEMQEESVSEA 58
Query: 940 AIQASPIQLAGRQVYIEERRP 960
+ GR + + E P
Sbjct: 59 IAKLDNTDFMGRTIRVTEANP 79
>pdb|2OOE|A Chain A, Crystal Structure Of Hat Domain Of Murine Cstf-77
Length = 530
Score = 29.6 bits (65), Expect = 9.2, Method: Compositional matrix adjust.
Identities = 50/254 (19%), Positives = 96/254 (37%), Gaps = 32/254 (12%)
Query: 222 KVVKLYERCLIACANYPEYWIRYVLCMEASGSM--------------DLAHNALARATHV 267
+V+ YE+CL+ ++P+ W +E S + D A N RA
Sbjct: 256 RVMFAYEQCLLVLGHHPDIWYEAAQYLEQSSKLLAEKGDMNNAKLFSDEAANIYERAIST 315
Query: 268 FVKRLPEIHLFAARFKEQNGDIDGARAAYQ--LVHTETSPGLLEAIIKHANMERRLGNLE 325
+K+ ++ A ++E + + Y L + P L+ I++ RR ++
Sbjct: 316 LLKKNMLLYFAYADYEESRMKYEKVHSIYNRLLAIEDIDPTLV--YIQYMKFARRAEGIK 373
Query: 326 DAFSLYEQAIAIEKGKEHSQTLPMLYAQYSRFLHLVSRNAEKARQILVDSLDHVQLSKPL 385
++++A +E ++T +Y + + S++ A +I L +
Sbjct: 374 SGRMIFKKA------REDARTRHHVYVTAALMEYYCSKDKSVAFKIFELGLKKYG---DI 424
Query: 386 LEALIHFESIQSSPKQIDFLEQLVDKFLMSNSDSPSTANAAEREELSCVFLEFLGLFGDA 445
E ++ + S + + L ++ L S S P + E+ FL F GD
Sbjct: 425 PEYVLAYIDYLSHLNEDNNTRVLFERVLTSGSLPPEKSG-----EIWARFLAFESNIGDL 479
Query: 446 QLIKKAEDRHARLF 459
I K E R F
Sbjct: 480 ASILKVEKRRFTAF 493
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
0.318 0.132 0.384
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 25,318,709
Number of Sequences: 62578
Number of extensions: 976464
Number of successful extensions: 2250
Number of sequences better than 100.0: 40
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 28
Number of HSP's that attempted gapping in prelim test: 2216
Number of HSP's gapped (non-prelim): 50
length of query: 1017
length of database: 14,973,337
effective HSP length: 108
effective length of query: 909
effective length of database: 8,214,913
effective search space: 7467355917
effective search space used: 7467355917
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)