Reference:
Altschul, Stephen F., Thomas L. Madden, Alejandro A. Schäffer,
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.
Query= Dr_sW_004_F08
(852 letters)
Database: Non-redundant SwissProt sequences
184,735 sequences; 68,354,980 total letters
Score E
Sequences producing significant alignments: (bits) Value
sp|Q921F2|TADBP_MOUSE TAR DNA-binding protein 43 (TDP-43) 137 3e-32
sp|Q13148|TADBP_HUMAN TAR DNA-binding protein 43 (TDP-43) 137 3e-32
sp|Q920Q6|MSI2H_MOUSE RNA-binding protein Musashi homolog 2... 66 1e-10
sp|Q96DH6|MSI2H_HUMAN RNA-binding protein Musashi homolog 2... 63 1e-09
sp|P51991|ROA3_HUMAN Heterogeneous nuclear ribonucleoprotei... 60 1e-08
sp|Q8BG05|ROA3_MOUSE Heterogeneous nuclear ribonucleoprotei... 60 1e-08
sp|P49312|ROA1_MOUSE Heterogeneous nuclear ribonucleoprotei... 59 1e-08
sp|P09651|ROA1_HUMAN Heterogeneous nuclear ribonucleoprotei... 59 1e-08
sp|P22626|ROA2_HUMAN Heterogeneous nuclear ribonucleoprotei... 59 2e-08
sp|O88569|ROA2_MOUSE Heterogeneous nuclear ribonucleoprotei... 59 2e-08
>sp|Q921F2|TADBP_MOUSE TAR DNA-binding protein 43 (TDP-43)
Length = 414
Score = 137 bits (346), Expect = 3e-32
Identities = 64/130 (49%), Positives = 90/130 (69%)
Frame = +1
Query: 19 ETSHSKGYAFIRFADYGAQVLCLAEKHLIDGRWCAVKVPFSKNEADKQEISKKIHVGYAS 198
+T HSKG+ F+RF +Y QV ++++H+IDGRWC K+P SK D+ S+K+ VG +
Sbjct: 140 KTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSPDEPLRSRKVFVGRCT 199
Query: 199 EDISMEDLRMAFEQYGYVTDIFIPKPFRNFAFVTFDSSDTAQSLIGQSINVNGHTLTIGS 378
ED++ E+L+ F QYG V D+FIPKPFR FAFVTF AQSL G+ + + G ++ I +
Sbjct: 200 EDMTAEELQQFFCQYGEVVDVFIPKPFRAFAFVTFADDKVAQSLCGEDLIIKGISVHISN 259
Query: 379 AVPKINSNRK 408
A PK NSNR+
Sbjct: 260 AEPKHNSNRQ 269
>sp|Q13148|TADBP_HUMAN TAR DNA-binding protein 43 (TDP-43)
Length = 414
Score = 137 bits (346), Expect = 3e-32
Identities = 64/130 (49%), Positives = 90/130 (69%)
Frame = +1
Query: 19 ETSHSKGYAFIRFADYGAQVLCLAEKHLIDGRWCAVKVPFSKNEADKQEISKKIHVGYAS 198
+T HSKG+ F+RF +Y QV ++++H+IDGRWC K+P SK D+ S+K+ VG +
Sbjct: 140 KTGHSKGFGFVRFTEYETQVKVMSQRHMIDGRWCDCKLPNSKQSQDEPLRSRKVFVGRCT 199
Query: 199 EDISMEDLRMAFEQYGYVTDIFIPKPFRNFAFVTFDSSDTAQSLIGQSINVNGHTLTIGS 378
ED++ ++LR F QYG V D+FIPKPFR FAFVTF AQSL G+ + + G ++ I +
Sbjct: 200 EDMTEDELREFFSQYGDVMDVFIPKPFRAFAFVTFADDQIAQSLCGEDLIIKGISVHISN 259
Query: 379 AVPKINSNRK 408
A PK NSNR+
Sbjct: 260 AEPKHNSNRQ 269
>sp|Q920Q6|MSI2H_MOUSE RNA-binding protein Musashi homolog 2 (Musashi-2)
Length = 346
Score = 65.9 bits (159), Expect = 1e-10
Identities = 77/274 (28%), Positives = 111/274 (40%), Gaps = 34/274 (12%)
Frame = +1
Query: 22 TSHSKGYAFIRFADYGAQVLCLAEKHL-IDGRWCAVKVPFSKNEADKQEI-SKKIHVGYA 195
T S+G+ F+ FAD + L + H +D + KV F + K +KKI VG
Sbjct: 58 TKRSRGFGFVTFADPASVDKVLGQPHHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGL 117
Query: 196 SEDISMEDLRMAFEQYGYVTDIFI-----PKPFRNFAFVTFDSSDTAQSLIGQSIN-VNG 357
S + +ED++ FEQ+G V D + R F FVTF++ D + + + +N
Sbjct: 118 SANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINN 177
Query: 358 HTLTIGSAVPK-------INSNRKGMPGHYPMYSNDNSMQTQAYQT------RYAPGMIP 498
+ A PK +G+P Y M + M Y R PG P
Sbjct: 178 KMVECKKAQPKEVMFPPGTRGRARGLP--YTMDAFMLGMGMLGYPNFVATYGRGYPGFAP 235
Query: 499 TYGAAWP----PSYDMAAAQKVARV-NSNNNPYNAYPGLLTGQTYVMSNGSRAG--QEAL 657
+YG +P +Y AA VA S N Y+A P + SN +R G A
Sbjct: 236 SYGYQFPGFPAAAYGPVAAAAVAAARGSVLNSYSAQPNFGAPASPAGSNPARPGGFPGAN 295
Query: 658 QQG------GYANQDMMHQNYMNQYSANDPSQHG 741
G G A+QD NY++ S S G
Sbjct: 296 SPGPVADLYGPASQDSGVGNYISAASPQPGSGFG 329
>sp|Q96DH6|MSI2H_HUMAN RNA-binding protein Musashi homolog 2 (Musashi-2)
Length = 328
Score = 62.8 bits (151), Expect = 1e-09
Identities = 73/266 (27%), Positives = 107/266 (40%), Gaps = 26/266 (9%)
Frame = +1
Query: 22 TSHSKGYAFIRFADYGAQVLCLAEKHL-IDGRWCAVKVPFSKNEADKQEI-SKKIHVGYA 195
T S+G+ F+ FAD + L + H +D + KV F + K +KKI VG
Sbjct: 58 TKRSRGFGFVTFADPASVDKVLGQPHHELDSKTIDPKVAFPRRAQPKMVTRTKKIFVGGL 117
Query: 196 SEDISMEDLRMAFEQYGYVTDIFI-----PKPFRNFAFVTFDSSDTAQSLIGQSIN-VNG 357
S + +ED++ FEQ+G V D + R F FVTF++ D + + + +N
Sbjct: 118 SANTVVEDVKQYFEQFGKVEDAMLMFDKTTNRHRGFGFVTFENEDVVEKVCEIHFHEINN 177
Query: 358 HTLTIGSAVPK-------INSNRKGMPGHYPMYSNDNSMQTQAYQT------RYAPGMIP 498
+ A PK +G+P Y M + M Y R PG P
Sbjct: 178 KMVECKKAQPKEVMFPPGTRGRARGLP--YTMDAFMLGMGMLGYPNFVATYGRGYPGFAP 235
Query: 499 TYGAAWP----PSYDMAAAQKVARV-NSNNNPYNAYPGLLTGQTYVMSNGSRAGQEALQQ 663
+YG +P +Y AA VA S +NP A PG G+ +
Sbjct: 236 SYGYQFPGFPAAAYGPVAAAAVAAARGSGSNP--ARPGGFP--------GANSPGPVADL 285
Query: 664 GGYANQDMMHQNYMNQYSANDPSQHG 741
G A+QD NY++ S S G
Sbjct: 286 YGPASQDSGVGNYISAASPQPGSGFG 311
>sp|P51991|ROA3_HUMAN Heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3)
Length = 378
Score = 59.7 bits (143), Expect = 1e-08
Identities = 43/135 (31%), Positives = 66/135 (48%), Gaps = 11/135 (8%)
Frame = +1
Query: 19 ETSHSKGYAFIRFA--DYGAQVLCLAEKHLIDGRWCAVKVPFSKNEADKQEIS---KKIH 183
+T S+G+ F+ ++ + +C A H +DGR K S+ ++ K KKI
Sbjct: 71 QTKRSRGFGFVTYSCVEEVDAAMC-ARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIF 129
Query: 184 VGYASEDISMEDLRMAFEQYGYVTDIFIPKPF-----RNFAFVTFDSSDTAQSLIGQSIN 348
VG ED +LR FE+YG + I + + R FAFVTFD DT ++ Q +
Sbjct: 130 VGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYH 189
Query: 349 -VNGHTLTIGSAVPK 390
+NGH + A+ K
Sbjct: 190 TINGHNCEVKKALSK 204
Score = 31.6 bits (70), Expect = 2.9
Identities = 23/95 (24%), Positives = 46/95 (48%), Gaps = 6/95 (6%)
Frame = +1
Query: 145 NEADKQEISKKIHVGYASEDISMEDLRMAFEQYGYVTDIFI-----PKPFRNFAFVTFDS 309
++ + E +K+ +G S + + + LR FE++G +TD + K R F FVT+
Sbjct: 26 HDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSC 85
Query: 310 -SDTAQSLIGQSINVNGHTLTIGSAVPKINSNRKG 411
+ ++ + V+G + AV + +S + G
Sbjct: 86 VEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPG 120
>sp|Q8BG05|ROA3_MOUSE Heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3)
sp|Q6URK4|ROA3_RAT Heterogeneous nuclear ribonucleoprotein A3 (hnRNP A3)
Length = 379
Score = 59.7 bits (143), Expect = 1e-08
Identities = 43/135 (31%), Positives = 66/135 (48%), Gaps = 11/135 (8%)
Frame = +1
Query: 19 ETSHSKGYAFIRFA--DYGAQVLCLAEKHLIDGRWCAVKVPFSKNEADKQEIS---KKIH 183
+T S+G+ F+ ++ + +C A H +DGR K S+ ++ K KKI
Sbjct: 71 QTKRSRGFGFVTYSCVEEVDAAMC-ARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIF 129
Query: 184 VGYASEDISMEDLRMAFEQYGYVTDIFIPKPF-----RNFAFVTFDSSDTAQSLIGQSIN 348
VG ED +LR FE+YG + I + + R FAFVTFD DT ++ Q +
Sbjct: 130 VGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYH 189
Query: 349 -VNGHTLTIGSAVPK 390
+NGH + A+ K
Sbjct: 190 TINGHNCEVKKALSK 204
Score = 31.6 bits (70), Expect = 2.9
Identities = 23/95 (24%), Positives = 46/95 (48%), Gaps = 6/95 (6%)
Frame = +1
Query: 145 NEADKQEISKKIHVGYASEDISMEDLRMAFEQYGYVTDIFI-----PKPFRNFAFVTFDS 309
++ + E +K+ +G S + + + LR FE++G +TD + K R F FVT+
Sbjct: 26 HDPKEPEQLRKLFIGGLSFETTDDSLREHFEKWGTLTDCVVMRDPQTKRSRGFGFVTYSC 85
Query: 310 -SDTAQSLIGQSINVNGHTLTIGSAVPKINSNRKG 411
+ ++ + V+G + AV + +S + G
Sbjct: 86 VEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPG 120
>sp|P49312|ROA1_MOUSE Heterogeneous nuclear ribonucleoprotein A1 (Helix-destabilizing
protein) (Single-strand binding protein) (hnRNP core
protein A1) (HDP-1) (Topoisomerase-inhibitor suppressed)
Length = 320
Score = 59.3 bits (142), Expect = 1e-08
Identities = 47/148 (31%), Positives = 68/148 (45%), Gaps = 15/148 (10%)
Frame = +1
Query: 22 TSHSKGYAFIRFADYGAQVLCL-AEKHLIDGRWCAVKVPFSKNEADKQEIS---KKIHVG 189
T S+G+ F+ +A + A H +DGR K S+ ++ + KKI VG
Sbjct: 51 TKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVG 110
Query: 190 YASEDISMEDLRMAFEQYGYVTDIFI-----PKPFRNFAFVTFDSSDTAQSLIGQSIN-V 351
ED LR FEQYG + I I R FAFVTFD D+ ++ Q + V
Sbjct: 111 GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTV 170
Query: 352 NGHTLTIGSAVPK-----INSNRKGMPG 420
NGH + A+ K +S+++G G
Sbjct: 171 NGHNCEVRKALSKQEMASASSSQRGRSG 198
Score = 40.0 bits (92), Expect = 0.008
Identities = 30/98 (30%), Positives = 51/98 (52%), Gaps = 7/98 (7%)
Frame = +1
Query: 139 SKNEADKQ-EISKKIHVGYASEDISMEDLRMAFEQYGYVTDIFI-----PKPFRNFAFVT 300
SK+E+ K+ E +K+ +G S + + E LR FEQ+G +TD + K R F FVT
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 301 FDSSDTAQSLI-GQSINVNGHTLTIGSAVPKINSNRKG 411
+ + + + + + V+G + AV + +S R G
Sbjct: 62 YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPG 99
>sp|P09651|ROA1_HUMAN Heterogeneous nuclear ribonucleoprotein A1 (Helix-destabilizing
protein) (Single-strand binding protein) (hnRNP core
protein A1)
Length = 372
Score = 59.3 bits (142), Expect = 1e-08
Identities = 47/148 (31%), Positives = 68/148 (45%), Gaps = 15/148 (10%)
Frame = +1
Query: 22 TSHSKGYAFIRFADYGAQVLCL-AEKHLIDGRWCAVKVPFSKNEADKQEIS---KKIHVG 189
T S+G+ F+ +A + A H +DGR K S+ ++ + KKI VG
Sbjct: 51 TKRSRGFGFVTYATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPGAHLTVKKIFVG 110
Query: 190 YASEDISMEDLRMAFEQYGYVTDIFI-----PKPFRNFAFVTFDSSDTAQSLIGQSIN-V 351
ED LR FEQYG + I I R FAFVTFD D+ ++ Q + V
Sbjct: 111 GIKEDTEEHHLRDYFEQYGKIEVIEIMTDRGSGKKRGFAFVTFDDHDSVDKIVIQKYHTV 170
Query: 352 NGHTLTIGSAVPK-----INSNRKGMPG 420
NGH + A+ K +S+++G G
Sbjct: 171 NGHNCEVRKALSKQEMASASSSQRGRSG 198
Score = 40.0 bits (92), Expect = 0.008
Identities = 30/98 (30%), Positives = 51/98 (52%), Gaps = 7/98 (7%)
Frame = +1
Query: 139 SKNEADKQ-EISKKIHVGYASEDISMEDLRMAFEQYGYVTDIFI-----PKPFRNFAFVT 300
SK+E+ K+ E +K+ +G S + + E LR FEQ+G +TD + K R F FVT
Sbjct: 2 SKSESPKEPEQLRKLFIGGLSFETTDESLRSHFEQWGTLTDCVVMRDPNTKRSRGFGFVT 61
Query: 301 FDSSDTAQSLI-GQSINVNGHTLTIGSAVPKINSNRKG 411
+ + + + + + V+G + AV + +S R G
Sbjct: 62 YATVEEVDAAMNARPHKVDGRVVEPKRAVSREDSQRPG 99
>sp|P22626|ROA2_HUMAN Heterogeneous nuclear ribonucleoproteins A2/B1 (hnRNP A2 / hnRNP
B1)
Length = 353
Score = 58.9 bits (141), Expect = 2e-08
Identities = 44/150 (29%), Positives = 68/150 (45%), Gaps = 15/150 (10%)
Frame = +1
Query: 22 TSHSKGYAFIRFADYGAQVLCLAEK-HLIDGRWCAVKVPFSKNEADKQEIS---KKIHVG 189
+ S+G+ F+ F+ +A + H IDGR K ++ E+ K KK+ VG
Sbjct: 58 SKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVG 117
Query: 190 YASEDISMEDLRMAFEQYGYVTDIFI-----PKPFRNFAFVTFDSSDTAQSLIGQSIN-V 351
ED LR FE+YG + I I R F FVTFD D ++ Q + +
Sbjct: 118 GIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTI 177
Query: 352 NGHTLTIGSAVPK-----INSNRKGMPGHY 426
NGH + A+ + + S+R G G++
Sbjct: 178 NGHNAEVRKALSRQEMQEVQSSRSGRGGNF 207
Score = 42.0 bits (97), Expect = 0.002
Identities = 27/100 (27%), Positives = 52/100 (52%), Gaps = 6/100 (6%)
Frame = +1
Query: 130 VPFSKNEADKQEISKKIHVGYASEDISMEDLRMAFEQYGYVTDIFI-----PKPFRNFAF 294
VP + + +K++ +K+ +G S + + E LR +EQ+G +TD + K R F F
Sbjct: 8 VPLERKKREKEQF-RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGF 66
Query: 295 VTFDS-SDTAQSLIGQSINVNGHTLTIGSAVPKINSNRKG 411
VTF S ++ ++ + +++G + AV + S + G
Sbjct: 67 VTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGKPG 106
>sp|O88569|ROA2_MOUSE Heterogeneous nuclear ribonucleoproteins A2/B1 (hnRNP A2 / hnRNP
B1)
Length = 341
Score = 58.9 bits (141), Expect = 2e-08
Identities = 44/150 (29%), Positives = 68/150 (45%), Gaps = 15/150 (10%)
Frame = +1
Query: 22 TSHSKGYAFIRFADYGAQVLCLAEK-HLIDGRWCAVKVPFSKNEADKQEIS---KKIHVG 189
+ S+G+ F+ F+ +A + H IDGR K ++ E+ K KK+ VG
Sbjct: 46 SKRSRGFGFVTFSSMAEVDAAMAARPHSIDGRVVEPKRAVAREESGKPGAHVTVKKLFVG 105
Query: 190 YASEDISMEDLRMAFEQYGYVTDIFI-----PKPFRNFAFVTFDSSDTAQSLIGQSIN-V 351
ED LR FE+YG + I I R F FVTFD D ++ Q + +
Sbjct: 106 GIKEDTEEHHLRDYFEEYGKIDTIEIITDRQSGKKRGFGFVTFDDHDPVDKIVLQKYHTI 165
Query: 352 NGHTLTIGSAVPK-----INSNRKGMPGHY 426
NGH + A+ + + S+R G G++
Sbjct: 166 NGHNAEVRKALSRQEMQEVQSSRSGRGGNF 195
Score = 38.5 bits (88), Expect = 0.024
Identities = 26/94 (27%), Positives = 49/94 (52%), Gaps = 6/94 (6%)
Frame = +1
Query: 148 EADKQEISKKIHVGYASEDISMEDLRMAFEQYGYVTDIFI-----PKPFRNFAFVTFDS- 309
E +K++ +K+ +G S + + E LR +EQ+G +TD + K R F FVTF S
Sbjct: 2 EREKEQF-RKLFIGGLSFETTEESLRNYYEQWGKLTDCVVMRDPASKRSRGFGFVTFSSM 60
Query: 310 SDTAQSLIGQSINVNGHTLTIGSAVPKINSNRKG 411
++ ++ + +++G + AV + S + G
Sbjct: 61 AEVDAAMAARPHSIDGRVVEPKRAVAREESGKPG 94
Database: Non-redundant SwissProt sequences
Posted date: Dec 6, 2005 7:40 AM
Number of letters in database: 68,354,980
Number of sequences in database: 184,735
Database: swissprot.01
Posted date: Dec 6, 2005 8:18 AM
Number of letters in database: 66,202,850
Number of sequences in database: 184,431
Lambda K H
0.314 0.129 0.387
Gapped
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 101,230,625
Number of Sequences: 369166
Number of extensions: 2158361
Number of successful extensions: 6658
Number of sequences better than 10.0: 10
Number of HSP's better than 10.0 without gapping: 6236
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 6618
length of database: 68,354,980
effective HSP length: 109
effective length of database: 48,218,865
effective search space used: 8390082510
frameshift window, decay const: 40, 0.1
T: 12
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.5 bits)