RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy10849
(267 letters)
>2l3k_A Rhombotin-2, linker, LIM domain-binding protein 1;
LMO2(LIM2)-LDB1(LID), chimera, fusion protein,
oncoprotein; NMR {Mus musculus} PDB: 2l6y_B 2l6z_C
Length = 123
Score = 105 bits (264), Expect = 4e-29
Identities = 33/117 (28%), Positives = 53/117 (45%), Gaps = 7/117 (5%)
Query: 15 FRLYGVK--CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFC 72
RL+G CA C R+ +EM MR + VYHL CF C C + G++++L + + C
Sbjct: 2 LRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIVC 61
Query: 73 RQDFEKEMYLMQQSSPSDDM----MLDENCRPRDGRRGPKRPRTILTSAQRRQFKSS 125
QD + + S S M+ G G + R ++T + QF ++
Sbjct: 62 EQDIYEWTKINGGSGGSGGSGGDVMVVGEPTLMGGEFGDEDER-LITRLENTQFDAA 117
>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding
protein 1; B-tandem zipper, protein binding; 1.30A {Mus
musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB:
2dfy_X 2xjz_I 2xjy_B
Length = 188
Score = 89.7 bits (222), Expect = 3e-22
Identities = 35/132 (26%), Positives = 53/132 (40%), Gaps = 9/132 (6%)
Query: 3 SHNSHVSCHPRGFRLYGV--KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKG 60
+ + + C RL+G C+ CG + E+VMRAQ +VYHL CF C C L G
Sbjct: 51 TKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPG 110
Query: 61 EQFILRSGQLFCRQDFEKEM------YLMQQSSPSDDMMLDENCRPRD-GRRGPKRPRTI 113
++F +G LFC D + S + P G +
Sbjct: 111 DRFHYINGSLFCEHDRPTALINGHLNSGGSGGSGGSGGDVMVVGEPTLMGGEFGDEDERL 170
Query: 114 LTSAQRRQFKSS 125
+T + QF ++
Sbjct: 171 ITRLENTQFDAA 182
Score = 47.3 bits (112), Expect = 9e-07
Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 2/61 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL-QKGEQFILRSGQLFCRQDFEKE 79
+CA CG ++ ++ A +H C C C L G +SG + CR D+ +
Sbjct: 7 RCAGCGGKIAD-RFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 65
Query: 80 M 80
Sbjct: 66 F 66
>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene,
transcription, developmental protein; 2.40A {Homo
sapiens} PDB: 2xjz_A
Length = 131
Score = 86.7 bits (215), Expect = 1e-21
Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 2/68 (2%)
Query: 15 FRLYGVK--CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFC 72
RL+G CA C R+ +EM MR + VYHL CF C C + G++++L + + C
Sbjct: 60 LRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVC 119
Query: 73 RQDFEKEM 80
QD +
Sbjct: 120 EQDIYEWT 127
Score = 51.7 bits (124), Expect = 1e-08
Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 2/59 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL-QKGEQFILRSGQLFCRQDFEK 78
C C + ++A +H C C +C L + G + + G+ CR+D+ +
Sbjct: 4 TCGGCQQNIGD-RYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 61
>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3;
intramolecular (fusion) protein-protein complex, protein
binding/transcription complex; NMR {Mus musculus}
Length = 182
Score = 84.2 bits (208), Expect = 3e-20
Identities = 27/67 (40%), Positives = 41/67 (61%), Gaps = 1/67 (1%)
Query: 15 FRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQF-ILRSGQLFCR 73
F+ +G KCA C + P ++V RAQ VYHL CF CV+C + L G++F ++ +L C+
Sbjct: 115 FKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCK 174
Query: 74 QDFEKEM 80
D+E
Sbjct: 175 ADYETAK 181
Score = 52.2 bits (125), Expect = 1e-08
Identities = 18/76 (23%), Positives = 27/76 (35%), Gaps = 3/76 (3%)
Query: 3 SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
G CA C +L +++A +H C C C PL E+
Sbjct: 44 DEGGSGGHMGSGGTPEIPMCAGCDQHIL-DRFILKALDRHWHSKCLKCSDCHVPL--AER 100
Query: 63 FILRSGQLFCRQDFEK 78
R ++C+ DF K
Sbjct: 101 CFSRGESVYCKDDFFK 116
>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein
ISL-1; protein-protein complex, LIM domain, Zn finger,
activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A
Length = 169
Score = 81.8 bits (202), Expect = 2e-19
Identities = 30/79 (37%), Positives = 44/79 (55%), Gaps = 1/79 (1%)
Query: 3 SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
S V C F+ +G KCA C + P ++V RAQ VYHL CF CV+C + L G++
Sbjct: 49 SRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDE 108
Query: 63 F-ILRSGQLFCRQDFEKEM 80
F ++ +L C+ D+E
Sbjct: 109 FYLMEDSRLVCKADYETAK 127
Score = 47.5 bits (113), Expect = 5e-07
Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
CA C +L +++A +H C C C PL E+ R ++C+ DF K
Sbjct: 8 MCAGCDQHIL-DRFILKALDRHWHSKCLKCSDCHVPL--AERCFSRGESVYCKDDFFK 62
Score = 29.8 bits (67), Expect = 0.51
Identities = 7/47 (14%), Positives = 9/47 (19%), Gaps = 2/47 (4%)
Query: 4 HNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVC 50
+S + C G M A S H
Sbjct: 113 EDSRLVCKADYETAKQGGSGGSGGSG--GGTPMVAASPERHDGGLQA 157
>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion,
acrosom; 2.62A {Homo sapiens}
Length = 126
Score = 69.0 bits (169), Expect = 4e-15
Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 3/68 (4%)
Query: 15 FRLYGVKCARCGDRLLPHEMVMRAQSHVYHLP--CFVCVICCQPLQKGEQFILRSGQLFC 72
+ + V C C + + P + + +H CF+C C + L G++F+ G +FC
Sbjct: 59 VKNHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVEGMVFC 117
Query: 73 RQDFEKEM 80
+ +K M
Sbjct: 118 SVECKKRM 125
Score = 53.9 bits (130), Expect = 1e-09
Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 2/58 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
+CA C D L+ +A++ +HL F C C L GE +++ + + C+ + K
Sbjct: 5 RCAGC-DELIFSNEYTQAENQNWHLKHFCCFDCDSILA-GEIYVMVNDKPVCKPCYVK 60
>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo
sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 77
Score = 64.3 bits (157), Expect = 7e-14
Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 1/63 (1%)
Query: 16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
L C RC P E ++ + +YH CFVC C Q F G+ +C D
Sbjct: 8 ALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP-EGLFYEFEGRKYCEHD 66
Query: 76 FEK 78
F+
Sbjct: 67 FQM 69
>1x6a_A LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc finger domain,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
g.39.1.3 g.39.1.3
Length = 81
Score = 64.4 bits (157), Expect = 7e-14
Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 3/74 (4%)
Query: 6 SHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL 65
S S + +G C C + M A YH CF C+ C ++ G+ + L
Sbjct: 2 SSGSSGKDYWGKFGEFCHGCSLLMTG--PFMVAGEFKYHPECFACMSCKVIIEDGDAYAL 59
Query: 66 R-SGQLFCRQDFEK 78
L+C + +
Sbjct: 60 VQHATLYCGKCHNE 73
>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1;
ILK, integrin-linked kinase, pinch, ankyrin repeat,
ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B
Length = 72
Score = 64.0 bits (156), Expect = 8e-14
Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 1/63 (1%)
Query: 16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
C RC P E ++ + +YH CFVC C Q F G+ +C D
Sbjct: 8 GSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP-EGLFYEFEGRKYCEHD 66
Query: 76 FEK 78
F+
Sbjct: 67 FQM 69
>1x61_A Thyroid receptor interacting protein 6; LIM domain,
OPA-interacting protein 1, zyxin related protein 1
(ZRP-1), structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 72
Score = 62.8 bits (153), Expect = 2e-13
Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
C CG+ ++ + A V+H+ CFVC C L+ G+ F + +C +
Sbjct: 7 GCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLR-GQHFYAVERRAYCEGCYVA 63
>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM
domains protein 1, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 82
Score = 62.4 bits (152), Expect = 4e-13
Identities = 16/73 (21%), Positives = 25/73 (34%), Gaps = 1/73 (1%)
Query: 6 SHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL 65
S S R KC C ++ + + + V+H CF C C Q + F
Sbjct: 2 SSGSSGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIG-TGSFFP 60
Query: 66 RSGQLFCRQDFEK 78
+ +C E
Sbjct: 61 KGEDFYCVTCHET 73
>1v6g_A Actin binding LIM protein 2; LIM domain, zinc binding domain,
ablim2, structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo
sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 81
Score = 61.0 bits (148), Expect = 1e-12
Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 2/60 (3%)
Query: 15 FRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQ 74
RLYG +C C + V+ A YH CFVC +C P G++ + C++
Sbjct: 11 QRLYGTRCFSCDQFIE--GEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQK 68
>2ehe_A Four and A half LIM domains 3; FHL-3, skeletal muscle LIM-
protein 2, SLIM 2, FHL3, SLIM2, structural genomics,
NPPSFA; NMR {Homo sapiens}
Length = 82
Score = 59.4 bits (144), Expect = 5e-12
Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 1/75 (1%)
Query: 6 SHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL 65
S S P + CA C + + + +H CF C C + L E F
Sbjct: 2 SSGSSGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLA-DEPFTC 60
Query: 66 RSGQLFCRQDFEKEM 80
+ +L C +
Sbjct: 61 QDSELLCNDCYCSAF 75
>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3
g.39.1.3
Length = 72
Score = 58.9 bits (143), Expect = 5e-12
Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 1/59 (1%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKE 79
C C ++P M + +H CF+C C QP+ + FI + Q FC +EK+
Sbjct: 7 GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPI-GTKSFIPKDNQNFCVPCYEKQ 64
>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken
structural genomics/proteomics initiative, RSGI,
NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 72
Score = 57.4 bits (139), Expect = 2e-11
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
C+ CG+ ++P + +H CF+C C QPL F+ G +C +E
Sbjct: 7 GCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLG-SRSFVPDKGAHYCVPCYEN 63
>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein
1, LIM domain, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3
Length = 101
Score = 57.4 bits (139), Expect = 5e-11
Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 1/62 (1%)
Query: 18 YGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFE 77
C C + + ++ +H CF C C PL E F+ + ++ C +
Sbjct: 4 GSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLA-NETFVAKDNKILCNKCTT 62
Query: 78 KE 79
+E
Sbjct: 63 RE 64
Score = 54.0 bits (130), Expect = 8e-10
Identities = 9/51 (17%), Positives = 20/51 (39%)
Query: 3 SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVIC 53
+ ++ + C+ R KC C ++ + + + V+H CF
Sbjct: 50 AKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100
>2cuq_A Four and A half LIM domains 3; structural genomics, NPPSFA,
national project on protein structural and functional
analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 80
Score = 55.8 bits (135), Expect = 1e-10
Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 3/73 (4%)
Query: 6 SHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL 65
S S P + +CARC L + + + +H C VC C PL G+QF
Sbjct: 2 SSGSSGPCYENKFAPRCARCSKTLT--QGGVTYRDQPWHRECLVCTGCQTPLA-GQQFTS 58
Query: 66 RSGQLFCRQDFEK 78
R +C F +
Sbjct: 59 RDEDPYCVACFGE 71
>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM
domain, structural genomics, NPPSFA; NMR {Homo sapiens}
SCOP: g.39.1.3 g.39.1.3
Length = 80
Score = 55.0 bits (133), Expect = 2e-10
Identities = 19/73 (26%), Positives = 26/73 (35%), Gaps = 3/73 (4%)
Query: 6 SHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL 65
S S ++ KC C +L E + A V+H CFVC C F
Sbjct: 2 SSGSSGKDFLAMFSPKCGGCNRPVL--ENYLSAMDTVWHPECFVCGDCFTSFS-TGSFFE 58
Query: 66 RSGQLFCRQDFEK 78
G+ FC +
Sbjct: 59 LDGRPFCELHYHH 71
>2egq_A FHL1 protein; LIM domain, four and A half LIM domains protein 1,
skeletal muscle LIM- protein 1, SLIM 1, structural
genomics NPPSFA; NMR {Homo sapiens}
Length = 77
Score = 54.0 bits (130), Expect = 5e-10
Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 4/67 (5%)
Query: 15 FRLYGVKCARCG---DRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLF 71
KCA C V+ + +H CF C C L ++F+ Q++
Sbjct: 11 KNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLA-NKRFVFHQEQVY 69
Query: 72 CRQDFEK 78
C +K
Sbjct: 70 CPDCAKK 76
>1nyp_A Pinch protein; LIM domain, protein recognition, cell adhesion;
NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 PDB: 1u5s_B
Length = 66
Score = 51.5 bits (124), Expect = 3e-09
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 3/58 (5%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
C C + V+ A +H+ FVC C +P G + R G +C + +
Sbjct: 7 ICGACRRPIE--GRVVNAMGKQWHVEHFVCAKCEKPFL-GHRHYERKGLAYCETHYNQ 61
>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3
g.39.1.3
Length = 72
Score = 51.0 bits (122), Expect = 4e-09
Identities = 13/64 (20%), Positives = 20/64 (31%), Gaps = 3/64 (4%)
Query: 17 LYGVKCARCGD--RLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQ 74
CA C + L + + +H CF C C L G F+ + C
Sbjct: 3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL-VGRGFLTERDDILCPD 61
Query: 75 DFEK 78
+
Sbjct: 62 CGKD 65
>2dj7_A Actin-binding LIM protein 3; LIM domain, Zn binding protein,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
g.39.1.3 g.39.1.3
Length = 80
Score = 50.5 bits (121), Expect = 8e-09
Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 4/74 (5%)
Query: 5 NSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFI 64
+S S P R CA C + + + + A +H+ CF C C L ++I
Sbjct: 2 SSGSSGKPIKIR-GPSHCAGCKEEIKHGQ-SLLALDKQWHVSCFKCQTCSVIL--TGEYI 57
Query: 65 LRSGQLFCRQDFEK 78
+ G +C D+
Sbjct: 58 SKDGVPYCESDYHA 71
>2dar_A PDZ and LIM domain protein 5; enigma homolog protein, structural
genomics, NPPSFA, national project on protein
structural and functional analyses; NMR {Homo sapiens}
SCOP: g.39.1.3 g.39.1.3
Length = 90
Score = 50.5 bits (121), Expect = 1e-08
Identities = 16/79 (20%), Positives = 25/79 (31%), Gaps = 4/79 (5%)
Query: 1 STSHNSHVSCHPRGFR-LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQK 59
S ++ V CA C + + A +H F C C +
Sbjct: 6 SGDQDTLVQRAEHIPAGKRTPMCAHCNQVIR--GPFLVALGKSWHPEEFNCAHCKNTMA- 62
Query: 60 GEQFILRSGQLFCRQDFEK 78
F+ G L+C +EK
Sbjct: 63 YIGFVEEKGALYCELCYEK 81
>2dlo_A Thyroid receptor-interacting protein 6; LIM domain,
OPA-interacting protein 1, zyxin related protein 1
(ZRP-1), structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 81
Score = 50.1 bits (120), Expect = 1e-08
Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 2/58 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
KCA C +L + ++RA YH CF CV+C + L + + Q+ C +DF +
Sbjct: 17 KCATCSQPIL--DRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHR 72
>2d8z_A Four and A half LIM domains 2; skeletal muscle LIM-protein 3,
LIM-domain protein DRAL, structural genomics, NPPSFA;
NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 70
Score = 49.3 bits (118), Expect = 2e-08
Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 3/58 (5%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
C +C + + + +H CFVC C + L G++F R +C F
Sbjct: 7 GCVQCKKPIT--TGGVTYREQPWHKECFVCTACRKQLS-GQRFTARDDFAYCLNCFCD 61
>1a7i_A QCRP2 (LIM1); LIM domain containing proteins, metal-binding
protein, zinc finger; NMR {Coturnix japonica} SCOP:
g.39.1.3 g.39.1.3 PDB: 2o10_A
Length = 81
Score = 49.7 bits (119), Expect = 2e-08
Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 2/58 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
KC CG + E V +H CF+C++C + L + +++C+ + K
Sbjct: 9 KCGACGRTVYHAEEVQ-CDGRSFHRCCFLCMVCRKNLDSTT-VAIHDAEVYCKSCYGK 64
>2cur_A Skeletal muscle LIM-protein 1; four and A half LIM domains
protein 1, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 69
Score = 48.9 bits (117), Expect = 3e-08
Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 3/58 (5%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
C +C + + Q +H CFVCV C + L G++F Q +C ++
Sbjct: 7 GCVKCNKAIT--SGGITYQDQPWHADCFVCVTCSKKLA-GQRFTAVEDQYYCVDCYKN 61
>2d8x_A Protein pinch; LIM domain, pinch protein, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3
g.39.1.3
Length = 70
Score = 48.6 bits (116), Expect = 3e-08
Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 3/60 (5%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80
C +CG+ ++ V++A ++ +H CF C +C + L F+ +G+ CR +E
Sbjct: 7 GCHQCGEFII--GRVIKAMNNSWHPECFRCDLCQEVLADIG-FVKNAGRHLCRPCHNREK 63
>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle;
NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3
g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A
Length = 192
Score = 51.2 bits (122), Expect = 4e-08
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 2/70 (2%)
Query: 9 SCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSG 68
+ C RCG + E V+ +H CF C C + L+ + G
Sbjct: 105 ASRMAQKVGGSDGCPRCGQAVYAAEKVI-GAGKSWHKSCFRCAKCGKSLE-STTLADKDG 162
Query: 69 QLFCRQDFEK 78
+++C+ + K
Sbjct: 163 EIYCKGCYAK 172
Score = 44.2 bits (104), Expect = 9e-06
Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 2/59 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKE 79
KC C + E V + + +H CF+C++C + L + +++C+ + K+
Sbjct: 9 KCGVCQKAVYFAEEV-QCEGSSFHKSCFLCMVCKKNLD-STTVAVHGDEIYCKSCYGKK 65
>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the
N-terminal LIM domain of LMO4...; fusion protein, LMO
proteins, metal binding protein; NMR {Mus musculus}
SCOP: g.39.1.3 g.39.1.3
Length = 122
Score = 49.6 bits (118), Expect = 5e-08
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 2/63 (3%)
Query: 17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL-QKGEQFILRSGQLFCRQD 75
L +CA CG ++ ++ A +H C C C L G +SG + CR D
Sbjct: 3 LSWKRCAGCGGKIA-DRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRND 61
Query: 76 FEK 78
+ +
Sbjct: 62 YIR 64
Score = 36.5 bits (84), Expect = 0.002
Identities = 11/77 (14%), Positives = 22/77 (28%), Gaps = 17/77 (22%)
Query: 15 FRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQ 74
RL+G A S + ++ +P G +F +L R
Sbjct: 63 IRLFGNSGA--------------GGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRL 108
Query: 75 DFEKEMYLMQQSSPSDD 91
+ + + D+
Sbjct: 109 ENTQ---FDAANGIDDE 122
>1x68_A FHL5 protein; four-and-A-half LIM protein 5, zinc finger domain,
AN actin- interacting protein, structural genomics,
NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 76
Score = 47.9 bits (114), Expect = 6e-08
Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 3/65 (4%)
Query: 17 LYGVKCARCGD--RLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQ 74
C C L + Q +H CF C C L G+ F+ ++ ++FC++
Sbjct: 3 SGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLV-GKGFLTQNKEIFCQK 61
Query: 75 DFEKE 79
Sbjct: 62 CGSGM 66
>2d8y_A Eplin protein; LIM domain, epithelial protein LOST in neoplasm,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
g.39.1.3 g.39.1.3
Length = 91
Score = 48.3 bits (115), Expect = 7e-08
Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 2/58 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
C C + P E ++ A V+H+ CF C C L G + G+++C+ F +
Sbjct: 17 TCVECQKTVYPMERLL-ANQQVFHISCFRCSYCNNKLSLGT-YASLHGRIYCKPHFNQ 72
>1x62_A C-terminal LIM domain protein 1; PDZ and LIM domain protein 1,
LIM domain protein CLP-36, contractIle protein,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
g.39.1.3 g.39.1.3
Length = 79
Score = 47.4 bits (113), Expect = 1e-07
Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 3/58 (5%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
C +CG ++ + ++ + H C+VC C L K + Q++C + +
Sbjct: 17 MCDKCGTGIV--GVFVKLRDRHRHPECYVCTDCGTNL-KQKGHFFVEDQIYCEKHARE 71
>2co8_A NEDD9 interacting protein with calponin homology and LIM domains;
zinc finger protein, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 82
Score = 47.3 bits (112), Expect = 2e-07
Identities = 17/61 (27%), Positives = 23/61 (37%), Gaps = 2/61 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGE-QFILRSGQLFCRQDFEKE 79
CA CG+ L E + H +H CF C C L G + G +C Q +
Sbjct: 17 LCALCGEHLYVLERLC-VNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQT 75
Query: 80 M 80
Sbjct: 76 D 76
>2l4z_A DNA endonuclease RBBP8, LIM domain transcription LMO4;
protein-protein interaction, LIM-interaction DOM LMO4,
RBBP8/CTIP, LIM-only protein; HET: DNA; NMR {Homo
sapiens}
Length = 123
Score = 48.2 bits (114), Expect = 2e-07
Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 2/79 (2%)
Query: 1 STSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL-QK 59
S H L +CA CG ++ ++ A +H C C C L
Sbjct: 43 SKLGGGGSGGHMGSGGLSWKRCAGCGGKIADRF-LLYAMDSYWHSRCLKCSSCQAQLGDI 101
Query: 60 GEQFILRSGQLFCRQDFEK 78
G +SG + CR D+ +
Sbjct: 102 GTSSYTKSGMILCRNDYIR 120
>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM
domain 3, structural genomics, NPPSFA; NMR {Mus
musculus} SCOP: g.39.1.3 g.39.1.3
Length = 89
Score = 46.7 bits (111), Expect = 2e-07
Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 3/58 (5%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
C +CG ++ V++A+ H CFVC C L K + + G+L+C
Sbjct: 27 LCDKCGSGIV--GAVVKARDKYRHPECFVCADCNLNL-KQKGYFFVEGELYCETHARA 81
>1iml_A CRIP, cysteine rich intestinal protein; metal-binding protein,
LIM domain protein; NMR {Rattus rattus} SCOP: g.39.1.3
g.39.1.3
Length = 76
Score = 45.8 bits (109), Expect = 4e-07
Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 2/61 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80
KC +C + E V + +H PC C C + L G+ +C M
Sbjct: 2 KCPKCDKEVYFAERVT-SLGKDWHRPCLKCEKCGKTL-TSGGHAEHEGKPYCNHPCYSAM 59
Query: 81 Y 81
+
Sbjct: 60 F 60
>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1;
LIM-interaction-domain (LID), metal binding protein;
NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3
Length = 114
Score = 46.6 bits (110), Expect = 4e-07
Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 2/59 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL-QKGEQFILRSGQLFCRQDFEK 78
C C + ++A +H C C +C L + G + + G+ CR+D+ +
Sbjct: 5 TCGGCQQNIG-DRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 62
Score = 33.5 bits (76), Expect = 0.019
Identities = 5/62 (8%), Positives = 10/62 (16%), Gaps = 2/62 (3%)
Query: 3 SHNSHVSCHPRGFRLYGVKCARCGDR--LLPHEMVMRAQSHVYHLPCFVCVICCQPLQKG 60
C RL G ++ E + + +
Sbjct: 49 YKLGRKLCRRDYLRLGGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQFDAA 108
Query: 61 EQ 62
Sbjct: 109 NG 110
>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics; NMR {Homo sapiens}
Length = 80
Score = 44.4 bits (105), Expect = 1e-06
Identities = 9/35 (25%), Positives = 15/35 (42%)
Query: 102 DGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKV 136
+ + KR RT +T Q + + P RK+
Sbjct: 12 EEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKM 46
Score = 30.9 bits (70), Expect = 0.082
Identities = 9/30 (30%), Positives = 14/30 (46%)
Query: 141 SKRAKNILTPNQRRQFKSSFEISSMPCRKV 170
KR + +TP Q + + S P RK+
Sbjct: 17 DKRLRTTITPEQLEILYQKYLLDSNPTRKM 46
>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
g.39.1.3 g.39.1.3
Length = 76
Score = 44.3 bits (105), Expect = 1e-06
Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 2/55 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
KC +C + E V + +H C C C + L G G+ FC +
Sbjct: 11 KCPKCDKTVYFAEKVS-SLGKDWHKFCLKCERCSKTLTPGG-HAEHDGKPFCHKP 63
>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics; NMR {Homo sapiens}
Length = 70
Score = 43.1 bits (102), Expect = 3e-06
Identities = 10/34 (29%), Positives = 16/34 (47%)
Query: 103 GRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKV 136
KRPRT +T Q R + F+++ P +
Sbjct: 3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQ 36
Score = 30.4 bits (69), Expect = 0.095
Identities = 9/34 (26%), Positives = 18/34 (52%)
Query: 137 STMNSKRAKNILTPNQRRQFKSSFEISSMPCRKV 170
S + KR + +T +Q R + F+I++ P +
Sbjct: 3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQ 36
>2iyb_E Testin, TESS, TES; LIM domain, SH3-binding, tumour supressor LIM
domain EVH1 DO cell motility, phosphorylation,
cytoskeleton; 2.35A {Homo sapiens}
Length = 65
Score = 42.5 bits (100), Expect = 5e-06
Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 3/65 (4%)
Query: 18 YGVKCARCGDRLLPHEMVMRAQSHVYHLP--CFVCVICCQPLQKGEQFILRSGQLFCRQD 75
+ V C C + + P + + +H CF+C C + L G++F+ G +FC +
Sbjct: 1 HAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI-GQKFMPVEGMVFCSVE 59
Query: 76 FEKEM 80
+K M
Sbjct: 60 CKKRM 64
>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary,
CPHD, POU domain, transcription factor,
transcription/DNA complex; HET: DNA; 2.30A {Rattus
norvegicus} SCOP: a.4.1.1 a.35.1.1
Length = 146
Score = 41.1 bits (96), Expect = 6e-05
Identities = 11/119 (9%), Positives = 29/119 (24%), Gaps = 12/119 (10%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80
K R + + + + LQ ++ K
Sbjct: 13 KVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLS------------FKNACKLK 60
Query: 81 YLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM 139
++ + + + ++ RT ++ A + + F KP +
Sbjct: 61 AILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMR 119
>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein,
structural genomics, riken structural
genomics/proteomics initiative, RSGI; NMR {Homo
sapiens} SCOP: g.39.1.3 g.39.1.3
Length = 73
Score = 39.3 bits (91), Expect = 6e-05
Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 2/52 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFC 72
C C + V+ A YH C +CV C Q +GE+ L+ ++
Sbjct: 7 GCDSCEKYIT--GRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWH 56
>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein,
homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP:
a.4.1.1
Length = 66
Score = 38.1 bits (89), Expect = 2e-04
Identities = 7/30 (23%), Positives = 14/30 (46%)
Query: 107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKV 136
R RT+L Q ++ + +P+P +
Sbjct: 3 TTRVRTVLNEKQLHTLRTCYAANPRPDALM 32
Score = 26.2 bits (58), Expect = 2.9
Identities = 5/32 (15%), Positives = 13/32 (40%)
Query: 139 MNSKRAKNILTPNQRRQFKSSFEISSMPCRKV 170
M + R + +L Q ++ + + P +
Sbjct: 1 MKTTRVRTVLNEKQLHTLRTCYAANPRPDALM 32
>2cor_A Pinch protein; LIM domain, particularly interesting NEW Cys- His
protein, LIM and senescent cell antigen-like domains 1,
structural genomics; NMR {Homo sapiens} SCOP: g.39.1.3
g.39.1.3
Length = 79
Score = 38.2 bits (89), Expect = 2e-04
Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 4/57 (7%)
Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
C +C + E + ++ YH F C C + L G+L+C +K
Sbjct: 18 CQKCHAIID--EQPLIFKNDPYHPDHFNCANCGKEL--TADARELKGELYCLPCHDK 70
>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the
DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 35.9 bits (83), Expect = 0.001
Identities = 11/34 (32%), Positives = 13/34 (38%)
Query: 103 GRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKV 136
KR RT Q R KS F ++ P K
Sbjct: 3 SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKD 36
>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription
factor DNA complex, pore, stem cells; HET: DNA; 2.80A
{Mus musculus} PDB: 1ocp_A
Length = 155
Score = 37.0 bits (85), Expect = 0.002
Identities = 17/78 (21%), Positives = 32/78 (41%), Gaps = 1/78 (1%)
Query: 67 SGQLFCRQDFEKEMYLMQQSSPSDDMM-LDENCRPRDGRRGPKRPRTILTSAQRRQFKSS 125
+ QL + + L + +D+ L E + + KR RT + + R ++
Sbjct: 55 ALQLSLKNMSKLRPLLEKWVEEADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETM 114
Query: 126 FEVSPKPCRKVSTMNSKR 143
F SPKP + T + +
Sbjct: 115 FLKSPKPSLQQITHIANQ 132
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 35.8 bits (82), Expect = 0.006
Identities = 13/66 (19%), Positives = 22/66 (33%), Gaps = 9/66 (13%)
Query: 83 MQQSSPSDDMMLDE---------NCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPC 133
M + P + L+E N + ++ RT + + +S F PKP
Sbjct: 66 MCKLKPLLNKWLEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPS 125
Query: 134 RKVSTM 139
T
Sbjct: 126 AHEITG 131
>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU
domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP:
a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A
1oct_C* 1pou_A 1pog_A 1hdp_A
Length = 160
Score = 32.6 bits (74), Expect = 0.070
Identities = 12/62 (19%), Positives = 22/62 (35%)
Query: 78 KEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVS 137
+ S S N +G ++ RT + + R + SF + KP +
Sbjct: 72 NDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDI 131
Query: 138 TM 139
T+
Sbjct: 132 TL 133
>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis,
programmed cell death; HET: DTP; 6.90A {Drosophila
melanogaster} PDB: 3iz8_A*
Length = 1221
Score = 31.0 bits (69), Expect = 0.47
Identities = 33/250 (13%), Positives = 67/250 (26%), Gaps = 65/250 (26%)
Query: 32 HEMVMRAQSHVYH--------LPCFVCVICCQPLQKGEQFILRSGQ---LFCRQDFEKEM 80
H M H Y FV C+ +Q + IL + + +D
Sbjct: 5 HHMDFETGEHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGT 64
Query: 81 YLM------QQSSPSDDMM---LDEN-----CRPRDGRRGPKRPRTILTSAQRRQFKSSF 126
+ +Q + L N + +R P + + R + +
Sbjct: 65 LRLFWTLLSKQEEMVQKFVEEVLRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDN- 123
Query: 127 EVSPKPCRKVSTMNSKRAKNILTPNQRRQFKSSFEISSMPCRKVGVHGHYLSLGM----- 181
+V K N R + L + R ++ E+ V + G+
Sbjct: 124 QVFAK-------YNVSRLQPYL---KLR--QALLELRPAK--NVLID------GVLGSGK 163
Query: 182 -SLQDSSDSIFASSTKPLNPNHPY--------SPDDSYAMHSNDSFCSSDISLDESTNLD 232
+ + D + + + SP+ M I + ++ D
Sbjct: 164 TWV--ALDVCLSYKVQCKMDFKIFWLNLKNCNSPETVLEMLQK--LL-YQIDPNWTSRSD 218
Query: 233 EGGSDSLSLD 242
+ L +
Sbjct: 219 HSSNIKLRIH 228
>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics; NMR {Homo sapiens}
Length = 70
Score = 28.5 bits (64), Expect = 0.49
Identities = 7/28 (25%), Positives = 11/28 (39%)
Query: 105 RGPKRPRTILTSAQRRQFKSSFEVSPKP 132
+ RT T Q R + F+ + P
Sbjct: 5 SSGRSSRTRFTDYQLRVLQDFFDANAYP 32
>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
acyl-carrier-protein, beta-ketoacyl RED beta-ketoacyl
synthase, dehydratase; 4.00A {Saccharomyces cerevisiae}
Length = 2006
Score = 30.8 bits (69), Expect = 0.51
Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 8/58 (13%)
Query: 192 ASSTKPLNPNHP---YS---PDDSY--AMHSNDSFCSSDISLDESTNLDEGGSDSLSL 241
A ST+PL +H + P S+ A + F E D+ + L
Sbjct: 3 AYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADDEPTTPAEL 60
>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex,
helix-turn-helix (HTH), DNA-binding, homeobox, nucleus,
transcription regulation; 2.51A {Homo sapiens}
Length = 151
Score = 28.8 bits (64), Expect = 1.0
Identities = 9/54 (16%), Positives = 18/54 (33%)
Query: 79 EMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKP 132
E +L + + + + ++ RT T + FE +P P
Sbjct: 65 EKWLNEAELRNQEGQQNLMEFVGGEPSKKRKRRTSFTPQAIEALNAYFEKNPLP 118
>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding
proteins/DNA), complex, DNA- binding protein, DNA; HET:
DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB:
1f43_A 1yrn_A*
Length = 61
Score = 27.2 bits (61), Expect = 1.2
Identities = 3/32 (9%), Positives = 10/32 (31%)
Query: 104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRK 135
+ + ++ ++ R + F K
Sbjct: 2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSK 33
>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
photosynthetic reaction center, peripheral antenna; HET:
CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
Length = 154
Score = 28.8 bits (63), Expect = 1.4
Identities = 5/25 (20%), Positives = 10/25 (40%), Gaps = 6/25 (24%)
Query: 193 SSTKPLNPNHPYSPDDSYAMHSNDS 217
+S K Y+ D + A+ +
Sbjct: 27 ASLKL------YADDSAPALAIKAT 45
>3rft_A Uronate dehydrogenase; apoenzyme, rossmann fold, NAD binding,
oxidoreductase; 1.90A {Agrobacterium tumefaciens} PDB:
3rfv_A* 3rfx_A*
Length = 267
Score = 28.1 bits (63), Expect = 2.5
Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 11/43 (25%)
Query: 190 IFASS---------TKPLNPNHPYSPDDSYAM--HSNDSFCSS 221
+FASS T+ L P+ P PD Y + ++
Sbjct: 107 VFASSNHTIGYYPQTERLGPDVPARPDGLYGVSKCFGENLARM 149
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 28.1 bits (61), Expect = 2.8
Identities = 6/47 (12%), Positives = 15/47 (31%)
Query: 86 SSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKP 132
S S ++ + +R R A ++ +++ P
Sbjct: 121 SQQSHGPGQSDDACSEPTNKKMRRNRFKWGPASQQILYQAYDRQKNP 167
>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with
the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 26.3 bits (58), Expect = 3.3
Identities = 8/33 (24%), Positives = 12/33 (36%)
Query: 95 DENCRPRDGRRGPKRPRTILTSAQRRQFKSSFE 127
P + +R RT+ T Q + FE
Sbjct: 5 SSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFE 37
>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken
structural genomics/proteomics initiative, RSGI,
structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 71
Score = 25.9 bits (57), Expect = 3.5
Identities = 6/30 (20%), Positives = 12/30 (40%), Gaps = 1/30 (3%)
Query: 107 PKRPRTILTSAQRRQFKSSF-EVSPKPCRK 135
R RT ++ +S +V P ++
Sbjct: 7 GPRSRTKISLEALGILQSFIHDVGLYPDQE 36
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for eukaryotic
structural genomics; NMR {Homo sapiens}
Length = 84
Score = 26.3 bits (58), Expect = 3.8
Identities = 6/41 (14%), Positives = 14/41 (34%), Gaps = 1/41 (2%)
Query: 87 SPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFE 127
P+ + + ++ RT+ +S Q F+
Sbjct: 3 QPTSAENSVAKKEDKVPVK-KQKTRTVFSSTQLCVLNDRFQ 42
>1d5y_A ROB transcription factor; protein-DNA complex, DNA,
transcription/DNA complex; HET: DNA; 2.70A {Escherichia
coli} SCOP: a.4.1.8 a.4.1.8 d.60.1.2
Length = 292
Score = 27.5 bits (61), Expect = 4.7
Identities = 16/104 (15%), Positives = 31/104 (29%), Gaps = 3/104 (2%)
Query: 120 RQFKSSFEVSPKPCRKVSTMNSKRAKNILTPNQRRQFKSSFEISSMPCRKV-GVHGHYLS 178
R FK F +P R+ ++ + L + + + ++ + GV Y
Sbjct: 88 RAFKKQFAQTPALYRRSPEWSAFGIRPPLRLGEFTMPE--HKFVTLEDTPLIGVTQSYSC 145
Query: 179 LGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFCSSD 222
+ D + N P P Y ++ D
Sbjct: 146 SLEQISDFRHEMRYQFWHDFLGNAPTIPPVLYGLNETRPSQDKD 189
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 25.4 bits (56), Expect = 4.8
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 107 PKRPRTILTSAQRRQFKSSFE 127
++PRTI +S Q + F+
Sbjct: 7 GRKPRTIYSSFQLAALQRRFQ 27
>3hcs_A TNF receptor-associated factor 6; cross-brace, beta-BETA-alpha,
coiled coil, cytoplasm, metal- binding, UBL conjugation,
UBL conjugation pathway; 2.20A {Homo sapiens}
Length = 170
Score = 27.0 bits (59), Expect = 5.0
Identities = 15/55 (27%), Positives = 21/55 (38%), Gaps = 2/55 (3%)
Query: 48 FVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLMQQSSPSDDMMLDENCRPRD 102
+ C IC L+ E G FC+ K + P D+ +L EN D
Sbjct: 19 YECPICLMALR--EAVQTPCGHRFCKACIIKSIRDAGHKCPVDNEILLENQLFPD 71
>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation,
DNA-binding, POU domain, diabetes, disease mutation,
MODY3, transcription/DNA comple; 2.60A {Homo sapiens}
SCOP: a.4.1.1 a.35.1.1
Length = 194
Score = 26.8 bits (58), Expect = 6.1
Identities = 7/56 (12%), Positives = 19/56 (33%)
Query: 77 EKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKP 132
++ Q + +++E + +R R A ++ ++E P
Sbjct: 85 KQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQILFQAYERQKNP 140
>1zfo_A LAsp-1; LIM domain, zinc-finger, metal-binding protein; NMR {Sus
scrofa} SCOP: g.39.1.4
Length = 31
Score = 24.2 bits (52), Expect = 7.7
Identities = 11/28 (39%), Positives = 13/28 (46%), Gaps = 1/28 (3%)
Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCF 48
CARCG + P E V +H CF
Sbjct: 5 NCARCGKIVYPTEKV-NCLDKFWHKACF 31
>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA
binding helix- turn-helix motif, structural genomics,
NPPSFA; NMR {Mus musculus}
Length = 80
Score = 25.1 bits (55), Expect = 8.6
Identities = 8/31 (25%), Positives = 12/31 (38%)
Query: 103 GRRGPKRPRTILTSAQRRQFKSSFEVSPKPC 133
+R RT T AQ ++ F + P
Sbjct: 3 SGSSGRRERTTFTRAQLDVLEALFAKTRYPD 33
>3itf_A Periplasmic adaptor protein CPXP; CPXR, CPXA, cpxrap, CPX-pathway,
envelope stress, transduction; HET: MSE; 1.45A
{Escherichia coli str} PDB: 3qzc_A
Length = 145
Score = 26.1 bits (57), Expect = 9.1
Identities = 4/16 (25%), Positives = 7/16 (43%)
Query: 146 NILTPNQRRQFKSSFE 161
+LTP Q+ +
Sbjct: 117 RLLTPEQQAVLNEKHQ 132
>3oeo_A Spheroplast protein Y; LTXXQ, extracytoplasmic stress
response-related, signaling P; 2.70A {Escherichia coli}
Length = 138
Score = 26.1 bits (57), Expect = 9.3
Identities = 10/16 (62%), Positives = 14/16 (87%)
Query: 146 NILTPNQRRQFKSSFE 161
NILTP Q++QF ++FE
Sbjct: 105 NILTPEQKKQFNANFE 120
Database: pdb70
Posted date: Sep 4, 2012 3:40 AM
Number of letters in database: 6,701,793
Number of sequences in database: 27,921
Lambda K H
0.319 0.132 0.408
Gapped
Lambda K H
0.267 0.0538 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 3,797,936
Number of extensions: 205732
Number of successful extensions: 681
Number of sequences better than 10.0: 1
Number of HSP's gapped: 616
Number of HSP's successfully gapped: 96
Length of query: 267
Length of database: 6,701,793
Length adjustment: 92
Effective length of query: 175
Effective length of database: 4,133,061
Effective search space: 723285675
Effective search space used: 723285675
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 56 (25.8 bits)