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= psy3727
(232 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 = 105 bits (261), Expect = 3e-23, Method: Compositional matrix adjust.
Identities = 49/76 (64%), Positives = 60/76 (78%), Gaps = 1/76 (1%)
Query: 77 SRHTVHMRGLPFRANERDVADFFRPVVPVHVDIHYE-NGRPSGEADVDFATHEDAMQAMS 135
+ H VHMRGLP++A E D+ +FF P+ PV V I +GR +GEADV+FATHE+A+ AMS
Sbjct: 45 TGHCVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMS 104
Query: 136 KDRTNMQHRYIELFLN 151
KDR NMQHRYIELFLN
Sbjct: 105 KDRANMQHRYIELFLN 120
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous Nuclear
Ribonucleoprotein H'
Length = 102
Score = 101 bits (251), Expect = 4e-22, Method: Compositional matrix adjust.
Identities = 47/74 (63%), Positives = 59/74 (79%), Gaps = 1/74 (1%)
Query: 79 HTVHMRGLPFRANERDVADFFRPVVPVHVDIHYE-NGRPSGEADVDFATHEDAMQAMSKD 137
H VHMRGLP+RA E D+ +FF P+ P+ V I +GR +GEADV+FATHEDA+ AM+KD
Sbjct: 16 HCVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKD 75
Query: 138 RTNMQHRYIELFLN 151
+ NMQHRY+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 = 64.3 bits (155), Expect = 6e-11, Method: Compositional matrix adjust.
Identities = 32/78 (41%), Positives = 46/78 (58%), Gaps = 1/78 (1%)
Query: 73 SSGPSRHTVHMRGLPFRANERDVADFFRPVVPVHVDI-HYENGRPSGEADVDFATHEDAM 131
SSG + HTV +RG PF E++V +F P+ PV + I +G +G VDF+ E+
Sbjct: 5 SSGTTCHTVKLRGAPFNVTEKNVMEFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVK 64
Query: 132 QAMSKDRTNMQHRYIELF 149
QA+ +R M RYIE+F
Sbjct: 65 QALKCNREYMGGRYIEVF 82
>pdb|2DB1|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein F Homolog
Length = 118
Score = 58.2 bits (139), Expect = 4e-09, Method: Compositional matrix adjust.
Identities = 32/81 (39%), Positives = 44/81 (54%), Gaps = 7/81 (8%)
Query: 75 GPSRHTVHMRGLPFRANERDVADFFR------PVVPVHVDIHYENGRPSGEADVDFATHE 128
G + V +RGLP+ + DV +F V VH I+ GR SGEA V+ + +
Sbjct: 14 GGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHF-IYTREGRQSGEAFVELESED 72
Query: 129 DAMQAMSKDRTNMQHRYIELF 149
D A+ KDR +M HRYIE+F
Sbjct: 73 DVKLALKKDRESMGHRYIEVF 93
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Hypothetical Protein Flj201171
Length = 123
Score = 56.6 bits (135), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 31/75 (41%), Positives = 41/75 (54%), Gaps = 6/75 (8%)
Query: 81 VHMRGLPFRANERDVADFFRPVVPVH------VDIHYENGRPSGEADVDFATHEDAMQAM 134
V MRGLPF A +V FF P+ + + Y +GRP+G+A V FA E A A+
Sbjct: 26 VRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPDGRPTGDAFVLFACEEYAQNAL 85
Query: 135 SKDRTNMQHRYIELF 149
K + + RYIELF
Sbjct: 86 RKHKDLLGKRYIELF 100
>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 = 55.8 bits (133), Expect = 2e-08, Method: Compositional matrix adjust.
Identities = 31/81 (38%), Positives = 42/81 (51%), Gaps = 7/81 (8%)
Query: 75 GPSRHTVHMRGLPFRANERDVADFFR------PVVPVHVDIHYENGRPSGEADVDFATHE 128
G V +RGLP+ + DV +F VH I+ GR SGEA V+ + +
Sbjct: 41 GGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHF-IYTREGRQSGEAFVELGSED 99
Query: 129 DAMQAMSKDRTNMQHRYIELF 149
D A+ KDR +M HRYIE+F
Sbjct: 100 DVKMALKKDRESMGHRYIEVF 120
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 55.5 bits (132), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 28/72 (38%), Positives = 44/72 (61%), Gaps = 3/72 (4%)
Query: 81 VHMRGLPFRANERDVADFFR--PVVPVHVDIHYE-NGRPSGEADVDFATHEDAMQAMSKD 137
V +RGLPF ++ ++ FF +VP + + + GR +GEA V FA+ E A +A+ K
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 77
Query: 138 RTNMQHRYIELF 149
+ + HRYIE+F
Sbjct: 78 KERIGHRYIEIF 89
>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 = 53.9 bits (128), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 27/72 (37%), Positives = 43/72 (59%), Gaps = 3/72 (4%)
Query: 81 VHMRGLPFRANERDVADFFR--PVVPVHVDIHYE-NGRPSGEADVDFATHEDAMQAMSKD 137
V +RGLPF + ++ FF +VP + + + G+ +GEA V FA+ E A +A+ K
Sbjct: 45 VRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKH 104
Query: 138 RTNMQHRYIELF 149
+ + HRYIE+F
Sbjct: 105 KERIGHRYIEVF 116
>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 = 51.2 bits (121), Expect = 5e-07, Method: Compositional matrix adjust.
Identities = 28/80 (35%), Positives = 41/80 (51%), Gaps = 5/80 (6%)
Query: 75 GPSRHTVHMRGLPFRANERDVADFFRPVVPVHVD-----IHYENGRPSGEADVDFATHED 129
G V +RGLP+ + +V FF + I+ GRPSGEA V+ + ++
Sbjct: 4 GGEGFVVKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDE 63
Query: 130 AMQAMSKDRTNMQHRYIELF 149
A+ KDR M HRY+E+F
Sbjct: 64 VKLALKKDRETMGHRYVEVF 83
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 47.4 bits (111), Expect = 7e-06, Method: Compositional matrix adjust.
Identities = 23/72 (31%), Positives = 40/72 (55%), Gaps = 3/72 (4%)
Query: 80 TVHMRGLPFRANERDVADFFRPVVPVHVDIHYE---NGRPSGEADVDFATHEDAMQAMSK 136
V+++GLPF A + V DFF+ + V I+ NG+ +GE V+F D A+ +
Sbjct: 27 CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR 86
Query: 137 DRTNMQHRYIEL 148
+ M +R+I++
Sbjct: 87 HKQYMGNRFIQV 98
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 43.9 bits (102), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/70 (37%), Positives = 39/70 (55%), Gaps = 3/70 (4%)
Query: 81 VHMRGLPFRANERDVADFFRP--VVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSKDR 138
V + G+PF A E DV DFF V VH+ + GR +G V F + +D +A+ ++R
Sbjct: 19 VSVHGMPFSAMENDVRDFFHGLRVDAVHL-LKDHVGRNNGNGLVKFLSPQDTFEALKRNR 77
Query: 139 TNMQHRYIEL 148
M RY+E+
Sbjct: 78 MLMIQRYVEV 87
>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 = 37.7 bits (86), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 76 PSRHTVHMRGLPFRANERDVADFFR--PVVPVHVDIHY-ENGRPSGEADVDFATHEDAMQ 132
P + ++ +PF + ++ DFF V+P V + Y E G P+GEA V F + ++A
Sbjct: 13 PGPTVIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
Query: 133 AM 134
A+
Sbjct: 73 AV 74
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 37.4 bits (85), Expect = 0.006, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 34/62 (54%), Gaps = 3/62 (4%)
Query: 76 PSRHTVHMRGLPFRANERDVADFFR--PVVPVHVDIHY-ENGRPSGEADVDFATHEDAMQ 132
P + ++ +PF + ++ DFF V+P V + Y E G P+GEA V F + ++A
Sbjct: 13 PGPTIIKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATA 72
Query: 133 AM 134
A+
Sbjct: 73 AV 74
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 37.4 bits (85), Expect = 0.007, Method: Compositional matrix adjust.
Identities = 20/74 (27%), Positives = 38/74 (51%), Gaps = 5/74 (6%)
Query: 81 VHMRGLPFRANERDVADFFRP--VVPVHVDIHY---ENGRPSGEADVDFATHEDAMQAMS 135
+ +GLP+ DV +FF + IH+ +G+ G+A ++ + +D +A+
Sbjct: 14 IRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALIEMESEQDVQKALE 73
Query: 136 KDRTNMQHRYIELF 149
K R M RY+E++
Sbjct: 74 KHRMYMGQRYVEVY 87
>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 = 37.0 bits (84), Expect = 0.010, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 3/62 (4%)
Query: 76 PSRHTVHMRGLPFRANERDVADFFR--PVVPVHVDIHY-ENGRPSGEADVDFATHEDAMQ 132
P + ++ PF + ++ DFF V+P V + Y E G P+GEA V F + ++A
Sbjct: 13 PGPTVIKVQNXPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGXPTGEAXVAFESRDEATA 72
Query: 133 AM 134
A+
Sbjct: 73 AV 74
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 36.6 bits (83), Expect = 0.011, Method: Compositional matrix adjust.
Identities = 21/73 (28%), Positives = 38/73 (52%), Gaps = 2/73 (2%)
Query: 79 HTVHMRGLPFRANERDVADFFRPVVPVHVDIHYENGRPSGEADVDFATHEDAMQAM-SKD 137
T+ + L + A E + + F + V +NG+ G A ++FA+ EDA +A+ S +
Sbjct: 16 KTLVLSNLSYSATEETLQEVFEKATFIKVP-QNQNGKSKGYAFIEFASFEDAKEALNSCN 74
Query: 138 RTNMQHRYIELFL 150
+ ++ R I L L
Sbjct: 75 KREIEGRAIRLEL 87
>pdb|1P1T|A Chain A, Nmr Structure Of The N-Terminal Rrm Domain Of Cleavage
Stimulation Factor 64 Kda Subunit
Length = 104
Score = 34.3 bits (77), Expect = 0.064, Method: Compositional matrix adjust.
Identities = 18/61 (29%), Positives = 28/61 (45%), Gaps = 3/61 (4%)
Query: 77 SRHTVHMRGLPFRANERDVADFFR---PVVPVHVDIHYENGRPSGEADVDFATHEDAMQA 133
S +V + +P+ A E + D F PVV + E G+P G ++ E A+ A
Sbjct: 7 SLRSVFVGNIPYEATEEQLKDIFSEVGPVVSFRLVYDRETGKPKGYGFCEYQDQETALSA 66
Query: 134 M 134
M
Sbjct: 67 M 67
>pdb|2CQG|A Chain A, Solution Structure Of The Rna Binding Domain Of Tar Dna-
Binding Protein-43
Length = 103
Score = 32.7 bits (73), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 85 GLPFRANERDVADFFRP---VVPVHVDIHYENGRPSGEADVDFATHEDAMQAMSK 136
GLP++ E+D+ ++F V+ V V + G G V F +E ++ MS+
Sbjct: 22 GLPWKTTEQDLKEYFSTFGEVLMVQVKKDLKTGHSKGFGFVRFTEYETQVKVMSQ 76
>pdb|1NO8|A Chain A, Solution Structure Of The Nuclear Factor Aly Rbd Domain
Length = 106
Score = 30.0 bits (66), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 17/53 (32%), Positives = 28/53 (52%), Gaps = 2/53 (3%)
Query: 86 LPFRANERDVADFFRPVVPVH-VDIHYE-NGRPSGEADVDFATHEDAMQAMSK 136
L F ++ D+ + F + +HY+ +GR G ADV F DA++AM +
Sbjct: 36 LDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQ 88
>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 = 1.3, Method: Compositional matrix adjust.
Identities = 21/71 (29%), Positives = 33/71 (46%), Gaps = 9/71 (12%)
Query: 73 SSG--PSRHT---VHMRGLPFRANERDVADFFRPVVPVHV----DIHYENGRPSGEADVD 123
SSG P + T + +R +PF+AN+R++ + F + G G VD
Sbjct: 5 SSGQVPKKQTTSKILVRNIPFQANQREIRELFSTFGELKTVRLPKKMTGTGAHRGFGFVD 64
Query: 124 FATHEDAMQAM 134
F T +DA +A
Sbjct: 65 FITKQDAKKAF 75
>pdb|2FC8|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 102
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 28/66 (42%), Gaps = 5/66 (7%)
Query: 73 SSGPS-----RHTVHMRGLPFRANERDVADFFRPVVPVHVDIHYENGRPSGEADVDFATH 127
SSGP+ T+ ++GL E + + F V + E G G VDF +
Sbjct: 5 SSGPNARSQPSKTLFVKGLSEDTTEETLKESFDGSVRARIVTDRETGSSKGFGFVDFNSE 64
Query: 128 EDAMQA 133
EDA A
Sbjct: 65 EDAKAA 70
>pdb|2CPE|A Chain A, Solution Structure Of The Rna Recognition Motif Of Ewing
Sarcoma(Ews) Protein
Length = 113
Score = 28.5 bits (62), Expect = 3.6, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 11/55 (20%)
Query: 81 VHMRGLPFRANERDVADFFRP--VVP---------VHVDIHYENGRPSGEADVDF 124
++++GL D+ADFF+ VV +H+ + E G+P G+A V +
Sbjct: 18 IYVQGLNDSVTLDDLADFFKQCGVVKMNKRTGQPMIHIYLDKETGKPKGDATVSY 72
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 28.1 bits (61), Expect = 4.7, Method: Compositional matrix adjust.
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 5/67 (7%)
Query: 82 HMRGLPFRANERDVADFFRPV----VPVHVDIHYENGRPSGEADVDFATHEDAMQAMSKD 137
H+ +PF + DV F + VHV + NG+ G+A V F +DA ++
Sbjct: 19 HITNIPFSITKMDVLQFLEGIPVDENAVHVLVD-NNGQGLGQALVQFKNEDDARKSERLH 77
Query: 138 RTNMQHR 144
R + R
Sbjct: 78 RKKLNGR 84
>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 = 27.3 bits (59), Expect = 6.6, Method: Compositional matrix adjust.
Identities = 16/53 (30%), Positives = 27/53 (50%), Gaps = 2/53 (3%)
Query: 86 LPFRANERDVADFFRPVVPVH-VDIHYE-NGRPSGEADVDFATHEDAMQAMSK 136
L F ++ D+ + F + +HY+ +GR G ADV F DA++A +
Sbjct: 37 LDFGVSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAXKQ 89
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 0.134 0.427
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,602,319
Number of Sequences: 62578
Number of extensions: 132601
Number of successful extensions: 297
Number of sequences better than 100.0: 25
Number of HSP's better than 100.0 without gapping: 13
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 273
Number of HSP's gapped (non-prelim): 25
length of query: 232
length of database: 14,973,337
effective HSP length: 96
effective length of query: 136
effective length of database: 8,965,849
effective search space: 1219355464
effective search space used: 1219355464
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)