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= 019258
(343 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4I79|A Chain A, Crystal Structure Of Human Nup43
pdb|4I79|B Chain B, Crystal Structure Of Human Nup43
Length = 399
Score = 61.2 bits (147), Expect = 7e-10, Method: Compositional matrix adjust.
Identities = 62/228 (27%), Positives = 89/228 (39%), Gaps = 40/228 (17%)
Query: 82 QSLVAASTLSGSLHVLSSAMQVLLSVDEN---SGFHVGP---------ISGVDLTGSECV 129
+ +VAAS+ L LSV++ + +H GP +GV E V
Sbjct: 105 ERIVAASSTGCVTVFLHHPNNQTLSVNQQWTTAHYHTGPGSPSYSSAPCTGVVCNNPEIV 164
Query: 130 SVGEDGRVNLVSVIGGGEFKRVYDGNGLVGFNCVKWASPTEFVTGGFGYGLQWWDLRRAG 189
+VGEDGR+NL E R D + V + E +T L+ WD R+ G
Sbjct: 165 TVGEDGRINLFRA-DHKEAVRTIDNADSSTLHAVTFLRTPEILTVNSIGQLKIWDFRQQG 223
Query: 190 SG-GPVLQFKGNFGSQGKASGMIHSVDIHPSRKHTCLAGGSSGTVFAWDLRWQQQSIVLS 248
+ +L G+ +H VD HP+++H GG G + WD+R
Sbjct: 224 NEPSQILSLTGD-------RVPLHCVDRHPNQQHVVATGGQDGMLSIWDVR--------- 267
Query: 249 GVGTGEAVTHSLSESEVWEVQYDCHTKSSNISSSRVLPAMFCSEDGIL 296
GT E+E+WEV + S CSEDG L
Sbjct: 268 -QGTMPVSLLKAHEAEMWEVHF---------HPSNPEHLFTCSEDGSL 305
>pdb|4A08|B Chain B, Structure Of Hsddb1-Drddb2 Bound To A 13 Bp Cpd-Duplex (
Purine At D-1 Position) At 3.0 A Resolution (Cpd 1)
pdb|4A09|B Chain B, Structure Of Hsddb1-Drddb2 Bound To A 15 Bp Cpd-Duplex
(Purine At D-1 Position) At 3.1 A Resolution (Cpd 2)
pdb|4A0A|B Chain B, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Cpd-Duplex (
Pyrimidine At D-1 Position) At 3.6 A Resolution (Cpd 3)
pdb|4A0B|B Chain B, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Cpd-Duplex (
Pyrimidine At D-1 Position) At 3.8 A Resolution (Cpd 4)
pdb|4A0B|D Chain D, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Cpd-Duplex (
Pyrimidine At D-1 Position) At 3.8 A Resolution (Cpd 4)
pdb|4A0K|D Chain D, Structure Of Ddb1-Ddb2-Cul4a-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
pdb|4A0L|B Chain B, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
pdb|4A0L|D Chain D, Structure Of Ddb1-Ddb2-Cul4b-Rbx1 Bound To A 12 Bp Abasic
Site Containing Dna-Duplex
Length = 382
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 211 IHSVDIHPSRKHTCLAGGSSGTVFAWDLRWQQQSIVLSGVGTGEAVT 257
+ S++ HP+ T G G + WD Q ++ + G+G G+A+T
Sbjct: 75 VTSLEWHPTHPTTVAVGSKGGDIILWDYDVQNKTSFIQGMGPGDAIT 121
>pdb|3EI1|B Chain B, Structure Of Hsddb1-Drddb2 Bound To A 14 Bp 6-4
Photoproduct Containing Dna-Duplex
pdb|3EI2|B Chain B, Structure Of Hsddb1-Drddb2 Bound To A 16 Bp Abasic Site
Containing Dna-Duplex
pdb|3EI3|B Chain B, Structure Of The Hsddb1-Drddb2 Complex
Length = 383
Score = 33.5 bits (75), Expect = 0.16, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 25/47 (53%)
Query: 211 IHSVDIHPSRKHTCLAGGSSGTVFAWDLRWQQQSIVLSGVGTGEAVT 257
+ S++ HP+ T G G + WD Q ++ + G+G G+A+T
Sbjct: 76 VTSLEWHPTHPTTVAVGSKGGDIILWDYDVQNKTSFIQGMGPGDAIT 122
>pdb|2PM9|A Chain A, Crystal Structure Of Yeast Sec1331 VERTEX ELEMENT OF THE
Copii Vesicular Coat
Length = 416
Score = 30.4 bits (67), Expect = 1.3, Method: Compositional matrix adjust.
Identities = 22/122 (18%), Positives = 48/122 (39%), Gaps = 6/122 (4%)
Query: 118 ISGVDLTGSECVSVGEDGRVNLVSVIGGGEFKRVYDGNGLVGFNCVKWASPTEFVTGGFG 177
+SG ++G+ + D + L S++ K + FN + W+ + + G
Sbjct: 29 VSGT-VSGTVDANFSTDSSLELWSLLAADSEKPIASLQVDSKFNDLDWSHNNKIIAGALD 87
Query: 178 YGLQWWDLRRAGSGGPVLQFKGNFGSQGKASGMIHSVDIHPSRKHTCLAGGSSGTVFAWD 237
G +L + F + S + +V + + + +GG++G +F WD
Sbjct: 88 NGSL--ELYSTNEANNAINSMARFSNH---SSSVKTVKFNAKQDNVLASGGNNGEIFIWD 142
Query: 238 LR 239
+
Sbjct: 143 MN 144
>pdb|4A11|B Chain B, Structure Of The Hsddb1-Hscsa Complex
Length = 408
Score = 30.0 bits (66), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 20/56 (35%), Positives = 28/56 (50%), Gaps = 2/56 (3%)
Query: 185 LRRAGSGGPVLQFKGNFGSQGKA--SGMIHSVDIHPSRKHTCLAGGSSGTVFAWDL 238
LRRA S VL + N + G I+++DI P L+GGS G + +DL
Sbjct: 18 LRRAESTRRVLGLELNKDRDVERIHGGGINTLDIEPVEGRYMLSGGSDGVIVLYDL 73
>pdb|3F3F|A Chain A, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21
pdb|3F3F|B Chain B, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21
pdb|3F3F|E Chain E, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21
pdb|3F3F|F Chain F, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21
pdb|3F3G|A Chain A, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P212121
pdb|3F3G|B Chain B, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P212121
pdb|3F3G|E Chain E, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P212121
pdb|3F3G|F Chain F, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P212121
Length = 351
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 97 LSSAMQV-LLSVDENSGFHVGPISGVDLTGSECVSVGEDGRVNLVSVIGGGEFK 149
L S +QV LLS ++ V +S +LTG+ S G+DG+V L EFK
Sbjct: 290 LQSNLQVELLSEHDDHNGEVWSVSW-NLTGTILSSAGDDGKVRLWKATYSNEFK 342
>pdb|3F3P|A Chain A, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21212
pdb|3F3P|B Chain B, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21212
pdb|3F3P|E Chain E, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21212
pdb|3F3P|F Chain F, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21212
pdb|3F3P|I Chain I, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21212
pdb|3F3P|J Chain J, Crystal Structure Of The Nucleoporin Pair Nup85-Seh1,
Space Group P21212
Length = 351
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 97 LSSAMQV-LLSVDENSGFHVGPISGVDLTGSECVSVGEDGRVNLVSVIGGGEFK 149
L S +QV LLS ++ V +S +LTG+ S G+DG+V L EFK
Sbjct: 290 LQSNLQVELLSEHDDHNGEVWSVSW-NLTGTILSSAGDDGKVRLWKATYSNEFK 342
>pdb|3EWE|A Chain A, Crystal Structure Of The Nup85SEH1 COMPLEX
pdb|3EWE|C Chain C, Crystal Structure Of The Nup85SEH1 COMPLEX
Length = 349
Score = 28.5 bits (62), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 2/54 (3%)
Query: 97 LSSAMQV-LLSVDENSGFHVGPISGVDLTGSECVSVGEDGRVNLVSVIGGGEFK 149
L S +QV LLS ++ V +S +LTG+ S G+DG+V L EFK
Sbjct: 288 LQSNLQVELLSEHDDHNGEVWSVSW-NLTGTILSSAGDDGKVRLWKATYSNEFK 340
>pdb|2IWF|A Chain A, Resting Form Of Pink Nitrous Oxide Reductase From
Achromobacter Cycloclastes
pdb|2IWF|B Chain B, Resting Form Of Pink Nitrous Oxide Reductase From
Achromobacter Cycloclastes
pdb|2IWK|A Chain A, Inhibitor-Bound Form Of Nitrous Oxide Reductase From
Achromobacter Cycloclastes At 1.7 Angstrom Resolution
pdb|2IWK|B Chain B, Inhibitor-Bound Form Of Nitrous Oxide Reductase From
Achromobacter Cycloclastes At 1.7 Angstrom Resolution
Length = 642
Score = 28.1 bits (61), Expect = 6.5, Method: Compositional matrix adjust.
Identities = 12/27 (44%), Positives = 16/27 (59%)
Query: 212 HSVDIHPSRKHTCLAGGSSGTVFAWDL 238
H ++ P RKH C+AG S TV D+
Sbjct: 327 HGCNMAPDRKHLCVAGKLSPTVTVLDV 353
>pdb|4G56|B Chain B, Crystal Structure Of Full Length Prmt5/mep50 Complexes
From Xenopus Laevis
pdb|4G56|D Chain D, Crystal Structure Of Full Length Prmt5/mep50 Complexes
From Xenopus Laevis
Length = 357
Score = 28.1 bits (61), Expect = 7.5, Method: Compositional matrix adjust.
Identities = 18/71 (25%), Positives = 29/71 (40%), Gaps = 10/71 (14%)
Query: 169 TEFVTGGFGYGLQWWDLRRAGSGGPVLQFKGNFGSQGKASGMIHSVDIHPSRKHTCLAGG 228
T+ V+GG + ++ WDL + K S S ++ V P + L+ G
Sbjct: 152 TQAVSGGKDFSVKVWDLSQ----------KAVLKSYNAHSSEVNCVAACPGKDTIFLSCG 201
Query: 229 SSGTVFAWDLR 239
G + WD R
Sbjct: 202 EDGRILLWDTR 212
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
0.316 0.132 0.407
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,198,672
Number of Sequences: 62578
Number of extensions: 488792
Number of successful extensions: 1180
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 12
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1159
Number of HSP's gapped (non-prelim): 30
length of query: 343
length of database: 14,973,337
effective HSP length: 100
effective length of query: 243
effective length of database: 8,715,537
effective search space: 2117875491
effective search space used: 2117875491
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: 52 (24.6 bits)