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= 039467
(687 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2QX5|A Chain A, Structure Of Nucleoporin Nic96
pdb|2QX5|B Chain B, Structure Of Nucleoporin Nic96
Length = 661
Score = 58.5 bits (140), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 80/356 (22%), Positives = 156/356 (43%), Gaps = 63/356 (17%)
Query: 64 LLEKKATVYAEVVKNLNNARQQGLPFKPATAFKGAYESLAIESSSGKSVNIQKI--WHLL 121
+L +K YA +V NN+RQ F A F ++I SS+ + N Q + W +L
Sbjct: 29 ILREKFENYARIVFQFNNSRQANGNFDIANEF------ISILSSANGTRNAQLLESWKIL 82
Query: 122 QTMMGEHATVQQTASRKMSLVIGARRHLEWGHEKYIMDTIQSHPAQAALGGVVGNLQRVR 181
++M S+ +++V +++LE +Y + + + + G+ N+ +++
Sbjct: 83 ESM----------KSKDINIVEVGKQYLEQQFLQYTDNLYKKNMNE----GLATNVNKIK 128
Query: 182 AFLRIRLR----DYGVLDFDIGDTRRQPPVDTTWQQIYFCLRTGYYDEARNVALSSRAS- 236
+F+ +L+ + + + + + P+ W I++ LR G EA V + ++A+
Sbjct: 129 SFIDTKLKKADKSWKISNLTVING---VPI---WALIFYLLRAGLIKEALQVLVENKANI 182
Query: 237 ----NQFAPLLTEWINTGGM-VPPEIAAAASEECDKMLRMGDRVGRAAYDKKKLLLYAII 291
F + ++ +P E + E ++ ++ D +L +Y +I
Sbjct: 183 KKVEQSFLTYFKAYASSKDHGLPVEYSTKLHTEYNQHIK-----SSLDGDPYRLAVYKLI 237
Query: 292 SGSRRQIDRLLRDLPTLFSTIEDFLWFKLSAIRDVPSEAPSVVLSDGLAPYSLDDLQVYL 351
R + R +++P + +IED+LW L I++ +E V YSL+D Q +
Sbjct: 238 G--RCDLSR--KNIPAVTLSIEDWLWMHLMLIKEKDAENDPVY-----ERYSLEDFQNII 288
Query: 352 NKFDPSYYTKNGKDPLVYPYVLLLSIQLLPAVLYLSKESGDEGYNIDAAHISIVLA 407
+ PS ++ Y LLLS A+ Y S +DA H++I LA
Sbjct: 289 ISYGPSRFSN------YYLQTLLLSGLYGLAIDYTYTFS-----EMDAVHLAIGLA 333
Score = 32.3 bits (72), Expect = 0.83, Method: Compositional matrix adjust.
Identities = 34/164 (20%), Positives = 72/164 (43%), Gaps = 9/164 (5%)
Query: 491 EAAGQCQEAGLYDKSIELQKRVGAFSMALDTINKCLSEAIFAMSRGRL----DGESQTAS 546
+AA + E G SI L + + + + +N LS+ + A + D S+T
Sbjct: 448 QAARRADEDGRIYDSILLYQLAEEYDIVITLVNSLLSDTLSASDLDQPLVGPDDNSETNP 507
Query: 547 LIHSGNEILEMEKYYPEVSLHEREQVLEQQTVLRQLEAILSVHKMARSGHYLDALREVAK 606
++ + M Y + + R+ ++ + + L I S+ ++ + + + L ++
Sbjct: 508 VLLAR----RMASIYFDNAGISRQIHVKNKEICMLLLNISSIRELYFNKQWQETLSQMEL 563
Query: 607 LPFLPF-DPRVPDAMVDVFQSLSPHVQACVPDLLRVALTCLDNV 649
L LPF D F +L ++ +P+LL + L+C+ N+
Sbjct: 564 LDLLPFSDELSARKKAQDFSNLDDNIVKNIPNLLIITLSCISNM 607
>pdb|2RFO|A Chain A, Crystral Structure Of The Nucleoporin Nic96
pdb|2RFO|B Chain B, Crystral Structure Of The Nucleoporin Nic96
Length = 651
Score = 58.2 bits (139), Expect = 1e-08, Method: Compositional matrix adjust.
Identities = 80/356 (22%), Positives = 156/356 (43%), Gaps = 63/356 (17%)
Query: 64 LLEKKATVYAEVVKNLNNARQQGLPFKPATAFKGAYESLAIESSSGKSVNIQKI--WHLL 121
+L +K YA +V NN+RQ F A F ++I SS+ + N Q + W +L
Sbjct: 19 ILREKFENYARIVFQFNNSRQANGNFDIANEF------ISILSSANGTRNAQLLESWKIL 72
Query: 122 QTMMGEHATVQQTASRKMSLVIGARRHLEWGHEKYIMDTIQSHPAQAALGGVVGNLQRVR 181
++M S+ +++V +++LE +Y + + + + G+ N+ +++
Sbjct: 73 ESM----------KSKDINIVEVGKQYLEQQFLQYTDNLYKKNMNE----GLATNVNKIK 118
Query: 182 AFLRIRLR----DYGVLDFDIGDTRRQPPVDTTWQQIYFCLRTGYYDEARNVALSSRAS- 236
+F+ +L+ + + + + + P+ W I++ LR G EA V + ++A+
Sbjct: 119 SFIDTKLKKADKSWKISNLTVING---VPI---WALIFYLLRAGLIKEALQVLVENKANI 172
Query: 237 ----NQFAPLLTEWINTGGM-VPPEIAAAASEECDKMLRMGDRVGRAAYDKKKLLLYAII 291
F + ++ +P E + E ++ ++ D +L +Y +I
Sbjct: 173 KKVEQSFLTYFKAYASSKDHGLPVEYSTKLHTEYNQHIK-----SSLDGDPYRLAVYKLI 227
Query: 292 SGSRRQIDRLLRDLPTLFSTIEDFLWFKLSAIRDVPSEAPSVVLSDGLAPYSLDDLQVYL 351
R + R +++P + +IED+LW L I++ +E V YSL+D Q +
Sbjct: 228 G--RCDLSR--KNIPAVTLSIEDWLWMHLMLIKEKDAENDPVY-----ERYSLEDFQNII 278
Query: 352 NKFDPSYYTKNGKDPLVYPYVLLLSIQLLPAVLYLSKESGDEGYNIDAAHISIVLA 407
+ PS ++ Y LLLS A+ Y S +DA H++I LA
Sbjct: 279 ISYGPSRFSN------YYLQTLLLSGLYGLAIDYTYTFS-----EMDAVHLAIGLA 323
Score = 32.3 bits (72), Expect = 0.87, Method: Compositional matrix adjust.
Identities = 34/164 (20%), Positives = 72/164 (43%), Gaps = 9/164 (5%)
Query: 491 EAAGQCQEAGLYDKSIELQKRVGAFSMALDTINKCLSEAIFAMSRGRL----DGESQTAS 546
+AA + E G SI L + + + + +N LS+ + A + D S+T
Sbjct: 438 QAARRADEDGRIYDSILLYQLAEEYDIVITLVNSLLSDTLSASDLDQPLVGPDDNSETNP 497
Query: 547 LIHSGNEILEMEKYYPEVSLHEREQVLEQQTVLRQLEAILSVHKMARSGHYLDALREVAK 606
++ + M Y + + R+ ++ + + L I S+ ++ + + + L ++
Sbjct: 498 VLLAR----RMASIYFDNAGISRQIHVKNKEICMLLLNISSIRELYFNKQWQETLSQMEL 553
Query: 607 LPFLPF-DPRVPDAMVDVFQSLSPHVQACVPDLLRVALTCLDNV 649
L LPF D F +L ++ +P+LL + L+C+ N+
Sbjct: 554 LDLLPFSDELSARKKAQDFSNLDDNIVKNIPNLLIITLSCISNM 597
>pdb|3GUW|A Chain A, Crystal Structure Of The Tatd-Like Protein (Af1765) From
Archaeoglobus Fulgidus, Northeast Structural Genomics
Consortium Target Gr121
pdb|3GUW|B Chain B, Crystal Structure Of The Tatd-Like Protein (Af1765) From
Archaeoglobus Fulgidus, Northeast Structural Genomics
Consortium Target Gr121
pdb|3GUW|C Chain C, Crystal Structure Of The Tatd-Like Protein (Af1765) From
Archaeoglobus Fulgidus, Northeast Structural Genomics
Consortium Target Gr121
pdb|3GUW|D Chain D, Crystal Structure Of The Tatd-Like Protein (Af1765) From
Archaeoglobus Fulgidus, Northeast Structural Genomics
Consortium Target Gr121
Length = 261
Score = 32.0 bits (71), Expect = 1.0, Method: Compositional matrix adjust.
Identities = 11/30 (36%), Positives = 18/30 (60%)
Query: 599 DALREVAKLPFLPFDPRVPDAMVDVFQSLS 628
+ ++EV L F P P+ P +DVF+ L+
Sbjct: 23 NGIKEVCSLAFFPVKPKYPQTXIDVFRKLT 52
>pdb|3MEA|A Chain A, Crystal Structure Of The Sgf29 In Complex With H3k4me3
Length = 180
Score = 29.6 bits (65), Expect = 5.3, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 30/66 (45%), Gaps = 3/66 (4%)
Query: 232 SSRASNQFAPLLTEWINTGGMVPPEIAAAASEECDKMLRMGDRVG---RAAYDKKKLLLY 288
SSR + F L WI G PP + A D + R GD+V +A ++ +L
Sbjct: 8 SSRENLYFQGTLPLWIGKPGDKPPPLCGAIPASGDYVARPGDKVAARVKAVDGDEQWILA 67
Query: 289 AIISGS 294
++S S
Sbjct: 68 EVVSYS 73
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 0.133 0.387
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 18,505,805
Number of Sequences: 62578
Number of extensions: 714805
Number of successful extensions: 1681
Number of sequences better than 100.0: 12
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 1676
Number of HSP's gapped (non-prelim): 14
length of query: 687
length of database: 14,973,337
effective HSP length: 105
effective length of query: 582
effective length of database: 8,402,647
effective search space: 4890340554
effective search space used: 4890340554
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: 55 (25.8 bits)