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= psy16116
(612 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Hypothetical Protein Flj201171
Length = 123
Score = 124 bits (311), Expect = 2e-28, Method: Compositional matrix adjust.
Identities = 62/106 (58%), Positives = 76/106 (71%), Gaps = 4/106 (3%)
Query: 427 NEAQAFLTRGAQVIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKA 486
NE FL++ QVI+RMRGLP+ TA++V+ FF C + G+EG+LFV PDG+
Sbjct: 12 NEVAQFLSKENQVIVRMRGLPFTATAEEVVAFFG----QHCPITGGKEGILFVTYPDGRP 67
Query: 487 TGDAFVLFEKEEEADKALSKHKESIGIRYIELFRSTTAEVQQVLNK 532
TGDAFVLF EE A AL KHK+ +G RYIELFRST AEVQQVLN+
Sbjct: 68 TGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAAEVQQVLNR 113
Score = 37.4 bits (85), Expect = 0.024, Method: Compositional matrix adjust.
Identities = 20/72 (27%), Positives = 39/72 (54%), Gaps = 5/72 (6%)
Query: 79 QGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKKQRYIEVFQCSGEDMNL 138
+G+ V G+P+G+AF+ E Y LR +++++ +RYIE+F+ + ++
Sbjct: 55 EGILFVTYPDGRPTGDAFVLFACEE--YAQNALRKHKDLL---GKRYIELFRSTAAEVQQ 109
Query: 139 VLNGVLPPTSPA 150
VLN + P+
Sbjct: 110 VLNRFSSASGPS 121
Score = 37.0 bits (84), Expect = 0.035, Method: Compositional matrix adjust.
Identities = 16/42 (38%), Positives = 26/42 (61%)
Query: 376 GRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGED 417
GR G+A V F +E+ AL++HK + KRYIE+ ++ +
Sbjct: 65 GRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELFRSTAAE 106
>pdb|2LXU|A Chain A, Solution Nmr Structure Of The Eukaryotic Rna Recognition
Motif, Rrm1, From The Heterogeneous Nuclear
Ribonucleoprotein H From Homo Sapiens, Northeast
Structural Genomics Consortium (Nesg) Target Hr8614a
Length = 108
Score = 82.4 bits (202), Expect = 7e-16, Method: Composition-based stats.
Identities = 36/98 (36%), Positives = 61/98 (62%), Gaps = 5/98 (5%)
Query: 436 GAQVIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFE 495
G ++++RGLP+ C+A +V FF + C + +G +G+ F+ +G+ +G+AFV E
Sbjct: 5 GEGFVVKVRGLPWSCSADEVQRFF-----SDCKIQNGAQGIRFIYTREGRPSGEAFVELE 59
Query: 496 KEEEADKALSKHKESIGIRYIELFRSTTAEVQQVLNKT 533
E+E AL K +E++G RY+E+F+S E+ VL T
Sbjct: 60 SEDEVKLALKKDRETMGHRYVEVFKSNNVEMDWVLKHT 97
Score = 52.4 bits (124), Expect = 7e-07, Method: Composition-based stats.
Identities = 27/71 (38%), Positives = 43/71 (60%), Gaps = 6/71 (8%)
Query: 79 QGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKKQRYIEVFQCSGEDMNL 138
QG+ +Y +G+PSGEAF++++SE LA L+ +R + RY+EVF+ + +M+
Sbjct: 38 QGIRFIYTREGRPSGEAFVELESEDEVKLA--LKKDRETM---GHRYVEVFKSNNVEMDW 92
Query: 139 VLNGVLPPTSP 149
VL P SP
Sbjct: 93 VLKHT-GPNSP 102
Score = 36.2 bits (82), Expect = 0.051, Method: Composition-based stats.
Identities = 17/51 (33%), Positives = 28/51 (54%)
Query: 364 GLGGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKAN 414
G G+ + GR +GEA V ++ +ALK+ + + RY+EV K+N
Sbjct: 36 GAQGIRFIYTREGRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVFKSN 86
>pdb|2HGM|A Chain A, Nmr Structure Of The Second Qrrm Domain Of Human Hnrnp F
pdb|2KG0|A Chain A, Structure Of The Second Qrrm Domain Of Hnrnp F In Complex
With A Agggau G-Tract Rna
Length = 126
Score = 80.9 bits (198), Expect = 2e-15, Method: Composition-based stats.
Identities = 41/87 (47%), Positives = 58/87 (66%), Gaps = 7/87 (8%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+R+RGLP+ CT ++++ FF +G E N G+ P+GK TG+AFV F +E A
Sbjct: 45 VRLRGLPFGCTKEEIVQFF-SGLEIVPN------GITLPVDPEGKITGEAFVQFASQELA 97
Query: 501 DKALSKHKESIGIRYIELFRSTTAEVQ 527
+KAL KHKE IG RYIE+F+S+ EV+
Sbjct: 98 EKALGKHKERIGHRYIEVFKSSQEEVR 124
Score = 43.5 bits (101), Expect = 3e-04, Method: Composition-based stats.
Identities = 22/51 (43%), Positives = 31/51 (60%)
Query: 367 GVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGED 417
G+ L + G+ GEA V+F QE + AL +HK I RYIEV K++ E+
Sbjct: 72 GITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVFKSSQEE 122
Score = 35.0 bits (79), Expect = 0.11, Method: Composition-based stats.
Identities = 24/74 (32%), Positives = 39/74 (52%), Gaps = 7/74 (9%)
Query: 63 EHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKK 122
E I++F IV G+ + + +G+ +GEAF+Q S+ A A +H +
Sbjct: 57 EEIVQFFSGL--EIVPNGITLPVDPEGKITGEAFVQFASQELAEKALG-KHKERI----G 109
Query: 123 QRYIEVFQCSGEDM 136
RYIEVF+ S E++
Sbjct: 110 HRYIEVFKSSQEEV 123
>pdb|2DB1|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein F Homolog
Length = 118
Score = 77.0 bits (188), Expect = 3e-14, Method: Composition-based stats.
Identities = 36/98 (36%), Positives = 59/98 (60%), Gaps = 5/98 (5%)
Query: 436 GAQVIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFE 495
G ++++RGLP+ C+ + V +F + C + DG GV F+ +G+ +G+AFV E
Sbjct: 15 GEGYVVKLRGLPWSCSIEDVQNFL-----SDCTIHDGVAGVHFIYTREGRQSGEAFVELE 69
Query: 496 KEEEADKALSKHKESIGIRYIELFRSTTAEVQQVLNKT 533
E++ AL K +ES+G RYIE+F+S E+ VL +
Sbjct: 70 SEDDVKLALKKDRESMGHRYIEVFKSHRTEMDWVLKHS 107
Score = 51.2 bits (121), Expect = 2e-06, Method: Composition-based stats.
Identities = 30/91 (32%), Positives = 49/91 (53%), Gaps = 5/91 (5%)
Query: 62 VEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGK 121
+E + FL + + GVH +Y +G+ SGEAF++++SE LA L+ +R +
Sbjct: 31 IEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLA--LKKDRESM--- 85
Query: 122 KQRYIEVFQCSGEDMNLVLNGVLPPTSPAIS 152
RYIEVF+ +M+ VL P ++ S
Sbjct: 86 GHRYIEVFKSHRTEMDWVLKHSGPNSASGPS 116
Score = 38.1 bits (87), Expect = 0.014, Method: Composition-based stats.
Identities = 18/51 (35%), Positives = 30/51 (58%)
Query: 364 GLGGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKAN 414
G+ GV + GR++GEA V ++ +ALK+ + + RYIEV K++
Sbjct: 46 GVAGVHFIYTREGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVFKSH 96
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 75.9 bits (185), Expect = 6e-14, Method: Composition-based stats.
Identities = 33/91 (36%), Positives = 55/91 (60%), Gaps = 5/91 (5%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
+IR +GLP+ CT + V++FF + C + +GE G+ F+ DGK GDA + E E++
Sbjct: 13 LIRAQGLPWSCTMEDVLNFF-----SDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQD 67
Query: 500 ADKALSKHKESIGIRYIELFRSTTAEVQQVL 530
KAL KH+ +G RY+E++ +V ++
Sbjct: 68 VQKALEKHRMYMGQRYVEVYEINNEDVDALM 98
Score = 46.2 bits (108), Expect = 5e-05, Method: Composition-based stats.
Identities = 25/88 (28%), Positives = 46/88 (52%), Gaps = 5/88 (5%)
Query: 62 VEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGK 121
+E +L F + G+H + N G+ G+A I+M+SE A + +H M
Sbjct: 25 MEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE-KHRMYM---- 79
Query: 122 KQRYIEVFQCSGEDMNLVLNGVLPPTSP 149
QRY+EV++ + ED++ ++ + +SP
Sbjct: 80 GQRYVEVYEINNEDVDALMKSLQVKSSP 107
Score = 42.0 bits (97), Expect = 0.001, Method: Composition-based stats.
Identities = 17/54 (31%), Positives = 33/54 (61%)
Query: 364 GLGGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGED 417
G G+ L+ G+R G+A++ ++ AL++H+ ++ +RY+EV + N ED
Sbjct: 40 GENGIHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVYEINNED 93
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 75.9 bits (185), Expect = 7e-14, Method: Composition-based stats.
Identities = 39/87 (44%), Positives = 58/87 (66%), Gaps = 7/87 (8%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+R+RGLP+ C+ ++++ FF +G E N G+ G++TG+AFV F +E A
Sbjct: 18 VRLRGLPFGCSKEEIVQFF-SGLEIVPN------GMTLPVDFQGRSTGEAFVQFASQEIA 70
Query: 501 DKALSKHKESIGIRYIELFRSTTAEVQ 527
+KAL KHKE IG RYIE+F+S+ AEV+
Sbjct: 71 EKALKKHKERIGHRYIEIFKSSRAEVR 97
Score = 44.7 bits (104), Expect = 1e-04, Method: Composition-based stats.
Identities = 22/48 (45%), Positives = 30/48 (62%)
Query: 367 GVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKAN 414
G+ L + GR GEA V+F QE + ALK+HK I RYIE+ K++
Sbjct: 45 GMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIFKSS 92
Score = 35.0 bits (79), Expect = 0.13, Method: Composition-based stats.
Identities = 24/70 (34%), Positives = 38/70 (54%), Gaps = 7/70 (10%)
Query: 63 EHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKK 122
E I++F IV G+ + + QG+ +GEAF+Q S+ A A L+ ++ I
Sbjct: 30 EEIVQFFSGL--EIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKA--LKKHKERI---G 82
Query: 123 QRYIEVFQCS 132
RYIE+F+ S
Sbjct: 83 HRYIEIFKSS 92
>pdb|2HGL|A Chain A, Nmr Structure Of The First Qrrm Domain Of Human Hnrnp F
pdb|2KFY|A Chain A, Nmr Structure Of The First Qrrm Of Hnrnp F In Complex With
Agggau G- Tract Rna
Length = 136
Score = 75.5 bits (184), Expect = 7e-14, Method: Composition-based stats.
Identities = 35/98 (35%), Positives = 58/98 (59%), Gaps = 5/98 (5%)
Query: 436 GAQVIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFE 495
G ++++RGLP+ C+ + V +F + C + DG GV F+ +G+ +G+AFV
Sbjct: 42 GEGFVVKLRGLPWSCSVEDVQNFL-----SDCTIHDGAAGVHFIYTREGRQSGEAFVELG 96
Query: 496 KEEEADKALSKHKESIGIRYIELFRSTTAEVQQVLNKT 533
E++ AL K +ES+G RYIE+F+S E+ VL +
Sbjct: 97 SEDDVKMALKKDRESMGHRYIEVFKSHRTEMDWVLKHS 134
Score = 48.9 bits (115), Expect = 8e-06, Method: Composition-based stats.
Identities = 28/79 (35%), Positives = 44/79 (55%), Gaps = 5/79 (6%)
Query: 62 VEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGK 121
VE + FL + + GVH +Y +G+ SGEAF+++ SE +A L+ +R +
Sbjct: 58 VEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMA--LKKDRESM--- 112
Query: 122 KQRYIEVFQCSGEDMNLVL 140
RYIEVF+ +M+ VL
Sbjct: 113 GHRYIEVFKSHRTEMDWVL 131
Score = 38.5 bits (88), Expect = 0.011, Method: Composition-based stats.
Identities = 19/51 (37%), Positives = 29/51 (56%)
Query: 364 GLGGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKAN 414
G GV + GR++GEA V ++ MALK+ + + RYIEV K++
Sbjct: 73 GAAGVHFIYTREGRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVFKSH 123
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 57.4 bits (137), Expect = 2e-08, Method: Composition-based stats.
Identities = 29/82 (35%), Positives = 48/82 (58%), Gaps = 7/82 (8%)
Query: 437 AQVIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEK 496
A + ++GLP+E K VIDFF+ +++ E+ + P+GKATG+ FV F
Sbjct: 24 AGFCVYLKGLPFEAENKHVIDFFK-----KLDIV--EDSIYIAYGPNGKATGEGFVEFRN 76
Query: 497 EEEADKALSKHKESIGIRYIEL 518
E + AL +HK+ +G R+I++
Sbjct: 77 EADYKAALCRHKQYMGNRFIQV 98
Score = 35.4 bits (80), Expect = 0.082, Method: Composition-based stats.
Identities = 20/74 (27%), Positives = 40/74 (54%), Gaps = 7/74 (9%)
Query: 63 EHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGKK 122
+H+++F + +IV +++ Y G+ +GE F++ +E + Y AA RH + M
Sbjct: 40 KHVIDFFKKL--DIVEDSIYIAYGPNGKATGEGFVEFRNE-ADYKAALCRHKQYM----G 92
Query: 123 QRYIEVFQCSGEDM 136
R+I+V + + M
Sbjct: 93 NRFIQVHPITKKGM 106
Score = 30.8 bits (68), Expect = 2.2, Method: Composition-based stats.
Identities = 13/35 (37%), Positives = 20/35 (57%)
Query: 376 GRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEV 410
G+ GE V F ++ AL RHK ++ R+I+V
Sbjct: 64 GKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQV 98
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein H'
Length = 102
Score = 54.3 bits (129), Expect = 2e-07, Method: Composition-based stats.
Identities = 30/84 (35%), Positives = 45/84 (53%), Gaps = 9/84 (10%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+ MRGLPY T + +FF ++ G PDG+ TG+A V F E+A
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLNPMRVHIEIG---------PDGRVTGEADVEFATHEDA 68
Query: 501 DKALSKHKESIGIRYIELFRSTTA 524
A++K K ++ RY+ELF ++TA
Sbjct: 69 VAAMAKDKANMQHRYVELFLNSTA 92
>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 = 53.5 bits (127), Expect = 3e-07, Method: Compositional matrix adjust.
Identities = 31/83 (37%), Positives = 45/83 (54%), Gaps = 9/83 (10%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+ MRGLPY+ T + +FF ++ G PDG+ TG+A V F EEA
Sbjct: 49 VHMRGLPYKATENDIYNFFSPLNPVRVHIEIG---------PDGRVTGEADVEFATHEEA 99
Query: 501 DKALSKHKESIGIRYIELFRSTT 523
A+SK + ++ RYIELF ++T
Sbjct: 100 VAAMSKDRANMQHRYIELFLNST 122
Score = 29.6 bits (65), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 7/54 (12%)
Query: 376 GRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDFINVAGGNNNEA 429
GR GEA V F E A+ + + ++ RYIE+ F+N G +N A
Sbjct: 83 GRVTGEADVEFATHEEAVAAMSKDRANMQHRYIEL-------FLNSTTGASNGA 129
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 49.7 bits (117), Expect = 4e-06, Method: Composition-based stats.
Identities = 27/84 (32%), Positives = 42/84 (50%), Gaps = 9/84 (10%)
Query: 441 IRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEA 500
+++RG P+ T K V++F + + V+ G TG FV F EEE
Sbjct: 13 VKLRGAPFNVTEKNVMEFLAPLKPVAIRI---------VRNAHGNKTGYIFVDFSNEEEV 63
Query: 501 DKALSKHKESIGIRYIELFRSTTA 524
+AL ++E +G RYIE+FR +
Sbjct: 64 KQALKCNREYMGGRYIEVFREKSG 87
Score = 29.3 bits (64), Expect = 7.4, Method: Composition-based stats.
Identities = 14/38 (36%), Positives = 22/38 (57%)
Query: 373 SAFGRRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEV 410
+A G + G V F ++E ALK ++ ++ RYIEV
Sbjct: 44 NAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEV 81
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 43.9 bits (102), Expect = 2e-04, Method: Composition-based stats.
Identities = 29/94 (30%), Positives = 47/94 (50%), Gaps = 1/94 (1%)
Query: 332 PTPGNPVALCPLVQNIWLSLLLNTIPGYEQVLGLGGVALCLSAFGRRNGEAIVRFIDQEH 391
P P NP L V + S + N + + L + V L GR NG +V+F+ +
Sbjct: 9 PLPINPDDLYVSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQD 68
Query: 392 RDMALKRHKHHIDKRYIEVTKANGEDFINVAGGN 425
ALKR++ + +RY+EV+ A ++ AGG+
Sbjct: 69 TFEALKRNRMLMIQRYVEVSPATERQWV-AAGGH 101
>pdb|3TU5|B Chain B, Actin Complex With Gelsolin Segment 1 Fused To Cobl
Segment
Length = 297
Score = 40.4 bits (93), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 31/111 (27%), Positives = 51/111 (45%), Gaps = 17/111 (15%)
Query: 19 GNLLGSDEQEIILLIYVIIDSYVNKVLITSQYKEPIQGFKKVLVEHILEFLGEFASNIVY 78
GN DE + V +D Y+N + Q++E +QGF+ FLG F S + Y
Sbjct: 84 GNECSQDESGAAAIFTVQLDDYLNGRAV--QHRE-VQGFESAT------FLGYFKSGLKY 134
Query: 79 QGVHMVYN--------SQGQPSGEAFIQMDSEHSAYLAAQLRHNRNMIFGK 121
+ + S+G+P ++++ +SE SA LAA H+ + K
Sbjct: 135 KKGGVASKLRKVAEQTSEGRPKKPSYVEAESERSALLAAIRGHSGTLSLRK 185
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 32.7 bits (73), Expect = 0.56, Method: Composition-based stats.
Identities = 25/86 (29%), Positives = 41/86 (47%), Gaps = 14/86 (16%)
Query: 435 RGAQVIIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLF 494
R A+ ++ + LPY+ T ++ + FE E + V K DGK+ G A++ F
Sbjct: 91 RDARTLL-AKNLPYKVTQDELKEVFEDAAE-----------IRLVSK-DGKSKGIAYIEF 137
Query: 495 EKEEEADKAL-SKHKESIGIRYIELF 519
+ E +A+K K I R I L+
Sbjct: 138 KTEADAEKTFEEKQGTEIDGRSISLY 163
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 32.7 bits (73), Expect = 0.59, Method: Composition-based stats.
Identities = 23/80 (28%), Positives = 42/80 (52%), Gaps = 8/80 (10%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
II+++ +P+ + +++DFF V+ G + + +K G TG+A V FE +E
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYG-----YQVIPGSVCLKYNEK--GMPTGEAMVAFESRDE 69
Query: 500 ADKA-LSKHKESIGIRYIEL 518
A A + + IG R ++L
Sbjct: 70 ATAAVIDLNDRPIGSRKVKL 89
Score = 30.0 bits (66), Expect = 3.7, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 60 VLVEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLA 108
V ++ IL+F + ++ V + YN +G P+GEA + +S A A
Sbjct: 27 VSIDEILDFF--YGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
>pdb|2EK6|A Chain A, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|B Chain B, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|C Chain C, Crystal Structure Of Human Rna-Binding Protein 12
pdb|2EK6|D Chain D, Crystal Structure Of Human Rna-Binding Protein 12
Length = 95
Score = 32.0 bits (71), Expect = 0.95, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 42/80 (52%), Gaps = 8/80 (10%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
+I+++ +P+ + +++DFF V+ G + + +K G TG+A V FE +E
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYG-----YQVIPGSVCLKYNEK--GMPTGEAMVAFESRDE 69
Query: 500 ADKA-LSKHKESIGIRYIEL 518
A A + + IG R ++L
Sbjct: 70 ATAAVIDLNDRPIGSRKVKL 89
Score = 30.0 bits (66), Expect = 4.0, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 60 VLVEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLA 108
V ++ IL+F + ++ V + YN +G P+GEA + +S A A
Sbjct: 27 VSIDEILDFF--YGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAA 73
>pdb|2DNO|A Chain A, Solution Structure Of Rna Binding Domain In Trinucleotide
Repeat Containing 4 Variant
Length = 102
Score = 30.8 bits (68), Expect = 2.3, Method: Composition-based stats.
Identities = 20/56 (35%), Positives = 27/56 (48%), Gaps = 10/56 (17%)
Query: 451 TAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKALS 505
T + V FE GT + C V+ G PDG + G AFV F+ EA A++
Sbjct: 25 TDEDVRKMFEPFGTIDECTVLRG---------PDGTSKGCAFVKFQTHAEAQAAIN 71
>pdb|3UJ0|A Chain A, Crystal Structure Of The Inositol 1,4,5-Trisphosphate
Receptor With Ligand Bound Form.
pdb|3UJ0|B Chain B, Crystal Structure Of The Inositol 1,4,5-Trisphosphate
Receptor With Ligand Bound Form.
pdb|3UJ4|A Chain A, Crystal Structure Of The Apo-Inositol 1,4,5-Trisphosphate
Receptor
pdb|3UJ4|B Chain B, Crystal Structure Of The Apo-Inositol 1,4,5-Trisphosphate
Receptor
Length = 604
Score = 30.8 bits (68), Expect = 2.6, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 31/69 (44%), Gaps = 4/69 (5%)
Query: 445 GLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKAT----GDAFVLFEKEEEA 500
G P ++ Q++D A NS N + VLF+K D K GD LF E+E
Sbjct: 190 GQPLHASSHQLVDNPGANEVNSVNANTSWKIVLFMKWSDNKDDILKGGDVVRLFHAEQEK 249
Query: 501 DKALSKHKE 509
+H++
Sbjct: 250 FLTADEHRK 258
>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 = 30.4 bits (67), Expect = 2.8, Method: Composition-based stats.
Identities = 21/77 (27%), Positives = 38/77 (49%), Gaps = 7/77 (9%)
Query: 445 GLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEEADKAL 504
GL ++ T K + D+F E V+D L + G++ G FVLF++ E DK +
Sbjct: 6 GLSWDTTKKDLKDYFSKFGE----VVDC---TLKLDPITGRSRGFGFVLFKESESVDKVM 58
Query: 505 SKHKESIGIRYIELFRS 521
+ + + + I+ R+
Sbjct: 59 DQKEHKLNGKVIDPKRA 75
>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 = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 4/34 (11%)
Query: 81 VHMVYNSQ-GQPSGEAFIQMDSE---HSAYLAAQ 110
+HMVY+ + G+P G AFI+ + E HSAY A
Sbjct: 132 IHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHAD 165
>pdb|2EK1|A Chain A, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|B Chain B, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|C Chain C, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|D Chain D, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|E Chain E, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|F Chain F, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|G Chain G, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
pdb|2EK1|H Chain H, Crystal Structure Of Rna-Binding Motif Of Human
Rna-Binding Protein 12
Length = 95
Score = 30.4 bits (67), Expect = 2.9, Method: Composition-based stats.
Identities = 22/80 (27%), Positives = 41/80 (51%), Gaps = 8/80 (10%)
Query: 440 IIRMRGLPYECTAKQVIDFFEAGTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFEKEEE 499
+I+++ P+ + +++DFF V+ G + + +K G TG+A V FE +E
Sbjct: 17 VIKVQNXPFTVSIDEILDFFYG-----YQVIPGSVCLKYNEK--GXPTGEAXVAFESRDE 69
Query: 500 ADKA-LSKHKESIGIRYIEL 518
A A + + IG R ++L
Sbjct: 70 ATAAVIDLNDRPIGSRKVKL 89
Score = 29.3 bits (64), Expect = 6.5, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 26/49 (53%), Gaps = 2/49 (4%)
Query: 60 VLVEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLA 108
V ++ IL+F + ++ V + YN +G P+GEA + +S A A
Sbjct: 27 VSIDEILDFF--YGYQVIPGSVCLKYNEKGXPTGEAXVAFESRDEATAA 73
>pdb|4F0J|A Chain A, Crystal Structure Of A Probable Hydrolytic Enzyme (Pa3053)
From Pseudomonas Aeruginosa Pao1 At 1.50 A Resolution
Length = 315
Score = 30.4 bits (67), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 21/84 (25%), Positives = 33/84 (39%), Gaps = 17/84 (20%)
Query: 50 YKEPIQGFKKVLVEHILEFLGEFASNIVYQGVHMVYNSQGQPSGEAFIQMDSEHSAYLAA 109
Y E ++GF H L+F SQGQP A++ + + +
Sbjct: 7 YGERLEGFDYAYPVHYLDF-----------------TSQGQPLSXAYLDVAPKKANGRTI 49
Query: 110 QLRHNRNMIFGKKQRYIEVFQCSG 133
L H +N G +R I+V +G
Sbjct: 50 LLXHGKNFCAGTWERTIDVLADAG 73
>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 = 29.6 bits (65), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 16/34 (47%), Positives = 22/34 (64%), Gaps = 4/34 (11%)
Query: 81 VHMVYNSQ-GQPSGEAFIQMDSE---HSAYLAAQ 110
+HMVY+ + G+P G AFI+ + E HSAY A
Sbjct: 132 IHMVYSKRSGKPRGYAFIEYEHERDMHSAYKHAD 165
>pdb|2LYV|A Chain A, Solution Structure Of The Two Rrm Domains Of Hnrnp A1
(up1) Using Segmental Isotope Labeling
Length = 197
Score = 29.6 bits (65), Expect = 4.9, Method: Composition-based stats.
Identities = 31/127 (24%), Positives = 48/127 (37%), Gaps = 19/127 (14%)
Query: 377 RRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDFINVAGGNNNEAQAFLTRG 436
R G V + E D A+ H +D R +E +A V+ ++ A LT
Sbjct: 54 RSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA-------VSREDSQRPGAHLTVK 106
Query: 437 AQVIIRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFE 495
I + G+ + + D+FE G +M + GK G AFV F+
Sbjct: 107 K---IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM--------TDRGSGKKRGFAFVTFD 155
Query: 496 KEEEADK 502
+ DK
Sbjct: 156 DHDSVDK 162
>pdb|1UP1|A Chain A, Up1, The Two Rna-Recognition Motif Domain Of Hnrnp A1
Length = 182
Score = 29.6 bits (65), Expect = 4.9, Method: Composition-based stats.
Identities = 31/127 (24%), Positives = 48/127 (37%), Gaps = 19/127 (14%)
Query: 377 RRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDFINVAGGNNNEAQAFLTRG 436
R G V + E D A+ H +D R +E +A V+ ++ A LT
Sbjct: 51 RSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA-------VSREDSQRPGAHLTVK 103
Query: 437 AQVIIRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFE 495
I + G+ + + D+FE G +M + GK G AFV F+
Sbjct: 104 K---IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM--------TDRGSGKKRGFAFVTFD 152
Query: 496 KEEEADK 502
+ DK
Sbjct: 153 DHDSVDK 159
>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 = 29.6 bits (65), Expect = 4.9, Method: Composition-based stats.
Identities = 31/127 (24%), Positives = 48/127 (37%), Gaps = 19/127 (14%)
Query: 377 RRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDFINVAGGNNNEAQAFLTRG 436
R G V + E D A+ H +D R +E +A V+ ++ A LT
Sbjct: 46 RSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA-------VSREDSQRPGAHLTVK 98
Query: 437 AQVIIRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFE 495
I + G+ + + D+FE G +M + GK G AFV F+
Sbjct: 99 K---IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM--------TDRGSGKKRGFAFVTFD 147
Query: 496 KEEEADK 502
+ DK
Sbjct: 148 DHDSVDK 154
>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 = 29.6 bits (65), Expect = 4.9, Method: Composition-based stats.
Identities = 31/127 (24%), Positives = 48/127 (37%), Gaps = 19/127 (14%)
Query: 377 RRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDFINVAGGNNNEAQAFLTRG 436
R G V + E D A+ H +D R +E +A V+ ++ A LT
Sbjct: 52 RSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA-------VSREDSQRPGAHLTVK 104
Query: 437 AQVIIRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFE 495
I + G+ + + D+FE G +M + GK G AFV F+
Sbjct: 105 K---IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM--------TDRGSGKKRGFAFVTFD 153
Query: 496 KEEEADK 502
+ DK
Sbjct: 154 DHDSVDK 160
>pdb|1HA1|A Chain A, Hnrnp A1 (Rbd1,2) From Homo Sapiens
Length = 184
Score = 29.6 bits (65), Expect = 4.9, Method: Composition-based stats.
Identities = 31/127 (24%), Positives = 48/127 (37%), Gaps = 19/127 (14%)
Query: 377 RRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDFINVAGGNNNEAQAFLTRG 436
R G V + E D A+ H +D R +E +A V+ ++ A LT
Sbjct: 53 RSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA-------VSREDSQRPGAHLTVK 105
Query: 437 AQVIIRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFE 495
I + G+ + + D+FE G +M + GK G AFV F+
Sbjct: 106 K---IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM--------TDRGSGKKRGFAFVTFD 154
Query: 496 KEEEADK 502
+ DK
Sbjct: 155 DHDSVDK 161
>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 = 29.6 bits (65), Expect = 4.9, Method: Composition-based stats.
Identities = 31/127 (24%), Positives = 48/127 (37%), Gaps = 19/127 (14%)
Query: 377 RRNGEAIVRFIDQEHRDMALKRHKHHIDKRYIEVTKANGEDFINVAGGNNNEAQAFLTRG 436
R G V + E D A+ H +D R +E +A V+ ++ A LT
Sbjct: 53 RSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRA-------VSREDSQRPGAHLTVK 105
Query: 437 AQVIIRMRGLPYECTAKQVIDFFEA-GTENSCNVMDGEEGVLFVKKPDGKATGDAFVLFE 495
I + G+ + + D+FE G +M + GK G AFV F+
Sbjct: 106 K---IFVGGIKEDTEEHHLRDYFEQYGKIEVIEIM--------TDRGSGKKRGFAFVTFD 154
Query: 496 KEEEADK 502
+ DK
Sbjct: 155 DHDSVDK 161
>pdb|2B25|A Chain A, Human Putative Trna(1-Methyladenosine)methyltransferase
pdb|2B25|B Chain B, Human Putative Trna(1-Methyladenosine)methyltransferase
Length = 336
Score = 29.3 bits (64), Expect = 7.1, Method: Compositional matrix adjust.
Identities = 15/41 (36%), Positives = 22/41 (53%)
Query: 364 GLGGVALCLSAFGRRNGEAIVRFIDQEHRDMALKRHKHHID 404
G GG++L LS G I + ++H D+A K +KH D
Sbjct: 115 GSGGMSLFLSKAVGSQGRVISFEVRKDHHDLAKKNYKHWRD 155
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
0.320 0.137 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,614,477
Number of Sequences: 62578
Number of extensions: 720777
Number of successful extensions: 1361
Number of sequences better than 100.0: 32
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 19
Number of HSP's that attempted gapping in prelim test: 1305
Number of HSP's gapped (non-prelim): 59
length of query: 612
length of database: 14,973,337
effective HSP length: 105
effective length of query: 507
effective length of database: 8,402,647
effective search space: 4260142029
effective search space used: 4260142029
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)