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= 025389
(253 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|5CSM|A Chain A, Yeast Chorismate Mutase, T226s Mutant, Complex With Trp
Length = 256
Score = 187 bits (474), Expect = 6e-48, Method: Compositional matrix adjust.
Identities = 98/251 (39%), Positives = 150/251 (59%), Gaps = 9/251 (3%)
Query: 7 LTLDLVRDSLIRQEDTIIFCLIERAKHPLNAPAYDQSYASF--PGFSGSLLQYIVQQSEA 64
L L +RD L+R ED+IIF IER+ Y+ ++ P F GS L + + E
Sbjct: 10 LNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGLEIPNFKGSFLDWALSNLEI 69
Query: 65 MQATAGRYENPEESPFFPDKLPHSFVPPFKYPQVLHPAGTSINKNKIIWDMYFNQLLPLF 124
+ R+E+P+E+PFFPDK+ SF+P YPQ+L P +N N I +Y +++PL
Sbjct: 70 AHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPLI 129
Query: 125 VA-EGDD-GNYASTATSDLACLQALSRRIHYGKFVAEVKFRDAPHEYELAIRAKDRDALM 182
+GDD N+ S AT D+ CLQ+LSRRIH+GKFVAE KF+ Y I++KD + +M
Sbjct: 130 SKRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIM 189
Query: 183 NLLTYENVEQMVKKRVEKKAMVLGQEVSLGNDGDKQARFKVDPSVVSRLYGDWIMPFTKL 242
+T VE+ + +R+ KKA V G + + +++ ++ P + ++Y + ++P TK
Sbjct: 190 KNITNSAVEEKILERLTKKAEVYGVDPT-----ERRIERRISPEYLVKIYKEIVIPITKE 244
Query: 243 VQVEYLLRRLD 253
V+VEYLLRRL+
Sbjct: 245 VEVEYLLRRLE 255
>pdb|3CSM|A Chain A, Structure Of Yeast Chorismate Mutase With Bound Trp And An
Endooxabicyclic Inhibitor
pdb|3CSM|B Chain B, Structure Of Yeast Chorismate Mutase With Bound Trp And An
Endooxabicyclic Inhibitor
Length = 256
Score = 186 bits (473), Expect = 7e-48, Method: Compositional matrix adjust.
Identities = 98/251 (39%), Positives = 150/251 (59%), Gaps = 9/251 (3%)
Query: 7 LTLDLVRDSLIRQEDTIIFCLIERAKHPLNAPAYDQSYASF--PGFSGSLLQYIVQQSEA 64
L L +RD L+R ED+IIF IER+ Y+ ++ P F GS L + + E
Sbjct: 10 LNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGLEIPNFKGSFLDWALSNLEI 69
Query: 65 MQATAGRYENPEESPFFPDKLPHSFVPPFKYPQVLHPAGTSINKNKIIWDMYFNQLLPLF 124
+ R+E+P+E+PFFPDK+ SF+P YPQ+L P +N N I +Y +++PL
Sbjct: 70 AHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPLI 129
Query: 125 VA-EGDD-GNYASTATSDLACLQALSRRIHYGKFVAEVKFRDAPHEYELAIRAKDRDALM 182
+GDD N+ S AT D+ CLQ+LSRRIH+GKFVAE KF+ Y I++KD + +M
Sbjct: 130 SKRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIM 189
Query: 183 NLLTYENVEQMVKKRVEKKAMVLGQEVSLGNDGDKQARFKVDPSVVSRLYGDWIMPFTKL 242
+T VE+ + +R+ KKA V G + + +++ ++ P + ++Y + ++P TK
Sbjct: 190 KNITNSAVEEKILERLTKKAEVYGVDPT-----ERRIERRITPEYLVKIYKEIVIPITKE 244
Query: 243 VQVEYLLRRLD 253
V+VEYLLRRL+
Sbjct: 245 VEVEYLLRRLE 255
>pdb|4CSM|A Chain A, Yeast Chorismate Mutase + Tyr + Endooxabicyclic Inhibitor
pdb|4CSM|B Chain B, Yeast Chorismate Mutase + Tyr + Endooxabicyclic Inhibitor
pdb|2CSM|A Chain A, Tyr-Bound T-State Of Yeast Chorismate Mutase
Length = 256
Score = 186 bits (473), Expect = 8e-48, Method: Compositional matrix adjust.
Identities = 100/251 (39%), Positives = 150/251 (59%), Gaps = 9/251 (3%)
Query: 7 LTLDLVRDSLIRQEDTIIFCLIERAKHPLNAPAYDQSYASF--PGFSGSLLQYIVQQSEA 64
L L +RD L+R ED+IIF IER+ Y+ ++ P F GS L + + E
Sbjct: 10 LNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGLEIPNFKGSFLDWALSNLEI 69
Query: 65 MQATAGRYENPEESPFFPDKLPHSFVPPFKYPQVLHPAGTSINKNKIIWDMYFNQLLPLF 124
+ R+E+P+E+PFFPDK+ SF+P YPQ+L P +N N I +Y +++PL
Sbjct: 70 AHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPLI 129
Query: 125 VA-EGDD-GNYASTATSDLACLQALSRRIHYGKFVAEVKFRDAPHEYELAIRAKDRDALM 182
+GDD N+ S AT D+ CLQ+LSRRIH+GKFVAE KF+ Y I++KD + +M
Sbjct: 130 SKRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIM 189
Query: 183 NLLTYENVEQMVKKRVEKKAMVLGQEVSLGNDGDKQARFKVDPSVVSRLYGDWIMPFTKL 242
+T VE+ + +R+ KKA V G V N+ ++ ++ P + ++Y + ++P TK
Sbjct: 190 KNITNSAVEEKILERLTKKAEVYG--VDPTNESGER---RITPEYLVKIYKEIVIPITKE 244
Query: 243 VQVEYLLRRLD 253
V+VEYLLRRL+
Sbjct: 245 VEVEYLLRRLE 255
>pdb|1CSM|A Chain A, The Crystal Structure Of Allosteric Chorismate Mutase At
2.2 Angstroms Resolution
pdb|1CSM|B Chain B, The Crystal Structure Of Allosteric Chorismate Mutase At
2.2 Angstroms Resolution
Length = 256
Score = 186 bits (471), Expect = 1e-47, Method: Compositional matrix adjust.
Identities = 100/251 (39%), Positives = 150/251 (59%), Gaps = 9/251 (3%)
Query: 7 LTLDLVRDSLIRQEDTIIFCLIERAKHPLNAPAYDQSYASF--PGFSGSLLQYIVQQSEA 64
L L +RD L+R ED+IIF IER+ Y+ ++ P F GS L + + E
Sbjct: 10 LNLQNIRDELVRMEDSIIFKFIERSHFATCPSVYEANHPGLEIPNFKGSFLDWALSNLEI 69
Query: 65 MQATAGRYENPEESPFFPDKLPHSFVPPFKYPQVLHPAGTSINKNKIIWDMYFNQLLPLF 124
+ R+E+P+E+PFFPDK+ SF+P YPQ+L P +N N I +Y +++PL
Sbjct: 70 AHSRIRRFESPDETPFFPDKIQKSFLPSINYPQILAPYAPEVNYNDKIKKVYIEKIIPLI 129
Query: 125 VA-EGDD-GNYASTATSDLACLQALSRRIHYGKFVAEVKFRDAPHEYELAIRAKDRDALM 182
+GDD N+ S AT D+ CLQ+LSRRIH+GKFVAE KF+ Y I++KD + +M
Sbjct: 130 SKRDGDDKNNFGSVATRDIECLQSLSRRIHFGKFVAEAKFQSDIPLYTKLIKSKDVEGIM 189
Query: 183 NLLTYENVEQMVKKRVEKKAMVLGQEVSLGNDGDKQARFKVDPSVVSRLYGDWIMPFTKL 242
+T VE+ + +R+ KKA V G V N+ ++ ++ P + ++Y + ++P TK
Sbjct: 190 KNITNSAVEEKILERLTKKAEVYG--VDPTNESGER---RIIPEYLVKIYKEIVIPITKE 244
Query: 243 VQVEYLLRRLD 253
V+VEYLLRRL+
Sbjct: 245 VEVEYLLRRLE 255
>pdb|2JS7|A Chain A, Solution Nmr Structure Of Human Myeloid Differentiation
Primary Response (Myd88). Northeast Structural Genomics
Target Hr2869a
Length = 160
Score = 30.8 bits (68), Expect = 0.74, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 32/72 (44%)
Query: 155 KFVAEVKFRDAPHEYELAIRAKDRDALMNLLTYENVEQMVKKRVEKKAMVLGQEVSLGND 214
+FV E+ + Y L + DRD L + ++++KR + +V+ + +
Sbjct: 29 QFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSDDYLQSKE 88
Query: 215 GDKQARFKVDPS 226
D Q +F + S
Sbjct: 89 CDFQTKFALSLS 100
>pdb|2Z5V|A Chain A, Solution Structure Of The Tir Domain Of Human Myd88
Length = 149
Score = 30.8 bits (68), Expect = 0.77, Method: Compositional matrix adjust.
Identities = 16/72 (22%), Positives = 32/72 (44%)
Query: 155 KFVAEVKFRDAPHEYELAIRAKDRDALMNLLTYENVEQMVKKRVEKKAMVLGQEVSLGND 214
+FV E+ + Y L + DRD L + ++++KR + +V+ + +
Sbjct: 26 QFVQEMIRQLEQTNYRLKLCVSDRDVLPGTCVWSIASELIEKRCRRMVVVVSDDYLQSKE 85
Query: 215 GDKQARFKVDPS 226
D Q +F + S
Sbjct: 86 CDFQTKFALSLS 97
>pdb|3BG0|A Chain A, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG0|D Chain D, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG0|E Chain E, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG0|H Chain H, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|A Chain A, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|D Chain D, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|E Chain E, Architecture Of A Coat For The Nuclear Pore Membrane
pdb|3BG1|H Chain H, Architecture Of A Coat For The Nuclear Pore Membrane
Length = 316
Score = 30.0 bits (66), Expect = 1.2, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 21/47 (44%)
Query: 165 APHEYELAIRAKDRDALMNLLTYENVEQMVKKRVEKKAMVLGQEVSL 211
APH+Y L + D ++LLTY Q K++ + VS
Sbjct: 112 APHDYGLILACGSSDGAISLLTYTGEGQWEVKKINNAHTIGCNAVSW 158
>pdb|1U2Z|A Chain A, Crystal Structure Of Histone K79 Methyltransferase Dot1p
From Yeast
pdb|1U2Z|B Chain B, Crystal Structure Of Histone K79 Methyltransferase Dot1p
From Yeast
pdb|1U2Z|C Chain C, Crystal Structure Of Histone K79 Methyltransferase Dot1p
From Yeast
Length = 433
Score = 29.6 bits (65), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 14/48 (29%), Positives = 25/48 (52%), Gaps = 3/48 (6%)
Query: 83 DKLPHSFVPPF---KYPQVLHPAGTSINKNKIIWDMYFNQLLPLFVAE 127
DK+P SF+ F Y + +HP + K + + +LLP F+++
Sbjct: 186 DKIPRSFIHDFLHIVYTRSIHPQANKLKHYKAFSNYVYGELLPNFLSD 233
>pdb|2RHQ|B Chain B, Phers From Staphylococcus Haemolyticus- Rational Protein
Engineering And Inhibitor Studies
Length = 795
Score = 29.3 bits (64), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 63 EAMQATAGRYENPEESPFFPD-------KLPHSFVPPFKYPQVLHPAGTSINKNKIIWDM 115
+AM A Y N E+ P FP ++ H VP + Q++H G I ++ +++D+
Sbjct: 688 DAMMQVAVGYINYEQIPKFPGVTRDIALEVNHD-VPSSELKQIIHNNGEDILQSTLVFDV 746
Query: 116 YFNQLL 121
Y + L
Sbjct: 747 YEGEHL 752
>pdb|2RHS|B Chain B, Phers From Staphylococcus Haemolyticus- Rational Protein
Engineering And Inhibitor Studies
pdb|2RHS|D Chain D, Phers From Staphylococcus Haemolyticus- Rational Protein
Engineering And Inhibitor Studies
Length = 800
Score = 29.3 bits (64), Expect = 2.1, Method: Compositional matrix adjust.
Identities = 19/66 (28%), Positives = 33/66 (50%), Gaps = 8/66 (12%)
Query: 63 EAMQATAGRYENPEESPFFPD-------KLPHSFVPPFKYPQVLHPAGTSINKNKIIWDM 115
+AM A Y N E+ P FP ++ H VP + Q++H G I ++ +++D+
Sbjct: 692 DAMMQVAVGYINYEQIPKFPGVTRDIALEVNHD-VPSSELKQIIHNNGEDILQSTLVFDV 750
Query: 116 YFNQLL 121
Y + L
Sbjct: 751 YEGEHL 756
>pdb|3QTG|A Chain A, Crystal Structure Of Pyruvate Kinase From Pyrobaculum
Aerophilum
pdb|3QTG|B Chain B, Crystal Structure Of Pyruvate Kinase From Pyrobaculum
Aerophilum
Length = 461
Score = 28.1 bits (61), Expect = 4.5, Method: Compositional matrix adjust.
Identities = 23/81 (28%), Positives = 36/81 (44%), Gaps = 10/81 (12%)
Query: 124 FVAEGDDGNYASTATSDLACLQALSRRIHYGKFVAEVKFRDAPHEYELAIRAKDRDALMN 183
V EG D + ++ A D+ L+A+S +VA LA KD D++ +
Sbjct: 167 IVVEGKDYDISTPAEEDVEALKAISPIRDNIDYVA----------ISLAKSCKDVDSVRS 216
Query: 184 LLTYENVEQMVKKRVEKKAMV 204
LLT + V ++E K V
Sbjct: 217 LLTELGFQSQVAVKIETKGAV 237
>pdb|1WAO|1 Chain 1, Pp5 Structure
pdb|1WAO|2 Chain 2, Pp5 Structure
pdb|1WAO|3 Chain 3, Pp5 Structure
pdb|1WAO|4 Chain 4, Pp5 Structure
Length = 477
Score = 27.3 bits (59), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 20/66 (30%), Positives = 33/66 (50%), Gaps = 15/66 (22%)
Query: 161 KFRDAPHEYELAIRAK--DRDALMNLLTYENVEQMVKKRVEKKAMVLGQEVSLGNDGDKQ 218
KFR A +YE ++ K D+DA M Y+ ++VK++ ++A+ GD+
Sbjct: 89 KFRAALRDYETVVKVKPHDKDAKMK---YQECNKIVKQKAFERAIA----------GDEH 135
Query: 219 ARFKVD 224
R VD
Sbjct: 136 KRSVVD 141
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
0.321 0.137 0.403
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 7,498,072
Number of Sequences: 62578
Number of extensions: 304803
Number of successful extensions: 597
Number of sequences better than 100.0: 18
Number of HSP's better than 100.0 without gapping: 7
Number of HSP's successfully gapped in prelim test: 11
Number of HSP's that attempted gapping in prelim test: 577
Number of HSP's gapped (non-prelim): 18
length of query: 253
length of database: 14,973,337
effective HSP length: 97
effective length of query: 156
effective length of database: 8,903,271
effective search space: 1388910276
effective search space used: 1388910276
T: 11
A: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)