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= psy12714
(117 letters)
Database: pdbaa
62,578 sequences; 14,973,337 total letters
Searching..................................................done
>pdb|2D8Y|A Chain A, Solution Structure Of The Lim Domain Of Epithelial Protein
Lost In Neoplasm
Length = 91
Score = 83.2 bits (204), Expect = 4e-17, Method: Compositional matrix adjust.
Identities = 35/69 (50%), Positives = 48/69 (69%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISR 94
C C K VYP+E++ + ++FH +CFRC+ C L + +Y +G +YC PHF QLF S+
Sbjct: 18 CVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK 77
Query: 95 GNYDEGFGS 103
GNYDEGFGS
Sbjct: 78 GNYDEGFGS 86
>pdb|2CO8|A Chain A, Solution Structures Of The Lim Domain Of Human Nedd9
Interacting Protein With Calponin Homology And Lim
Domains
Length = 82
Score = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 24/60 (40%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 32 SSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMN--NGHLYCLPHFKQ 89
LC C + +Y LE++ +G FHR+CFRC C L Y + +GH YCL H Q
Sbjct: 15 GDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQ 74
>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein,
Nmr, Minimized Structure
Length = 113
Score = 52.0 bits (123), Expect = 8e-08, Method: Compositional matrix adjust.
Identities = 26/73 (35%), Positives = 37/73 (50%), Gaps = 1/73 (1%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISR 94
C AC VY EK+ GK +H+ CFRC +C L + T G +YC + + F +
Sbjct: 39 CSACGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPK 98
Query: 95 G-NYDEGFGSDQH 106
G Y +G G+ H
Sbjct: 99 GFGYGQGAGALVH 111
>pdb|1IBI|A Chain A, Quail Cysteine And Glycine-Rich Protein, Nmr, 15 Minimized
Model Structures
pdb|1QLI|A Chain A, Quail Cysteine And Glycine-Rich Protein, Nmr, Minimized
Average Structure
Length = 113
Score = 49.7 bits (117), Expect = 4e-07, Method: Compositional matrix adjust.
Identities = 25/73 (34%), Positives = 36/73 (49%), Gaps = 1/73 (1%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFISR 94
C C VY EK+ GK +H+ CFRC +C L + T G +YC + + F +
Sbjct: 39 CSRCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPK 98
Query: 95 G-NYDEGFGSDQH 106
G Y +G G+ H
Sbjct: 99 GFGYGQGAGALVH 111
>pdb|1A7I|A Chain A, Amino-Terminal Lim Domain From Quail Cysteine And Glycine-
Rich Protein, Nmr, Minimized Average Structure
Length = 81
Score = 48.1 bits (113), Expect = 1e-06, Method: Compositional matrix adjust.
Identities = 26/81 (32%), Positives = 43/81 (53%), Gaps = 4/81 (4%)
Query: 24 PSNGTGNPSSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
P+ G GN C AC + VY E+++ DG+ FHR CF C C L + +++ +YC
Sbjct: 2 PNWGGGNK---CGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYC 58
Query: 84 LPHFKQLFISRG-NYDEGFGS 103
+ + + +G Y +G G+
Sbjct: 59 KSCYGKKYGPKGYGYGQGAGT 79
>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The
Cysteine Rich Protein Crp
Length = 85
Score = 44.7 bits (104), Expect = 1e-05, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%)
Query: 32 SSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91
S C C + VY EK+ GK +H++CFRC +C L + +G +YC + + F
Sbjct: 8 SDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNF 67
>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1
Length = 192
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 20/60 (33%), Positives = 31/60 (51%)
Query: 32 SSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91
S C C + VY EK+ GK +H++CFRC +C L + +G +YC + + F
Sbjct: 115 SDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNF 174
Score = 37.7 bits (86), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 16/49 (32%), Positives = 26/49 (53%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C C K VY E+++ +G FH++CF C C L + ++ +YC
Sbjct: 10 CGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYC 58
>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of
MlpCRP3
Length = 58
Score = 44.3 bits (103), Expect = 2e-05, Method: Compositional matrix adjust.
Identities = 22/57 (38%), Positives = 29/57 (50%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91
C C K VY EK+ GK +H+ CFRC C L + T +G LYC + + F
Sbjct: 2 CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNF 58
>pdb|1IML|A Chain A, Cysteine Rich Intestinal Protein, Nmr, 48 Structures
Length = 76
Score = 41.2 bits (95), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 20/62 (32%), Positives = 33/62 (53%), Gaps = 1/62 (1%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC-LPHFKQLFIS 93
C C+K+VY E++ + GK +HR C +C +C L + + G YC P + +F
Sbjct: 3 CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGP 62
Query: 94 RG 95
+G
Sbjct: 63 KG 64
>pdb|2O10|A Chain A, Solution Structure Of The N-Terminal Lim Domain Of
MlpCRP3
Length = 60
Score = 40.4 bits (93), Expect = 2e-04, Method: Compositional matrix adjust.
Identities = 18/49 (36%), Positives = 26/49 (53%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
C AC K VY E+I+ +G+ FH+ CF C C L + + +YC
Sbjct: 4 CGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYC 52
>pdb|2CU8|A Chain A, Solution Structure Of The Lim Domain Of Human
Cysteine-Rich Protein 2
Length = 76
Score = 39.3 bits (90), Expect = 6e-04, Method: Compositional matrix adjust.
Identities = 21/63 (33%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 32 SSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC-LPHFKQL 90
+S C C+K VY EK+ + GK +H+ C +C +C L + ++G +C P + L
Sbjct: 9 ASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATL 68
Query: 91 FIS 93
F S
Sbjct: 69 FGS 71
>pdb|3F6Q|B Chain B, Crystal Structure Of Integrin-Linked Kinase Ankyrin
Repeat Domain In Complex With Pinch1 Lim1 Domain
Length = 72
Score = 38.5 bits (88), Expect = 0.001, Method: Compositional matrix adjust.
Identities = 22/64 (34%), Positives = 30/64 (46%), Gaps = 1/64 (1%)
Query: 29 GNPSSLCFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
G+ S+ C C P EKI ++G+L+H CF C QC + G YC F
Sbjct: 8 GSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDF 67
Query: 88 KQLF 91
+ LF
Sbjct: 68 QMLF 71
>pdb|3IXE|B Chain B, Structural Basis Of Competition Between Pinch1 And
Pinch2 For Binding To The Ankyrin Repeat Domain Of
Integrin-Linked Kinase
Length = 72
Score = 37.4 bits (85), Expect = 0.002, Method: Compositional matrix adjust.
Identities = 20/64 (31%), Positives = 32/64 (50%), Gaps = 1/64 (1%)
Query: 29 GNPSSLCFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
G+ +++C C + P E+I ++G+L+H CF C QC + G YC F
Sbjct: 8 GSANAVCQRCQARFSPAERIVNSNGELYHEHCFVCAQCFRPFPEGLFYEFEGRKYCEHDF 67
Query: 88 KQLF 91
+ LF
Sbjct: 68 QMLF 71
>pdb|1WYH|A Chain A, Solution Structure Of The Lim Domain From Human Skeletal
Muscle Lim-Protein 2
Length = 72
Score = 36.2 bits (82), Expect = 0.005, Method: Compositional matrix adjust.
Identities = 16/47 (34%), Positives = 25/47 (53%)
Query: 47 KIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFIS 93
K+E G+ +H CF C+ C L S+ + G YC+P ++ F S
Sbjct: 21 KLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFAS 67
>pdb|1G47|A Chain A, 1st Lim Domain Of Pinch Protein
Length = 77
Score = 35.4 bits (80), Expect = 0.008, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 32 SSLCFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQL 90
S+ C C P EKI ++G+L+H CF C QC + G YC F+ L
Sbjct: 11 SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQML 70
Query: 91 F 91
F
Sbjct: 71 F 71
>pdb|2KBX|B Chain B, Solution Structure Of Ilk-Pinch Complex
Length = 70
Score = 35.4 bits (80), Expect = 0.009, Method: Compositional matrix adjust.
Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 32 SSLCFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQL 90
S+ C C P EKI ++G+L+H CF C QC + G YC F+ L
Sbjct: 7 SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQML 66
Query: 91 F 91
F
Sbjct: 67 F 67
>pdb|1X4K|A Chain A, Solution Structure Of Lim Domain In Lim-Protein 3
Length = 72
Score = 34.7 bits (78), Expect = 0.014, Method: Compositional matrix adjust.
Identities = 18/63 (28%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 32 SSLCFACNKKVYP-LEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQL 90
SS C C K + P K+E G +H CF C +C + +S+ + +C+P +++
Sbjct: 5 SSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQ 64
Query: 91 FIS 93
S
Sbjct: 65 HAS 67
>pdb|2CUQ|A Chain A, Solution Structure Of Second Lim Domain From Human
Skeletal Muscle Lim-Protein 2
Length = 80
Score = 33.1 bits (74), Expect = 0.045, Method: Compositional matrix adjust.
Identities = 15/39 (38%), Positives = 21/39 (53%)
Query: 55 FHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFIS 93
+HR C CT C T L + +T + YC+ F +LF S
Sbjct: 37 WHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFAS 75
>pdb|1ZFO|A Chain A, Amino-Terminal Lim-Domain Peptide Of Lasp-1, Nmr
Length = 31
Score = 31.2 bits (69), Expect = 0.14, Method: Compositional matrix adjust.
Identities = 13/26 (50%), Positives = 16/26 (61%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACF 60
C C K VYP EK+ K +H+ACF
Sbjct: 6 CARCGKIVYPTEKVNCLDKFWHKACF 31
>pdb|1X63|A Chain A, Solution Structure Of The Second Lim Domain Of Skeletal
Muscle Lim Protein 1
Length = 82
Score = 30.8 bits (68), Expect = 0.19, Method: Compositional matrix adjust.
Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 1/60 (1%)
Query: 35 CFACNKKVYPLEK-IETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFIS 93
C C K + ++ +E G ++H+ CF C+ C V+ S+ YC+ + F S
Sbjct: 18 CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFAS 77
>pdb|2D8Z|A Chain A, Solution Structure Of The Third Lim Domain Of Four And A
Half Lim Domains Protein 2 (Fhl-2)
Length = 70
Score = 30.4 bits (67), Expect = 0.23, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 28/62 (45%), Gaps = 1/62 (1%)
Query: 32 SSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91
SS C C K + + + +H+ CF CT C L + +T + YCL F L+
Sbjct: 5 SSGCVQCKKPI-TTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLY 63
Query: 92 IS 93
S
Sbjct: 64 AS 65
>pdb|2CUP|A Chain A, Solution Structure Of The Skeletal Muscle Lim-Protein 1
Length = 101
Score = 29.6 bits (65), Expect = 0.41, Method: Compositional matrix adjust.
Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)
Query: 32 SSLCFACNKKVYPLEK-IETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
SS C C K + K + + +H CFRC +C L E++ + + C
Sbjct: 5 SSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILC 57
>pdb|2LXD|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For
Lmo2(Lim2)- Ldb1(Lid)
Length = 125
Score = 29.3 bits (64), Expect = 0.57, Method: Compositional matrix adjust.
Identities = 14/54 (25%), Positives = 26/54 (48%), Gaps = 2/54 (3%)
Query: 32 SSLCFACNKKVYPLE-KIETDGKLFHRACFRCTQCCTVLRM-ESYTMNNGHLYC 83
LC +C+K++ E + K++H CF+C C + + Y + N + C
Sbjct: 10 DGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIVC 63
>pdb|2CUR|A Chain A, Solution Structure Of Skeletal Muscle Lim-Protein 1
Length = 69
Score = 29.3 bits (64), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 19/62 (30%), Positives = 27/62 (43%), Gaps = 2/62 (3%)
Query: 32 SSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91
SS C CNK + I + +H CF C C L + +T YC+ +K F
Sbjct: 5 SSGCVKCNKAITS-GGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKN-F 62
Query: 92 IS 93
+S
Sbjct: 63 VS 64
>pdb|1X64|A Chain A, Solution Structure Of The Lim Domain Of Alpha-Actinin-2
Associated Lim Protein
Length = 89
Score = 29.3 bits (64), Expect = 0.62, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 22/55 (40%), Gaps = 1/55 (1%)
Query: 34 LCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFK 88
LC C + ++ K H CF C C L+ + Y G LYC H +
Sbjct: 27 LCDKCGSGIVGAV-VKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHAR 80
>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 = 28.9 bits (63), Expect = 0.80, Method: Compositional matrix adjust.
Identities = 11/35 (31%), Positives = 19/35 (54%), Gaps = 1/35 (2%)
Query: 32 SSLCFACNKKVYPLE-KIETDGKLFHRACFRCTQC 65
LC +C+K++ E + K++H CF+C C
Sbjct: 8 DGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAAC 42
>pdb|2EHE|A Chain A, Solution Structure Of The First Lim Domain From Human
Four And A Half Lim Domains Protein 3
Length = 82
Score = 28.1 bits (61), Expect = 1.4, Method: Compositional matrix adjust.
Identities = 14/43 (32%), Positives = 20/43 (46%)
Query: 51 DGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLFIS 93
+ + FH CFRC +C L E +T + L C + F S
Sbjct: 35 EDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSS 77
>pdb|1NYP|A Chain A, 4th Lim Domain Of Pinch Protein
pdb|1U5S|B Chain B, Nmr Structure Of The Complex Between Nck-2 Sh3 Domain
And Pinch-1 Lim4 Domain
Length = 66
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 18/60 (30%), Positives = 26/60 (43%), Gaps = 5/60 (8%)
Query: 34 LCFACNKKVYPLEK--IETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQLF 91
+C AC + P+E + GK +H F C +C + G YC H+ QLF
Sbjct: 7 ICGACRR---PIEGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLF 63
>pdb|1X68|A Chain A, Solution Structures Of The C-Terminal Lim Domain Of
Human Fhl5 Protein
Length = 76
Score = 27.7 bits (60), Expect = 1.6, Method: Compositional matrix adjust.
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 3/55 (5%)
Query: 32 SSLCFACNKKVYPLEK---IETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYC 83
SS C AC+K + L I +H CF C +C L + + N ++C
Sbjct: 5 SSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFC 59
>pdb|1FCX|A Chain A, Isotype Selectivity Of The Human Retinoic Acid Nuclear
Receptor Hrar: The Complex With The Rargamma-Selective
Retinoid Bms184394
pdb|1FCZ|A Chain A, Isotype Selectivity Of The Human Retinoic Acid Nuclear
Receptor Hrar: The Complex With The Panagonist Retinoid
Bms181156
pdb|1FD0|A Chain A, Isotype Selectivity Of The Human Retinoic Acid Nuclear
Receptor Hrar: The Complex With The Rargamma-Selective
Retinoid Sr11254
Length = 235
Score = 27.7 bits (60), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 16 IILNQPEAPSNGTGNPSSLCFACNKKVYPLEKIETDGKLFHRACFRC 62
+ LN+ + + G G + L FA ++ PLE +T+ L C C
Sbjct: 110 LTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLIC 156
>pdb|2LBD|A Chain A, Ligand-Binding Domain Of The Human Retinoic Acid Receptor
Gamma Bound To All-Trans Retinoic Acid
pdb|3LBD|A Chain A, Ligand-binding Domain Of The Human Retinoic Acid Receptor
Gamma Bound To 9-cis Retinoic Acid
pdb|4LBD|A Chain A, Ligand-binding Domain Of The Human Retinoic Acid Receptor
Gamma Bound To The Synthetic Agonist Bms961
Length = 267
Score = 27.3 bits (59), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 16 IILNQPEAPSNGTGNPSSLCFACNKKVYPLEKIETDGKLFHRACFRC 62
+ LN+ + + G G + L FA ++ PLE +T+ L C C
Sbjct: 136 LTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLIC 182
>pdb|2XJY|A Chain A, Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21
Crystal Form
pdb|2XJZ|A Chain A, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|B Chain B, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|C Chain C, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|D Chain D, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
pdb|2XJZ|E Chain E, Crystal Structure Of The Lmo2:ldb1-Lid Complex, C2 Crystal
Form
Length = 131
Score = 27.3 bits (59), Expect = 1.9, Method: Compositional matrix adjust.
Identities = 11/37 (29%), Positives = 19/37 (51%), Gaps = 1/37 (2%)
Query: 30 NPSSLCFACNKKVYPLE-KIETDGKLFHRACFRCTQC 65
LC +C+K++ E + K++H CF+C C
Sbjct: 64 GQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAAC 100
>pdb|1FCY|A Chain A, Isotype Selectivity Of The Human Retinoic Acid Nuclear
Receptor Hrar: The Complex With The RarbetaGAMMA-
Selective Retinoid Cd564
Length = 236
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 16 IILNQPEAPSNGTGNPSSLCFACNKKVYPLEKIETDGKLFHRACFRC 62
+ LN+ + + G G + L FA ++ PLE +T+ L C C
Sbjct: 111 LTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLIC 157
>pdb|1EXA|A Chain A, Enantiomer Discrimination Illustrated By Crystal
Structures Of The Human Retinoic Acid Receptor Hrargamma
Ligand Binding Domain: The Complex With The Active
R-Enantiomer Bms270394.
pdb|1EXX|A Chain A, Enantiomer Discrimination Illustrated By Crystal
Structures Of The Human Retinoic Acid Receptor Hrargamma
Ligand Binding Domain: The Complex With The Inactive
S-Enantiomer Bms270395
Length = 246
Score = 27.3 bits (59), Expect = 2.0, Method: Compositional matrix adjust.
Identities = 14/47 (29%), Positives = 23/47 (48%)
Query: 16 IILNQPEAPSNGTGNPSSLCFACNKKVYPLEKIETDGKLFHRACFRC 62
+ LN+ + + G G + L FA ++ PLE +T+ L C C
Sbjct: 115 LTLNRTQMHNAGFGPLTDLVFAFAGQLLPLEMDDTETGLLSAICLIC 161
>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin
Length = 80
Score = 26.6 bits (57), Expect = 3.3, Method: Compositional matrix adjust.
Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 5/57 (8%)
Query: 35 CFACNKKVYP--LEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQ 89
C CN+ V L ++T ++H CF C C T S+ +G +C H+
Sbjct: 18 CGGCNRPVLENYLSAMDT---VWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHH 71
>pdb|2DAR|A Chain A, Solution Structure Of First Lim Domain Of Enigma-Like
Pdz And Lim Domains Protein
Length = 90
Score = 26.6 bits (57), Expect = 3.9, Method: Compositional matrix adjust.
Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 3/67 (4%)
Query: 28 TGNPSSLCFACNKKVY-PLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPH 86
G + +C CN+ + P + GK +H F C C + + G LYC
Sbjct: 21 AGKRTPMCAHCNQVIRGPF--LVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELC 78
Query: 87 FKQLFIS 93
+++ F S
Sbjct: 79 YEKFFAS 85
>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 = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 32 SSLCFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLR-MESYTMNNGHLYC 83
S C AC + + E + G ++H CF C+ C L + + NG L+C
Sbjct: 67 SGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFC 120
>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid
Domain
Length = 188
Score = 26.6 bits (57), Expect = 4.0, Method: Compositional matrix adjust.
Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 2/54 (3%)
Query: 32 SSLCFACNKKVYPLEKI-ETDGKLFHRACFRCTQCCTVLR-MESYTMNNGHLYC 83
S C AC + + E + G ++H CF C+ C L + + NG L+C
Sbjct: 69 SGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFC 122
>pdb|1XAP|A Chain A, Structure Of The Ligand Binding Domain Of The Retinoic
Acid Receptor Beta
pdb|4DM6|A Chain A, Crystal Structure Of Rarb Lbd Homodimer In Complex With
Ttnpb
pdb|4DM6|B Chain B, Crystal Structure Of Rarb Lbd Homodimer In Complex With
Ttnpb
pdb|4DM8|A Chain A, Crystal Structure Of Rarb Lbd In Complex With 9cis
Retinoic Acid
pdb|4DM8|B Chain B, Crystal Structure Of Rarb Lbd In Complex With 9cis
Retinoic Acid
Length = 267
Score = 26.2 bits (56), Expect = 4.6, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 22/47 (46%)
Query: 16 IILNQPEAPSNGTGNPSSLCFACNKKVYPLEKIETDGKLFHRACFRC 62
+ LN+ + + G G + L F ++ PLE +T+ L C C
Sbjct: 136 LTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLIC 182
>pdb|2EGQ|A Chain A, Solution Structure Of The Fourth Lim Domain From Human
Four And A Half Lim Domains 1
Length = 77
Score = 26.2 bits (56), Expect = 5.0, Method: Compositional matrix adjust.
Identities = 11/43 (25%), Positives = 21/43 (48%)
Query: 48 IETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQL 90
+ +G+ +H CF C +C L + + + +YC K+L
Sbjct: 35 VAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKKL 77
>pdb|2XQN|T Chain T, Complex Of The 2nd And 3rd Lim Domains Of Tes With The
Evh1 Domain Of Mena And The N-Terminal Domain Of
Actin-Like Protein Arp7a
Length = 126
Score = 26.2 bits (56), Expect = 5.1, Method: Compositional matrix adjust.
Identities = 14/53 (26%), Positives = 25/53 (47%)
Query: 35 CFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLPHF 87
C C++ ++ E + + + +H F C C ++L E Y M N C P +
Sbjct: 6 CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCY 58
>pdb|2D8X|A Chain A, Solution Structure Of The Second Lim Domain Of
Particularly Interesting New Cys-His Protein (Pinch)
Length = 70
Score = 25.8 bits (55), Expect = 6.0, Method: Compositional matrix adjust.
Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 1/54 (1%)
Query: 32 SSLCFACNKKVYPLEKIETDGKLFHRACFRCTQCCTVLRMESYTMNNGHLYCLP 85
SS C C + + I+ +H CFRC C VL + N G C P
Sbjct: 5 SSGCHQCGEFIIG-RVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRP 57
>pdb|1XDK|B Chain B, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING
Domain Heterodimer In Complex With 9-Cis Retinoic Acid
And A Fragment Of The Trap220 Coactivator
pdb|1XDK|F Chain F, Crystal Structure Of The RarbetaRXRALPHA LIGAND BINDING
Domain Heterodimer In Complex With 9-Cis Retinoic Acid
And A Fragment Of The Trap220 Coactivator
Length = 303
Score = 25.4 bits (54), Expect = 7.4, Method: Compositional matrix adjust.
Identities = 13/47 (27%), Positives = 22/47 (46%)
Query: 16 IILNQPEAPSNGTGNPSSLCFACNKKVYPLEKIETDGKLFHRACFRC 62
+ LN+ + + G G + L F ++ PLE +T+ L C C
Sbjct: 138 LTLNRTQMHNAGFGPLTDLVFTFANQLLPLEMDDTETGLLSAICLIC 184
>pdb|1X62|A Chain A, Solution Structure Of The Lim Domain Of Carboxyl
Terminal Lim Domain Protein 1
Length = 79
Score = 25.4 bits (54), Expect = 7.9, Method: Compositional matrix adjust.
Identities = 10/34 (29%), Positives = 17/34 (50%)
Query: 56 HRACFRCTQCCTVLRMESYTMNNGHLYCLPHFKQ 89
H C+ CT C T L+ + + +YC H ++
Sbjct: 38 HPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARE 71
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 0.135 0.439
Lambda K H
0.267 0.0410 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3,815,100
Number of Sequences: 62578
Number of extensions: 139774
Number of successful extensions: 288
Number of sequences better than 100.0: 48
Number of HSP's better than 100.0 without gapping: 40
Number of HSP's successfully gapped in prelim test: 8
Number of HSP's that attempted gapping in prelim test: 241
Number of HSP's gapped (non-prelim): 50
length of query: 117
length of database: 14,973,337
effective HSP length: 80
effective length of query: 37
effective length of database: 9,967,097
effective search space: 368782589
effective search space used: 368782589
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: 45 (21.9 bits)