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= 043980
(233 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3OZI|A Chain A, Crystal Structure Of The Tir Domain From The Flax Disease
Resistance Protein L6
pdb|3OZI|B Chain B, Crystal Structure Of The Tir Domain From The Flax Disease
Resistance Protein L6
Length = 204
Score = 110 bits (276), Expect = 5e-25, Method: Compositional matrix adjust.
Identities = 56/115 (48%), Positives = 79/115 (68%), Gaps = 2/115 (1%)
Query: 24 KYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTF-IDDQLNRGDEISQSLVNAIEASAISV 82
+YEVF+SFRG DTR++FT LY +L R I TF DD+L +G EI +L+ AI+ S I V
Sbjct: 35 EYEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLKGKEIGPNLLRAIDQSKIYV 94
Query: 83 IIFSESYTSSRWCVDELVKILECKKEYA-QIVIPVLYRVDPSDVRNQTGSFGDSF 136
I S Y S+WC+ EL +I+ ++E +I++P+ Y VDPSDVR+QTG + +F
Sbjct: 95 PIISSGYADSKWCLMELAEIVRRQEEDPRRIILPIFYMVDPSDVRHQTGCYKKAF 149
>pdb|3JRN|A Chain A, Crystal Structure Of Tir Domain From Arabidopsis Thaliana
Length = 176
Score = 110 bits (274), Expect = 8e-25, Method: Compositional matrix adjust.
Identities = 54/114 (47%), Positives = 76/114 (66%), Gaps = 1/114 (0%)
Query: 24 KYEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDD-QLNRGDEISQSLVNAIEASAISV 82
KY+VF+SFRG DTR F S LY L R+SI+TF DD +L G S L + IE S +V
Sbjct: 8 KYDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIEVSRFAV 67
Query: 83 IIFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSF 136
++ SE+Y +S WC+DELV I++ +K+ + V+P+ Y V+P+ VR QTG + F
Sbjct: 68 VVVSENYAASSWCLDELVTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQF 121
>pdb|3H16|A Chain A, Crystal Structure Of A Bacteria Tir Domain, Pdtir From
Paracoccus Denitrificans
pdb|3H16|B Chain B, Crystal Structure Of A Bacteria Tir Domain, Pdtir From
Paracoccus Denitrificans
pdb|3H16|C Chain C, Crystal Structure Of A Bacteria Tir Domain, Pdtir From
Paracoccus Denitrificans
pdb|3H16|D Chain D, Crystal Structure Of A Bacteria Tir Domain, Pdtir From
Paracoccus Denitrificans
Length = 154
Score = 39.3 bits (90), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 23/114 (20%), Positives = 51/114 (44%), Gaps = 2/114 (1%)
Query: 25 YEVFVSFRGEDTRDKFTSHLYSALSRQSIQTFIDD-QLNRGDEISQSLVNAIEASAISVI 83
+++F+S ED D F L L + + DD L GD + +S+ + +S ++
Sbjct: 21 HDIFISHAWEDKAD-FVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIV 79
Query: 84 IFSESYTSSRWCVDELVKILECKKEYAQIVIPVLYRVDPSDVRNQTGSFGDSFS 137
+ S + W EL + + + ++P+ ++V +V + + + D +
Sbjct: 80 VLSTHFFKKEWPQKELDGLFQLESSGRSRILPIWHKVSKDEVASFSPTMADKLA 133
>pdb|2KRI|A Chain A, Structure Of A Complex Between Domain V Of Beta2-
Glycoprotein I And The Fourth Ligand-Binding Module From
Ldlr Determined With Haddock
pdb|3OP8|A Chain A, Crystal Structure Of The Domain V From Beta2-Glycoprotein
I
pdb|3OP8|B Chain B, Crystal Structure Of The Domain V From Beta2-Glycoprotein
I
Length = 85
Score = 27.7 bits (60), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 12/77 (15%)
Query: 50 RQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEY 109
R IQ + + GD++S N + SYT C+D +++ +C KE+
Sbjct: 18 RVKIQEKFKNGMLHGDKVSFFCKNKEKKC---------SYTEDAQCIDGTIEVPKCFKEH 68
Query: 110 AQIVIPVLYRVDPSDVR 126
+ + ++ D SDV+
Sbjct: 69 SSL---AFWKTDASDVK 82
>pdb|1C1Z|A Chain A, Crystal Structure Of Human Beta-2-Glycoprotein-I
(Apolipoprotein-H)
Length = 326
Score = 27.7 bits (60), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 12/77 (15%)
Query: 50 RQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEY 109
R IQ + + GD++S N + SYT C+D +++ +C KE+
Sbjct: 260 RVKIQEKFKNGMLHGDKVSFFCKNKEKKC---------SYTEDAQCIDGTIEVPKCFKEH 310
Query: 110 AQIVIPVLYRVDPSDVR 126
+ + ++ D SDV+
Sbjct: 311 SSL---AFWKTDASDVK 324
>pdb|1G4F|A Chain A, Nmr Structure Of The Fifth Domain Of Human Beta2-
Glycoprotein I
pdb|1G4G|A Chain A, Nmr Structure Of The Fifth Domain Of Human Beta2-
Glycoprotein I
Length = 86
Score = 27.7 bits (60), Expect = 5.6, Method: Compositional matrix adjust.
Identities = 19/77 (24%), Positives = 35/77 (45%), Gaps = 12/77 (15%)
Query: 50 RQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSSRWCVDELVKILECKKEY 109
R IQ + + GD++S N + SYT C+D +++ +C KE+
Sbjct: 20 RVKIQEKFKNGMLHGDKVSFFCKNKEKKC---------SYTEDAQCIDGTIEVPKCFKEH 70
Query: 110 AQIVIPVLYRVDPSDVR 126
+ + ++ D SDV+
Sbjct: 71 SSL---AFWKTDASDVK 84
>pdb|3JS3|A Chain A, Crystal Structure Of Type I 3-Dehydroquinate Dehydratase
(Arod) From Clostridium Difficile With Covalent Reaction
Intermediate
pdb|3JS3|B Chain B, Crystal Structure Of Type I 3-Dehydroquinate Dehydratase
(Arod) From Clostridium Difficile With Covalent Reaction
Intermediate
pdb|3JS3|C Chain C, Crystal Structure Of Type I 3-Dehydroquinate Dehydratase
(Arod) From Clostridium Difficile With Covalent Reaction
Intermediate
pdb|3JS3|D Chain D, Crystal Structure Of Type I 3-Dehydroquinate Dehydratase
(Arod) From Clostridium Difficile With Covalent Reaction
Intermediate
pdb|4H3D|A Chain A, 1.95 Angstrom Crystal Structure Of Of Type I
3-Dehydroquinate Dehydratase (Arod) From Clostridium
Difficile With Covalent Modified Comenic Acid.
pdb|4H3D|B Chain B, 1.95 Angstrom Crystal Structure Of Of Type I
3-Dehydroquinate Dehydratase (Arod) From Clostridium
Difficile With Covalent Modified Comenic Acid.
pdb|4H3D|C Chain C, 1.95 Angstrom Crystal Structure Of Of Type I
3-Dehydroquinate Dehydratase (Arod) From Clostridium
Difficile With Covalent Modified Comenic Acid.
pdb|4H3D|D Chain D, 1.95 Angstrom Crystal Structure Of Of Type I
3-Dehydroquinate Dehydratase (Arod) From Clostridium
Difficile With Covalent Modified Comenic Acid
Length = 258
Score = 27.3 bits (59), Expect = 6.9, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 28/57 (49%), Gaps = 1/57 (1%)
Query: 36 TRDKFTSHLYSALSRQSIQTFIDDQLNRGDEISQSLVNAIEASAISVIIFSESYTSS 92
+RD +T+ L +S + ID +L GDE+ +VN + VII + + +
Sbjct: 97 SRDYYTT-LNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKT 152
>pdb|1XR7|A Chain A, Crystal Structure Of Rna-Dependent Rna Polymerase 3d From
Human Rhinovirus Serotype 16
pdb|1XR7|B Chain B, Crystal Structure Of Rna-Dependent Rna Polymerase 3d From
Human Rhinovirus Serotype 16
Length = 460
Score = 27.3 bits (59), Expect = 7.8, Method: Compositional matrix adjust.
Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 5/60 (8%)
Query: 35 DTRDKFTSHLYSALSRQSIQ----TFIDDQLNRGDEISQSLVNAIEASAIS-VIIFSESY 89
+ + K S L AL + + TF+ D+L + D+I+ IEAS+I+ I+F Y
Sbjct: 132 NNKTKDISKLKLALDKYGVDLPMITFLKDELRKKDKIAAGKTRVIEASSINDTILFRTVY 191
>pdb|1TP7|A Chain A, Crystal Structure Of The Rna-Dependent Rna Polymerase From
Human Rhinovirus 16
pdb|1TP7|B Chain B, Crystal Structure Of The Rna-Dependent Rna Polymerase From
Human Rhinovirus 16
pdb|1TP7|C Chain C, Crystal Structure Of The Rna-Dependent Rna Polymerase From
Human Rhinovirus 16
pdb|1TP7|D Chain D, Crystal Structure Of The Rna-Dependent Rna Polymerase From
Human Rhinovirus 16
Length = 460
Score = 27.3 bits (59), Expect = 8.1, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 55 TFIDDQLNRGDEISQSLVNAIEASAIS-VIIFSESY 89
TF+ D+L + D+I+ IEAS+I+ I+F Y
Sbjct: 156 TFLKDELRKKDKIAAGKTRVIEASSINDTILFRTVY 191
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 0.369
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 5,172,698
Number of Sequences: 62578
Number of extensions: 166620
Number of successful extensions: 406
Number of sequences better than 100.0: 10
Number of HSP's better than 100.0 without gapping: 3
Number of HSP's successfully gapped in prelim test: 7
Number of HSP's that attempted gapping in prelim test: 400
Number of HSP's gapped (non-prelim): 10
length of query: 233
length of database: 14,973,337
effective HSP length: 96
effective length of query: 137
effective length of database: 8,965,849
effective search space: 1228321313
effective search space used: 1228321313
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: 50 (23.9 bits)