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= 002269
(944 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2Q5X|A Chain A, Crystal Structure Of The C-Terminal Domain Of Hnup98
Length = 155
Score = 99.0 bits (245), Expect = 1e-20, Method: Compositional matrix adjust.
Identities = 57/153 (37%), Positives = 89/153 (58%), Gaps = 8/153 (5%)
Query: 43 VLCSPDYYTEPLLNDLGKREVIDPGYSSRVPDFTVGRLGYGYVKFLGNTDVRWLDLDQIV 102
+L YYT P ++DL K + + V DFT+GR GYG + F G+ ++ L+LD IV
Sbjct: 3 ILTKVGYYTIPSMDDLAK--ITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIV 60
Query: 103 KFGRHEIVVYEDESSKPEVGQGLNKAAEVTL---FLQGRYLSLKLKEGD---SDDFVKKM 156
R E+VVY D++ KP VG+GLN+ AEVTL + + +K D ++ ++
Sbjct: 61 HIRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRL 120
Query: 157 KERTERQGARFVSFDPVSGEWKFLVVHFSRFGL 189
+ + +QGA+F + P +G W F V HF+++GL
Sbjct: 121 EAVSRKQGAQFKEYRPETGSWVFKVSHFAKYGL 153
>pdb|1KO6|A Chain A, Crystal Structure Of C-Terminal Autoproteolytic Domain Of
Nucleoporin Nup98
pdb|1KO6|C Chain C, Crystal Structure Of C-Terminal Autoproteolytic Domain Of
Nucleoporin Nup98
Length = 187
Score = 94.4 bits (233), Expect = 3e-19, Method: Compositional matrix adjust.
Identities = 56/148 (37%), Positives = 86/148 (58%), Gaps = 8/148 (5%)
Query: 43 VLCSPDYYTEPLLNDLGKREVIDPGYSSRVPDFTVGRLGYGYVKFLGNTDVRWLDLDQIV 102
+L YYT P ++DL K + + V DFT+GR GYG + F G+ ++ L+LD IV
Sbjct: 42 ILTKVGYYTIPSMDDLAK--ITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIV 99
Query: 103 KFGRHEIVVYEDESSKPEVGQGLNKAAEVTL---FLQGRYLSLKLKEGD--SD-DFVKKM 156
R E+VVY D++ KP VG+GLN+ AEVTL + + +K D +D ++ ++
Sbjct: 100 HIRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRL 159
Query: 157 KERTERQGARFVSFDPVSGEWKFLVVHF 184
+ + +QGA+F + P +G W F V HF
Sbjct: 160 EAVSRKQGAQFKEYRPETGSWVFKVSHF 187
>pdb|2Q5Y|A Chain A, Crystal Structure Of The C-Terminal Domain Of Hnup98
pdb|2Q5Y|C Chain C, Crystal Structure Of The C-Terminal Domain Of Hnup98
Length = 152
Score = 93.2 bits (230), Expect = 6e-19, Method: Compositional matrix adjust.
Identities = 55/148 (37%), Positives = 84/148 (56%), Gaps = 8/148 (5%)
Query: 43 VLCSPDYYTEPLLNDLGKREVIDPGYSSRVPDFTVGRLGYGYVKFLGNTDVRWLDLDQIV 102
+L YYT P ++DL K + + V DFT+GR GYG + F G+ ++ L+LD IV
Sbjct: 7 ILTKVGYYTIPSMDDLAK--ITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIV 64
Query: 103 KFGRHEIVVYEDESSKPEVGQGLNKAAEVTL---FLQGRYLSLKLKEGD---SDDFVKKM 156
R E+VVY D++ KP VG+GLN+ AEVTL + + +K D ++ ++
Sbjct: 65 HIRRKEVVVYLDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRL 124
Query: 157 KERTERQGARFVSFDPVSGEWKFLVVHF 184
+ + +QGA+F + P +G W F V HF
Sbjct: 125 EAVSRKQGAQFKEYRPETGSWVFKVSHF 152
>pdb|3TKN|C Chain C, Structure Of The Nup82-Nup159-Nup98 Heterotrimer
pdb|3TKN|F Chain F, Structure Of The Nup82-Nup159-Nup98 Heterotrimer
pdb|3TKN|I Chain I, Structure Of The Nup82-Nup159-Nup98 Heterotrimer
Length = 152
Score = 93.2 bits (230), Expect = 7e-19, Method: Compositional matrix adjust.
Identities = 55/148 (37%), Positives = 84/148 (56%), Gaps = 8/148 (5%)
Query: 43 VLCSPDYYTEPLLNDLGKREVIDPGYSSRVPDFTVGRLGYGYVKFLGNTDVRWLDLDQIV 102
VL YYT P ++DL K + + V DFT+GR GYG + F G+ ++ L+LD IV
Sbjct: 7 VLTKVGYYTIPSMDDLAK--ITNEKGECIVSDFTIGRKGYGSIYFEGDVNLTNLNLDDIV 64
Query: 103 KFGRHEIVVYEDESSKPEVGQGLNKAAEVTL---FLQGRYLSLKLKEGD---SDDFVKKM 156
R E++VY D++ KP VG+GLN+ AEVTL + + +K D ++ ++
Sbjct: 65 HIRRKEVIVYVDDNQKPPVGEGLNRKAEVTLDGVWPTDKTSRCLIKSPDRLADINYEGRL 124
Query: 157 KERTERQGARFVSFDPVSGEWKFLVVHF 184
+ + +QGA+F + P +G W F V HF
Sbjct: 125 EAVSRKQGAQFKEYRPETGSWVFKVSHF 152
>pdb|3KEP|A Chain A, Crystal Structure Of The Autoproteolytic Domain From The
Nuclear Pore Complex Component Nup145 From Saccharomyces
Cerevisiae
pdb|3KEP|B Chain B, Crystal Structure Of The Autoproteolytic Domain From The
Nuclear Pore Complex Component Nup145 From Saccharomyces
Cerevisiae
pdb|3KES|A Chain A, Crystal Structure Of The Autoproteolytic Domain From The
Nuclear Pore Complex Component Nup145 From Saccharomyces
Cerevisiae In The Hexagonal, P61 Space Group
pdb|3KES|B Chain B, Crystal Structure Of The Autoproteolytic Domain From The
Nuclear Pore Complex Component Nup145 From Saccharomyces
Cerevisiae In The Hexagonal, P61 Space Group
Length = 174
Score = 51.6 bits (122), Expect = 2e-06, Method: Compositional matrix adjust.
Identities = 38/128 (29%), Positives = 58/128 (45%), Gaps = 18/128 (14%)
Query: 72 VPDFTVGRLGYGYVKFLGNTDVRWLD-------LDQIVKFGRHEIV-VYEDESSKPEVGQ 123
V +F +GR GYG + F + D+ +IV F + V VY DE++KP +G
Sbjct: 42 VSNFVIGRRGYGCITFQHDVDLTAFTKSFREELFGKIVIFRSSKTVEVYPDEATKPXIGH 101
Query: 124 GLNKAAEVTL-------FLQGRYLSLKLKEGDSDDFVKKMKERTERQGARFVSFDPVSGE 176
GLN A +TL + K + F +K++ E ++S++P G
Sbjct: 102 GLNVPAIITLENVYPVDKKTKKPXKDTTKFAEFQVFDRKLRSXRE---XNYISYNPFGGT 158
Query: 177 WKFLVVHF 184
W F V HF
Sbjct: 159 WTFKVNHF 166
>pdb|3PBP|B Chain B, Structure Of The Yeast Heterotrimeric Nup82-Nup159-Nup116
Nucleoporin Complex
pdb|3PBP|E Chain E, Structure Of The Yeast Heterotrimeric Nup82-Nup159-Nup116
Nucleoporin Complex
pdb|3PBP|H Chain H, Structure Of The Yeast Heterotrimeric Nup82-Nup159-Nup116
Nucleoporin Complex
pdb|3PBP|K Chain K, Structure Of The Yeast Heterotrimeric Nup82-Nup159-Nup116
Nucleoporin Complex
Length = 148
Score = 51.6 bits (122), Expect = 2e-06, Method: Composition-based stats.
Identities = 38/143 (26%), Positives = 68/143 (47%), Gaps = 10/143 (6%)
Query: 48 DYYTEPLLNDLGKREVIDPGYSSRVPDFTVGRLGYGYVKFLGNTDVRWLDLDQ----IVK 103
+YY P L+ L ++ +VP VG YG ++FL D+ + L I+
Sbjct: 4 NYYISPSLDTLSSYSLLQ---LRKVPHLVVGHKSYGKIEFLEPVDLAGIPLTSLGGVIIT 60
Query: 104 FGRHEIVVYEDESSKPEVGQGLNKAAEVTLF--LQGRYLSLKLKEGDSDDFVKKMKERTE 161
F ++Y + ++P+ G+G+N A +T F + K + + VK+ ER +
Sbjct: 61 FEPKTCIIYANLPNRPKRGEGINVRARITCFNCYPVDKSTRKPIKDPNHQLVKRHIERLK 120
Query: 162 RQ-GARFVSFDPVSGEWKFLVVH 183
+ ++F S+D SG + F+V H
Sbjct: 121 KNPNSKFESYDADSGTYVFIVNH 143
>pdb|2AIV|A Chain A, Multiple Conformations In The Ligand-Binding Site Of The
Yeast Nuclear Pore Targeting Domain Of Nup116p
Length = 149
Score = 51.6 bits (122), Expect = 2e-06, Method: Composition-based stats.
Identities = 38/143 (26%), Positives = 68/143 (47%), Gaps = 10/143 (6%)
Query: 48 DYYTEPLLNDLGKREVIDPGYSSRVPDFTVGRLGYGYVKFLGNTDVRWLDLDQ----IVK 103
+YY P L+ L ++ +VP VG YG ++FL D+ + L I+
Sbjct: 5 NYYISPSLDTLSSYSLLQ---LRKVPHLVVGHKSYGKIEFLEPVDLAGIPLTSLGGVIIT 61
Query: 104 FGRHEIVVYEDESSKPEVGQGLNKAAEVTLF--LQGRYLSLKLKEGDSDDFVKKMKERTE 161
F ++Y + ++P+ G+G+N A +T F + K + + VK+ ER +
Sbjct: 62 FEPKTCIIYANLPNRPKRGEGINVRARITCFNCYPVDKSTRKPIKDPNHQLVKRHIERLK 121
Query: 162 RQ-GARFVSFDPVSGEWKFLVVH 183
+ ++F S+D SG + F+V H
Sbjct: 122 KNPNSKFESYDADSGTYVFIVNH 144
>pdb|3NF5|A Chain A, Crystal Structure Of The C-Terminal Domain Of Nuclear Pore
Complex Component Nup116 From Candida Glabrata
pdb|3NF5|B Chain B, Crystal Structure Of The C-Terminal Domain Of Nuclear Pore
Complex Component Nup116 From Candida Glabrata
Length = 164
Score = 47.0 bits (110), Expect = 5e-05, Method: Composition-based stats.
Identities = 41/148 (27%), Positives = 67/148 (45%), Gaps = 20/148 (13%)
Query: 48 DYYTEPLLNDLG---KREVIDPGYSSRVPDFTVGRLGYGYVKFLGNTDVRWLDL----DQ 100
+YY P L+ L K E+ +V + VG YG ++FL D+ + L D
Sbjct: 15 NYYISPSLDTLATLSKYEI------QKVENLVVGNKQYGKIEFLDPVDLSDIPLGSICDD 68
Query: 101 IVKFGRHEIVVYEDESSKPEVGQGLNKAAEVTLFLQGRYLSLKLKEGDSDDFVKKMKERT 160
+V F +++Y + ++ PE G+GLN A ++ + Y K D ++ ER
Sbjct: 69 LVVFQPXSVLLYNNSTNVPEKGKGLNVRARISCY--NCYPLDKSTRKPIKDPNHRIXERY 126
Query: 161 ERQGAR-----FVSFDPVSGEWKFLVVH 183
+ + F S+DP SG + F V H
Sbjct: 127 SEKLKKIPHTHFESYDPASGTYCFTVDH 154
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
0.318 0.135 0.402
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 29,424,563
Number of Sequences: 62578
Number of extensions: 1298630
Number of successful extensions: 2620
Number of sequences better than 100.0: 9
Number of HSP's better than 100.0 without gapping: 5
Number of HSP's successfully gapped in prelim test: 4
Number of HSP's that attempted gapping in prelim test: 2600
Number of HSP's gapped (non-prelim): 9
length of query: 944
length of database: 14,973,337
effective HSP length: 108
effective length of query: 836
effective length of database: 8,214,913
effective search space: 6867667268
effective search space used: 6867667268
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 56 (26.2 bits)