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= 035500
(606 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4E54|B Chain B, Damaged Dna Induced Uv-Damaged Dna-Binding Protein
(Uv-Ddb) Dimerization And Its Roles In Chromatinized Dna
Repair
Length = 435
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 53/227 (23%), Positives = 90/227 (39%), Gaps = 46/227 (20%)
Query: 406 RSLSAAKLGSSAWP---------LLHPVSSFSHIYKEGNKRVRPRQFEYNPSNPSLMAFG 456
R+L KLG ++WP LH + S+ + K R ++P++PS +A G
Sbjct: 79 RTLHQHKLGRASWPSVQQGLQQSFLHTLDSYRILQKAAPFDRRATSLAWHPTHPSTVAVG 138
Query: 457 TLDGEVIVINHENGNVACYIPSIGGTNSVLGLCWLKKYPSKLVAGSDSGCVRLFDLNHIP 516
+ G++++ N + +I IG S+ GL + ++ A S G RL D
Sbjct: 139 SKGGDIMLWNFGIKDKPTFIKGIGAGGSITGLKFNPLNTNQFYASSMEGTTRLQDFKGNI 198
Query: 517 PKV-------------ADARGNSSVATYYD---------------------FEQLTSVHV 542
+V D +S + D +++T V +
Sbjct: 199 LRVFASSDTINIWFCSLDVSASSRMVVTGDNVGNVILLNMDGKELWNLRMHKKKVTHVAL 258
Query: 543 NSTDDQFLASG-YSKNVALYDINT--EKPLQLFTDMHREPINVAKFS 586
N D FLA+ + V ++D+ K L++ HR P+N A FS
Sbjct: 259 NPCCDWFLATASVDQTVKIWDLRQVRGKASFLYSLPHRHPVNAACFS 305
>pdb|4E5Z|B Chain B, Damaged Dna Induced Uv-Damaged Dna-Binding Protein
(Uv-Ddb) Dimerization And Its Roles In Chromatinized Dna
Repair
Length = 436
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 53/227 (23%), Positives = 90/227 (39%), Gaps = 46/227 (20%)
Query: 406 RSLSAAKLGSSAWP---------LLHPVSSFSHIYKEGNKRVRPRQFEYNPSNPSLMAFG 456
R+L KLG ++WP LH + S+ + K R ++P++PS +A G
Sbjct: 79 RTLHQHKLGRASWPSVQQGLQQSFLHTLDSYRILQKAAPFDRRATSLAWHPTHPSTVAVG 138
Query: 457 TLDGEVIVINHENGNVACYIPSIGGTNSVLGLCWLKKYPSKLVAGSDSGCVRLFDLNHIP 516
+ G++++ N + +I IG S+ GL + ++ A S G RL D
Sbjct: 139 SKGGDIMLWNFGIKDKPTFIKGIGAGGSITGLKFNPLNTNQFYASSMEGTTRLQDFKGNI 198
Query: 517 PKV-------------ADARGNSSVATYYD---------------------FEQLTSVHV 542
+V D +S + D +++T V +
Sbjct: 199 LRVFASSDTINIWFCSLDVSASSRMVVTGDNVGNVILLNMDGKELWNLRMHKKKVTHVAL 258
Query: 543 NSTDDQFLASG-YSKNVALYDINT--EKPLQLFTDMHREPINVAKFS 586
N D FLA+ + V ++D+ K L++ HR P+N A FS
Sbjct: 259 NPCCDWFLATASVDQTVKIWDLRQVRGKASFLYSLPHRHPVNAACFS 305
>pdb|3EI4|B Chain B, Structure Of The Hsddb1-Hsddb2 Complex
pdb|3EI4|D Chain D, Structure Of The Hsddb1-Hsddb2 Complex
pdb|3EI4|F Chain F, Structure Of The Hsddb1-Hsddb2 Complex
Length = 436
Score = 50.8 bits (120), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 53/227 (23%), Positives = 90/227 (39%), Gaps = 46/227 (20%)
Query: 406 RSLSAAKLGSSAWP---------LLHPVSSFSHIYKEGNKRVRPRQFEYNPSNPSLMAFG 456
R+L KLG ++WP LH + S+ + K R ++P++PS +A G
Sbjct: 80 RTLHQHKLGRASWPSVQQGLQQSFLHTLDSYRILQKAAPFDRRATSLAWHPTHPSTVAVG 139
Query: 457 TLDGEVIVINHENGNVACYIPSIGGTNSVLGLCWLKKYPSKLVAGSDSGCVRLFDLNHIP 516
+ G++++ N + +I IG S+ GL + ++ A S G RL D
Sbjct: 140 SKGGDIMLWNFGIKDKPTFIKGIGAGGSITGLKFNPLNTNQFYASSMEGTTRLQDFKGNI 199
Query: 517 PKV-------------ADARGNSSVATYYD---------------------FEQLTSVHV 542
+V D +S + D +++T V +
Sbjct: 200 LRVFASSDTINIWFCSLDVSASSRMVVTGDNVGNVILLNMDGKELWNLRMHKKKVTHVAL 259
Query: 543 NSTDDQFLASG-YSKNVALYDINT--EKPLQLFTDMHREPINVAKFS 586
N D FLA+ + V ++D+ K L++ HR P+N A FS
Sbjct: 260 NPCCDWFLATASVDQTVKIWDLRQVRGKASFLYSLPHRHPVNAACFS 306
>pdb|1A9N|A Chain A, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
pdb|1A9N|C Chain C, Crystal Structure Of The Spliceosomal U2b''-U2a' Protein
Complex Bound To A Fragment Of U2 Small Nuclear Rna
Length = 176
Score = 36.2 bits (82), Expect = 0.058, Method: Composition-based stats.
Identities = 18/53 (33%), Positives = 32/53 (60%)
Query: 302 ANVKLKKYISHHPSPICFEKHYREYMIASLPQLEVLDNLPIGRLDREIAKSVF 354
A++K Y+ +P+ +KHYR Y+I +PQ+ VLD + +R+ A+ +F
Sbjct: 110 ASLKSLTYLCILRNPVTNKKHYRLYVIYKVPQVRVLDFQKVKLKERQEAEKMF 162
>pdb|3CFV|B Chain B, Structural Basis Of The Interaction Of Rbap46RBAP48 WITH
Histone H4
pdb|3CFV|A Chain A, Structural Basis Of The Interaction Of Rbap46RBAP48 WITH
Histone H4
Length = 414
Score = 33.5 bits (75), Expect = 0.32, Method: Compositional matrix adjust.
Identities = 43/163 (26%), Positives = 67/163 (41%), Gaps = 27/163 (16%)
Query: 445 YNPSNPSLMAFGTLDGEVIVINHE--------NGNVACYIPSIGGTNSVLGLCWLKKYPS 496
Y P NP ++A T +V+V ++ +G + G GL W
Sbjct: 134 YXPQNPHIIATKTPSSDVLVFDYTKHPAKPDPSGECNPDLRLRGHQKEGYGLSWNSNLSG 193
Query: 497 KLVAGSDSGCVRLFDLNHIPP--KVADAR----GNSSVATYYDFEQL-TSVHVNSTDDQF 549
L++ SD V L+D+N P K+ DA+ G+S+V + L S+ + DDQ
Sbjct: 194 HLLSASDDHTVCLWDINAGPKEGKIVDAKAIFTGHSAVVEDVAWHLLHESLFGSVADDQK 253
Query: 550 LASGYSKNVALYDI---NTEKPLQLFTDMHREPINVAKFSHHS 589
L ++D T KP L D H +N F+ +S
Sbjct: 254 L--------XIWDTRSNTTSKPSHL-VDAHTAEVNCLSFNPYS 287
>pdb|3CFS|B Chain B, Structural Basis Of The Interaction Of Rbap46RBAP48 WITH
Histone H4
Length = 414
Score = 33.1 bits (74), Expect = 0.45, Method: Compositional matrix adjust.
Identities = 43/163 (26%), Positives = 67/163 (41%), Gaps = 27/163 (16%)
Query: 445 YNPSNPSLMAFGTLDGEVIVINHE--------NGNVACYIPSIGGTNSVLGLCWLKKYPS 496
Y P NP ++A T +V+V ++ +G + G GL W
Sbjct: 134 YMPQNPHIIATKTPSSDVLVFDYTKHPAKPDPSGECNPDLRLRGHQKEGYGLSWNSNLSG 193
Query: 497 KLVAGSDSGCVRLFDLNHIPP--KVADAR----GNSSVATYYDFEQL-TSVHVNSTDDQF 549
L++ SD V L+D+N P K+ DA+ G+S+V + L S+ + DDQ
Sbjct: 194 HLLSASDDHTVCLWDINAGPKEGKIVDAKAIFTGHSAVVEDVAWHLLHESLFGSVADDQK 253
Query: 550 LASGYSKNVALYDI---NTEKPLQLFTDMHREPINVAKFSHHS 589
L ++D T KP L D H +N F+ +S
Sbjct: 254 L--------MIWDTRSNTTSKPSHL-VDAHTAEVNCLSFNPYS 287
>pdb|3FMO|A Chain A, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
pdb|3FMP|A Chain A, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
pdb|3FMP|C Chain C, Crystal Structure Of The Nucleoporin Nup214 In Complex
With The Dead- Box Helicase Ddx19
Length = 450
Score = 33.1 bits (74), Expect = 0.46, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 443 FEYNPSNPSLMAFGTLDGEVIVIN-HENGNVACYIPSIGGTNSVLGLCWLKKYPSKLVAG 501
++NP+ PS++A DG + V+ E V +PS T +V +CW K +L G
Sbjct: 155 MKWNPTVPSMVAVCLADGSIAVLQVTETVKVCATLPS---TVAVTSVCWSPKG-KQLAVG 210
Query: 502 SDSGCV 507
+G V
Sbjct: 211 KQNGTV 216
>pdb|2OIT|A Chain A, Crystal Structure Of The N-Terminal Domain Of The Human
Proto-Oncogene Nup214CAN
Length = 434
Score = 33.1 bits (74), Expect = 0.51, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 443 FEYNPSNPSLMAFGTLDGEVIVIN-HENGNVACYIPSIGGTNSVLGLCWLKKYPSKLVAG 501
++NP+ PS++A DG + V+ E V +PS T +V +CW K +L G
Sbjct: 155 MKWNPTVPSMVAVCLADGSIAVLQVTETVKVCATLPS---TVAVTSVCWSPKG-KQLAVG 210
Query: 502 SDSGCV 507
+G V
Sbjct: 211 KQNGTV 216
>pdb|3FHC|A Chain A, Crystal Structure Of Human Dbp5 In Complex With Nup214
Length = 405
Score = 32.7 bits (73), Expect = 0.54, Method: Compositional matrix adjust.
Identities = 21/66 (31%), Positives = 33/66 (50%), Gaps = 5/66 (7%)
Query: 443 FEYNPSNPSLMAFGTLDGEVIVIN-HENGNVACYIPSIGGTNSVLGLCWLKKYPSKLVAG 501
++NP+ PS++A DG + V+ E V +PS T +V +CW K +L G
Sbjct: 155 MKWNPTVPSMVAVCLADGSIAVLQVTETVKVCATLPS---TVAVTSVCWSPKG-KQLAVG 210
Query: 502 SDSGCV 507
+G V
Sbjct: 211 KQNGTV 216
>pdb|3GFC|A Chain A, Crystal Structure Of Histone-Binding Protein Rbbp4
pdb|2XU7|A Chain A, Structural Basis For Rbap48 Binding To Fog-1
pdb|2XU7|B Chain B, Structural Basis For Rbap48 Binding To Fog-1
Length = 425
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 41/163 (25%), Positives = 68/163 (41%), Gaps = 27/163 (16%)
Query: 445 YNPSNPSLMAFGTLDGEVIVINHE--------NGNVACYIPSIGGTNSVLGLCWLKKYPS 496
Y P NP ++A T +V+V ++ +G + G GL W
Sbjct: 132 YMPQNPCIIATKTPSSDVLVFDYTKHPSKPDPSGECNPDLRLRGHQKEGYGLSWNPNLSG 191
Query: 497 KLVAGSDSGCVRLFDLNHIPP--KVADAR----GNSSVATYYDFEQL-TSVHVNSTDDQF 549
L++ SD + L+D++ +P KV DA+ G+++V + L S+ + DDQ
Sbjct: 192 HLLSASDDHTICLWDISAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQK 251
Query: 550 LASGYSKNVALYDI---NTEKPLQLFTDMHREPINVAKFSHHS 589
L ++D NT KP D H +N F+ +S
Sbjct: 252 L--------MIWDTRSNNTSKPSH-SVDAHTAEVNCLSFNPYS 285
>pdb|2WLI|A Chain A, Potassium Channel From Magnetospirillum Magnetotacticum
Length = 301
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 15/57 (26%), Positives = 30/57 (52%)
Query: 389 SSKPKQPNIHRTQHFFSRSLSAAKLGSSAWPLLHPVSSFSHIYKEGNKRVRPRQFEY 445
S ++ + R H +R+ S + + S +W ++HP+ S IY E ++ +R E+
Sbjct: 183 SEISQEGMVFRRFHDLTRTRSRSPIFSLSWTVMHPIDHHSPIYGETDETLRNSHSEF 239
>pdb|3PFY|A Chain A, The Catalytic Domain Of Human Otud5
Length = 185
Score = 30.0 bits (66), Expect = 4.4, Method: Composition-based stats.
Identities = 18/57 (31%), Positives = 31/57 (54%), Gaps = 4/57 (7%)
Query: 530 TYYDFEQLTSVHVNSTDDQFLASGYSKNVALYDINTEKPLQLFTDMHR---EPINVA 583
TY + ++ + H N + Q A Y++ V +Y +TE P+ F +H+ EPI V+
Sbjct: 114 TYINRKRKNNCHGNHIEXQAXAEXYNRPVEVYQYSTE-PINTFHGIHQNEDEPIRVS 169
>pdb|2XYI|A Chain A, Crystal Structure Of Nurf55 In Complex With A H4 Peptide
Length = 430
Score = 29.3 bits (64), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 66/160 (41%), Gaps = 21/160 (13%)
Query: 445 YNPSNPSLMAFGTLDGEVIVINHE--------NGNVACYIPSIGGTNSVLGLCWLKKYPS 496
Y P N ++A T +V+V ++ +G + G GL W
Sbjct: 136 YMPQNACVIATKTPSSDVLVFDYTKHPSKPEPSGECQPDLRLRGHQKEGYGLSWNPNLNG 195
Query: 497 KLVAGSDSGCVRLFDLNHIPP--KVADAR----GNSSVATYYDFEQL-TSVHVNSTDDQF 549
L++ SD + L+D+N P +V DA+ G+++V + L S+ + DDQ
Sbjct: 196 YLLSASDDHTICLWDINATPKEHRVIDAKNIFTGHTAVVEDVAWHLLHESLFGSVADDQK 255
Query: 550 LASGYSKNVALYDINTEKPLQLFTDMHREPINVAKFSHHS 589
L ++N NT KP D H +N F+ +S
Sbjct: 256 LMIWDTRNN-----NTSKPSHT-VDAHTAEVNCLSFNPYS 289
>pdb|3C99|A Chain A, Structural Basis Of Histone H4 Recognition By P55
pdb|3C9C|A Chain A, Structural Basis Of Histone H4 Recognition By P55
Length = 432
Score = 28.9 bits (63), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 66/160 (41%), Gaps = 21/160 (13%)
Query: 445 YNPSNPSLMAFGTLDGEVIVINHE--------NGNVACYIPSIGGTNSVLGLCWLKKYPS 496
Y P N ++A T +V+V ++ +G + G GL W
Sbjct: 138 YMPQNACVIATKTPSSDVLVFDYTKHPSKPEPSGECQPDLRLRGHQKEGYGLSWNPNLNG 197
Query: 497 KLVAGSDSGCVRLFDLNHIPP--KVADAR----GNSSVATYYDFEQL-TSVHVNSTDDQF 549
L++ SD + L+D+N P +V DA+ G+++V + L S+ + DDQ
Sbjct: 198 YLLSASDDHTICLWDINATPKEHRVIDAKNIFTGHTAVVEDVAWHLLHESLFGSVADDQK 257
Query: 550 LASGYSKNVALYDINTEKPLQLFTDMHREPINVAKFSHHS 589
L ++N NT KP D H +N F+ +S
Sbjct: 258 LMIWDTRNN-----NTSKPSHT-VDAHTAEVNCLSFNPYS 291
>pdb|2YBA|A Chain A, Crystal Structure Of Nurf55 In Complex With Histone H3
pdb|2YBA|B Chain B, Crystal Structure Of Nurf55 In Complex With Histone H3
pdb|2YB8|B Chain B, Crystal Structure Of Nurf55 In Complex With Su(Z)12
Length = 422
Score = 28.9 bits (63), Expect = 8.4, Method: Compositional matrix adjust.
Identities = 40/160 (25%), Positives = 66/160 (41%), Gaps = 21/160 (13%)
Query: 445 YNPSNPSLMAFGTLDGEVIVINHE--------NGNVACYIPSIGGTNSVLGLCWLKKYPS 496
Y P N ++A T +V+V ++ +G + G GL W
Sbjct: 140 YMPQNACVIATKTPSSDVLVFDYTKHPSKPEPSGECQPDLRLRGHQKEGYGLSWNPNLNG 199
Query: 497 KLVAGSDSGCVRLFDLNHIPP--KVADAR----GNSSVATYYDFEQL-TSVHVNSTDDQF 549
L++ SD + L+D+N P +V DA+ G+++V + L S+ + DDQ
Sbjct: 200 YLLSASDDHTICLWDINATPKEHRVIDAKNIFTGHTAVVEDVAWHLLHESLFGSVADDQK 259
Query: 550 LASGYSKNVALYDINTEKPLQLFTDMHREPINVAKFSHHS 589
L ++N NT KP D H +N F+ +S
Sbjct: 260 LMIWDTRNN-----NTSKPSHT-VDAHTAEVNCLSFNPYS 293
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 0.404
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 17,517,660
Number of Sequences: 62578
Number of extensions: 722447
Number of successful extensions: 1754
Number of sequences better than 100.0: 26
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 16
Number of HSP's that attempted gapping in prelim test: 1731
Number of HSP's gapped (non-prelim): 33
length of query: 606
length of database: 14,973,337
effective HSP length: 104
effective length of query: 502
effective length of database: 8,465,225
effective search space: 4249542950
effective search space used: 4249542950
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: 54 (25.4 bits)