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= psy10467
(304 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1WG5|A Chain A, Solution Structure Of The First Rrm Domain In
Heterogeneous Nuclear Ribonucleoprotein H
Length = 104
Score = 96.7 bits (239), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 41/74 (55%), Positives = 57/74 (77%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
+RL+GLP+ C KE++ +F GLEIVPNG+T+P D+ GR TG A++QF +E AEKAL +H
Sbjct: 18 VRLRGLPFGCSKEEIVQFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKH 77
Query: 205 KEKIGHRLVTLVMS 218
KE+IGHR + + S
Sbjct: 78 KERIGHRYIEIFKS 91
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 27/56 (48%), Positives = 39/56 (69%), Gaps = 2/56 (3%)
Query: 22 QFFK--PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
QFF IVP + L D GRS+GEA V+F+S + A++AL++HK +G RYIE++
Sbjct: 34 QFFSGLEIVPNGMTLPVDFQGRSTGEAFVQFASQEIAEKALKKHKERIGHRYIEIF 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 = 94.4 bits (233), Expect = 8e-20, Method: Compositional matrix adjust.
Identities = 42/83 (50%), Positives = 59/83 (71%)
Query: 136 SGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKE 195
S + + +RL+GLP+ C KE++ +F GLEIVPNGIT+P D G+ TG A++QF +E
Sbjct: 36 SADSANDGFVRLRGLPFGCTKEEIVQFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQE 95
Query: 196 NAEKALLRHKEKIGHRLVTLVMS 218
AEKAL +HKE+IGHR + + S
Sbjct: 96 LAEKALGKHKERIGHRYIEVFKS 118
Score = 50.8 bits (120), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/56 (46%), Positives = 37/56 (66%), Gaps = 2/56 (3%)
Query: 22 QFFK--PIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
QFF IVP I L D G+ +GEA V+F+S + A++AL +HK +G RYIE++
Sbjct: 61 QFFSGLEIVPNGITLPVDPEGKITGEAFVQFASQELAEKALGKHKERIGHRYIEVF 116
>pdb|1WEL|A Chain A, Solution Structure Of Rna Binding Domain In Np_006038
Length = 124
Score = 57.0 bits (136), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 28/103 (27%), Positives = 58/103 (56%), Gaps = 10/103 (9%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
C+ L+GLP+E + + V F + L+IV + I I + G+ TG +++F ++ + + AL R
Sbjct: 27 CVYLKGLPFEAENKHVIDFFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCR 86
Query: 204 HKEKIGHRLVTLVMSGAQWFLSPPLTNETPISRLDLTGSPVRS 246
HK+ +G+R + + P+T + + ++D+ ++S
Sbjct: 87 HKQYMGNRFIQV----------HPITKKGMLEKIDMIRKRLQS 119
Score = 40.0 bits (92), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 22/55 (40%), Positives = 34/55 (61%), Gaps = 2/55 (3%)
Query: 23 FFKP--IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
FFK IV +I + G+++GE VEF + D + AL RHK MG+R+I+++
Sbjct: 45 FFKKLDIVEDSIYIAYGPNGKATGEGFVEFRNEADYKAALCRHKQYMGNRFIQVH 99
>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 = 54.7 bits (130), Expect = 6e-08, Method: Compositional matrix adjust.
Identities = 24/64 (37%), Positives = 39/64 (60%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEGTS 81
FF P+ PV + + GR +GEADVEF++ ++A A+ + ++NM RYIEL++ T
Sbjct: 65 NFFSPLNPVRVHIEIGPDGRVTGEADVEFATHEEAVAAMSKDRANMQHRYIELFLNSTTG 124
Query: 82 SKEA 85
+
Sbjct: 125 ASNG 128
Score = 46.2 bits (108), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 24/75 (32%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
C+ ++GLPY+ + D+ F L V I I D GR TG A ++F E A A+ +
Sbjct: 48 CVHMRGLPYKATENDIYNFFSPLNPVRVHIEIGPD--GRVTGEADVEFATHEEAVAAMSK 105
Query: 204 HKEKIGHRLVTLVMS 218
+ + HR + L ++
Sbjct: 106 DRANMQHRYIELFLN 120
>pdb|1WEZ|A Chain A, Solution Structure Of Rrm Domain In Heterogeneous
Nuclear Ribonucleoprotein H'
Length = 102
Score = 53.9 bits (128), Expect = 1e-07, Method: Compositional matrix adjust.
Identities = 23/55 (41%), Positives = 37/55 (67%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYM 76
FF P+ P+ + + GR +GEADVEF++ +DA A+ + K+NM RY+EL++
Sbjct: 34 NFFSPLNPMRVHIEIGPDGRVTGEADVEFATHEDAVAAMAKDKANMQHRYVELFL 88
Score = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/75 (33%), Positives = 39/75 (52%), Gaps = 2/75 (2%)
Query: 144 CMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
C+ ++GLPY + D+ F L + I I D GR TG A ++F E+A A+ +
Sbjct: 17 CVHMRGLPYRATENDIYNFFSPLNPMRVHIEIGPD--GRVTGEADVEFATHEDAVAAMAK 74
Query: 204 HKEKIGHRLVTLVMS 218
K + HR V L ++
Sbjct: 75 DKANMQHRYVELFLN 89
>pdb|2DB1|A Chain A, Solution Structure Of The Rna Binding Domain In
Heterogeneous Nuclear Ribonucleoprotein F Homolog
Length = 118
Score = 47.4 bits (111), Expect = 9e-06, Method: Compositional matrix adjust.
Identities = 25/89 (28%), Positives = 47/89 (52%), Gaps = 2/89 (2%)
Query: 132 GAVLSGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPN--GITIPHDYAGRCTGVAYI 189
G +L + ++L+GLP+ C EDV+ FL I G+ + GR +G A++
Sbjct: 7 GMMLGPEGGEGYVVKLRGLPWSCSIEDVQNFLSDCTIHDGVAGVHFIYTREGRQSGEAFV 66
Query: 190 QFVDKENAEKALLRHKEKIGHRLVTLVMS 218
+ +++ + AL + +E +GHR + + S
Sbjct: 67 ELESEDDVKLALKKDRESMGHRYIEVFKS 95
Score = 41.2 bits (95), Expect = 8e-04, Method: Compositional matrix adjust.
Identities = 19/36 (52%), Positives = 26/36 (72%)
Query: 40 GRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
GR SGEA VE S DD + AL++ + +MG RYIE++
Sbjct: 58 GRQSGEAFVELESEDDVKLALKKDRESMGHRYIEVF 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 = 47.4 bits (111), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 25/93 (26%), Positives = 48/93 (51%), Gaps = 2/93 (2%)
Query: 128 LKRQGAVLSGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPN--GITIPHDYAGRCTG 185
+ R +L + ++L+GLP+ C EDV+ FL I G+ + GR +G
Sbjct: 30 MGRGSMMLGPEGGEGFVVKLRGLPWSCSVEDVQNFLSDCTIHDGAAGVHFIYTREGRQSG 89
Query: 186 VAYIQFVDKENAEKALLRHKEKIGHRLVTLVMS 218
A+++ +++ + AL + +E +GHR + + S
Sbjct: 90 EAFVELGSEDDVKMALKKDRESMGHRYIEVFKS 122
Score = 42.0 bits (97), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 19/36 (52%), Positives = 26/36 (72%)
Query: 40 GRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
GR SGEA VE S DD + AL++ + +MG RYIE++
Sbjct: 85 GRQSGEAFVELGSEDDVKMALKKDRESMGHRYIEVF 120
>pdb|2CPY|A Chain A, Solution Structure Of Rna Binding Domain 3 In Rna Binding
Motif Protein 12
Length = 114
Score = 47.0 bits (110), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 21/70 (30%), Positives = 40/70 (57%)
Query: 142 QCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKAL 201
+ C + +P+ K DV +FLEG+ + N + + D G+ G A +QF ++++A K+
Sbjct: 15 KVCAHITNIPFSITKMDVLQFLEGIPVDENAVHVLVDNNGQGLGQALVQFKNEDDARKSE 74
Query: 202 LRHKEKIGHR 211
H++K+ R
Sbjct: 75 RLHRKKLNGR 84
Score = 32.0 bits (71), Expect = 0.48, Method: Compositional matrix adjust.
Identities = 28/97 (28%), Positives = 46/97 (47%), Gaps = 16/97 (16%)
Query: 3 FSFYVIDILIHITYCLLCSQFFKPIVPVN---ILLLTDDAGRSSGEADVEFSSVDDAQRA 59
FS +D+L QF + I PV+ + +L D+ G+ G+A V+F + DDA+++
Sbjct: 25 FSITKMDVL----------QFLEGI-PVDENAVHVLVDNNGQGLGQALVQFKNEDDARKS 73
Query: 60 --LQRHKSNMGDRYIELYMEEGTSSKEANGRGTGGFG 94
L R K N + ++ + E E N G G
Sbjct: 74 ERLHRKKLNGREAFVHVVTLEDMREIEKNPPAQGKSG 110
>pdb|2LMI|A Chain A, Nmr Structure Of The Protein Bc040485 From Homo Sapiens
Length = 107
Score = 45.1 bits (105), Expect = 5e-05, Method: Compositional matrix adjust.
Identities = 28/86 (32%), Positives = 42/86 (48%), Gaps = 2/86 (2%)
Query: 132 GAVLSGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIV--PNGITIPHDYAGRCTGVAYI 189
G+ L D +R QGLP+ C EDV F I NGI + G+ G A I
Sbjct: 1 GSKLEEEVDDVFLIRAQGLPWSCTMEDVLNFFSDCRIRNGENGIHFLLNRDGKRRGDALI 60
Query: 190 QFVDKENAEKALLRHKEKIGHRLVTL 215
+ +++ +KAL +H+ +G R V +
Sbjct: 61 EMESEQDVQKALEKHRMYMGQRYVEV 86
Score = 40.8 bits (94), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 18/44 (40%), Positives = 28/44 (63%)
Query: 32 ILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
I L + G+ G+A +E S D Q+AL++H+ MG RY+E+Y
Sbjct: 44 IHFLLNRDGKRRGDALIEMESEQDVQKALEKHRMYMGQRYVEVY 87
>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 = 44.7 bits (104), Expect = 7e-05, Method: Compositional matrix adjust.
Identities = 26/98 (26%), Positives = 49/98 (50%), Gaps = 11/98 (11%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIV--PNGITIPHDYAGRCTGVAYIQFVDKENAEKALL 202
++++GLP+ C ++V++F +I GI + GR +G A+++ ++ + AL
Sbjct: 10 VKVRGLPWSCSADEVQRFFSDCKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLALK 69
Query: 203 RHKEKIGHRLVTLVMSGA---QWFL------SPPLTNE 231
+ +E +GHR V + S W L SP N+
Sbjct: 70 KDRETMGHRYVEVFKSNNVEMDWVLKHTGPNSPDTAND 107
Score = 38.5 bits (88), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 17/36 (47%), Positives = 25/36 (69%)
Query: 40 GRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
GR SGEA VE S D+ + AL++ + MG RY+E++
Sbjct: 48 GRPSGEAFVELESEDEVKLALKKDRETMGHRYVEVF 83
>pdb|2DHA|A Chain A, Solution Structure Of The Second Rna Recognition Motif In
Hypothetical Protein Flj201171
Length = 123
Score = 44.3 bits (103), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 29/89 (32%), Positives = 45/89 (50%), Gaps = 9/89 (10%)
Query: 138 SAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNG------ITIPHDYAGRCTGVAYIQF 191
S +Q +R++GLP+ E+V F + G +T P GR TG A++ F
Sbjct: 19 SKENQVIVRMRGLPFTATAEEVVAFFGQHCPITGGKEGILFVTYPD---GRPTGDAFVLF 75
Query: 192 VDKENAEKALLRHKEKIGHRLVTLVMSGA 220
+E A+ AL +HK+ +G R + L S A
Sbjct: 76 ACEEYAQNALRKHKDLLGKRYIELFRSTA 104
Score = 42.7 bits (99), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 21/44 (47%), Positives = 30/44 (68%)
Query: 32 ILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELY 75
IL +T GR +G+A V F+ + AQ AL++HK +G RYIEL+
Sbjct: 57 ILFVTYPDGRPTGDAFVLFACEEYAQNALRKHKDLLGKRYIELF 100
>pdb|2DGW|A Chain A, Solution Structure Of The Second Rna Recognition Motif
In Rna-Binding Protein 19
Length = 91
Score = 43.9 bits (102), Expect = 1e-04, Method: Composition-based stats.
Identities = 20/61 (32%), Positives = 38/61 (62%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEEGTS 81
+F P+ PV I ++ + G +G V+FS+ ++ ++AL+ ++ MG RYIE++ E+
Sbjct: 29 EFLAPLKPVAIRIVRNAHGNKTGYIFVDFSNEEEVKQALKCNREYMGGRYIEVFREKSGP 88
Query: 82 S 82
S
Sbjct: 89 S 89
>pdb|2CQP|A Chain A, Solution Structure Of The Rna Binding Domain Of
Rna-Binding Protein 12
Length = 98
Score = 40.4 bits (93), Expect = 0.001, Method: Composition-based stats.
Identities = 18/74 (24%), Positives = 41/74 (55%), Gaps = 1/74 (1%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
+++Q +P+ +++ F G +++P + + ++ G TG A + F ++ A A++
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77
Query: 205 KEK-IGHRLVTLVM 217
++ IG R V LV+
Sbjct: 78 NDRPIGSRKVKLVL 91
Score = 32.0 bits (71), Expect = 0.39, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 32/57 (56%), Gaps = 1/57 (1%)
Query: 27 IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRA-LQRHKSNMGDRYIELYMEEGTSS 82
++P ++ L ++ G +GEA V F S D+A A + + +G R ++L + G SS
Sbjct: 41 VIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDLNDRPIGSRKVKLVLGSGPSS 97
>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 = 38.1 bits (87), Expect = 0.007, Method: Composition-based stats.
Identities = 17/72 (23%), Positives = 39/72 (54%), Gaps = 1/72 (1%)
Query: 145 MRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRH 204
+++Q +P+ +++ F G +++P + + ++ G TG A + F ++ A A++
Sbjct: 18 IKVQNMPFTVSIDEILDFFYGYQVIPGSVCLKYNEKGMPTGEAMVAFESRDEATAAVIDL 77
Query: 205 KEK-IGHRLVTL 215
++ IG R V L
Sbjct: 78 NDRPIGSRKVKL 89
>pdb|2DO4|A Chain A, Solution Structure Of The Rna Binding Domain Of Squamous
Cell Carcinoma Antigen Recognized By T Cells 3
Length = 100
Score = 36.2 bits (82), Expect = 0.023, Method: Composition-based stats.
Identities = 15/57 (26%), Positives = 36/57 (63%), Gaps = 1/57 (1%)
Query: 147 LQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLR 203
+ GLP+ C KE++E+ + V + + + + AG+ G+AY+++ ++ A +A+++
Sbjct: 22 ISGLPFSCTKEELEEICKAHGTVKD-LRLVTNRAGKPKGLAYVEYENESQASQAVMK 77
>pdb|2CQD|A Chain A, Solution Structure Of The Rna Recognition Motif In Rna-
Binding Region Containing Protein 1
Length = 116
Score = 34.3 bits (77), Expect = 0.087, Method: Compositional matrix adjust.
Identities = 14/52 (26%), Positives = 23/52 (44%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKA 200
GLPY + K+ EG + + I G+ G ++ D+ AE+A
Sbjct: 24 GLPYHTTDASLRKYFEGFGDIEEAVVITDRQTGKSRGYGFVTMADRAAAERA 75
>pdb|2DNN|A Chain A, Solution Structure Of Rna Binding Domain In Rna-Binding
Protein 12
Length = 109
Score = 33.9 bits (76), Expect = 0.13, Method: Compositional matrix adjust.
Identities = 19/53 (35%), Positives = 29/53 (54%)
Query: 22 QFFKPIVPVNILLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIEL 74
FF + + LL D GR++G V+F S D AL+R++ M RY+E+
Sbjct: 35 DFFHGLRVDAVHLLKDHVGRNNGNGLVKFLSPQDTFEALKRNRMLMIQRYVEV 87
>pdb|4EGL|A Chain A, Crystal Structure Of Two Tandem Rna Recognition Motifs Of
Human Antigen R
Length = 177
Score = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 29/66 (43%)
Query: 136 SGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKE 195
S + + + GLP ++DVE + N + G GVA+I+F +
Sbjct: 82 SSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRS 141
Query: 196 NAEKAL 201
AE+A+
Sbjct: 142 EAEEAI 147
>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 = 33.5 bits (75), Expect = 0.15, Method: Compositional matrix adjust.
Identities = 17/66 (25%), Positives = 29/66 (43%)
Query: 136 SGSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKE 195
S + + + GLP ++DVE + N + G GVA+I+F +
Sbjct: 82 SSEVIKDANLYISGLPRTMTQKDVEDMFSRFGRIINSRVLVDQTTGLSRGVAFIRFDKRS 141
Query: 196 NAEKAL 201
AE+A+
Sbjct: 142 EAEEAI 147
>pdb|3SDE|A Chain A, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 32.7 bits (73), Expect = 0.29, Method: Compositional matrix adjust.
Identities = 17/45 (37%), Positives = 28/45 (62%), Gaps = 1/45 (2%)
Query: 19 LCSQFFKPIVPV-NILLLTDDAGRSSGEADVEFSSVDDAQRALQR 62
L Q F PV +++ DD GR++G+ VEF++ A++AL+R
Sbjct: 112 LLEQAFSQFGPVEKAVVVVDDRGRATGKGFVEFAAKPPARKALER 156
>pdb|2DNZ|A Chain A, Solution Structure Of The Second Rna Binding Domain Of
Rna Binding Motif Protein 23
Length = 95
Score = 31.6 bits (70), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 22/60 (36%), Positives = 34/60 (56%), Gaps = 3/60 (5%)
Query: 5 FYVIDILIHITYCLLCSQFFKPIVPV-NILLLTD-DAGRSSGEADVEFSSVDDAQRALQR 62
YV + +IT +L F+P + NI+L+ D D GRS G + FS + A+RAL++
Sbjct: 8 LYVGSLHFNITEDML-RGIFEPFGKIDNIVLMKDSDTGRSKGYGFITFSDSECARRALEQ 66
>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 = 30.8 bits (68), Expect = 1.1, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 32/66 (48%), Gaps = 2/66 (3%)
Query: 137 GSAVDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKE 195
G D + + + Y E++E G V N +TI D ++G G AYI+F DKE
Sbjct: 1 GXEADARSIYVGNVDYGATAEELEAHFHGCGSV-NRVTILCDKFSGHPKGFAYIEFSDKE 59
Query: 196 NAEKAL 201
+ +L
Sbjct: 60 SVRTSL 65
>pdb|3SDE|B Chain B, Crystal Structure Of A Paraspeckle-Protein Heterodimer,
Pspc1NONO
Length = 261
Score = 29.6 bits (65), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/30 (46%), Positives = 20/30 (66%)
Query: 33 LLLTDDAGRSSGEADVEFSSVDDAQRALQR 62
+++ DD GR SG+ VEFS A++AL R
Sbjct: 127 VVIVDDRGRPSGKGIVEFSGKPAARKALDR 156
>pdb|2DGS|A Chain A, Solution Structure Of The Second Rna Binding Domain In
Daz- Associated Protein 1
Length = 99
Score = 29.6 bits (65), Expect = 2.4, Method: Composition-based stats.
Identities = 13/60 (21%), Positives = 30/60 (50%)
Query: 149 GLPYECKKEDVEKFLEGLEIVPNGITIPHDYAGRCTGVAYIQFVDKENAEKALLRHKEKI 208
G+P+ C + ++ ++ + +V + I R G +I F D+++ ++A+ H I
Sbjct: 17 GIPHNCGETELREYFKKFGVVTEVVMIYDAEKQRPRGFGFITFEDEQSVDQAVNMHFHDI 76
>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 = 28.9 bits (63), Expect = 3.5, Method: Compositional matrix adjust.
Identities = 20/63 (31%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 140 VDQCCMRLQGLPYECKKEDVEKFLEGLEIVPNGITIPHD-YAGRCTGVAYIQFVDKENAE 198
D + + + Y E++E G V N +TI D ++G G AYI+F DKE+
Sbjct: 3 ADARSIYVGNVDYGATAEELEAHFHGCGSV-NRVTILCDKFSGHPKGFAYIEFSDKESVR 61
Query: 199 KAL 201
+L
Sbjct: 62 TSL 64
>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 = 28.5 bits (62), Expect = 4.7, Method: Composition-based stats.
Identities = 15/49 (30%), Positives = 28/49 (57%), Gaps = 1/49 (2%)
Query: 27 IVPVNILLLTDDAGRSSGEADVEFSSVDDAQRA-LQRHKSNMGDRYIEL 74
++P ++ L ++ G +GEA V F S D+A A + + +G R ++L
Sbjct: 41 VIPGSVCLKYNEKGXPTGEAXVAFESRDEATAAVIDLNDRPIGSRKVKL 89
>pdb|2FC9|A Chain A, Solution Structure Of The Rrm_1 Domain Of Ncl Protein
Length = 101
Score = 28.1 bits (61), Expect = 6.3, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 2/53 (3%)
Query: 40 GRSSGEADVEFSSVDDAQRALQR-HKSNMGDRYIELYMEEGTSSKEANGRGTG 91
G+S G A +EF+S +DA+ AL +K + R I L + +G +G +G
Sbjct: 50 GKSKGYAFIEFASFEDAKEALNSCNKREIEGRAIRLEL-QGPRGSPNSGPSSG 101
>pdb|3SXL|A Chain A, Sex-Lethal Rna Recognition Domains 1 And 2 From
Drosophila Melanogaster
pdb|3SXL|B Chain B, Sex-Lethal Rna Recognition Domains 1 And 2 From
Drosophila Melanogaster
pdb|3SXL|C Chain C, Sex-Lethal Rna Recognition Domains 1 And 2 From
Drosophila Melanogaster
Length = 184
Score = 28.1 bits (61), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 16/41 (39%), Positives = 24/41 (58%), Gaps = 2/41 (4%)
Query: 23 FFKPIVPVNILLLTDD--AGRSSGEADVEFSSVDDAQRALQ 61
F+ I P+N + D G S G A V+F+S D+QRA++
Sbjct: 34 LFRAIGPINTCRIXRDYKTGYSFGYAFVDFTSEXDSQRAIK 74
>pdb|2CJK|A Chain A, Structure Of The Rna Binding Domain Of Hrp1 In Complex
With Rna
pdb|2KM8|C Chain C, Interdomain Rrm Packing Contributes To Rna Recognition In
The Rna15, Hrp1, Anchor Rna 3' Processing Ternary
Complex
Length = 167
Score = 27.7 bits (60), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 16/46 (34%), Positives = 21/46 (45%)
Query: 33 LLLTDDAGRSSGEADVEFSSVDDAQRALQRHKSNMGDRYIELYMEE 78
L+L D G+S G V + S D R Q + DR IE+ E
Sbjct: 119 LMLDKDTGQSRGFGFVTYDSADAVDRVCQNKFIDFKDRKIEIKRAE 164
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
0.323 0.138 0.431
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,185,078
Number of Sequences: 62578
Number of extensions: 374687
Number of successful extensions: 986
Number of sequences better than 100.0: 39
Number of HSP's better than 100.0 without gapping: 27
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 929
Number of HSP's gapped (non-prelim): 65
length of query: 304
length of database: 14,973,337
effective HSP length: 98
effective length of query: 206
effective length of database: 8,840,693
effective search space: 1821182758
effective search space used: 1821182758
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 51 (24.3 bits)