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= 042466
(178 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|3JRN|A Chain A, Crystal Structure Of Tir Domain From Arabidopsis Thaliana
Length = 176
Score = 133 bits (334), Expect = 6e-32, Method: Compositional matrix adjust.
Identities = 73/167 (43%), Positives = 105/167 (62%), Gaps = 8/167 (4%)
Query: 10 KYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDD-QLNRGDEISESLVNAIEASAISV 68
KYDVF+SFRG DTR NF S LY L R++I+TF DD +L G S L + IE S +V
Sbjct: 8 KYDVFLSFRGHDTRHNFISFLYKELVRRSIRTFKDDKELENGQRFSPELKSPIEVSRFAV 67
Query: 69 IIFSESYPSSRWCLDELVKILECKKEYAQILIPVFYRVDPSDVRNQTGSFGDSFSKLEER 128
++ SE+Y +S WCLDELV I++ +K+ + ++P+FY V+P+ VR QTG + F K R
Sbjct: 68 VVVSENYAASSWCLDELVTIMDFEKKGSITVMPIFYGVEPNHVRWQTGVLAEQFKKHASR 127
Query: 129 FKENSKKLQTWRKALKEAASLSGFPSQSIRINNKSKRILQYISNKIS 175
E+ +K+ WR+AL A LSG S + +++ I+N+IS
Sbjct: 128 --EDPEKVLKWRQALTNFAQLSGDCS-----GDDDSKLVDKIANEIS 167
>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 = 129 bits (325), Expect = 6e-31, Method: Compositional matrix adjust.
Identities = 72/167 (43%), Positives = 103/167 (61%), Gaps = 7/167 (4%)
Query: 10 KYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTF-IDDQLNRGDEISESLVNAIEASAISV 68
+Y+VF+SFRG DTR+ FT LY +L R I TF DD+L +G EI +L+ AI+ S I V
Sbjct: 35 EYEVFLSFRGPDTREQFTDFLYQSLRRYKIHTFRDDDELLKGKEIGPNLLRAIDQSKIYV 94
Query: 69 IIFSESYPSSRWCLDELVKILECKKEYA-QILIPVFYRVDPSDVRNQTGSFGDSFSKLEE 127
I S Y S+WCL EL +I+ ++E +I++P+FY VDPSDVR+QTG + +F K
Sbjct: 95 PIISSGYADSKWCLMELAEIVRRQEEDPRRIILPIFYMVDPSDVRHQTGCYKKAFRKHAN 154
Query: 128 RFKENSKKLQTWRKALKEAASLSGFPSQSIRINNKSKRILQYISNKI 174
+F + + +Q W+ ALK+ L G+ I N+K I +S I
Sbjct: 155 KF--DGQTIQNWKDALKKVGDLKGW---HIGKNDKQGAIADKVSADI 196
>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 = 39.7 bits (91), Expect = 9e-04, Method: Compositional matrix adjust.
Identities = 24/114 (21%), Positives = 51/114 (44%), Gaps = 2/114 (1%)
Query: 11 YDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDD-QLNRGDEISESLVNAIEASAISVI 69
+D+F+S ED D F L L + + DD L GD + S+ + +S ++
Sbjct: 21 HDIFISHAWEDKAD-FVEALAHTLRAAGAEVWYDDFSLRPGDSLRRSIDKGLGSSRFGIV 79
Query: 70 IFSESYPSSRWCLDELVKILECKKEYAQILIPVFYRVDPSDVRNQTGSFGDSFS 123
+ S + W EL + + + ++P++++V +V + + + D +
Sbjct: 80 VLSTHFFKKEWPQKELDGLFQLESSGRSRILPIWHKVSKDEVASFSPTMADKLA 133
>pdb|2J67|A Chain A, The Tir Domain Of Human Toll-Like Receptor 10 (Tlr10)
pdb|2J67|B Chain B, The Tir Domain Of Human Toll-Like Receptor 10 (Tlr10)
Length = 178
Score = 30.0 bits (66), Expect = 0.66, Method: Compositional matrix adjust.
Identities = 20/83 (24%), Positives = 40/83 (48%), Gaps = 4/83 (4%)
Query: 6 RNNKKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFI---DDQLNRGDEISESLVNAIE 62
+ N ++ F+S+ D+ + L L +++ I + + G ISE++V+ IE
Sbjct: 31 KRNVRFHAFISYSEHDSL-WVKNELIPNLEKEDGSILICLYESYFDPGKSISENIVSFIE 89
Query: 63 ASAISVIIFSESYPSSRWCLDEL 85
S S+ + S ++ + WC E
Sbjct: 90 KSYKSIFVLSPNFVQNEWCHYEF 112
>pdb|2Q8Y|A Chain A, Structural Insight Into The Enzymatic Mechanism Of The
Phophothreonine Lyase
pdb|2Z8P|A Chain A, Structural Basis For The Catalytic Mechanism Of
Phosphothreonine Lyase
Length = 241
Score = 28.9 bits (63), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 23/87 (26%)
Query: 7 NNKKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRG---DEISESLVNAIEA 63
NN YDVF+ R E S Q+ F D+ + D + ++
Sbjct: 79 NNHGYDVFIHARRE--------------SPQSQGKFAGDKFHISVLRDMVPQAF------ 118
Query: 64 SAISVIIFSESYPSSRWCLDELVKILE 90
A+S ++FSE P +W + ++ K+++
Sbjct: 119 QALSGLLFSEDSPVDKWAVTDMEKVVQ 145
>pdb|3F9S|A Chain A, Crystal Structure Of A Putative Polyketide Cyclase
(Lferr_0659) From Acidithiobacillus Ferrooxidans Atcc At
1.76 A Resolution
pdb|3F9S|B Chain B, Crystal Structure Of A Putative Polyketide Cyclase
(Lferr_0659) From Acidithiobacillus Ferrooxidans Atcc At
1.76 A Resolution
Length = 146
Score = 28.1 bits (61), Expect = 2.5, Method: Compositional matrix adjust.
Identities = 13/66 (19%), Positives = 26/66 (39%)
Query: 111 VRNQTGSFGDSFSKLEERFKENSKKLQTWRKALKEAASLSGFPSQSIRINNKSKRILQYI 170
V+ +F D ++ F + + TW + GFPS +I + +
Sbjct: 60 VKTLRAAFPDQCFDIQGLFADGDAVVXTWLWTATHKEDIPGFPSTGKQIKXSGATVYYFD 119
Query: 171 SNKISG 176
N+++G
Sbjct: 120 GNRLTG 125
>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 = 28.1 bits (61), Expect = 2.9, Method: Compositional matrix adjust.
Identities = 20/82 (24%), Positives = 38/82 (46%), Gaps = 4/82 (4%)
Query: 22 TRDNFTSHLYSALSRQNIQTFIDDQLNRGDEISESLVNAIEASAISVIIFSESY---PSS 78
+RD +T+ L +S + ID +L GDE+ + +VN + VII + + P
Sbjct: 97 SRDYYTT-LNKEISNTGLVDLIDVELFMGDEVIDEVVNFAHKKEVKVIISNHDFNKTPKK 155
Query: 79 RWCLDELVKILECKKEYAQILI 100
+ L ++ E + +I +
Sbjct: 156 EEIVSRLCRMQELGADLPKIAV 177
>pdb|1QBB|A Chain A, Bacterial Chitobiase Complexed With Chitobiose (Dinag)
pdb|1QBA|A Chain A, Bacterial Chitobiase, Glycosyl Hydrolase Family 20
Length = 858
Score = 27.7 bits (60), Expect = 4.0, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 109 SDVRNQTGSFGDSFSKLEERFKENSKKLQTWRKALKEAASLSGFPSQSIRIN 160
+D+ + FG SKL + ++Q W+ LK+A S F + + +N
Sbjct: 561 ADMEHLPSYFGQEVSKLVK--AHGIDRMQAWQDGLKDAESSKAFATSRVGVN 610
>pdb|1C7S|A Chain A, Beta-N-Acetylhexosaminidase Mutant D539a Complexed With
Di- N-Acetyl-Beta-D-Glucosamine (Chitobiase)
Length = 858
Score = 27.3 bits (59), Expect = 4.1, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 109 SDVRNQTGSFGDSFSKLEERFKENSKKLQTWRKALKEAASLSGFPSQSIRIN 160
+D+ + FG SKL + ++Q W+ LK+A S F + + +N
Sbjct: 561 ADMEHLPSYFGQEVSKLVK--AHGIDRMQAWQDGLKDAESSKAFATSRVGVN 610
>pdb|1C7T|A Chain A, Beta-N-Acetylhexosaminidase Mutant E540d Complexed With
Di- N Acetyl-D-Glucosamine (Chitobiase)
Length = 858
Score = 27.3 bits (59), Expect = 4.2, Method: Composition-based stats.
Identities = 14/52 (26%), Positives = 25/52 (48%), Gaps = 2/52 (3%)
Query: 109 SDVRNQTGSFGDSFSKLEERFKENSKKLQTWRKALKEAASLSGFPSQSIRIN 160
+D+ + FG SKL + ++Q W+ LK+A S F + + +N
Sbjct: 561 ADMEHLPSYFGQEVSKLVK--AHGIDRMQAWQDGLKDAESSKAFATSRVGVN 610
>pdb|2Z8M|A Chain A, Structural Basis For The Catalytic Mechanism Of
Phosphothreonine Lyase
pdb|2Z8M|B Chain B, Structural Basis For The Catalytic Mechanism Of
Phosphothreonine Lyase
pdb|2Z8N|A Chain A, Structural Basis For The Catalytic Mechanism Of
Phosphothreonine Lyase
pdb|2Z8N|B Chain B, Structural Basis For The Catalytic Mechanism Of
Phosphothreonine Lyase
Length = 241
Score = 27.3 bits (59), Expect = 4.4, Method: Compositional matrix adjust.
Identities = 21/87 (24%), Positives = 38/87 (43%), Gaps = 23/87 (26%)
Query: 7 NNKKYDVFVSFRGEDTRDNFTSHLYSALSRQNIQTFIDDQLNRG---DEISESLVNAIEA 63
NN YDVF+ R E S Q+ F D+ + D + ++
Sbjct: 79 NNHGYDVFIHARRE--------------SPQSQGKFAGDKFHISVLRDMVPQAF------ 118
Query: 64 SAISVIIFSESYPSSRWCLDELVKILE 90
A+S ++FSE P +W + ++ K+++
Sbjct: 119 QALSGLLFSEDSPVDKWKVTDMEKVVQ 145
>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 = 27.3 bits (59), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 74 SYPSSRWCLDELVKILECKKEYAQILIPVFYRVDPSDVR 112
SY C+D +++ +C KE++ + F++ D SDV+
Sbjct: 47 SYTEDAQCIDGTIEVPKCFKEHSSL---AFWKTDASDVK 82
>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 = 27.3 bits (59), Expect = 4.8, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 74 SYPSSRWCLDELVKILECKKEYAQILIPVFYRVDPSDVR 112
SY C+D +++ +C KE++ + F++ D SDV+
Sbjct: 49 SYTEDAQCIDGTIEVPKCFKEHSSL---AFWKTDASDVK 84
>pdb|2VUG|A Chain A, The Structure Of An Archaeal Homodimeric Rna Ligase
pdb|2VUG|B Chain B, The Structure Of An Archaeal Homodimeric Rna Ligase
Length = 389
Score = 26.9 bits (58), Expect = 5.4, Method: Compositional matrix adjust.
Identities = 17/55 (30%), Positives = 28/55 (50%), Gaps = 6/55 (10%)
Query: 128 RFKENSKKLQTWRKALKEAASLSGFPSQSIRINNKS--KRILQ----YISNKISG 176
RFK+++ KL+ + E + GFP IN +S +RI + Y+ K+ G
Sbjct: 51 RFKDSAGKLRRGTVVIDEEYVIPGFPHIKRIINLRSGIRRIFKRGEFYVEEKVDG 105
>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 = 26.9 bits (58), Expect = 5.9, Method: Compositional matrix adjust.
Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 5/53 (9%)
Query: 28 SHLYSALSRQNIQ----TFIDDQLNRGDEISESLVNAIEASAIS-VIIFSESY 75
S L AL + ++ TF+ D+L + D+I+ IEAS+I+ I+F Y
Sbjct: 139 SKLKLALDKYDVDLPXITFLKDELRKKDKIAAGKTRVIEASSINDTILFRTVY 191
>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 = 26.9 bits (58), Expect = 6.7, Method: Compositional matrix adjust.
Identities = 14/36 (38%), Positives = 22/36 (61%), Gaps = 1/36 (2%)
Query: 41 TFIDDQLNRGDEISESLVNAIEASAIS-VIIFSESY 75
TF+ D+L + D+I+ IEAS+I+ I+F Y
Sbjct: 156 TFLKDELRKKDKIAAGKTRVIEASSINDTILFRTVY 191
>pdb|1C1Z|A Chain A, Crystal Structure Of Human Beta-2-Glycoprotein-I
(Apolipoprotein-H)
Length = 326
Score = 26.6 bits (57), Expect = 8.2, Method: Compositional matrix adjust.
Identities = 12/39 (30%), Positives = 23/39 (58%), Gaps = 3/39 (7%)
Query: 74 SYPSSRWCLDELVKILECKKEYAQILIPVFYRVDPSDVR 112
SY C+D +++ +C KE++ + F++ D SDV+
Sbjct: 289 SYTEDAQCIDGTIEVPKCFKEHSSL---AFWKTDASDVK 324
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
0.316 0.130 0.362
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 4,798,057
Number of Sequences: 62578
Number of extensions: 176932
Number of successful extensions: 561
Number of sequences better than 100.0: 23
Number of HSP's better than 100.0 without gapping: 10
Number of HSP's successfully gapped in prelim test: 13
Number of HSP's that attempted gapping in prelim test: 546
Number of HSP's gapped (non-prelim): 23
length of query: 178
length of database: 14,973,337
effective HSP length: 92
effective length of query: 86
effective length of database: 9,216,161
effective search space: 792589846
effective search space used: 792589846
T: 11
A: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)