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= 012811
(456 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4GZ2|A Chain A, Mus Musculus Tdp2 Excluded Ssdna Complex
pdb|4GZ2|B Chain B, Mus Musculus Tdp2 Excluded Ssdna Complex
Length = 255
Score = 88.2 bits (217), Expect = 9e-18, Method: Compositional matrix adjust.
Identities = 80/280 (28%), Positives = 126/280 (45%), Gaps = 43/280 (15%)
Query: 183 SGSLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGY 242
S ++ +++N+ + + R + + + L+SPD++ QE+ P L K + Y
Sbjct: 7 SSTISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRA--ASY 64
Query: 243 RCSVPNEMADSRGYFCMQL---SKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVA 299
NE GYF L +++ KS PF N+ M R L V + G + +
Sbjct: 65 TIITGNE----EGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNE-FCLM 119
Query: 300 TSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPN---VIFCGDMNWDDKLDGK-FP 355
TSHLES + S ER+ Q K + +++ P+ VIF GD N D+ K
Sbjct: 120 TSHLES--------TREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGG 171
Query: 356 LPDGWVDAWTEL-RPGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLRDFKII--RIDMI 412
LPD DAW L +P +T+DTK+N L + R DR + +I +D++
Sbjct: 172 LPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLV 231
Query: 413 GVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTIS 452
G+E KL+ PSDH+GLL T++
Sbjct: 232 GLE------------------KLDCGRFPSDHWGLLCTLN 253
>pdb|4GYZ|A Chain A, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|B Chain B, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|C Chain C, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|D Chain D, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|E Chain E, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|F Chain F, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|G Chain G, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|H Chain H, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GYZ|I Chain I, Mus Musculus Tdp2 Bound To Damp And Mg2+
pdb|4GZ0|A Chain A, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|B Chain B, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|E Chain E, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|K Chain K, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|G Chain G, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ0|I Chain I, Mus Musculus Tdp2-Dna Substrate Analog (5'-6-Aminohexanol)
Complex
pdb|4GZ1|A Chain A, Mus Musculus Tdp2 Reaction Product (5'-Phosphorylated
Dna)-Mg2+ Complex At 1.5 Angstroms Resolution
pdb|4GZ1|B Chain B, Mus Musculus Tdp2 Reaction Product (5'-Phosphorylated
Dna)-Mg2+ Complex At 1.5 Angstroms Resolution
Length = 256
Score = 88.2 bits (217), Expect = 1e-17, Method: Compositional matrix adjust.
Identities = 80/280 (28%), Positives = 126/280 (45%), Gaps = 43/280 (15%)
Query: 183 SGSLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGY 242
S ++ +++N+ + + R + + + L+SPD++ QE+ P L K + Y
Sbjct: 7 SSTISFITWNIDGLDGCNLPERARGVCSCLALYSPDVVFLQEVIPPYCAYLKKRA--ASY 64
Query: 243 RCSVPNEMADSRGYFCMQL---SKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVA 299
NE GYF L +++ KS PF N+ M R L V + G + +
Sbjct: 65 TIITGNE----EGYFTAILLKKGRVKFKSQEIIPFPNTKMMRNLLCVNVSLGGNE-FCLM 119
Query: 300 TSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPN---VIFCGDMNWDDKLDGK-FP 355
TSHLES + S ER+ Q K + +++ P+ VIF GD N D+ K
Sbjct: 120 TSHLES--------TREHSAERIRQLKTVLGKMQEAPDSTTVIFAGDTNLRDQEVIKCGG 171
Query: 356 LPDGWVDAWTEL-RPGENGWTYDTKSNKMLSGNRTLQKRLDRFICSLRDFKII--RIDMI 412
LPD DAW L +P +T+DTK+N L + R DR + +I +D++
Sbjct: 172 LPDNVFDAWEFLGKPKHCQYTWDTKANNNLRIPAAYKHRFDRIFFRAEEGHLIPQSLDLV 231
Query: 413 GVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTIS 452
G+E KL+ PSDH+GLL T++
Sbjct: 232 GLE------------------KLDCGRFPSDHWGLLCTLN 253
>pdb|4FPV|A Chain A, Crystal Structure Of D. Rerio Tdp2 Complexed With Single
Strand Dna Product
pdb|4FPV|B Chain B, Crystal Structure Of D. Rerio Tdp2 Complexed With Single
Strand Dna Product
Length = 257
Score = 73.6 bits (179), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 81/287 (28%), Positives = 128/287 (44%), Gaps = 39/287 (13%)
Query: 176 NSESGAVSGSLKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCK 235
++S L I+S+NV + L + R + + + L++PD++ QE+ P L K
Sbjct: 1 TAKSEVEDSKLSIISWNVDGLDTLNLADRARGLCSYLALYTPDVVFLQELIPAYVQYLKK 60
Query: 236 SSWWKGYRCSVPNEMADSRGYFC-MQLSKLQAKSFTCEP--FRNSIMGRELCVAEVEVQG 292
+ S GYF + L K + K E F + M R L +A+V G
Sbjct: 61 RA------VSYLFFEGSDDGYFTGIMLRKSRVKFLESEIICFPTTQMMRNLLIAQVTFSG 114
Query: 293 KKPLVVATSHLESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPN---VIFCGDMNW-DD 348
+K L + TSHLES C S+ER +Q + + +K+ P VIF GD N D
Sbjct: 115 QK-LYLMTSHLES-CKNQ-------SQERTKQLRVVLQKIKEAPEDAIVIFAGDTNLRDA 165
Query: 349 KLDGKFPLPDGWVDAWTELRPGEN-GWTYDTKSNKMLSGNRTLQKRLDR-FICSLRDFKI 406
++ LP G D W +L E+ +T+DTK+N + + R DR F+ S +
Sbjct: 166 EVANVGGLPAGVCDVWEQLGKQEHCRYTWDTKANSNKTVPYVSRCRFDRIFLRSAKTAPP 225
Query: 407 IRIDMIGVEAIPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTISN 453
+ D + A+ G M+KL+ SDH+G+ T +
Sbjct: 226 VTPDHM---ALIG------------MEKLDCGRYTSDHWGIYCTFNT 257
>pdb|4F1H|A Chain A, Crystal Structure Of Tdp2 From Danio Rerio Complexed With
A Single Strand Dna
Length = 250
Score = 73.6 bits (179), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 80/277 (28%), Positives = 125/277 (45%), Gaps = 39/277 (14%)
Query: 186 LKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCS 245
L I+S+NV + L + R + + + L++PD++ QE+ P L K + S
Sbjct: 4 LSIISWNVDGLDTLNLADRARGLCSYLALYTPDVVFLQELIPAYVQYLKKRA------VS 57
Query: 246 VPNEMADSRGYFC-MQLSKLQAKSFTCEP--FRNSIMGRELCVAEVEVQGKKPLVVATSH 302
GYF + L K + K E F + M R L +A+V G+K L + TSH
Sbjct: 58 YLFFEGSDDGYFTGIMLRKSRVKFLESEIICFPTTQMMRNLLIAQVTFSGQK-LYLMTSH 116
Query: 303 LESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPN---VIFCGDMNW-DDKLDGKFPLPD 358
LES C S+ER +Q + + +K+ P VIF GD N D ++ LP
Sbjct: 117 LES-CKNQ-------SQERTKQLRVVLQKIKEAPEDAIVIFAGDTNLRDAEVANVGGLPA 168
Query: 359 GWVDAWTELRPGEN-GWTYDTKSNKMLSGNRTLQKRLDR-FICSLRDFKIIRIDMIGVEA 416
G D W +L E+ +T+DTK+N + + R DR F+ S + + D + A
Sbjct: 169 GVCDVWEQLGKQEHCRYTWDTKANSNKTVPYVSRCRFDRIFLRSAKTAPPVTPDHM---A 225
Query: 417 IPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTISN 453
+ G M+KL+ SDH+G+ T +
Sbjct: 226 LIG------------MEKLDCGRYTSDHWGIYCTFNT 250
>pdb|4F1H|B Chain B, Crystal Structure Of Tdp2 From Danio Rerio Complexed With
A Single Strand Dna
Length = 251
Score = 73.6 bits (179), Expect = 2e-13, Method: Compositional matrix adjust.
Identities = 80/277 (28%), Positives = 125/277 (45%), Gaps = 39/277 (14%)
Query: 186 LKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCS 245
L I+S+NV + L + R + + + L++PD++ QE+ P L K + S
Sbjct: 5 LSIISWNVDGLDTLNLADRARGLCSYLALYTPDVVFLQELIPAYVQYLKKRA------VS 58
Query: 246 VPNEMADSRGYFC-MQLSKLQAKSFTCEP--FRNSIMGRELCVAEVEVQGKKPLVVATSH 302
GYF + L K + K E F + M R L +A+V G+K L + TSH
Sbjct: 59 YLFFEGSDDGYFTGIMLRKSRVKFLESEIICFPTTQMMRNLLIAQVTFSGQK-LYLMTSH 117
Query: 303 LESPCPGPPTWDQMFSKERVEQAKEAINLLKKNPN---VIFCGDMNW-DDKLDGKFPLPD 358
LES C S+ER +Q + + +K+ P VIF GD N D ++ LP
Sbjct: 118 LES-CKNQ-------SQERTKQLRVVLQKIKEAPEDAIVIFAGDTNLRDAEVANVGGLPA 169
Query: 359 GWVDAWTELRPGEN-GWTYDTKSNKMLSGNRTLQKRLDR-FICSLRDFKIIRIDMIGVEA 416
G D W +L E+ +T+DTK+N + + R DR F+ S + + D + A
Sbjct: 170 GVCDVWEQLGKQEHCRYTWDTKANSNKTVPYVSRCRFDRIFLRSAKTAPPVTPDHM---A 226
Query: 417 IPGLLYVKEKKVRKEMQKLELPVLPSDHYGLLLTISN 453
+ G M+KL+ SDH+G+ T +
Sbjct: 227 LIG------------MEKLDCGRYTSDHWGIYCTFNT 251
>pdb|4FVA|A Chain A, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2
pdb|4FVA|B Chain B, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2
pdb|4FVA|C Chain C, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2
pdb|4FVA|D Chain D, Crystal Structure Of Truncated Caenorhabditis Elegans Tdp2
Length = 256
Score = 51.6 bits (122), Expect = 8e-07, Method: Compositional matrix adjust.
Identities = 58/222 (26%), Positives = 99/222 (44%), Gaps = 21/222 (9%)
Query: 186 LKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCS 245
+ ++S+N+ + + RMK + +++ +PDI+ QE+ D+ Y+
Sbjct: 14 VSVMSWNIDGLDGRSLLTRMKAVAHIVKNVNPDILFLQEVVDR--DLAPIDKLQSLYKIY 71
Query: 246 VPNEMADSRGYFCMQLSKL-QAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLE 304
N+ + Y + +SK+ + F+NS M R L + E + G K ++ T HLE
Sbjct: 72 YSNK--GCQYYTAILVSKMFDVEKHDVIHFQNSGMYRTLQILEGSIGGLKVFLLNT-HLE 128
Query: 305 SPCPGPPTWDQMFS--KERVEQAKEAINLLKKNPN--VIFCGDMNWDDKLDGKFPLPDGW 360
S P F ++V + ++ +NP V F GD+N D+ + +PDG
Sbjct: 129 STREHRPQRCAQFGFCMDKVRE------IIAQNPGALVFFGGDLNLRDEEVSR--VPDGV 180
Query: 361 VDAWTELRPGEN--GWTYDTKSNKMLSGNRTLQKRLDRFICS 400
DAW E +N +T+DT N G + R DR S
Sbjct: 181 KDAW-EAAGSDNKTKFTWDTFKNDNKQGFHGAKMRFDRLYWS 221
>pdb|4GEW|A Chain A, Crystal Structure Of Tdp2 From C. Elegans
Length = 362
Score = 51.6 bits (122), Expect = 9e-07, Method: Compositional matrix adjust.
Identities = 58/222 (26%), Positives = 99/222 (44%), Gaps = 21/222 (9%)
Query: 186 LKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCS 245
+ ++S+N+ + + RMK + +++ +PDI+ QE+ D+ Y+
Sbjct: 120 VSVMSWNIDGLDGRSLLTRMKAVAHIVKNVNPDILFLQEVVDR--DLAPIDKLQSLYKIY 177
Query: 246 VPNEMADSRGYFCMQLSKL-QAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLE 304
N+ + Y + +SK+ + F+NS M R L + E + G K ++ T HLE
Sbjct: 178 YSNK--GCQYYTAILVSKMFDVEKHDVIHFQNSGMYRTLQILEGSIGGLKVFLLNT-HLE 234
Query: 305 SPCPGPPTWDQMFS--KERVEQAKEAINLLKKNPN--VIFCGDMNWDDKLDGKFPLPDGW 360
S P F ++V + ++ +NP V F GD+N D+ + +PDG
Sbjct: 235 STREHRPQRCAQFGFCMDKVRE------IIAQNPGALVFFGGDLNLRDEEVSR--VPDGV 286
Query: 361 VDAWTELRPGEN--GWTYDTKSNKMLSGNRTLQKRLDRFICS 400
DAW E +N +T+DT N G + R DR S
Sbjct: 287 KDAW-EAAGSDNKTKFTWDTFKNDNKQGFHGAKMRFDRLYWS 327
>pdb|4F1I|A Chain A, Crystal Structure Of Semet Tdp2 From Caenorhabditis
Elegans
Length = 362
Score = 45.1 bits (105), Expect = 8e-05, Method: Compositional matrix adjust.
Identities = 56/222 (25%), Positives = 95/222 (42%), Gaps = 21/222 (9%)
Query: 186 LKILSYNVWFREDLEMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCS 245
+ + S+N+ + + R K + +++ +PDI+ QE+ D+ Y+
Sbjct: 120 VSVXSWNIDGLDGRSLLTRXKAVAHIVKNVNPDILFLQEVVDR--DLAPIDKLQSLYKIY 177
Query: 246 VPNEMADSRGYFCMQLSK-LQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLVVATSHLE 304
N+ + Y + +SK + F+NS R L + E + G K ++ T HLE
Sbjct: 178 YSNKGC--QYYTAILVSKXFDVEKHDVIHFQNSGXYRTLQILEGSIGGLKVFLLNT-HLE 234
Query: 305 SPCPGPPTWDQMFS--KERVEQAKEAINLLKKNPN--VIFCGDMNWDDKLDGKFPLPDGW 360
S P F ++V + ++ +NP V F GD+N D+ + +PDG
Sbjct: 235 STREHRPQRCAQFGFCXDKVRE------IIAQNPGALVFFGGDLNLRDEEVSR--VPDGV 286
Query: 361 VDAWTELRPGEN--GWTYDTKSNKMLSGNRTLQKRLDRFICS 400
DAW E +N +T+DT N G + R DR S
Sbjct: 287 KDAW-EAAGSDNKTKFTWDTFKNDNKQGFHGAKXRFDRLYWS 327
>pdb|2OKV|A Chain A, C-Myc Dna Unwinding Element Binding Protein
pdb|2OKV|B Chain B, C-Myc Dna Unwinding Element Binding Protein
pdb|2OKV|C Chain C, C-Myc Dna Unwinding Element Binding Protein
pdb|2OKV|D Chain D, C-Myc Dna Unwinding Element Binding Protein
Length = 209
Score = 35.8 bits (81), Expect = 0.051, Method: Compositional matrix adjust.
Identities = 32/109 (29%), Positives = 53/109 (48%), Gaps = 20/109 (18%)
Query: 230 YDILCKSSW-----WKG----YRCSVPNEMADSRGYFCMQLSKLQAKSFTCEPFRNSIMG 280
Y+ILC S + KG + ++P E A+ G++ L +L+ K++ E ++ G
Sbjct: 72 YEILCVSQFTLQCVLKGNKPDFHLAMPTEQAE--GFYNSFLEQLR-KTYRPELIKDGKFG 128
Query: 281 RELCVAEVEVQGKKPLVVATSHLESPCPGPPTWD--QMFSKERVEQAKE 327
+V +Q P+ + LESP PG T D Q+ E+ +Q KE
Sbjct: 129 ---AYMQVHIQNDGPVTI---ELESPAPGTATSDPKQLSKLEKQQQRKE 171
>pdb|2OHF|A Chain A, Crystal Structure Of Human Ola1 In Complex With Amppcp
Length = 396
Score = 32.7 bits (73), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 30/107 (28%), Positives = 43/107 (40%), Gaps = 15/107 (14%)
Query: 97 LCNTRAPVSGLSSFEDLTDPA---LDSELDSSVGSVFLPLQLKACTG----KRKIRDQD- 148
LC P S + +F ++ D A + +G+ FL + AC G R D D
Sbjct: 74 LCQYHKPASKIPAFLNVVDIAGLVKGAHNGQGLGNAFLS-HISACDGIFHLTRAFEDDDI 132
Query: 149 --CDGDFDGFR----VTNSVSIKDDTTSGPSADNSESGAVSGSLKIL 189
+G D R + + +KD+ GP D E AV G K L
Sbjct: 133 THVEGSVDPIRDIEIIHEELQLKDEEMIGPIIDKLEKVAVRGGDKKL 179
>pdb|1ES6|A Chain A, Crystal Structure Of The Matrix Protein Of Ebola Virus
Length = 296
Score = 32.3 bits (72), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 23/69 (33%), Positives = 39/69 (56%), Gaps = 7/69 (10%)
Query: 385 SGNRTLQKRLDRFICSLRDFKIIRID----MIGVEAIPGLLYVK--EKKVRKEMQKLELP 438
S + T +++ + SL+DFKI+ ID ++G+E +P L +K KKV + + +P
Sbjct: 198 SADLTSPEKIQAIMTSLQDFKIVPIDPTKNIMGIE-VPETLVLKLTGKKVTSKNGQPIIP 256
Query: 439 VLPSDHYGL 447
VL + GL
Sbjct: 257 VLLPKYIGL 265
>pdb|1NJ3|A Chain A, Structure And Ubiquitin Interactions Of The Conserved
Nzf Domain Of Npl4
pdb|1Q5W|A Chain A, Ubiquitin Recognition By Npl4 Zinc-Fingers
Length = 31
Score = 32.0 bits (71), Expect = 0.65, Method: Composition-based stats.
Identities = 12/27 (44%), Positives = 18/27 (66%), Gaps = 1/27 (3%)
Query: 33 GSSMSSWACKKCTFLNSPSRKSTCQIC 59
GS+ + WAC+ CTF+N P C++C
Sbjct: 1 GSTSAMWACQHCTFMNQPG-TGHCEMC 26
Score = 29.3 bits (64), Expect = 4.9, Method: Composition-based stats.
Identities = 9/21 (42%), Positives = 14/21 (66%)
Query: 79 WSCKACTFLNPYNNTSCELCN 99
W+C+ CTF+N CE+C+
Sbjct: 7 WACQHCTFMNQPGTGHCEMCS 27
>pdb|2E7G|A Chain A, Solution Structure Of Putative Ribosome-Binding Factor A
(Rbfa) From Human Mutochondrial Precursor
Length = 129
Score = 30.8 bits (68), Expect = 1.5, Method: Composition-based stats.
Identities = 21/98 (21%), Positives = 45/98 (45%), Gaps = 5/98 (5%)
Query: 200 EMHPRMKTIGDLIQLHSPDIICFQEITPNIYDILCKSSWWKGYRCSVPNEMADSRGYFCM 259
E H R++ + L+ D++C E++ +YD+ + S + S+ + + R Y+
Sbjct: 10 EDHARLRALNGLLYKALTDLLCTPEVSQELYDLNVELS-----KVSLTPDFSACRAYWKT 64
Query: 260 QLSKLQAKSFTCEPFRNSIMGRELCVAEVEVQGKKPLV 297
LS Q R++ R L +++ ++ P+V
Sbjct: 65 TLSAEQNAHMEAVLQRSAAHMRHLLMSQQTLRNVPPIV 102
>pdb|3B08|B Chain B, Crystal Structure Of The Mouse Hoil1-L-Nzf In Complex With
Linear Di- Ubiquitin
pdb|3B08|E Chain E, Crystal Structure Of The Mouse Hoil1-L-Nzf In Complex With
Linear Di- Ubiquitin
pdb|3B08|H Chain H, Crystal Structure Of The Mouse Hoil1-L-Nzf In Complex With
Linear Di- Ubiquitin
pdb|3B08|K Chain K, Crystal Structure Of The Mouse Hoil1-L-Nzf In Complex With
Linear Di- Ubiquitin
pdb|3B0A|B Chain B, Crystal Structure Of The Mouse Hoil1-L-Nzf In Complex With
Linear Di- Ubiquitin
pdb|3B0A|E Chain E, Crystal Structure Of The Mouse Hoil1-L-Nzf In Complex With
Linear Di- Ubiquitin
Length = 64
Score = 30.0 bits (66), Expect = 3.2, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 79 WSCKACTFLNPYNNTSCELCNTRAP 103
W C CTF+N CE+C P
Sbjct: 9 WQCPGCTFINKPTRPGCEMCCRARP 33
Score = 29.6 bits (65), Expect = 3.3, Method: Composition-based stats.
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 39 WACKKCTFLNSPSRKSTCQIC 59
W C CTF+N P+R C++C
Sbjct: 9 WQCPGCTFINKPTRPG-CEMC 28
>pdb|3VKG|A Chain A, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein
Motor Domain
pdb|3VKG|B Chain B, X-Ray Structure Of An Mtbd Truncation Mutant Of Dynein
Motor Domain
Length = 3245
Score = 29.6 bits (65), Expect = 4.1, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 59/129 (45%), Gaps = 20/129 (15%)
Query: 313 WDQMFSKERVEQAKEAINLLKKNPNV-IFCGDMN-WDDKLDGKFPLPDGWVDAWTELRPG 370
WD +F+K + + +I+ +K +P +F + N WDD+L+ L D W+D
Sbjct: 195 WDDLFNK--LAEHLNSISAMKMSPYYKVFEEEANHWDDRLNKVRSLLDVWIDV------- 245
Query: 371 ENGWTYDTKSNKMLSG----NRTLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEK 426
+ W Y + SG N+ L RF +F I + G I +L + +
Sbjct: 246 QRRWVY---LEGIFSGSGDINQLLPAESTRFKSINSEFIAILKKVSGAPLILEVLAI--E 300
Query: 427 KVRKEMQKL 435
++++ M++L
Sbjct: 301 RIQQTMERL 309
>pdb|3VKH|A Chain A, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
pdb|3VKH|B Chain B, X-Ray Structure Of A Functional Full-Length Dynein Motor
Domain
Length = 3367
Score = 29.3 bits (64), Expect = 4.2, Method: Compositional matrix adjust.
Identities = 32/129 (24%), Positives = 59/129 (45%), Gaps = 20/129 (15%)
Query: 313 WDQMFSKERVEQAKEAINLLKKNPNV-IFCGDMN-WDDKLDGKFPLPDGWVDAWTELRPG 370
WD +F+K + + +I+ +K +P +F + N WDD+L+ L D W+D
Sbjct: 195 WDDLFNK--LAEHLNSISAMKMSPYYKVFEEEANHWDDRLNKVRSLLDVWIDV------- 245
Query: 371 ENGWTYDTKSNKMLSG----NRTLQKRLDRFICSLRDFKIIRIDMIGVEAIPGLLYVKEK 426
+ W Y + SG N+ L RF +F I + G I +L + +
Sbjct: 246 QRRWVY---LEGIFSGSGDINQLLPAESTRFKSINSEFIAILKKVSGAPLILEVLAI--E 300
Query: 427 KVRKEMQKL 435
++++ M++L
Sbjct: 301 RIQQTMERL 309
>pdb|2CRC|A Chain A, Solution Structure Of The Zf-Ranbp Domain Of The Protein
Hbv Associated Factor
Length = 52
Score = 28.9 bits (63), Expect = 6.7, Method: Composition-based stats.
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 79 WSCKACTFLNPYNNTSCELCNTRAP 103
W C CTF+N CE+C P
Sbjct: 11 WQCPGCTFINKPTRPGCEMCCRARP 35
Score = 28.5 bits (62), Expect = 7.9, Method: Composition-based stats.
Identities = 10/21 (47%), Positives = 14/21 (66%), Gaps = 1/21 (4%)
Query: 39 WACKKCTFLNSPSRKSTCQIC 59
W C CTF+N P+R C++C
Sbjct: 11 WQCPGCTFINKPTRPG-CEMC 30
>pdb|3A9J|C Chain C, Crystal Structure Of The Mouse Tab2-Nzf In Complex With
Lys63-Linked Di-Ubiquitin
Length = 34
Score = 28.9 bits (63), Expect = 6.9, Method: Composition-based stats.
Identities = 11/20 (55%), Positives = 12/20 (60%)
Query: 79 WSCKACTFLNPYNNTSCELC 98
W+C ACTFLN CE C
Sbjct: 9 WNCTACTFLNHPALIRCEQC 28
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
0.319 0.135 0.424
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 13,818,082
Number of Sequences: 62578
Number of extensions: 575590
Number of successful extensions: 1151
Number of sequences better than 100.0: 24
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1124
Number of HSP's gapped (non-prelim): 32
length of query: 456
length of database: 14,973,337
effective HSP length: 102
effective length of query: 354
effective length of database: 8,590,381
effective search space: 3040994874
effective search space used: 3040994874
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: 53 (25.0 bits)