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= psy2754
(367 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|1M3V|A Chain A, Flin4: Fusion Of The Lim Binding Domain Of Ldb1 And The N-
Terminal Lim Domain Of Lmo4
Length = 122
Score = 72.4 bits (176), Expect = 3e-13, Method: Composition-based stats.
Identities = 34/41 (82%), Positives = 38/41 (92%), Gaps = 1/41 (2%)
Query: 289 DVMVVGEPSLMGGEFGDEDERLITRLENTQYDAGANCLDHD 329
DVMVVGEP+LMGGEFGDEDERLITRLENTQ+DA AN +D +
Sbjct: 83 DVMVVGEPTLMGGEFGDEDERLITRLENTQFDA-ANGIDDE 122
>pdb|2DFY|X Chain X, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim
Domains 1 And 2 With The Lim Interacting Domain Of Ldb1
pdb|2DFY|C Chain C, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim
Domains 1 And 2 With The Lim Interacting Domain Of Ldb1
Length = 195
Score = 70.9 bits (172), Expect = 1e-12, Method: Compositional matrix adjust.
Identities = 36/47 (76%), Positives = 40/47 (85%), Gaps = 1/47 (2%)
Query: 289 DVMVVGEPSLMGGEFGDEDERLITRLENTQYDAGANCLDHDPHFSDS 335
DVMVVGEP+LMGGEFGDEDERLITRLENTQ+DA AN +D + S S
Sbjct: 147 DVMVVGEPTLMGGEFGDEDERLITRLENTQFDA-ANGIDDETRESGS 192
>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
Domain
Length = 188
Score = 70.1 bits (170), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 34/39 (87%), Positives = 37/39 (94%), Gaps = 1/39 (2%)
Query: 289 DVMVVGEPSLMGGEFGDEDERLITRLENTQYDAGANCLD 327
DVMVVGEP+LMGGEFGDEDERLITRLENTQ+DA AN +D
Sbjct: 149 DVMVVGEPTLMGGEFGDEDERLITRLENTQFDA-ANGID 186
>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex
Length = 182
Score = 69.7 bits (169), Expect = 2e-12, Method: Compositional matrix adjust.
Identities = 34/39 (87%), Positives = 37/39 (94%), Gaps = 1/39 (2%)
Query: 289 DVMVVGEPSLMGGEFGDEDERLITRLENTQYDAGANCLD 327
DVMVVGEP+LMGGEFGDEDERLITRLENTQ+DA AN +D
Sbjct: 6 DVMVVGEPTLMGGEFGDEDERLITRLENTQFDA-ANGID 43
>pdb|2XJY|B Chain B, Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21
Crystal Form
Length = 35
Score = 69.7 bits (169), Expect = 3e-12, Method: Composition-based stats.
Identities = 31/33 (93%), Positives = 33/33 (100%)
Query: 289 DVMVVGEPSLMGGEFGDEDERLITRLENTQYDA 321
DVMVVGEP+LMGGEFGDEDERLITRLENTQ+DA
Sbjct: 3 DVMVVGEPTLMGGEFGDEDERLITRLENTQFDA 35
>pdb|2LXD|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
Lmo2(Lim2)- Ldb1(Lid)
Length = 125
Score = 69.7 bits (169), Expect = 3e-12, Method: Compositional matrix adjust.
Identities = 34/39 (87%), Positives = 37/39 (94%), Gaps = 1/39 (2%)
Query: 289 DVMVVGEPSLMGGEFGDEDERLITRLENTQYDAGANCLD 327
DVMVVGEP+LMGGEFGDEDERLITRLENTQ+DA AN +D
Sbjct: 86 DVMVVGEPTLMGGEFGDEDERLITRLENTQFDA-ANGID 123
>pdb|2XJZ|I Chain I, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|J Chain J, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|K Chain K, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|L Chain L, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|M Chain M, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
Length = 36
Score = 69.3 bits (168), Expect = 3e-12, Method: Composition-based stats.
Identities = 31/33 (93%), Positives = 33/33 (100%)
Query: 289 DVMVVGEPSLMGGEFGDEDERLITRLENTQYDA 321
DVMVVGEP+LMGGEFGDEDERLITRLENTQ+DA
Sbjct: 4 DVMVVGEPTLMGGEFGDEDERLITRLENTQFDA 36
>pdb|1J2O|A Chain A, Structure Of Flin2, A Complex Containing The N-Terminal
Lim Domain Of Lmo2 And Ldb1-Lid
Length = 114
Score = 68.6 bits (166), Expect = 5e-12, Method: Compositional matrix adjust.
Identities = 34/41 (82%), Positives = 38/41 (92%), Gaps = 1/41 (2%)
Query: 289 DVMVVGEPSLMGGEFGDEDERLITRLENTQYDAGANCLDHD 329
DVMVVGEP+LMGGEFGDEDERLITRLENTQ+DA AN +D +
Sbjct: 75 DVMVVGEPTLMGGEFGDEDERLITRLENTQFDA-ANGIDDE 114
>pdb|2L6Y|B Chain B, Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid
pdb|2L6Z|C Chain C, Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid With Fog
Length = 96
Score = 30.8 bits (68), Expect = 1.4, Method: Composition-based stats.
Identities = 12/13 (92%), Positives = 13/13 (100%)
Query: 289 DVMVVGEPSLMGG 301
DVMVVGEP+LMGG
Sbjct: 84 DVMVVGEPTLMGG 96
>pdb|3EO8|A Chain A, Crystal Structure Of Blub-Like Flavoprotein
(Yp_001089088.1) From Clostridium Difficile 630 At 1.74
A Resolution
pdb|3EO8|B Chain B, Crystal Structure Of Blub-Like Flavoprotein
(Yp_001089088.1) From Clostridium Difficile 630 At 1.74
A Resolution
pdb|3EO8|C Chain C, Crystal Structure Of Blub-Like Flavoprotein
(Yp_001089088.1) From Clostridium Difficile 630 At 1.74
A Resolution
pdb|3EO8|D Chain D, Crystal Structure Of Blub-Like Flavoprotein
(Yp_001089088.1) From Clostridium Difficile 630 At 1.74
A Resolution
pdb|3EO8|E Chain E, Crystal Structure Of Blub-Like Flavoprotein
(Yp_001089088.1) From Clostridium Difficile 630 At 1.74
A Resolution
pdb|3EO8|F Chain F, Crystal Structure Of Blub-Like Flavoprotein
(Yp_001089088.1) From Clostridium Difficile 630 At 1.74
A Resolution
Length = 219
Score = 30.4 bits (67), Expect = 1.8, Method: Compositional matrix adjust.
Identities = 22/87 (25%), Positives = 41/87 (47%), Gaps = 8/87 (9%)
Query: 153 IKSWHFAVRQHRELVPRT--IVGMQDPSMLEQLTK------NITRQGITNSTLNYLRLCV 204
I++WHF V + R+L + ++ + +L + K N R+ + N TL YL+ V
Sbjct: 43 IQNWHFVVIKRRDLXEKIADVITKKQQEILVEXDKVSVDKANRFRKFVKNFTLFYLKAPV 102
Query: 205 ILEPMQELMSRHKAYALSPRDCLKTTL 231
++ ++ + Y L D K T+
Sbjct: 103 LVLVFTKVYNPSGYYELELIDAPKETI 129
>pdb|3S98|A Chain A, Human Ifnar1
Length = 306
Score = 29.3 bits (64), Expect = 3.2, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 34/84 (40%), Gaps = 4/84 (4%)
Query: 163 HRELVPRTIVGMQDPSMLEQLTKNITRQGITNSTLNYLRLCVILEPMQELMSRHKAYALS 222
H E + IV P + + + T S + + + E ++ + SRHK Y LS
Sbjct: 108 HLEAEDKAIVIHISPGTKDSVXWALDGLSFTYSLVIWKNSSGVEERIENIYSRHKIYKLS 167
Query: 223 PRD--CLKT--TLFQKWQRMVAPP 242
P CLK L W+ V P
Sbjct: 168 PETTYCLKVKAALLTSWKIGVYSP 191
>pdb|4EAZ|A Chain A, Vgll1-Tead4 Structure
pdb|4EAZ|B Chain B, Vgll1-Tead4 Structure
Length = 223
Score = 28.9 bits (63), Expect = 4.9, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 133 TKVCTEGRLILEFTFDDLMRIKSWHFAVRQHRELVPRTIVG-------MQDPSMLEQLTK 185
TKVC+ G+ ++E + R ++ H+ R HR + ++ + + M+ + +
Sbjct: 121 TKVCSFGKQVVEKVETEYARYENGHYLYRIHRSPLCEYMINFIHKLKHLPEKYMMNSVLE 180
Query: 186 NIT-RQGITNSTLNYLRLCV 204
N T Q +TN LC+
Sbjct: 181 NFTILQVVTNRDTQETLLCI 200
>pdb|3SE3|A Chain A, Human Ifna2-Ifnar Ternary Complex
pdb|3SE4|A Chain A, Human Ifnw-Ifnar Ternary Complex
Length = 414
Score = 28.9 bits (63), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 23/84 (27%), Positives = 34/84 (40%), Gaps = 4/84 (4%)
Query: 163 HRELVPRTIVGMQDPSMLEQLTKNITRQGITNSTLNYLRLCVILEPMQELMSRHKAYALS 222
H E + IV P + + + T S + + + E ++ + SRHK Y LS
Sbjct: 112 HLEAEDKAIVIHISPGTKDSVMWALDGLSFTYSLVIWKNSSGVEERIENIYSRHKIYKLS 171
Query: 223 PRD--CLKT--TLFQKWQRMVAPP 242
P CLK L W+ V P
Sbjct: 172 PETTYCLKVKAALLTSWKIGVYSP 195
>pdb|3JUA|A Chain A, Structural Basis Of Yap Recognition By Tead4 In The Hippo
Pathway
pdb|3JUA|C Chain C, Structural Basis Of Yap Recognition By Tead4 In The Hippo
Pathway
pdb|3JUA|E Chain E, Structural Basis Of Yap Recognition By Tead4 In The Hippo
Pathway
pdb|3JUA|G Chain G, Structural Basis Of Yap Recognition By Tead4 In The Hippo
Pathway
Length = 220
Score = 28.5 bits (62), Expect = 5.7, Method: Compositional matrix adjust.
Identities = 19/80 (23%), Positives = 37/80 (46%), Gaps = 8/80 (10%)
Query: 133 TKVCTEGRLILEFTFDDLMRIKSWHFAVRQHRELVPRTIVG-------MQDPSMLEQLTK 185
TKVC+ G+ ++E + R ++ H+ R HR + ++ + + M+ + +
Sbjct: 118 TKVCSFGKQVVEKVETEYARYENGHYLYRIHRSPLCEYMINFIHKLKHLPEKYMMNSVLE 177
Query: 186 NIT-RQGITNSTLNYLRLCV 204
N T Q +TN LC+
Sbjct: 178 NFTILQVVTNRDTQETLLCI 197
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
0.320 0.136 0.429
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 11,160,712
Number of Sequences: 62578
Number of extensions: 445782
Number of successful extensions: 947
Number of sequences better than 100.0: 15
Number of HSP's better than 100.0 without gapping: 9
Number of HSP's successfully gapped in prelim test: 6
Number of HSP's that attempted gapping in prelim test: 938
Number of HSP's gapped (non-prelim): 15
length of query: 367
length of database: 14,973,337
effective HSP length: 100
effective length of query: 267
effective length of database: 8,715,537
effective search space: 2327048379
effective search space used: 2327048379
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: 52 (24.6 bits)