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= 024584
(265 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 82.8 bits (203), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 38/80 (47%), Positives = 55/80 (68%)
Query: 178 LKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRAMCKD 237
+++RGLPF K EIVQFF +I+ + I + P+GK TGEA+V+F S E A++A+ K
Sbjct: 45 VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKH 104
Query: 238 KMTIGSRYVELFPSTPDEAR 257
K IG RY+E+F S+ +E R
Sbjct: 105 KERIGHRYIEVFKSSQEEVR 124
Score = 73.9 bits (180), Expect = 8e-14, Method: Compositional matrix adjust.
Identities = 36/78 (46%), Positives = 52/78 (66%), Gaps = 3/78 (3%)
Query: 61 VRLRGLPFNCTDIDICKFFAGLDIVD---VLLVNKNGRFSGEAFVVFAGPIQVEFALQRD 117
VRLRGLPF CT +I +FF+GL+IV L V+ G+ +GEAFV FA E AL +
Sbjct: 45 VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKH 104
Query: 118 RQNMGRRYVEVFRCKRQD 135
++ +G RY+EVF+ +++
Sbjct: 105 KERIGHRYIEVFKSSQEE 122
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 73.9 bits (180), Expect = 7e-14, Method: Compositional matrix adjust.
Identities = 34/89 (38%), Positives = 55/89 (61%)
Query: 164 KRYNDKDQMEHTEILKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVE 223
KR + E + ++GLPF + ++ FFK I+ED I+IA P+GKATGE +VE
Sbjct: 14 KRSRSRSPHEAGFCVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVE 73
Query: 224 FVSVEEAKRAMCKDKMTIGSRYVELFPST 252
F + + K A+C+ K +G+R++++ P T
Sbjct: 74 FRNEADYKAALCRHKQYMGNRFIQVHPIT 102
Score = 50.4 bits (119), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 27/71 (38%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 61 VRLRGLPFNCTDIDICKFFAGLDIVD---VLLVNKNGRFSGEAFVVFAGPIQVEFALQRD 117
V L+GLPF + + FF LDIV+ + NG+ +GE FV F + AL R
Sbjct: 28 VYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRH 87
Query: 118 RQNMGRRYVEV 128
+Q MG R+++V
Sbjct: 88 KQYMGNRFIQV 98
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 73.2 bits (178), Expect = 1e-13, Method: Compositional matrix adjust.
Identities = 35/82 (42%), Positives = 54/82 (65%)
Query: 178 LKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRAMCKD 237
+++RGLPF K EIVQFF +I+ + + + G++TGEA+V+F S E A++A+ K
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 77
Query: 238 KMTIGSRYVELFPSTPDEARRA 259
K IG RY+E+F S+ E R +
Sbjct: 78 KERIGHRYIEIFKSSRAEVRTS 99
Score = 72.4 bits (176), Expect = 3e-13, Method: Compositional matrix adjust.
Identities = 36/78 (46%), Positives = 52/78 (66%), Gaps = 3/78 (3%)
Query: 61 VRLRGLPFNCTDIDICKFFAGLDIVD---VLLVNKNGRFSGEAFVVFAGPIQVEFALQRD 117
VRLRGLPF C+ +I +FF+GL+IV L V+ GR +GEAFV FA E AL++
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 77
Query: 118 RQNMGRRYVEVFRCKRQD 135
++ +G RY+E+F+ R +
Sbjct: 78 KERIGHRYIEIFKSSRAE 95
>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 = 68.6 bits (166), Expect = 4e-12, Method: Compositional matrix adjust.
Identities = 34/87 (39%), Positives = 50/87 (57%), Gaps = 2/87 (2%)
Query: 178 LKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRAMCKD 237
+ MRGLP+ +++I FF + ++HI PDG+ TGEA VEF + EEA AM KD
Sbjct: 49 VHMRGLPYKATENDIYNFFSPLNPV--RVHIEIGPDGRVTGEADVEFATHEEAVAAMSKD 106
Query: 238 KMTIGSRYVELFPSTPDEARRAESRSR 264
+ + RY+ELF ++ A S+
Sbjct: 107 RANMQHRYIELFLNSTTGASNGAYSSQ 133
Score = 58.9 bits (141), Expect = 3e-09, Method: Compositional matrix adjust.
Identities = 33/90 (36%), Positives = 49/90 (54%), Gaps = 1/90 (1%)
Query: 61 VRLRGLPFNCTDIDICKFFAGLDIVDVLL-VNKNGRFSGEAFVVFAGPIQVEFALQRDRQ 119
V +RGLP+ T+ DI FF+ L+ V V + + +GR +GEA V FA + A+ +DR
Sbjct: 49 VHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRA 108
Query: 120 NMGRRYVEVFRCKRQDYYNAVASEVNYEGI 149
NM RY+E+F N S +G+
Sbjct: 109 NMQHRYIELFLNSTTGASNGAYSSQVMQGM 138
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Hypothetical Protein Flj201171
Length = 123
Score = 68.2 bits (165), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 37/93 (39%), Positives = 55/93 (59%), Gaps = 3/93 (3%)
Query: 173 EHTEILKMRGLPFSVKKSEIVQFFKDYKII---EDKIHIACRPDGKATGEAYVEFVSVEE 229
E+ I++MRGLPF+ E+V FF + I ++ I PDG+ TG+A+V F E
Sbjct: 21 ENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEY 80
Query: 230 AKRAMCKDKMTIGSRYVELFPSTPDEARRAESR 262
A+ A+ K K +G RY+ELF ST E ++ +R
Sbjct: 81 AQNALRKHKDLLGKRYIELFRSTAAEVQQVLNR 113
Score = 50.4 bits (119), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 28/77 (36%), Positives = 46/77 (59%), Gaps = 6/77 (7%)
Query: 60 VVRLRGLPFNCTDIDICKFFAGLDIVD-----VLLVN-KNGRFSGEAFVVFAGPIQVEFA 113
+VR+RGLPF T ++ FF + +L V +GR +G+AFV+FA + A
Sbjct: 25 IVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNA 84
Query: 114 LQRDRQNMGRRYVEVFR 130
L++ + +G+RY+E+FR
Sbjct: 85 LRKHKDLLGKRYIELFR 101
>pdb|2DB1|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein F Homolog
Length = 118
Score = 67.4 bits (163), Expect = 7e-12, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 50/81 (61%), Gaps = 5/81 (6%)
Query: 60 VVRLRGLPFNCTDIDICKFFAGLDIVDVL-----LVNKNGRFSGEAFVVFAGPIQVEFAL 114
VV+LRGLP++C+ D+ F + I D + + + GR SGEAFV V+ AL
Sbjct: 19 VVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL 78
Query: 115 QRDRQNMGRRYVEVFRCKRQD 135
++DR++MG RY+EVF+ R +
Sbjct: 79 KKDRESMGHRYIEVFKSHRTE 99
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 27/77 (35%), Positives = 47/77 (61%), Gaps = 2/77 (2%)
Query: 177 ILKMRGLPFSVKKSEIVQFFKDYKIIED--KIHIACRPDGKATGEAYVEFVSVEEAKRAM 234
++K+RGLP+S ++ F D I + +H +G+ +GEA+VE S ++ K A+
Sbjct: 19 VVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFVELESEDDVKLAL 78
Query: 235 CKDKMTIGSRYVELFPS 251
KD+ ++G RY+E+F S
Sbjct: 79 KKDRESMGHRYIEVFKS 95
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein H'
Length = 102
Score = 67.0 bits (162), Expect = 9e-12, Method: Compositional matrix adjust.
Identities = 33/72 (45%), Positives = 45/72 (62%), Gaps = 2/72 (2%)
Query: 178 LKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRAMCKD 237
+ MRGLP+ +++I FF + ++HI PDG+ TGEA VEF + E+A AM KD
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLNPM--RVHIEIGPDGRVTGEADVEFATHEDAVAAMAKD 75
Query: 238 KMTIGSRYVELF 249
K + RYVELF
Sbjct: 76 KANMQHRYVELF 87
Score = 54.3 bits (129), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 29/70 (41%), Positives = 43/70 (61%), Gaps = 1/70 (1%)
Query: 61 VRLRGLPFNCTDIDICKFFAGLDIVDVLL-VNKNGRFSGEAFVVFAGPIQVEFALQRDRQ 119
V +RGLP+ T+ DI FF+ L+ + V + + +GR +GEA V FA A+ +D+
Sbjct: 18 VHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKA 77
Query: 120 NMGRRYVEVF 129
NM RYVE+F
Sbjct: 78 NMQHRYVELF 87
>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 = 66.2 bits (160), Expect = 2e-11, Method: Compositional matrix adjust.
Identities = 33/81 (40%), Positives = 49/81 (60%), Gaps = 5/81 (6%)
Query: 60 VVRLRGLPFNCTDIDICKFFAGLDIVDV-----LLVNKNGRFSGEAFVVFAGPIQVEFAL 114
VV+LRGLP++C+ D+ F + I D + + GR SGEAFV V+ AL
Sbjct: 46 VVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL 105
Query: 115 QRDRQNMGRRYVEVFRCKRQD 135
++DR++MG RY+EVF+ R +
Sbjct: 106 KKDRESMGHRYIEVFKSHRTE 126
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/81 (34%), Positives = 48/81 (59%), Gaps = 2/81 (2%)
Query: 177 ILKMRGLPFSVKKSEIVQFFKDYKIIEDK--IHIACRPDGKATGEAYVEFVSVEEAKRAM 234
++K+RGLP+S ++ F D I + +H +G+ +GEA+VE S ++ K A+
Sbjct: 46 VVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL 105
Query: 235 CKDKMTIGSRYVELFPSTPDE 255
KD+ ++G RY+E+F S E
Sbjct: 106 KKDRESMGHRYIEVFKSHRTE 126
>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 = 63.2 bits (152), Expect = 2e-10, Method: Compositional matrix adjust.
Identities = 31/76 (40%), Positives = 49/76 (64%), Gaps = 5/76 (6%)
Query: 60 VVRLRGLPFNCTDIDICKFFAGLDIVDV-----LLVNKNGRFSGEAFVVFAGPIQVEFAL 114
VV++RGLP++C+ ++ +FF+ I + + + GR SGEAFV +V+ AL
Sbjct: 9 VVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLAL 68
Query: 115 QRDRQNMGRRYVEVFR 130
++DR+ MG RYVEVF+
Sbjct: 69 KKDRETMGHRYVEVFK 84
Score = 62.0 bits (149), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 33/78 (42%), Positives = 48/78 (61%), Gaps = 2/78 (2%)
Query: 177 ILKMRGLPFSVKKSEIVQFFKDYKIIE--DKIHIACRPDGKATGEAYVEFVSVEEAKRAM 234
++K+RGLP+S E+ +FF D KI I +G+ +GEA+VE S +E K A+
Sbjct: 9 VVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLAL 68
Query: 235 CKDKMTIGSRYVELFPST 252
KD+ T+G RYVE+F S
Sbjct: 69 KKDRETMGHRYVEVFKSN 86
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 57.8 bits (138), Expect = 6e-09, Method: Compositional matrix adjust.
Identities = 32/74 (43%), Positives = 48/74 (64%), Gaps = 1/74 (1%)
Query: 60 VVRLRGLPFNCTDIDICKFFAGLDIVDVLLV-NKNGRFSGEAFVVFAGPIQVEFALQRDR 118
V+LRG PFN T+ ++ +F A L V + +V N +G +G FV F+ +V+ AL+ +R
Sbjct: 12 TVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNR 71
Query: 119 QNMGRRYVEVFRCK 132
+ MG RY+EVFR K
Sbjct: 72 EYMGGRYIEVFREK 85
Score = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 26/76 (34%), Positives = 44/76 (57%), Gaps = 4/76 (5%)
Query: 174 HTEILKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRA 233
HT +K+RG PF+V + +++F K + I I G TG +V+F + EE K+A
Sbjct: 11 HT--VKLRGAPFNVTEKNVMEFLAPLKPV--AIRIVRNAHGNKTGYIFVDFSNEEEVKQA 66
Query: 234 MCKDKMTIGSRYVELF 249
+ ++ +G RY+E+F
Sbjct: 67 LKCNREYMGGRYIEVF 82
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 56.2 bits (134), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 47/75 (62%), Gaps = 2/75 (2%)
Query: 177 ILKMRGLPFSVKKSEIVQFFKDYKII--EDKIHIACRPDGKATGEAYVEFVSVEEAKRAM 234
+++ +GLP+S +++ FF D +I E+ IH DGK G+A +E S ++ ++A+
Sbjct: 13 LIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL 72
Query: 235 CKDKMTIGSRYVELF 249
K +M +G RYVE++
Sbjct: 73 EKHRMYMGQRYVEVY 87
Score = 53.9 bits (128), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 27/81 (33%), Positives = 47/81 (58%), Gaps = 5/81 (6%)
Query: 60 VVRLRGLPFNCTDIDICKFFAGLDIVD-----VLLVNKNGRFSGEAFVVFAGPIQVEFAL 114
++R +GLP++CT D+ FF+ I + L+N++G+ G+A + V+ AL
Sbjct: 13 LIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKAL 72
Query: 115 QRDRQNMGRRYVEVFRCKRQD 135
++ R MG+RYVEV+ +D
Sbjct: 73 EKHRMYMGQRYVEVYEINNED 93
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 48.1 bits (113), Expect = 4e-06, Method: Compositional matrix adjust.
Identities = 28/73 (38%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 177 ILKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRAMCK 236
I+K++ +PF+V EI+ FF Y++I + + G TGEA V F S +EA A+
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 237 -DKMTIGSRYVEL 248
+ IGSR V+L
Sbjct: 77 LNDRPIGSRKVKL 89
Score = 28.9 bits (63), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 60 VVRLRGLPFNCTDIDICKFFAGLDIVD---VLLVNKNGRFSGEAFVVF 104
+++++ +PF + +I FF G ++ L N+ G +GEA V F
Sbjct: 17 IIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64
>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 = 47.8 bits (112), Expect = 6e-06, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 42/73 (57%), Gaps = 1/73 (1%)
Query: 177 ILKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRAMCK 236
++K++ +PF+V EI+ FF Y++I + + G TGEA V F S +EA A+
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVID 76
Query: 237 -DKMTIGSRYVEL 248
+ IGSR V+L
Sbjct: 77 LNDRPIGSRKVKL 89
Score = 29.6 bits (65), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 26/48 (54%), Gaps = 3/48 (6%)
Query: 60 VVRLRGLPFNCTDIDICKFFAGLDIVD---VLLVNKNGRFSGEAFVVF 104
V++++ +PF + +I FF G ++ L N+ G +GEA V F
Sbjct: 17 VIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAF 64
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 47.8 bits (112), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 29/80 (36%), Positives = 42/80 (52%), Gaps = 1/80 (1%)
Query: 61 VRLRGLPFNCTDIDICKFFAGLDIVDV-LLVNKNGRFSGEAFVVFAGPIQVEFALQRDRQ 119
V + G+PF+ + D+ FF GL + V LL + GR +G V F P AL+R+R
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRM 78
Query: 120 NMGRRYVEVFRCKRQDYYNA 139
M +RYVEV + + A
Sbjct: 79 LMIQRYVEVSPATERQWVAA 98
Score = 47.4 bits (111), Expect = 8e-06, Method: Compositional matrix adjust.
Identities = 21/75 (28%), Positives = 44/75 (58%), Gaps = 2/75 (2%)
Query: 178 LKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRAMCKD 237
+ + G+PFS ++++ FF ++ D +H+ G+ G V+F+S ++ A+ ++
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGLRV--DAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRN 76
Query: 238 KMTIGSRYVELFPST 252
+M + RYVE+ P+T
Sbjct: 77 RMLMIQRYVEVSPAT 91
>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 = 46.6 bits (109), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 27/73 (36%), Positives = 41/73 (56%), Gaps = 1/73 (1%)
Query: 177 ILKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRAMCK 236
++K++ PF+V EI+ FF Y++I + + G TGEA V F S +EA A+
Sbjct: 17 VIKVQNXPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGXPTGEAXVAFESRDEATAAVID 76
Query: 237 -DKMTIGSRYVEL 248
+ IGSR V+L
Sbjct: 77 LNDRPIGSRKVKL 89
Score = 27.7 bits (60), Expect = 7.7, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 60 VVRLRGLPFNCTDIDICKFFAGLDIVD---VLLVNKNGRFSGEAFVVF 104
V++++ PF + +I FF G ++ L N+ G +GEA V F
Sbjct: 17 VIKVQNXPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGXPTGEAXVAF 64
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 41.2 bits (95), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 35/54 (64%)
Query: 180 MRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRA 233
+ +PFS+ K +++QF + + E+ +H+ +G+ G+A V+F + ++A+++
Sbjct: 20 ITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKS 73
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 35.0 bits (79), Expect = 0.044, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 1/60 (1%)
Query: 182 GLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRAMCKDKMTI 241
GLP+ + + ++F+ + IE+ + I R GK+ G +V A+RA CKD I
Sbjct: 24 GLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA-CKDPNPI 82
Score = 28.5 bits (62), Expect = 3.7, Method: Compositional matrix adjust.
Identities = 15/44 (34%), Positives = 25/44 (56%), Gaps = 3/44 (6%)
Query: 65 GLPFNCTDIDICKFFAGL-DIVDVLLVN--KNGRFSGEAFVVFA 105
GLP++ TD + K+F G DI + +++ + G+ G FV A
Sbjct: 24 GLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMA 67
>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 = 32.7 bits (73), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 163 AKRYNDKDQMEHTEILKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYV 222
AKR N + E IL +R LP+ + E+ F Y I +I + P+ + G AYV
Sbjct: 6 AKRANIRLPPEVNRILMIRNLPYKITAEEMYDIFGKYGPIR-QIRVGNTPETR--GTAYV 62
Query: 223 EFVSVEEAKRA 233
+ + +AK A
Sbjct: 63 VYEDIFDAKNA 73
>pdb|1FJE|B Chain B, Solution Structure Of Nucleolin Rbd12 In Complex With Snre
Rna
pdb|1RKJ|A Chain A, Solution Structure Of The Complex Formed By The Two N-
Terminal Rna-Binding Domains Of Nucleolin And A Pre-Rrna
Target
Length = 175
Score = 32.7 bits (73), Expect = 0.21, Method: Compositional matrix adjust.
Identities = 27/103 (26%), Positives = 46/103 (44%), Gaps = 13/103 (12%)
Query: 149 IYDNDFHGSPPPSRAKRYNDKDQMEHTEILKMRGLPFSVKKSEIVQFFKDYKIIEDKIHI 208
++ N+ P R D ++ L + L F++ + E+ + F ED + I
Sbjct: 78 VFGNEIKLEKPKGR-----DSKKVRAARTLLAKNLSFNITEDELKEVF------EDALEI 126
Query: 209 -ACRPDGKATGEAYVEFVSVEEAKRAM-CKDKMTIGSRYVELF 249
DGK+ G AY+EF S +A++ + K I R V L+
Sbjct: 127 RLVSQDGKSKGIAYIEFKSEADAEKNLEEKQGAEIDGRSVSLY 169
>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 = 32.7 bits (73), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 23/71 (32%), Positives = 35/71 (49%), Gaps = 3/71 (4%)
Query: 163 AKRYNDKDQMEHTEILKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYV 222
AKR N + E IL +R LP+ + E+ F Y I +I + P+ + G AYV
Sbjct: 6 AKRANIRLPPEVNRILYIRNLPYKITAEEMYDIFGKYGPIR-QIRVGNTPETR--GTAYV 62
Query: 223 EFVSVEEAKRA 233
+ + +AK A
Sbjct: 63 VYEDIFDAKNA 73
>pdb|3BBO|O Chain O, Homology Model For The Spinach Chloroplast 50s Subunit
Fitted To 9.4a Cryo-Em Map Of The 70s Chlororibosome
Length = 135
Score = 32.3 bits (72), Expect = 0.26, Method: Compositional matrix adjust.
Identities = 15/48 (31%), Positives = 25/48 (52%)
Query: 215 KATGEAYVEFVSVEEAKRAMCKDKMTIGSRYVELFPSTPDEARRAESR 262
+A A++ +E +RAM ++ G +V +FP P R AE+R
Sbjct: 35 QALEPAWITSRQIEAGRRAMTRNARRGGKIWVRIFPDKPVTVRPAETR 82
>pdb|2KRR|A Chain A, Solution Structure Of The Rbd1,2 Domains From Human
Nucleoli
Length = 180
Score = 31.6 bits (70), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 40/73 (54%), Gaps = 6/73 (8%)
Query: 178 LKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRAMCKD 237
L + LP+ V + E+ + F+D +I + + DGK+ G AY+EF + +A++ +
Sbjct: 96 LLAKNLPYKVTQDELKEVFEDAA----EIRLVSK-DGKSKGIAYIEFKTEADAEKTFEEK 150
Query: 238 KMT-IGSRYVELF 249
+ T I R + L+
Sbjct: 151 QGTEIDGRSISLY 163
>pdb|2DNG|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 4h
Length = 103
Score = 31.6 bits (70), Expect = 0.47, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 32/66 (48%), Gaps = 1/66 (1%)
Query: 183 LPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRAMCKDKMTIG 242
LPF+ + +I FKD I ++ + + K G YVEF V+ K A+ D +G
Sbjct: 23 LPFNTVQGDIDAIFKDLSIRSVRL-VRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLG 81
Query: 243 SRYVEL 248
R + +
Sbjct: 82 DRSLRV 87
Score = 28.9 bits (63), Expect = 3.4, Method: Compositional matrix adjust.
Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 66 LPFNCTDIDICKFFAGLDIVDVLLV--NKNGRFSGEAFVVFAGPIQVEFALQRDRQNMGR 123
LPFN DI F L I V LV +F G +V F ++ AL D +G
Sbjct: 23 LPFNTVQGDIDAIFKDLSIRSVRLVRDKDTDKFKGFCYVEFDEVDSLKEALTYDGALLGD 82
Query: 124 RY--VEVFRCKRQD 135
R V++ ++QD
Sbjct: 83 RSLRVDIAEGRKQD 96
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 31.2 bits (69), Expect = 0.60, Method: Compositional matrix adjust.
Identities = 20/76 (26%), Positives = 38/76 (50%), Gaps = 5/76 (6%)
Query: 174 HTEILKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRA 233
++ L + L +S + + + F+ I+ + +GK+ G A++EF S E+AK A
Sbjct: 14 ESKTLVLSNLSYSATEETLQEVFEKATFIK----VPQNQNGKSKGYAFIEFASFEDAKEA 69
Query: 234 MCK-DKMTIGSRYVEL 248
+ +K I R + L
Sbjct: 70 LNSCNKREIEGRAIRL 85
>pdb|1FJC|A Chain A, Solution Structure Of Nucleolin Rbd2
Length = 96
Score = 30.0 bits (66), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 23/74 (31%), Positives = 37/74 (50%), Gaps = 8/74 (10%)
Query: 178 LKMRGLPFSVKKSEIVQFFKDYKIIEDKIHI-ACRPDGKATGEAYVEFVSVEEAKRAM-C 235
L + L F++ + E+ + F ED + I DGK+ G AY+EF S +A++ +
Sbjct: 19 LLAKNLSFNITEDELKEVF------EDALEIRLVSQDGKSKGIAYIEFKSEADAEKNLEE 72
Query: 236 KDKMTIGSRYVELF 249
K I R V L+
Sbjct: 73 KQGAEIDGRSVSLY 86
>pdb|2CPH|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
Of Hypothetical Rna-Binding Protein Rbm19
Length = 107
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 18/78 (23%), Positives = 37/78 (47%), Gaps = 4/78 (5%)
Query: 173 EHTEILKMRGLPFSVKKSEIVQFFKDYKIIED-KIHIACRPDGKATGEAYVEFVSVEEAK 231
+ T + +R +PF + EI + F + ++ ++ G G +V+F++ ++AK
Sbjct: 13 QTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVDFITKQDAK 72
Query: 232 R---AMCKDKMTIGSRYV 246
+ A+C G R V
Sbjct: 73 KAFNALCHSTHLYGRRLV 90
>pdb|2DNH|A Chain A, Solution Structure Of Rna Binding Domain In Bruno-Like 5
Rna Binding Protein
Length = 105
Score = 29.3 bits (64), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/44 (31%), Positives = 28/44 (63%), Gaps = 1/44 (2%)
Query: 191 EIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRAM 234
++++ F+ + +I D+ + PDG + G A+V+F S EA+ A+
Sbjct: 31 DVLRLFQPFGVI-DECTVLRGPDGSSKGCAFVKFSSHTEAQAAI 73
>pdb|1F0X|A Chain A, Crystal Structure Of D-Lactate Dehydrogenase, A Peripheral
Membrane Respiratory Enzyme.
pdb|1F0X|B Chain B, Crystal Structure Of D-Lactate Dehydrogenase, A Peripheral
Membrane Respiratory Enzyme
Length = 571
Score = 28.1 bits (61), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 16/38 (42%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 160 PSRAKRYNDKDQMEHTEILKMRGLPFSVKKSEIVQFFK 197
P R K + DK EH +LKM G KS +V +FK
Sbjct: 378 PPRMKNWRDK--YEHHLLLKMAGDGVGEAKSWLVDYFK 413
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 27.7 bits (60), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 18/66 (27%), Positives = 32/66 (48%), Gaps = 3/66 (4%)
Query: 174 HTEILKMRGLPFSVKKSEIVQFFKDYKIIEDKIHIACRPDGKATGEAYVEFVSVEEAKRA 233
H L ++ L V + Q F + +E + + G+ATG+ +VEF + A++A
Sbjct: 95 HGAALTVKNLSPVVSNELLEQAFSQFGPVEKAV-VVVDDRGRATGKGFVEFAAKPPARKA 153
Query: 234 M--CKD 237
+ C D
Sbjct: 154 LERCGD 159
>pdb|2DHG|A Chain A, Solution Structure Of The C-Terminal Rna Recognition Motif
In Trna Selenocysteine Associated Protein
Length = 104
Score = 27.7 bits (60), Expect = 7.6, Method: Compositional matrix adjust.
Identities = 18/62 (29%), Positives = 31/62 (50%), Gaps = 9/62 (14%)
Query: 205 KIHIACR-------PDGKATGEAYVEFVSVEEAKRAM--CKDKMTIGSRYVELFPSTPDE 255
K++ +CR G + G +V+F E KRA+ C+ + +GS+ V L + P
Sbjct: 32 KVYPSCRGGKVVLDQTGVSKGYGFVKFTDELEQKRALTECQGAVGLGSKPVRLSVAIPKA 91
Query: 256 AR 257
+R
Sbjct: 92 SR 93
>pdb|2J76|E Chain E, Solution Structure And Rna Interactions Of The Rna
Recognition Motif From Eukaryotic Translation Initiation
Factor 4b
Length = 100
Score = 27.3 bits (59), Expect = 9.7, Method: Compositional matrix adjust.
Identities = 20/69 (28%), Positives = 33/69 (47%), Gaps = 3/69 (4%)
Query: 63 LRGLPFNCTDIDICKFFAGLDIVDVLLVNKNG---RFSGEAFVVFAGPIQVEFALQRDRQ 119
L LP++ T+ I +FF GL+I V L + R G + F + AL + +
Sbjct: 24 LGNLPYDVTEESIKEFFRGLNISAVRLPREPSNPERLKGFGYAEFEDLDSLLSALSLNEE 83
Query: 120 NMGRRYVEV 128
++G R + V
Sbjct: 84 SLGNRRIRV 92
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
0.321 0.138 0.405
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,458,218
Number of Sequences: 62578
Number of extensions: 282630
Number of successful extensions: 760
Number of sequences better than 100.0: 34
Number of HSP's better than 100.0 without gapping: 19
Number of HSP's successfully gapped in prelim test: 15
Number of HSP's that attempted gapping in prelim test: 697
Number of HSP's gapped (non-prelim): 56
length of query: 265
length of database: 14,973,337
effective HSP length: 97
effective length of query: 168
effective length of database: 8,903,271
effective search space: 1495749528
effective search space used: 1495749528
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: 50 (23.9 bits)