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= psy3068
(152 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>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 = 102 bits (253), Expect = 1e-22, Method: Compositional matrix adjust.
Identities = 53/91 (58%), Positives = 63/91 (69%), Gaps = 2/91 (2%)
Query: 38 GPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYK-NGRPSGEA 96
G GD S GH VHMRGLP++ E DI +FFSP+ PV V I +GR +GEA
Sbjct: 31 GRGSGDSEFTVQSTTGH-CVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEA 89
Query: 97 DVYFATHEDAMQAMSKDRTNIRHRYIELFLN 127
DV FATHE+A+ AMSKDR N++HRYIELFLN
Sbjct: 90 DVEFATHEEAVAAMSKDRANMQHRYIELFLN 120
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein H'
Length = 102
Score = 98.2 bits (243), Expect = 2e-21, Method: Compositional matrix adjust.
Identities = 46/74 (62%), Positives = 58/74 (78%), Gaps = 1/74 (1%)
Query: 55 HTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYK-NGRPSGEADVYFATHEDAMQAMSKD 113
H VHMRGLP+R E DI +FFSP+ P+ V I +GR +GEADV FATHEDA+ AM+KD
Sbjct: 16 HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKD 75
Query: 114 RTNIRHRYIELFLN 127
+ N++HRY+ELFLN
Sbjct: 76 KANMQHRYVELFLN 89
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Rna-Binding Protein 19
Length = 91
Score = 60.5 bits (145), Expect = 3e-10, Method: Compositional matrix adjust.
Identities = 31/78 (39%), Positives = 47/78 (60%), Gaps = 1/78 (1%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDI-NYKNGRPSGEADVYFATHEDAM 107
SSG HTV +RG PF V EK++++F +P+ PV + I +G +G V F+ E+
Sbjct: 5 SSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVK 64
Query: 108 QAMSKDRTNIRHRYIELF 125
QA+ +R + RYIE+F
Sbjct: 65 QALKCNREYMGGRYIEVF 82
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 60.1 bits (144), Expect = 4e-10, Method: Compositional matrix adjust.
Identities = 32/73 (43%), Positives = 50/73 (68%), Gaps = 5/73 (6%)
Query: 57 VHMRGLPFRVNEKDIVDFFS--PVVP--VYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
V +RGLPF ++++IV FFS +VP + + ++++ GR +GEA V FA+ E A +A+ K
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQ-GRSTGEAFVQFASQEIAEKALKK 76
Query: 113 DRTNIRHRYIELF 125
+ I HRYIE+F
Sbjct: 77 HKERIGHRYIEIF 89
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Hypothetical Protein Flj201171
Length = 123
Score = 58.9 bits (141), Expect = 1e-09, Method: Compositional matrix adjust.
Identities = 30/75 (40%), Positives = 42/75 (56%), Gaps = 6/75 (8%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVPV------YVDINYKNGRPSGEADVYFATHEDAMQAM 110
V MRGLPF +++V FF P+ + + Y +GRP+G+A V FA E A A+
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 111 SKDRTNIRHRYIELF 125
K + + RYIELF
Sbjct: 86 RKHKDLLGKRYIELF 100
>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 = 57.8 bits (138), Expect = 2e-09, Method: Compositional matrix adjust.
Identities = 31/72 (43%), Positives = 45/72 (62%), Gaps = 3/72 (4%)
Query: 57 VHMRGLPFRVNEKDIVDFFS--PVVPVYVDINYK-NGRPSGEADVYFATHEDAMQAMSKD 113
V +RGLPF +++IV FFS +VP + + G+ +GEA V FA+ E A +A+ K
Sbjct: 45 VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKH 104
Query: 114 RTNIRHRYIELF 125
+ I HRYIE+F
Sbjct: 105 KERIGHRYIEVF 116
>pdb|2DB1|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein F Homolog
Length = 118
Score = 52.0 bits (123), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 34/98 (34%), Positives = 50/98 (51%), Gaps = 17/98 (17%)
Query: 34 GGFAGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFS------PVVPVYVDINY 87
G GP G+ +V V +RGLP+ + +D+ +F S V V+ I
Sbjct: 7 GMMLGPEGGEGYV----------VKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHF-IYT 55
Query: 88 KNGRPSGEADVYFATHEDAMQAMSKDRTNIRHRYIELF 125
+ GR SGEA V + +D A+ KDR ++ HRYIE+F
Sbjct: 56 REGRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVF 93
>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 = 51.6 bits (122), Expect = 2e-07, Method: Compositional matrix adjust.
Identities = 28/75 (37%), Positives = 41/75 (54%), Gaps = 5/75 (6%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPVV----PVYVDINY-KNGRPSGEADVYFATHEDAMQAM 110
V +RGLP+ + +D+ +F S V Y + GR SGEA V + +D A+
Sbjct: 46 VVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSGEAFVELGSEDDVKMAL 105
Query: 111 SKDRTNIRHRYIELF 125
KDR ++ HRYIE+F
Sbjct: 106 KKDRESMGHRYIEVF 120
>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 = 48.1 bits (113), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 26/75 (34%), Positives = 39/75 (52%), Gaps = 5/75 (6%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPV-----VPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
V +RGLP+ + ++ FFS I + GRPSGEA V + ++ A+
Sbjct: 9 VVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLAL 68
Query: 111 SKDRTNIRHRYIELF 125
KDR + HRY+E+F
Sbjct: 69 KKDRETMGHRYVEVF 83
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 22/72 (30%), Positives = 39/72 (54%), Gaps = 3/72 (4%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSP--VVPVYVDINYK-NGRPSGEADVYFATHEDAMQAMSK 112
V+++GLPF K ++DFF +V + I Y NG+ +GE V F D A+ +
Sbjct: 27 CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR 86
Query: 113 DRTNIRHRYIEL 124
+ + +R+I++
Sbjct: 87 HKQYMGNRFIQV 98
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 45/80 (56%), Gaps = 6/80 (7%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFF--SPVVPVYVDINY-KNGRPSGEADVYFATHEDAMQ 108
PG + ++ +PF V+ +I+DFF V+P V + Y + G P+GEA V F + ++A
Sbjct: 13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
Query: 109 AM--SKDRTNIRHRYIELFL 126
A+ DR I R ++L L
Sbjct: 73 AVIDLNDRP-IGSRKVKLVL 91
>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 = 40.4 bits (93), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 37/62 (59%), Gaps = 3/62 (4%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFF--SPVVPVYVDINY-KNGRPSGEADVYFATHEDAMQ 108
PG + ++ +PF V+ +I+DFF V+P V + Y + G P+GEA V F + ++A
Sbjct: 13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
Query: 109 AM 110
A+
Sbjct: 73 AV 74
>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 = 40.0 bits (92), Expect = 5e-04, Method: Compositional matrix adjust.
Identities = 22/62 (35%), Positives = 36/62 (58%), Gaps = 3/62 (4%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFF--SPVVPVYVDINY-KNGRPSGEADVYFATHEDAMQ 108
PG + ++ PF V+ +I+DFF V+P V + Y + G P+GEA V F + ++A
Sbjct: 13 PGPTVIKVQNXPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGXPTGEAXVAFESRDEATA 72
Query: 109 AM 110
A+
Sbjct: 73 AV 74
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 37.7 bits (86), Expect = 0.003, Method: Compositional matrix adjust.
Identities = 21/69 (30%), Positives = 36/69 (52%), Gaps = 1/69 (1%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPV-VPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRT 115
V + G+PF E D+ DFF + V + GR +G V F + +D +A+ ++R
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRM 78
Query: 116 NIRHRYIEL 124
+ RY+E+
Sbjct: 79 LMIQRYVEV 87
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 36.2 bits (82), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 18/75 (24%), Positives = 41/75 (54%), Gaps = 7/75 (9%)
Query: 57 VHMRGLPFRVNEKDIVDFFSPVVP------VYVDINYKNGRPSGEADVYFATHEDAMQAM 110
+ +GLP+ +D+++FFS ++ +N ++G+ G+A + + +D +A+
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLN-RDGKRRGDALIEMESEQDVQKAL 72
Query: 111 SKDRTNIRHRYIELF 125
K R + RY+E++
Sbjct: 73 EKHRMYMGQRYVEVY 87
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/69 (31%), Positives = 36/69 (52%), Gaps = 4/69 (5%)
Query: 61 GLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTNI 117
GLP++ E+D+ ++FS V+ V V + K G G V F +E ++ MS+ R I
Sbjct: 22 GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ-RHMI 80
Query: 118 RHRYIELFL 126
R+ + L
Sbjct: 81 DGRWCDCKL 89
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 35.0 bits (79), Expect = 0.018, Method: Compositional matrix adjust.
Identities = 22/74 (29%), Positives = 37/74 (50%), Gaps = 2/74 (2%)
Query: 54 HHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM-SK 112
T+ + L + E+ + + F + V N +NG+ G A + FA+ EDA +A+ S
Sbjct: 15 SKTLVLSNLSYSATEETLQEVFEKATFIKVPQN-QNGKSKGYAFIEFASFEDAKEALNSC 73
Query: 113 DRTNIRHRYIELFL 126
++ I R I L L
Sbjct: 74 NKREIEGRAIRLEL 87
>pdb|2F3J|A Chain A, The Solution Structure Of The Ref2-I Mrna Export Factor
(Residues 1-155)
Length = 177
Score = 33.9 bits (76), Expect = 0.037, Method: Compositional matrix adjust.
Identities = 28/95 (29%), Positives = 49/95 (51%), Gaps = 14/95 (14%)
Query: 31 DRPGGFAGPRP-GDRWVNE------SSGPGHHT---VHMRGLPFRVNEKDIVDFFS---P 77
+RP ++ P+P D+W ++ G G T + + L F V++ DI + F+
Sbjct: 55 NRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGVSDADIQELFAEFGT 114
Query: 78 VVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
+ VD + ++GR G ADV+F DA++AM +
Sbjct: 115 LKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 148
>pdb|2YKA|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hvs
Orf57 Peptide
Length = 124
Score = 32.7 bits (73), Expect = 0.082, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 62 LPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
L F V++ DI + F+ + VD + ++GR G ADV+F DA++AM +
Sbjct: 43 LDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 95
>pdb|2KT5|A Chain A, Rrm Domain Of Mrna Export Adaptor Ref2-I Bound To Hsv-1
Icp27 Peptide
Length = 124
Score = 32.7 bits (73), Expect = 0.083, Method: Compositional matrix adjust.
Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 4/54 (7%)
Query: 62 LPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSK 112
L F V++ DI + F+ + VD + ++GR G ADV+F DA++AM +
Sbjct: 43 LDFGVSDADIQELFAEFGTLKKAAVDYD-RSGRSLGTADVHFERRADALKAMKQ 95
>pdb|2DGV|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 92
Score = 31.2 bits (69), Expect = 0.25, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 49 SSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPV-YVDINYKNGRPSGEADVYFATHEDAM 107
S G + +R LPF K + D F+ V Y DI +NG+ G V F + E A
Sbjct: 3 SGSSGACQIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAE 62
Query: 108 QAM 110
+A
Sbjct: 63 RAC 65
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 30.8 bits (68), Expect = 0.31, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 2/53 (3%)
Query: 62 LPFRVNEKDIVDFFSPVVPVY-VDINY-KNGRPSGEADVYFATHEDAMQAMSK 112
L F V++ DI + F+ + ++Y ++GR G ADV+F DA++AM +
Sbjct: 36 LDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 88
>pdb|2KXN|B Chain B, Nmr Structure Of Human Tra2beta1 Rrm In Complex With
Aagaac Rna
Length = 129
Score = 30.8 bits (68), Expect = 0.35, Method: Compositional matrix adjust.
Identities = 24/79 (30%), Positives = 39/79 (49%), Gaps = 6/79 (7%)
Query: 42 GDRWVNESSGPG-HHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEAD 97
G R V + P + + + GL E+D+ + FS P+ V + + ++ R G A
Sbjct: 33 GSRHVGNRANPDPNCCLGVFGLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAF 92
Query: 98 VYFATHEDAMQAMSKDRTN 116
VYF +DA +A K+R N
Sbjct: 93 VYFENVDDAKEA--KERAN 109
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 30.4 bits (67), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 19/75 (25%), Positives = 36/75 (48%), Gaps = 11/75 (14%)
Query: 56 TVHMRGLPFRVNEKDIVDFFSPV------VPVYVDINYKNGRPSGEADVYFATHEDAMQA 109
H+ +PF + + D++ F + V V VD NG+ G+A V F +DA ++
Sbjct: 17 CAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVD---NNGQGLGQALVQFKNEDDARKS 73
Query: 110 --MSKDRTNIRHRYI 122
+ + + N R ++
Sbjct: 74 ERLHRKKLNGREAFV 88
>pdb|2DH9|A Chain A, Solution Structure Of The C-Terminal Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein M
Length = 89
Score = 30.4 bits (67), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 53 GHHTVHMRGLPFRVNEKDIVDFFSPVVPV-YVDINYKNGRPSGEADVYFATHEDAMQAM 110
G + +R LPF K + D F+ V Y DI +NG+ G V F + E A +A
Sbjct: 4 GSSGIFVRNLPFDFTWKMLKDKFNECGHVLYADIKMENGKSKGCGVVKFESPEVAERAC 62
>pdb|2RRA|A Chain A, Solution Structure Of Rna Binding Domain In Human Tra2
Beta Protein In Complex With Rna (Gaagaa)
Length = 99
Score = 30.0 bits (66), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTN 116
GL E+D+ + FS P+ V + + ++ R G A VYF +DA +A K+R N
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA--KERAN 78
>pdb|2CQC|A Chain A, Solution Structure Of The Rna Recognition Motif In
ArginineSERINE-Rich Splicing Factor 10
Length = 95
Score = 30.0 bits (66), Expect = 0.52, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTN 116
GL E+D+ + FS P+ V + + ++ R G A VYF +DA +A K+R N
Sbjct: 22 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA--KERAN 78
>pdb|2RRB|A Chain A, Refinement Of Rna Binding Domain In Human Tra2 Beta
Protein
Length = 96
Score = 30.0 bits (66), Expect = 0.58, Method: Compositional matrix adjust.
Identities = 20/59 (33%), Positives = 31/59 (52%), Gaps = 5/59 (8%)
Query: 61 GLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMSKDRTN 116
GL E+D+ + FS P+ V + + ++ R G A VYF +DA +A K+R N
Sbjct: 19 GLSLYTTERDLREVFSKYGPIADVSIVYDQQSRRSRGFAFVYFENVDDAKEA--KERAN 75
>pdb|1N8P|A Chain A, Crystal Structure Of Cystathionine Gamma-lyase From Yeast
pdb|1N8P|B Chain B, Crystal Structure Of Cystathionine Gamma-lyase From Yeast
pdb|1N8P|C Chain C, Crystal Structure Of Cystathionine Gamma-lyase From Yeast
pdb|1N8P|D Chain D, Crystal Structure Of Cystathionine Gamma-lyase From Yeast
Length = 393
Score = 28.9 bits (63), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 29/71 (40%), Gaps = 3/71 (4%)
Query: 37 AGPRPGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYKNGRPSGEA 96
A P P D W+ G T+H+R ++ I +F + V +NY +
Sbjct: 236 AIPSPFDAWLTHR---GLKTLHLRVRQAALSANKIAEFLAADKENVVAVNYPGLKTHPNY 292
Query: 97 DVYFATHEDAM 107
DV H DA+
Sbjct: 293 DVVLKQHRDAL 303
>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 = 28.5 bits (62), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 30/53 (56%), Gaps = 2/53 (3%)
Query: 62 LPFRVNEKDIVDFFSPVVPVY-VDINY-KNGRPSGEADVYFATHEDAMQAMSK 112
L F V++ DI + F+ + ++Y ++GR G ADV+F DA++A +
Sbjct: 37 LDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQ 89
>pdb|2CQ0|A Chain A, Solution Structure Of Rna Binding Domain In Eukaryotic
Translation Initiation Factor 3 Subunit 4
Length = 103
Score = 28.1 bits (61), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 8/71 (11%)
Query: 49 SSGPGHH-----TVHMRGLPFRVNEKDIVDFFSP---VVPVYVDINYKNGRPSGEADVYF 100
SSGP T+ + L E D+ + F P + +Y+ + G+ G A + F
Sbjct: 5 SSGPNRRADDNATIRVTNLSEDTRETDLQELFRPFGSISRIYLAKDKTTGQSKGFAFISF 64
Query: 101 ATHEDAMQAMS 111
EDA +A++
Sbjct: 65 HRREDAARAIA 75
>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 = 28.1 bits (61), Expect = 2.2, Method: Compositional matrix adjust.
Identities = 16/62 (25%), Positives = 30/62 (48%), Gaps = 3/62 (4%)
Query: 52 PGHHTVHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQ 108
P V++ +P+ E+ I+D S PV+ + + + + GR G A + F E +
Sbjct: 2 PPSRVVYLGSIPYDQTEEQILDLCSNVGPVINLKMMFDPQTGRSKGYAFIEFRDLESSAS 61
Query: 109 AM 110
A+
Sbjct: 62 AV 63
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 27.3 bits (59), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 16/59 (27%), Positives = 26/59 (44%), Gaps = 3/59 (5%)
Query: 55 HTVHMRGLPFRVNE---KDIVDFFSPVVPVYVDINYKNGRPSGEADVYFATHEDAMQAM 110
+V + +P+ E KDI PVV + + + G+P G + E A+ AM
Sbjct: 9 RSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSAM 67
>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 = 27.3 bits (59), Expect = 3.1, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 57 VHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
+++ GLP + +KD+ D FS ++ V ++ G G A + F +A +A++
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 27.3 bits (59), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 15/58 (25%), Positives = 30/58 (51%), Gaps = 3/58 (5%)
Query: 57 VHMRGLPFRVNEKDIVDFFS---PVVPVYVDINYKNGRPSGEADVYFATHEDAMQAMS 111
+++ GLP + +KD+ D FS ++ V ++ G G A + F +A +A++
Sbjct: 91 LYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRSEAEEAIT 148
>pdb|2DIC|A Chain A, Solution Structure Of The 12th Filamin Domain From Human
Filamin-B
Length = 105
Score = 27.3 bits (59), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/33 (48%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 41 PGDRWVNESSGPGHHTVHMRGLPFRVNEKDIVD 73
PGD VN + G H+ G PFRV KD+VD
Sbjct: 75 PGDYDVNITYG----GAHIPGSPFRVPVKDVVD 103
>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 = 26.9 bits (58), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 30/66 (45%), Gaps = 10/66 (15%)
Query: 51 GPGHHTVHMRGLPFRVNEKDIVDFFSPVVPVYVDINYK------NGRPSGEADVYFATHE 104
GP V++ +P+ E+ I+D S V PV IN K GR G A + F E
Sbjct: 1 GP-SRVVYLGSIPYDQTEEQILDLCSNVGPV---INLKMMFDPQTGRSKGYAFIEFRDLE 56
Query: 105 DAMQAM 110
+ A+
Sbjct: 57 SSASAV 62
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 0.138 0.448
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,266,547
Number of Sequences: 62578
Number of extensions: 173192
Number of successful extensions: 356
Number of sequences better than 100.0: 42
Number of HSP's better than 100.0 without gapping: 21
Number of HSP's successfully gapped in prelim test: 21
Number of HSP's that attempted gapping in prelim test: 320
Number of HSP's gapped (non-prelim): 42
length of query: 152
length of database: 14,973,337
effective HSP length: 90
effective length of query: 62
effective length of database: 9,341,317
effective search space: 579161654
effective search space used: 579161654
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: 47 (22.7 bits)