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= 004632
(741 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|4G24|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G26|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Ca
Length = 501
Score = 43.9 bits (102), Expect = 4e-04, Method: Compositional matrix adjust.
Identities = 37/135 (27%), Positives = 56/135 (41%), Gaps = 17/135 (12%)
Query: 542 DMYAKCGDLQTAQRVFDSMSERNVVSWS---------------AMIDCYGMHGQLNDAAS 586
DM +K GD+ A R++D + RN V S A + G L+
Sbjct: 34 DMCSKKGDVLEALRLYDE-ARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPG-LSRGFD 91
Query: 587 LFKQMLDSGIKPNEVTFMNILWACSHSGSVEEGKFYFNAMRIFGVEPDLQHYACMVDLLS 646
+FKQM+ + PNE TF N E M+ FG++P L+ Y +
Sbjct: 92 IFKQMIVDKVVPNEATFTNGARLAVAKDDPEMAFDMVKQMKAFGIQPRLRSYGPALFGFC 151
Query: 647 RSGDIEGAFKMIHSM 661
R GD + A+++ M
Sbjct: 152 RKGDADKAYEVDAHM 166
>pdb|4G23|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana With Mn
pdb|4G25|A Chain A, Crystal Structure Of Proteinaceous Rnase P 1 (Prorp1) From
A. Thaliana, Semet Substituted Form With Sr
Length = 501
Score = 37.7 bits (86), Expect = 0.025, Method: Compositional matrix adjust.
Identities = 33/131 (25%), Positives = 52/131 (39%), Gaps = 17/131 (12%)
Query: 542 DMYAKCGDLQTAQRVFDSMSERNVVSWS---------------AMIDCYGMHGQLNDAAS 586
D +K GD+ A R++D + RN V S A + G L+
Sbjct: 34 DXCSKKGDVLEALRLYDE-ARRNGVQLSQYHYNVLLYVCSLAEAATESSPNPG-LSRGFD 91
Query: 587 LFKQMLDSGIKPNEVTFMNILWACSHSGSVEEGKFYFNAMRIFGVEPDLQHYACMVDLLS 646
+FKQ + + PNE TF N E + FG++P L+ Y +
Sbjct: 92 IFKQXIVDKVVPNEATFTNGARLAVAKDDPEXAFDXVKQXKAFGIQPRLRSYGPALFGFC 151
Query: 647 RSGDIEGAFKM 657
R GD + A+++
Sbjct: 152 RKGDADKAYEV 162
>pdb|1W3B|A Chain A, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha.
pdb|1W3B|B Chain B, The Superhelical Tpr Domain Of O-Linked Glcnac Transferase
Reveals Structural Similarities To Importin Alpha
Length = 388
Score = 33.5 bits (75), Expect = 0.49, Method: Compositional matrix adjust.
Identities = 68/292 (23%), Positives = 118/292 (40%), Gaps = 66/292 (22%)
Query: 402 VASSLSACGNV----GSLQLGLQIHGHVIKIDCKDEFVQSSLIDMYSKCGFKNLAYLL-- 455
+A + S GNV G LQ ++ + H +++ K +F+ G+ NLA L
Sbjct: 66 LAEAYSNLGNVYKERGQLQEAIEHYRHALRL--KPDFID----------GYINLAAALVA 113
Query: 456 ---FERIQQK--SVVMWNS-MICGFYQNGNSLEAINLFHQMYLNCLEMDEVTFLTAIQ-- 507
E Q S + +N + C GN L+A L LE + +L AI+
Sbjct: 114 AGDMEGAVQAYVSALQYNPDLYCVRSDLGNLLKA--------LGRLEEAKACYLKAIETQ 165
Query: 508 -----ACSNIG-----QLEKGKWVHHKLISYGVRKDIYIDTALTDMYAKCGDLQTAQRVF 557
A SN+G Q E +HH K + +D D Y G++ R+F
Sbjct: 166 PNFAVAWSNLGCVFNAQGEIWLAIHH------FEKAVTLDPNFLDAYINLGNVLKEARIF 219
Query: 558 D----------SMSERNVVSWSAMIDCYGMHGQLNDAASLFKQMLDSGIKPN-EVTFMNI 606
D S+S + V + Y G ++ A +++ ++ ++P+ + N+
Sbjct: 220 DRAVAAYLRALSLSPNHAVVHGNLACVYYEQGLIDLAIDTYRRAIE--LQPHFPDAYCNL 277
Query: 607 LWACSHSGSVEEGKFYFN-AMRIFGVEPDLQHYACMVDLLSRSGDIEGAFKM 657
A GSV E + +N A+R+ D + ++ G+IE A ++
Sbjct: 278 ANALKEKGSVAEAEDCYNTALRLCPTHAD--SLNNLANIKREQGNIEEAVRL 327
>pdb|1F08|A Chain A, Crystal Structure Of The Dna-Binding Domain Of The
Replication Initiation Protein E1 From Papillomavirus
pdb|1F08|B Chain B, Crystal Structure Of The Dna-Binding Domain Of The
Replication Initiation Protein E1 From Papillomavirus
pdb|1KSX|A Chain A, Crystal Structures Of Two Intermediates In The Assembly Of
The Papillomavirus Replication Initiation Complex
pdb|1KSX|B Chain B, Crystal Structures Of Two Intermediates In The Assembly Of
The Papillomavirus Replication Initiation Complex
pdb|1KSX|E Chain E, Crystal Structures Of Two Intermediates In The Assembly Of
The Papillomavirus Replication Initiation Complex
pdb|1KSX|F Chain F, Crystal Structures Of Two Intermediates In The Assembly Of
The Papillomavirus Replication Initiation Complex
pdb|1KSX|I Chain I, Crystal Structures Of Two Intermediates In The Assembly Of
The Papillomavirus Replication Initiation Complex
pdb|1KSX|J Chain J, Crystal Structures Of Two Intermediates In The Assembly Of
The Papillomavirus Replication Initiation Complex
pdb|1KSX|M Chain M, Crystal Structures Of Two Intermediates In The Assembly Of
The Papillomavirus Replication Initiation Complex
pdb|1KSX|N Chain N, Crystal Structures Of Two Intermediates In The Assembly Of
The Papillomavirus Replication Initiation Complex
Length = 148
Score = 30.8 bits (68), Expect = 2.7, Method: Composition-based stats.
Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 4/96 (4%)
Query: 239 VMYSKCGDLLSAERTFVKIEKRCTTSWTAMIS--CYNRSGWFQKALESFVKMLEVKEEPN 296
V + +LL + +F++++KR T + C+N + + ML V+EE
Sbjct: 47 VFFEASFELLKKQCSFLQMQKRSHEGGTCAVYLICFNTAKSRETVRNLMANMLNVREECL 106
Query: 297 LITLITVLGSCAGLGWLREGKSVHCQIIRKGMGPEY 332
++ + G A L W + S+ ++ G PE+
Sbjct: 107 MLQPPKIRGLSAALFWFKS--SLSPATLKHGALPEW 140
>pdb|1KSY|A Chain A, Crystal Structures Of Two Intermediates In The Assembly Of
The Papillomavirus Replication Initiation Complex
pdb|1KSY|B Chain B, Crystal Structures Of Two Intermediates In The Assembly Of
The Papillomavirus Replication Initiation Complex
pdb|1KSY|C Chain C, Crystal Structures Of Two Intermediates In The Assembly Of
The Papillomavirus Replication Initiation Complex
Length = 154
Score = 30.8 bits (68), Expect = 2.7, Method: Composition-based stats.
Identities = 22/96 (22%), Positives = 43/96 (44%), Gaps = 4/96 (4%)
Query: 239 VMYSKCGDLLSAERTFVKIEKRCTTSWTAMIS--CYNRSGWFQKALESFVKMLEVKEEPN 296
V + +LL + +F++++KR T + C+N + + ML V+EE
Sbjct: 47 VFFEASFELLKKQCSFLQMQKRSHEGGTCAVYLICFNTAKSRETVRNLMANMLNVREECL 106
Query: 297 LITLITVLGSCAGLGWLREGKSVHCQIIRKGMGPEY 332
++ + G A L W + S+ ++ G PE+
Sbjct: 107 MLQPPKIRGLSAALFWFKS--SLSPATLKHGALPEW 140
>pdb|3KD7|A Chain A, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|B Chain B, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|C Chain C, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|D Chain D, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
pdb|3KD7|E Chain E, Designed Tpr Module (Ctpr390) In Complex With Its
Peptide-Ligand (Hsp90 Peptide)
Length = 125
Score = 30.4 bits (67), Expect = 3.6, Method: Composition-based stats.
Identities = 25/93 (26%), Positives = 41/93 (44%), Gaps = 20/93 (21%)
Query: 233 LGNSFIVMYSKCGDLLSAERTFVK---IEKRCTTSWTAMISCYNRSGWFQKALESFVKML 289
LGN+ Y K GD A + K ++ ++W + + Y + G +QKA+E + K L
Sbjct: 15 LGNA----YYKQGDYQKAIEYYQKALELDPNNASAWYNLGNAYYKQGDYQKAIEYYQKAL 70
Query: 290 EVKEEPNLITLITVLGSCAGLGWLREGKSVHCQ 322
E+ +PN W R G + + Q
Sbjct: 71 EL--DPN-----------NAKAWYRRGNAYYKQ 90
>pdb|3SPA|A Chain A, Crystal Structure Of Human Mitochondrial Rna Polymerase
Length = 1134
Score = 29.6 bits (65), Expect = 6.3, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 3/54 (5%)
Query: 361 ERNILS---WNMLISEYARKGMSKEALELLVQMQTWGLMPDSFSVASSLSACGN 411
+R +L+ +N ++ +AR+G KE + +L ++ GL PD S A++L G
Sbjct: 159 KRKLLTLDMYNAVMLGWARQGAFKELVYVLFMVKDAGLTPDLLSYAAALQCMGR 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
0.323 0.137 0.423
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 22,303,908
Number of Sequences: 62578
Number of extensions: 900890
Number of successful extensions: 2151
Number of sequences better than 100.0: 11
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 10
Number of HSP's that attempted gapping in prelim test: 2139
Number of HSP's gapped (non-prelim): 17
length of query: 741
length of database: 14,973,337
effective HSP length: 106
effective length of query: 635
effective length of database: 8,340,069
effective search space: 5295943815
effective search space used: 5295943815
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.8 bits)