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= 012935
(453 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3SIU|B Chain B, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Monomeric Form
pdb|3SIU|E Chain E, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Monomeric Form
pdb|3SIV|B Chain B, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
pdb|3SIV|E Chain E, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
pdb|3SIV|H Chain H, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
pdb|3SIV|K Chain K, Structure Of A Hprp31-15.5k-U4atac 5' Stem Loop Complex,
Dimeric Form
Length = 254
Score = 245 bits (626), Expect = 3e-65, Method: Compositional matrix adjust.
Identities = 128/249 (51%), Positives = 170/249 (68%), Gaps = 2/249 (0%)
Query: 57 EDDPEYQLIVDCNVLSVDIENEIVIIHNFIRDKYRLKFPELESLVHHPIDYARVVKKIGN 116
E PEY++IVD N L+V+IENE+ IIH FIRDKY +FPELESLV + +DY R VK++GN
Sbjct: 6 EAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLVPNALDYIRTVKELGN 65
Query: 117 EMDLTL--VDLEGLLPSAIIMVVSVTASTTSGKPLPEDVLQKTIXXXXXXXXXXXXXXXX 174
+D +L+ +L +A IMVVSVTASTT G+ L E+ L++
Sbjct: 66 SLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLSEEELERLEEACDMALELNASKHRI 125
Query: 175 XXFVESRMSYIAPNLSAIVGSAVAAKLMGTAGGLSALAKMPACNVQLLGAKKKNLAGFST 234
+VESRMS+IAPNLS I+G++ AAK+MG AGGL+ L+KMPACN+ LLGA++K L+GFS+
Sbjct: 126 YEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTNLSKMPACNIMLLGAQRKTLSGFSS 185
Query: 235 ATSQFRVGYLEQTEIFQSTPPPLRMRACRLLAAKSTLAARVDSTRGDPSGTAGRSFREEI 294
+ GY+ ++I QS PP LR +A RL+AAK TLAARVDS G G ++EI
Sbjct: 186 TSVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCTLAARVDSFHESTEGKVGYELKDEI 245
Query: 295 HKKIEKWQE 303
+K +KWQE
Sbjct: 246 ERKFDKWQE 254
>pdb|2OZB|B Chain B, Structure Of A Human Prp31-15.5k-U4 Snrna Complex
pdb|2OZB|E Chain E, Structure Of A Human Prp31-15.5k-U4 Snrna Complex
Length = 260
Score = 245 bits (625), Expect = 4e-65, Method: Compositional matrix adjust.
Identities = 128/250 (51%), Positives = 171/250 (68%), Gaps = 2/250 (0%)
Query: 56 LEDDPEYQLIVDCNVLSVDIENEIVIIHNFIRDKYRLKFPELESLVHHPIDYARVVKKIG 115
+E PEY++IVD N L+V+IENE+ IIH FIRDKY +FPELESLV + +DY R VK++G
Sbjct: 11 VEAAPEYRVIVDANNLTVEIENELNIIHKFIRDKYSKRFPELESLVPNALDYIRTVKELG 70
Query: 116 NEMDLTL--VDLEGLLPSAIIMVVSVTASTTSGKPLPEDVLQKTIXXXXXXXXXXXXXXX 173
N +D +L+ +L +A IMVVSVTASTT G+ L E+ L++
Sbjct: 71 NSLDKCKNNENLQQILTNATIMVVSVTASTTQGQQLSEEELERLEEACDMALELNASKHR 130
Query: 174 XXXFVESRMSYIAPNLSAIVGSAVAAKLMGTAGGLSALAKMPACNVQLLGAKKKNLAGFS 233
+VESRMS+IAPNLS I+G++ AAK+MG AGGL+ L+KMPACN+ LLGA++K L+GFS
Sbjct: 131 IYEYVESRMSFIAPNLSIIIGASTAAKIMGVAGGLTNLSKMPACNIMLLGAQRKTLSGFS 190
Query: 234 TATSQFRVGYLEQTEIFQSTPPPLRMRACRLLAAKSTLAARVDSTRGDPSGTAGRSFREE 293
+ + GY+ ++I QS PP LR +A RL+AAK TLAARVDS G G ++E
Sbjct: 191 STSVLPHTGYIYHSDIVQSLPPDLRRKAARLVAAKCTLAARVDSFHESTEGKVGYELKDE 250
Query: 294 IHKKIEKWQE 303
I +K +KWQE
Sbjct: 251 IERKFDKWQE 260
>pdb|3NMU|A Chain A, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
pdb|3NMU|B Chain B, Crystal Structure Of Substrate-Bound Halfmer Box CD RNP
pdb|3NVI|A Chain A, Structure Of N-Terminal Truncated Nop5658 BOUND WITH L7AE
AND BOX CD Rna
pdb|3NVI|C Chain C, Structure Of N-Terminal Truncated Nop5658 BOUND WITH L7AE
AND BOX CD Rna
Length = 379
Score = 83.6 bits (205), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 65/228 (28%), Positives = 104/228 (45%), Gaps = 10/228 (4%)
Query: 74 DIENEIVIIHNFIRDKYRLKFPELESLV-HHPIDYARVVKKIGNEMDLTLVDLEGL-LPS 131
D++ I ++ +R+ Y L FPEL+ L+ HP Y VK +G+ ++ L L L
Sbjct: 150 DVDKVINLLVARLREWYSLHFPELDELLPKHP-QYVAFVKTVGHRDNINEEVLRELGLSE 208
Query: 132 AIIMVVSVTASTTSGKPLPEDVLQKTIXXXXXXXXXXXXXXXXXXFVESRMSYIAPNLSA 191
I + T G + + ++ +++ M +APNL A
Sbjct: 209 EKIKKILEAKEKTMGAWMDQTDIEVVRQLAEEIDRLYQLRKKLEDYIDRAMDDVAPNLKA 268
Query: 192 IVGSAVAAKLMGTAGGLSALAKMPACNVQLLGAKKKNLAGFSTATSQFRVGYLEQTEIFQ 251
+VG+ +AA+L+ AGGL LA MP+ +Q+LGA+K T + G + Q
Sbjct: 269 LVGAKLAARLISLAGGLRELAMMPSSTIQVLGAEKALFRHLRTGAKPPKHGVIYQYPAIN 328
Query: 252 STPPPLRMRACRLLAAKSTLAARVDSTRGDPSGTAGRSFREEIHKKIE 299
+P R + R LA K +AARVD +G EE+ K++E
Sbjct: 329 RSPWWQRGKIARALAGKLAIAARVDY-------FSGEYIAEELKKELE 369
>pdb|2NNW|A Chain A, Alternative Conformations Of Nop56/58-fibrillarin Complex
And Implication For Induced-fit Assenly Of Box C/d Rnps
pdb|2NNW|C Chain C, Alternative Conformations Of Nop56/58-fibrillarin Complex
And Implication For Induced-fit Assenly Of Box C/d Rnps
Length = 376
Score = 83.6 bits (205), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 65/228 (28%), Positives = 104/228 (45%), Gaps = 10/228 (4%)
Query: 74 DIENEIVIIHNFIRDKYRLKFPELESLV-HHPIDYARVVKKIGNEMDLTLVDLEGL-LPS 131
D++ I ++ +R+ Y L FPEL+ L+ HP Y VK +G+ ++ L L L
Sbjct: 150 DVDKVINLLVARLREWYSLHFPELDELLPKHP-QYVAFVKTVGHRDNINEEVLRELGLSE 208
Query: 132 AIIMVVSVTASTTSGKPLPEDVLQKTIXXXXXXXXXXXXXXXXXXFVESRMSYIAPNLSA 191
I + T G + + ++ +++ M +APNL A
Sbjct: 209 EKIKKILEAKEKTMGAWMDQTDIEVVRQLAEEIDRLYQLRKKLEDYIDRAMDDVAPNLKA 268
Query: 192 IVGSAVAAKLMGTAGGLSALAKMPACNVQLLGAKKKNLAGFSTATSQFRVGYLEQTEIFQ 251
+VG+ +AA+L+ AGGL LA MP+ +Q+LGA+K T + G + Q
Sbjct: 269 LVGAKLAARLISLAGGLRELAMMPSSTIQVLGAEKALFRHLRTGAKPPKHGVIYQYPAIN 328
Query: 252 STPPPLRMRACRLLAAKSTLAARVDSTRGDPSGTAGRSFREEIHKKIE 299
+P R + R LA K +AARVD +G EE+ K++E
Sbjct: 329 RSPWWQRGKIARALAGKLAIAARVDY-------FSGEYIAEELKKELE 369
>pdb|3NVK|A Chain A, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
pdb|3NVK|F Chain F, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
Length = 376
Score = 83.6 bits (205), Expect = 2e-16, Method: Compositional matrix adjust.
Identities = 65/228 (28%), Positives = 104/228 (45%), Gaps = 10/228 (4%)
Query: 74 DIENEIVIIHNFIRDKYRLKFPELESLV-HHPIDYARVVKKIGNEMDLTLVDLEGL-LPS 131
D++ I ++ +R+ Y L FPEL+ L+ HP Y VK +G+ ++ L L L
Sbjct: 150 DVDKVINLLVARLREWYSLHFPELDELLPKHP-QYVAFVKTVGHRDNINEEVLRELGLSE 208
Query: 132 AIIMVVSVTASTTSGKPLPEDVLQKTIXXXXXXXXXXXXXXXXXXFVESRMSYIAPNLSA 191
I + T G + + ++ +++ M +APNL A
Sbjct: 209 EKIKKILEAKEKTMGAWMDQTDIEVVRQLAEEIDRLYQLRKKLEDYIDRAMDDVAPNLKA 268
Query: 192 IVGSAVAAKLMGTAGGLSALAKMPACNVQLLGAKKKNLAGFSTATSQFRVGYLEQTEIFQ 251
+VG+ +AA+L+ AGGL LA MP+ +Q+LGA+K T + G + Q
Sbjct: 269 LVGAKLAARLISLAGGLRELAMMPSSTIQVLGAEKALFRHLRTGAKPPKHGVIYQYPAIN 328
Query: 252 STPPPLRMRACRLLAAKSTLAARVDSTRGDPSGTAGRSFREEIHKKIE 299
+P R + R LA K +AARVD +G EE+ K++E
Sbjct: 329 RSPWWQRGKIARALAGKLAIAARVDY-------FSGEYIAEELKKELE 369
>pdb|3ICX|A Chain A, Crystal Structure Of Sulfolobus Solfataricus Nop5
(135-380)
pdb|3ICX|B Chain B, Crystal Structure Of Sulfolobus Solfataricus Nop5
(135-380)
pdb|3ICX|C Chain C, Crystal Structure Of Sulfolobus Solfataricus Nop5
(135-380)
Length = 255
Score = 82.8 bits (203), Expect = 3e-16, Method: Compositional matrix adjust.
Identities = 69/231 (29%), Positives = 111/231 (48%), Gaps = 4/231 (1%)
Query: 74 DIENEIVIIHNFIRDKYRLKFPELESLVHHPIDYARVVKKIGNEMDLTLVDLEGL-LPSA 132
DI+ I + +R+ Y + FPEL+ L+ +YA +V + G+ LT+ L+ L
Sbjct: 16 DIDKTINLFSERLREWYSIHFPELDKLIEDHEEYATIVSRFGDRGFLTIDSLKELGFNEQ 75
Query: 133 IIMVVSVTASTTSGKPLPEDVLQKTIXXXXXXXXXXXXXXXXXXFVESRMSYIAPNLSAI 192
I + A + G + ED L ++E M +APN++A+
Sbjct: 76 RINRILDAAKKSIGADISEDDLSAMRMIANTILDLYNIRRNLNNYLEGVMKEVAPNVTAL 135
Query: 193 VGSAVAAKLMGTAGGLSALAKMPACNVQLLGAKKKNLAGFSTATSQFRVGYLEQTEIFQS 252
VG A+ A+L+ AG L LAKMPA +Q+LGA+K + + G + Q +
Sbjct: 136 VGPALGARLLSIAGSLDELAKMPASTIQVLGAEKALFRALRSGGRPPKHGIIFQYPAIHT 195
Query: 253 TPPPLRMRACRLLAAKSTLAARVDSTRGDPSGTAGRSFREEIHKKIEKWQE 303
+P R + R LAAK +AARVD+ G G E++ K+I++ +E
Sbjct: 196 SPRWQRGKIARALAAKLAIAARVDAFSGR---FIGDQLNEQLKKRIDEIKE 243
>pdb|3ID5|A Chain A, Crystal Structure Of Sulfolobus Solfataricus CD RNP
ASSEMBLED WITH Nop5, Fibrillarin, L7ae And A Split Half
CD RNA
pdb|3ID5|E Chain E, Crystal Structure Of Sulfolobus Solfataricus CD RNP
ASSEMBLED WITH Nop5, Fibrillarin, L7ae And A Split Half
CD RNA
pdb|3PLA|A Chain A, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
pdb|3PLA|B Chain B, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
pdb|3PLA|K Chain K, Crystal Structure Of A Catalytically Active
Substrate-Bound Box CD Rnp From Sulfolobus Solfataricus
Length = 388
Score = 82.8 bits (203), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 69/231 (29%), Positives = 111/231 (48%), Gaps = 4/231 (1%)
Query: 74 DIENEIVIIHNFIRDKYRLKFPELESLVHHPIDYARVVKKIGNEMDLTLVDLEGL-LPSA 132
DI+ I + +R+ Y + FPEL+ L+ +YA +V + G+ LT+ L+ L
Sbjct: 149 DIDKTINLFSERLREWYSIHFPELDKLIEDHEEYATIVSRFGDRGFLTIDSLKELGFNEQ 208
Query: 133 IIMVVSVTASTTSGKPLPEDVLQKTIXXXXXXXXXXXXXXXXXXFVESRMSYIAPNLSAI 192
I + A + G + ED L ++E M +APN++A+
Sbjct: 209 RINRILDAAKKSIGADISEDDLSAMRMIANTILDLYNIRRNLNNYLEGVMKEVAPNVTAL 268
Query: 193 VGSAVAAKLMGTAGGLSALAKMPACNVQLLGAKKKNLAGFSTATSQFRVGYLEQTEIFQS 252
VG A+ A+L+ AG L LAKMPA +Q+LGA+K + + G + Q +
Sbjct: 269 VGPALGARLLSIAGSLDELAKMPASTIQVLGAEKALFRALRSGGRPPKHGIIFQYPAIHT 328
Query: 253 TPPPLRMRACRLLAAKSTLAARVDSTRGDPSGTAGRSFREEIHKKIEKWQE 303
+P R + R LAAK +AARVD+ G G E++ K+I++ +E
Sbjct: 329 SPRWQRGKIARALAAKLAIAARVDAFSGR---FIGDQLNEQLKKRIDEIKE 376
>pdb|3NVM|A Chain A, Structural Basis For Substrate Placement By An Archaeal
Box CD Ribonucleoprotein Particle
Length = 371
Score = 82.4 bits (202), Expect = 4e-16, Method: Compositional matrix adjust.
Identities = 66/234 (28%), Positives = 108/234 (46%), Gaps = 18/234 (7%)
Query: 70 VLSVDIENEIVIIHNFIRDKYRLKFPELESLV-HHPIDYARVVKKIGNEMDLT---LVDL 125
+ +++ ++I ++ +R+ Y L FPEL+ L+ HP Y VK +G+ ++ L +L
Sbjct: 142 IQAIEALDDINLLVARLREWYSLHFPELDELLPKHP-QYVAFVKTVGHRDNINEEVLREL 200
Query: 126 EGLLPSAIIMVVSVTASTTSGKPLPEDVLQKTIXXXXXXXXXXXXXXXXXXFVESRMSYI 185
GL I ++ T + Q I +++ M +
Sbjct: 201 -GLSEEKIKKILEAKEKTMGAW-----MDQTDIEVVRQLAEEIQLRKKLEDYIDRAMDDV 254
Query: 186 APNLSAIVGSAVAAKLMGTAGGLSALAKMPACNVQLLGAKKKNLAGFSTATSQFRVGYLE 245
APNL A+VG+ +AA+L+ AGGL LA MP+ +Q+LGA+K T + G +
Sbjct: 255 APNLKALVGAKLAARLISLAGGLRELAMMPSSTIQVLGAEKALFRHLRTGAKPPKHGVIY 314
Query: 246 QTEIFQSTPPPLRMRACRLLAAKSTLAARVDSTRGDPSGTAGRSFREEIHKKIE 299
Q +P R + R LA K +AARVD +G EE+ K++E
Sbjct: 315 QYPAINRSPWWQRGKIARALAGKLAIAARVDY-------FSGEYIAEELKKELE 361
>pdb|3GQU|A Chain A, Pyrococcus Horikoshii Nop5 Rna Binding Domain
pdb|3GQX|B Chain B, Pyrococcus Horikoshii Nop5 Rna Binding Domain From A
Twinned Crystal Form
pdb|3GQX|A Chain A, Pyrococcus Horikoshii Nop5 Rna Binding Domain From A
Twinned Crystal Form
Length = 169
Score = 68.9 bits (167), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 41/123 (33%), Positives = 64/123 (52%), Gaps = 7/123 (5%)
Query: 177 FVESRMSYIAPNLSAIVGSAVAAKLMGTAGGLSALAKMPACNVQLLGAKKKNLAGFSTAT 236
+++ M +APNL A+VG+ + A+L+ AGGL LA +P+ +Q+LGA+K T
Sbjct: 25 YIDKAMDDVAPNLKALVGAKLGARLISLAGGLKELAMLPSSTIQVLGAEKALFRHLRTGA 84
Query: 237 SQFRVGYLEQTEIFQSTPPPLRMRACRLLAAKSTLAARVDSTRGDPSGTAGRSFREEIHK 296
+ G + Q +P R + R LA K +AARVD G+ EE+ K
Sbjct: 85 KPPKHGVIYQYPAINRSPWWQRGKIARALAGKLAIAARVDYFSGE-------YIAEELKK 137
Query: 297 KIE 299
++E
Sbjct: 138 ELE 140
>pdb|1NT2|B Chain B, Crystal Structure Of FibrillarinNOP5P COMPLEX
Length = 258
Score = 56.2 bits (134), Expect = 3e-08, Method: Compositional matrix adjust.
Identities = 42/128 (32%), Positives = 68/128 (53%), Gaps = 8/128 (6%)
Query: 178 VESRMSYIAPNLSAIVGSAVAAKLMGTAGGLSALAKMPACNVQLLGAKKKNLAGFSTATS 237
+E M IAPN++ +VG+ VAAKL+ AG + L ++PA +Q++GA+K F+
Sbjct: 131 IEEVMEKIAPNMTELVGAKVAAKLLERAGSMERLVRLPASKIQVIGAEKSLYKAFARMKK 190
Query: 238 QFRVGYLEQTEIF-----QSTPPPLRMRACRLLAAKSTLAARVDSTRGDPSGTAGRSFR- 291
+ + IF ++ P R + R LAAK +AA++D RG+ + S R
Sbjct: 191 GKKAKIPKHGIIFLHPFIRTLPKAKRGKMARFLAAKLAIAAKIDYFRGEIDESLYESIRR 250
Query: 292 --EEIHKK 297
EE+ +K
Sbjct: 251 RYEELRRK 258
>pdb|3ID6|A Chain A, Crystal Structure Of Sulfolobus Solfataricus Nop5 (1-262)
And Fibrillarin Complex
Length = 268
Score = 34.3 bits (77), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 18/55 (32%), Positives = 31/55 (56%)
Query: 74 DIENEIVIIHNFIRDKYRLKFPELESLVHHPIDYARVVKKIGNEMDLTLVDLEGL 128
DI+ I + +R+ Y + FPEL+ L+ +YA +V + G+ LT+ L+ L
Sbjct: 149 DIDKTINLFSERLREWYSIHFPELDKLIEDHEEYATIVSRFGDRGFLTIDSLKEL 203
>pdb|2DAT|A Chain A, Solution Structure Of The Bromodomain Of Human SwiSNF
Related Matrix Associated Actin Dependent Regulator Of
Cromatin Subfamily A Member 2
Length = 123
Score = 30.8 bits (68), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 85 FIRDKYRLKFPELESLVHHPIDYARVVKKIGNEMDLTLVDLE 126
FI+ R + PE L+ P+D+ ++ ++I N +L DLE
Sbjct: 40 FIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLGDLE 81
>pdb|2GRC|A Chain A, 1.5 A Structure Of Bromodomain From Human Brg1 Protein, A
Central Atpase Of SwiSNF REMODELING COMPLEX
Length = 129
Score = 30.4 bits (67), Expect = 2.3, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 85 FIRDKYRLKFPELESLVHHPIDYARVVKKIGNEMDLTLVDLE 126
FI+ R + PE L+ P+D+ ++ ++I N +L DLE
Sbjct: 39 FIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLE 80
>pdb|3UVD|A Chain A, Crystal Structure Of The Bromodomain Of Human
Transcription Activator Brg1 (Smarca4) In Complex With
N-Methyl-2-Pyrrolidone
Length = 124
Score = 30.0 bits (66), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 85 FIRDKYRLKFPELESLVHHPIDYARVVKKIGNEMDLTLVDLE 126
FI+ R + PE L+ P+D+ ++ ++I N +L DLE
Sbjct: 40 FIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLE 81
>pdb|2H60|A Chain A, Solution Structure Of Human Brg1 Bromodomain
Length = 128
Score = 30.0 bits (66), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 85 FIRDKYRLKFPELESLVHHPIDYARVVKKIGNEMDLTLVDLE 126
FI+ R + PE L+ P+D+ ++ ++I N +L DLE
Sbjct: 35 FIQLPSRKELPEYYELIRKPVDFKKIKERIRNHKYRSLNDLE 76
>pdb|1D3Y|A Chain A, Structure Of The Dna Topoisomerase Vi A Subunit
pdb|1D3Y|B Chain B, Structure Of The Dna Topoisomerase Vi A Subunit
Length = 301
Score = 28.9 bits (63), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 22/78 (28%), Positives = 38/78 (48%), Gaps = 21/78 (26%)
Query: 23 VSKLQKSQRFTD------IMQKVEAAL------------QNGSDISNHGMVLEDDPEYQL 64
VSK RF D +++ +EAAL ++GS + ++E+ PE +L
Sbjct: 36 VSKNWGEARFDDQQASNNVIEDLEAALGVLREHLGFIPEEDGSSVVGPLKIIEETPEGEL 95
Query: 65 IVDCNVL---SVDIENEI 79
+VDC L + +I N++
Sbjct: 96 VVDCTKLGTGAYNIPNDV 113
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
0.315 0.131 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 9,706,250
Number of Sequences: 62578
Number of extensions: 314349
Number of successful extensions: 860
Number of sequences better than 100.0: 16
Number of HSP's better than 100.0 without gapping: 15
Number of HSP's successfully gapped in prelim test: 1
Number of HSP's that attempted gapping in prelim test: 834
Number of HSP's gapped (non-prelim): 16
length of query: 453
length of database: 14,973,337
effective HSP length: 102
effective length of query: 351
effective length of database: 8,590,381
effective search space: 3015223731
effective search space used: 3015223731
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 53 (25.0 bits)