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= 040681
(594 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4HXT|A Chain A, Crystal Structure Of Engineered Protein. Northeast
Structural Genomics Consortium Target Or329
Length = 252
Score = 38.1 bits (87), Expect = 0.015, Method: Compositional matrix adjust.
Identities = 33/95 (34%), Positives = 48/95 (50%), Gaps = 2/95 (2%)
Query: 175 EAAIELASLAKDNDRNKKIIVEEGGVPPLLKLLKXXXXXXXXXXXXXXLYNIAND-QERV 233
EAA LA++A D K IV+ GGV L+KLL L NIA+ E +
Sbjct: 63 EAARALANIASGPDEAIKAIVDAGGVEVLVKLL-TSTDSEVQKEAARALANIASGPDEAI 121
Query: 234 RVIVSELGVPTIVNVLSDSIMKVQIQVASLVARMA 268
+ IV GV +V +L+ + +VQ + A +A +A
Sbjct: 122 KAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIA 156
Score = 35.0 bits (79), Expect = 0.12, Method: Compositional matrix adjust.
Identities = 32/95 (33%), Positives = 47/95 (49%), Gaps = 2/95 (2%)
Query: 175 EAAIELASLAKDNDRNKKIIVEEGGVPPLLKLLKXXXXXXXXXXXXXXLYNIAND-QERV 233
EAA +LA +A K IV+ GGV L+KLL L NIA+ E +
Sbjct: 21 EAARDLAEIASGPASAIKAIVDAGGVEVLVKLL-TSTDSEVQKEAARALANIASGPDEAI 79
Query: 234 RVIVSELGVPTIVNVLSDSIMKVQIQVASLVARMA 268
+ IV GV +V +L+ + +VQ + A +A +A
Sbjct: 80 KAIVDAGGVEVLVKLLTSTDSEVQKEAARALANIA 114
>pdb|3TJ3|A Chain A, Structure Of Importin A5 Bound To The N-Terminus Of Nup50
pdb|3TJ3|B Chain B, Structure Of Importin A5 Bound To The N-Terminus Of Nup50
Length = 447
Score = 33.5 bits (75), Expect = 0.36, Method: Compositional matrix adjust.
Identities = 24/102 (23%), Positives = 42/102 (41%), Gaps = 1/102 (0%)
Query: 192 KIIVEEGGVPPLLKLLKXXXXXXXXXXXXXXLYNIANDQE-RVRVIVSELGVPTIVNVLS 250
++I G V ++ LK L NIA+ + R+++ VP + +LS
Sbjct: 55 EVISTPGVVARFVEFLKRKENCTLQFESAWVLTNIASGNSLQTRIVIQAGAVPIFIELLS 114
Query: 251 DSIMKVQIQVASLVARMAEHDALAQDDFARENVIRPLVTLLS 292
VQ Q + +A + +D N++ PL+ L S
Sbjct: 115 SEFEDVQEQAVWALGNIAGDSTMCRDYVLDCNILPPLLQLFS 156
>pdb|2YNS|A Chain A, Rimp_alpha_b54nls
pdb|2YNS|B Chain B, Rimp_alpha_b54nls
pdb|4B8O|A Chain A, Rimp_alpha_sv40tagnls
pdb|4B8P|A Chain A, Rimp_alpha_a89nls
pdb|4B8P|B Chain B, Rimp_alpha_a89nls
Length = 490
Score = 33.5 bits (75), Expect = 0.37, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 173 RIEAAIELASLAKDNDRNKKIIVEEGGVPPLLKLLKXXXXXXXXXXXXXXLYNIANDQER 232
+ EAA L ++A N K++++ G VP +KLL L N+A D +
Sbjct: 97 QFEAAWALTNIASGTSENTKVVIDHGAVPIFVKLLG-SSSDDVREQAVWALGNVAGDSPK 155
Query: 233 VRVIV 237
R +V
Sbjct: 156 CRDLV 160
>pdb|2JDQ|A Chain A, C-Terminal Domain Of Influenza A Virus Polymerase Pb2
Subunit In Complex With Human Importin Alpha5
pdb|2JDQ|B Chain B, C-Terminal Domain Of Influenza A Virus Polymerase Pb2
Subunit In Complex With Human Importin Alpha5
Length = 450
Score = 33.5 bits (75), Expect = 0.38, Method: Compositional matrix adjust.
Identities = 24/102 (23%), Positives = 42/102 (41%), Gaps = 1/102 (0%)
Query: 192 KIIVEEGGVPPLLKLLKXXXXXXXXXXXXXXLYNIANDQE-RVRVIVSELGVPTIVNVLS 250
++I G V ++ LK L NIA+ + R+++ VP + +LS
Sbjct: 58 EVISTPGVVARFVEFLKRKENCTLQFESAWVLTNIASGNSLQTRIVIQAGAVPIFIELLS 117
Query: 251 DSIMKVQIQVASLVARMAEHDALAQDDFARENVIRPLVTLLS 292
VQ Q + +A + +D N++ PL+ L S
Sbjct: 118 SEFEDVQEQAVWALGNIAGDSTMCRDYVLDCNILPPLLQLFS 159
>pdb|4B8J|A Chain A, Rimp_alpha1a
Length = 528
Score = 32.7 bits (73), Expect = 0.55, Method: Compositional matrix adjust.
Identities = 19/65 (29%), Positives = 30/65 (46%), Gaps = 1/65 (1%)
Query: 173 RIEAAIELASLAKDNDRNKKIIVEEGGVPPLLKLLKXXXXXXXXXXXXXXLYNIANDQER 232
+ EAA L ++A N K++++ G VP +KLL L N+A D +
Sbjct: 135 QFEAAWALTNIASGTSENTKVVIDHGAVPIFVKLLG-SSSDDVREQAVWALGNVAGDSPK 193
Query: 233 VRVIV 237
R +V
Sbjct: 194 CRDLV 198
>pdb|1H80|A Chain A, 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate-3,6-Anhydro-D-
Galactose-2-Sulfate 4 Galactohydrolase
pdb|1H80|B Chain B, 1,3-Alpha-1,4-Beta-D-Galactose-4-Sulfate-3,6-Anhydro-D-
Galactose-2-Sulfate 4 Galactohydrolase
pdb|1KTW|A Chain A, Iota-carrageenase Complexed To Iota-carrageenan Fragments
pdb|1KTW|B Chain B, Iota-carrageenase Complexed To Iota-carrageenan Fragments
Length = 464
Score = 32.7 bits (73), Expect = 0.67, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 43/95 (45%), Gaps = 7/95 (7%)
Query: 350 RENEKPEVKIKLKIACAEALWMLARGSVANSRRISETKGLLCLAKL-VEKEQGELQFNCL 408
R++ K V+ KL CA+ + G + R+++ L AKL E G
Sbjct: 294 RQSWKQAVESKLGRGCAQTPYARGNGGTRWAARVTQKDACLDKAKLEYGIEPGSFG---T 350
Query: 409 MTIMEITAAAESNADLRRAA---FKTNSPAAKAVV 440
+ + ++TA NADL++ F T++P K V
Sbjct: 351 VKVFDVTARFGYNADLKQDQLDYFSTSNPMCKRVC 385
>pdb|3LMW|A Chain A, Crystal Structure Of Iota-Carrageenase Family Gh82 From A.
Fortis In Absence Of Chloride Ions
pdb|3LMW|B Chain B, Crystal Structure Of Iota-Carrageenase Family Gh82 From A.
Fortis In Absence Of Chloride Ions
Length = 473
Score = 32.3 bits (72), Expect = 0.72, Method: Compositional matrix adjust.
Identities = 26/95 (27%), Positives = 43/95 (45%), Gaps = 7/95 (7%)
Query: 350 RENEKPEVKIKLKIACAEALWMLARGSVANSRRISETKGLLCLAKL-VEKEQGELQFNCL 408
R++ K V+ KL CA+ + G + R+++ L AKL E G
Sbjct: 295 RQSWKQAVESKLGRGCAQTPYARGNGGTRWAARVTQKDACLDKAKLEYGIEPGSFG---T 351
Query: 409 MTIMEITAAAESNADLRRAA---FKTNSPAAKAVV 440
+ + ++TA NADL++ F T++P K V
Sbjct: 352 VKVFDVTARFGYNADLKQDQLDYFSTSNPMCKRVC 386
>pdb|1EE5|A Chain A, Yeast Karyopherin (Importin) Alpha In A Complex With A
Nucleoplasmin Nls Peptide
Length = 424
Score = 32.3 bits (72), Expect = 0.85, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 50/95 (52%), Gaps = 12/95 (12%)
Query: 451 DSPTLQIPAIKSIGSLARTFPARETRVI---GPLVAH---LSHRNQEVATEAAIALQKFA 504
+S +Q PA++++G++ T +T+V+ G L A LS + + EA +
Sbjct: 225 ESTLVQTPALRAVGNIV-TGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNIT 283
Query: 505 SPENFLCTEHSKAIIEFNAVPPLMRLLR-GNDRTQ 538
+ TE +A+I+ N +PPL++LL D+T+
Sbjct: 284 AGN----TEQIQAVIDANLIPPLVKLLEVAEDKTK 314
>pdb|1EE4|A Chain A, Crystal Structure Of Yeast Karyopherin (Importin) Alpha In
A Complex With A C-Myc Nls Peptide
pdb|1EE4|B Chain B, Crystal Structure Of Yeast Karyopherin (Importin) Alpha In
A Complex With A C-Myc Nls Peptide
Length = 423
Score = 32.3 bits (72), Expect = 0.86, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 50/95 (52%), Gaps = 12/95 (12%)
Query: 451 DSPTLQIPAIKSIGSLARTFPARETRVI---GPLVAH---LSHRNQEVATEAAIALQKFA 504
+S +Q PA++++G++ T +T+V+ G L A LS + + EA +
Sbjct: 225 ESTLVQTPALRAVGNIV-TGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNIT 283
Query: 505 SPENFLCTEHSKAIIEFNAVPPLMRLLR-GNDRTQ 538
+ TE +A+I+ N +PPL++LL D+T+
Sbjct: 284 AGN----TEQIQAVIDANLIPPLVKLLEVAEDKTK 314
>pdb|2C1T|A Chain A, Structure Of The Kap60p:nup2 Complex
pdb|2C1T|B Chain B, Structure Of The Kap60p:nup2 Complex
Length = 454
Score = 32.0 bits (71), Expect = 0.92, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 50/95 (52%), Gaps = 12/95 (12%)
Query: 451 DSPTLQIPAIKSIGSLARTFPARETRVI---GPLVAH---LSHRNQEVATEAAIALQKFA 504
+S +Q PA++++G++ T +T+V+ G L A LS + + EA +
Sbjct: 224 ESTLVQTPALRAVGNIV-TGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNIT 282
Query: 505 SPENFLCTEHSKAIIEFNAVPPLMRLLR-GNDRTQ 538
+ TE +A+I+ N +PPL++LL D+T+
Sbjct: 283 AGN----TEQIQAVIDANLIPPLVKLLEVAEDKTK 313
>pdb|1UN0|A Chain A, Crystal Structure Of Yeast Karyopherin (Importin) Alpha In
Complex With A Nup2p N-Terminal Fragment
pdb|1UN0|B Chain B, Crystal Structure Of Yeast Karyopherin (Importin) Alpha In
Complex With A Nup2p N-Terminal Fragment
Length = 443
Score = 32.0 bits (71), Expect = 0.95, Method: Compositional matrix adjust.
Identities = 27/95 (28%), Positives = 50/95 (52%), Gaps = 12/95 (12%)
Query: 451 DSPTLQIPAIKSIGSLARTFPARETRVI---GPLVAH---LSHRNQEVATEAAIALQKFA 504
+S +Q PA++++G++ T +T+V+ G L A LS + + EA +
Sbjct: 224 ESTLVQTPALRAVGNIV-TGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNIT 282
Query: 505 SPENFLCTEHSKAIIEFNAVPPLMRLLR-GNDRTQ 538
+ TE +A+I+ N +PPL++LL D+T+
Sbjct: 283 AGN----TEQIQAVIDANLIPPLVKLLEVAEDKTK 313
>pdb|1BK5|A Chain A, Karyopherin Alpha From Saccharomyces Cerevisiae
pdb|1BK5|B Chain B, Karyopherin Alpha From Saccharomyces Cerevisiae
Length = 422
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 11/87 (12%)
Query: 451 DSPTLQIPAIKSIGSLARTFPARETRVI---GPLVAH---LSHRNQEVATEAAIALQKFA 504
+S +Q PA++++G++ T +T+V+ G L A LS + + EA +
Sbjct: 223 ESTLVQTPALRAVGNIV-TGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNIT 281
Query: 505 SPENFLCTEHSKAIIEFNAVPPLMRLL 531
+ TE +A+I+ N +PPL++LL
Sbjct: 282 AGN----TEQIQAVIDANLIPPLVKLL 304
>pdb|1BK6|A Chain A, Karyopherin Alpha (Yeast) + Sv40 T Antigen Nls
pdb|1BK6|B Chain B, Karyopherin Alpha (Yeast) + Sv40 T Antigen Nls
Length = 422
Score = 31.6 bits (70), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 11/87 (12%)
Query: 451 DSPTLQIPAIKSIGSLARTFPARETRVI---GPLVAH---LSHRNQEVATEAAIALQKFA 504
+S +Q PA++++G++ T +T+V+ G L A LS + + EA +
Sbjct: 223 ESTLVQTPALRAVGNIV-TGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNIT 281
Query: 505 SPENFLCTEHSKAIIEFNAVPPLMRLL 531
+ TE +A+I+ N +PPL++LL
Sbjct: 282 AGN----TEQIQAVIDANLIPPLVKLL 304
>pdb|1WA5|B Chain B, Crystal Structure Of The Exportin Cse1p Complexed With Its
Cargo (Kap60p) And Rangtp
Length = 530
Score = 31.2 bits (69), Expect = 1.7, Method: Compositional matrix adjust.
Identities = 25/87 (28%), Positives = 46/87 (52%), Gaps = 11/87 (12%)
Query: 451 DSPTLQIPAIKSIGSLARTFPARETRVI---GPLVAH---LSHRNQEVATEAAIALQKFA 504
+S +Q PA++++G++ T +T+V+ G L A LS + + EA +
Sbjct: 311 ESTLVQTPALRAVGNIV-TGNDLQTQVVINAGVLPALRLLLSSPKENIKKEACWTISNIT 369
Query: 505 SPENFLCTEHSKAIIEFNAVPPLMRLL 531
+ TE +A+I+ N +PPL++LL
Sbjct: 370 AGN----TEQIQAVIDANLIPPLVKLL 392
>pdb|3QKU|A Chain A, Mre11 Rad50 Binding Domain In Complex With Rad50 And
Amp-Pnp
pdb|3QKU|B Chain B, Mre11 Rad50 Binding Domain In Complex With Rad50 And
Amp-Pnp
Length = 359
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 246 VNVLSDSIMKVQIQVASLVARMAEHDALAQDDFARENVIRPLVTLLSFET 295
++ + ++ I + ++ R + DA+ + D ARE V+R ++ L FET
Sbjct: 119 ISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLDKFET 168
>pdb|3QKR|A Chain A, Mre11 Rad50 Binding Domain Bound To Rad50
pdb|3QKS|A Chain A, Mre11 Rad50 Binding Domain Bound To Rad50
Length = 203
Score = 30.4 bits (67), Expect = 2.7, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 246 VNVLSDSIMKVQIQVASLVARMAEHDALAQDDFARENVIRPLVTLLSFET 295
++ + ++ I + ++ R + DA+ + D ARE V+R ++ L FET
Sbjct: 119 ISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLDKFET 168
>pdb|3QKT|A Chain A, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|B Chain B, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|C Chain C, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
pdb|3QKT|D Chain D, Rad50 Abc-Atpase With Adjacent Coiled-Coil Region In
Complex With Amp- Pnp
Length = 339
Score = 30.4 bits (67), Expect = 2.8, Method: Compositional matrix adjust.
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 246 VNVLSDSIMKVQIQVASLVARMAEHDALAQDDFARENVIRPLVTLLSFET 295
++ + ++ I + ++ R + DA+ + D ARE V+R ++ L FET
Sbjct: 119 ISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLDKFET 168
>pdb|1II8|A Chain A, Crystal Structure Of The P. Furiosus Rad50 Atpase Domain
Length = 195
Score = 30.0 bits (66), Expect = 3.4, Method: Composition-based stats.
Identities = 14/50 (28%), Positives = 28/50 (56%)
Query: 246 VNVLSDSIMKVQIQVASLVARMAEHDALAQDDFARENVIRPLVTLLSFET 295
++ + ++ I + ++ R + DA+ + D ARE V+R ++ L FET
Sbjct: 119 ISAFMEKLIPYNIFLNAIYIRQGQIDAILESDEAREKVVREVLNLDKFET 168
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 0.131 0.363
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 14,546,291
Number of Sequences: 62578
Number of extensions: 524827
Number of successful extensions: 1439
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 11
Number of HSP's successfully gapped in prelim test: 12
Number of HSP's that attempted gapping in prelim test: 1395
Number of HSP's gapped (non-prelim): 53
length of query: 594
length of database: 14,973,337
effective HSP length: 104
effective length of query: 490
effective length of database: 8,465,225
effective search space: 4147960250
effective search space used: 4147960250
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: 54 (25.4 bits)