RPS-BLAST 2.2.26 [Sep-21-2011]
Database: pdb70
27,921 sequences; 6,701,793 total letters
Searching..................................................done
Query= psy4325
(306 letters)
>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 = 192 bits (489), Expect = 1e-61
Identities = 93/166 (56%), Positives = 111/166 (66%), Gaps = 6/166 (3%)
Query: 70 IPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFKRFG 129
IP C GC ILDRFILK L+R WH++CLKC +C PLAE+CF+R ++CK+DFFKRFG
Sbjct: 6 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFG 65
Query: 130 TKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEA 189
TKCA C++GIPPTQVVRRAQD VYHL+CFACV+C RQL TGDEFYLMED +LVCK DYE
Sbjct: 66 TKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYET 125
Query: 190 AKA-KDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVR 234
AK G T + A E +P + +
Sbjct: 126 AKQGGSGGS-----GGSGGGTPMVAASPERHDGGLQANPVEVQSYQ 166
>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 = 190 bits (485), Expect = 9e-61
Identities = 88/123 (71%), Positives = 102/123 (82%)
Query: 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFKRF 128
IP C GC ILDRFILK L+R WH++CLKC +C PLAE+CF+R ++CK+DFFKRF
Sbjct: 59 EIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRF 118
Query: 129 GTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
GTKCA C++GIPPTQVVRRAQD VYHL+CFACV+C RQL TGDEFYLMED +LVCK DYE
Sbjct: 119 GTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYE 178
Query: 189 AAK 191
AK
Sbjct: 179 TAK 181
Score = 57.2 bits (138), Expect = 4e-10
Identities = 17/87 (19%), Positives = 26/87 (29%), Gaps = 4/87 (4%)
Query: 103 CGAPLAEKCFARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVM 162
A G CAGC+ I ++ +A D +H C C
Sbjct: 34 TQFDAANGIDDEGGSGGHMGSGGTPEIPMCAGCDQHILDRFIL-KALDRHWHSKCLKCSD 92
Query: 163 CARQLNTGDEFYLMEDRKLVCKPDYEA 189
C L + + + CK D+
Sbjct: 93 CHVPL--AERCFS-RGESVYCKDDFFK 116
>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene,
transcription, developmental protein; 2.40A {Homo
sapiens} PDB: 2xjz_A
Length = 131
Score = 167 bits (424), Expect = 3e-52
Identities = 44/125 (35%), Positives = 64/125 (51%), Gaps = 6/125 (4%)
Query: 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDFF 125
S+ CGGC I DR+ LK +++ WH CL C CG L E + + + G C+ D+
Sbjct: 1 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 60
Query: 126 KRFGTK--CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
+ FG CA C+ I ++ R +D VYHL CF C C + GD + L+ +VC
Sbjct: 61 RLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINS-DIVC 119
Query: 184 KPDYE 188
+ D
Sbjct: 120 EQDIY 124
Score = 52.1 bits (125), Expect = 9e-09
Identities = 17/67 (25%), Positives = 30/67 (44%), Gaps = 1/67 (1%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAA 190
C GC+ I ++ A D +H +C +C +C +L + + +C+ DY
Sbjct: 4 TCGGCQQNIGDRYFLK-AIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL 62
Query: 191 KAKDGNC 197
+DG C
Sbjct: 63 FGQDGLC 69
Score = 49.7 bits (119), Expect = 6e-08
Identities = 12/64 (18%), Positives = 24/64 (37%), Gaps = 3/64 (4%)
Query: 71 PKCGGCGDLIL-DRFILKVLERTWHARCLKCHECGAPLA--EKCFARNGLLFCKEDFFKR 127
C C I ++V ++ +H C KC C ++ N + C++D ++
Sbjct: 67 GLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEW 126
Query: 128 FGTK 131
Sbjct: 127 TKIN 130
>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 = 162 bits (410), Expect = 2e-49
Identities = 56/188 (29%), Positives = 82/188 (43%), Gaps = 17/188 (9%)
Query: 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDFF 125
S +C GCG I DRF+L ++ WH+RCLKC C A L + + ++G++ C+ D+
Sbjct: 4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63
Query: 126 KRFG--TKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
+ FG C+ C IP +++V RAQ VYHL CF C C +L GD F+ + + L C
Sbjct: 64 RLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYI-NGSLFC 122
Query: 184 KPDYEAAKAKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVR-------EQ 236
+ D A G + + TL R Q
Sbjct: 123 EHDRPTALINGHLNSGGSGGSGGSGGDVMVVGEPTLM----GGEFGDEDERLITRLENTQ 178
Query: 237 LSQDTGLD 244
G+D
Sbjct: 179 FDAANGID 186
>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion,
acrosom; 2.62A {Homo sapiens}
Length = 126
Score = 142 bits (360), Expect = 1e-42
Identities = 31/124 (25%), Positives = 52/124 (41%), Gaps = 5/124 (4%)
Query: 68 ASIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFK 126
+ P+C GC +LI + + WH + C +C + LA + + N CK + K
Sbjct: 1 SEKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVK 60
Query: 127 RFGTKCAGCEMGIPPTQVVRRAQDLVYHLN--CFACVMCARQLNTGDEFYLMEDRKLVCK 184
C GC I P + +H + CF C C++ L G +F +E + C
Sbjct: 61 NHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVEG-MVFCS 118
Query: 185 PDYE 188
+ +
Sbjct: 119 VECK 122
Score = 51.3 bits (123), Expect = 2e-08
Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 4/62 (6%)
Query: 71 PKCGGCGDLILDR-FILKVLERTWHA--RCLKCHECGAPLAEKCF-ARNGLLFCKEDFFK 126
C GC + I + +WHA C C C L + F G++FC + K
Sbjct: 64 VVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKK 123
Query: 127 RF 128
R
Sbjct: 124 RM 125
Score = 49.7 bits (119), Expect = 6e-08
Identities = 21/59 (35%), Positives = 30/59 (50%), Gaps = 3/59 (5%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEA 189
+CAGC+ I + + A++ +HL F C C L E Y+M + K VCKP Y
Sbjct: 5 RCAGCDELIFSNEYTQ-AENQNWHLKHFCCFDCDSIL--AGEIYVMVNDKPVCKPCYVK 60
>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 = 128 bits (324), Expect = 3e-37
Identities = 32/145 (22%), Positives = 57/145 (39%), Gaps = 7/145 (4%)
Query: 122 EDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKL 181
E F F K ++G T V + + L F K
Sbjct: 6 EQFANEF--KVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLS--FKNACKLKA 61
Query: 182 VCKPDYEAAKAKDGNC---LDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLS 238
+ E A+ + ++ ++ RTTI+ + L+ + KP+ +++
Sbjct: 62 ILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMA 121
Query: 239 QDTGLDMRVVQVWFQNRRAKEKRLK 263
++ L+ VV+VWF NRR +EKR+K
Sbjct: 122 EELNLEKEVVRVWFCNRRQREKRVK 146
>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 = 124 bits (313), Expect = 4e-36
Identities = 25/95 (26%), Positives = 38/95 (40%), Gaps = 2/95 (2%)
Query: 71 PKCGGCGDLIL-DRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRF 128
C C I D + R WH C +C +C PLA + F A++ + C + +
Sbjct: 6 SGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTRED 65
Query: 129 GTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMC 163
KC GC I + V+H +CF+
Sbjct: 66 SPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100
Score = 54.0 bits (130), Expect = 1e-09
Identities = 13/63 (20%), Positives = 23/63 (36%), Gaps = 2/63 (3%)
Query: 127 RFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPD 186
+ C C I ++ +H CF C C L +E ++ +D K++C
Sbjct: 3 SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPL--ANETFVAKDNKILCNKC 60
Query: 187 YEA 189
Sbjct: 61 TTR 63
Score = 38.5 bits (90), Expect = 3e-04
Identities = 11/36 (30%), Positives = 15/36 (41%), Gaps = 3/36 (8%)
Query: 71 PKCGGCGDLIL--DRFILKVLERTWHARCLKCHECG 104
PKC GC I+ D+ + + WH C G
Sbjct: 67 PKCKGCFKAIVAGDQNV-EYKGTVWHKDCFSGPSSG 101
>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 = 124 bits (312), Expect = 1e-35
Identities = 37/136 (27%), Positives = 60/136 (44%), Gaps = 20/136 (14%)
Query: 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDFF 125
S +C GCG I DRF+L ++ WH+RCLKC C A L + + ++G++ C+ D+
Sbjct: 4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63
Query: 126 KRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKP 185
+ FG AG G + ++ G EF ED +L+ +
Sbjct: 64 RLFGNSGAGGSGGHMG--------------SGGDVMVVGEPTLMGGEFG-DEDERLITRL 108
Query: 186 DYEAAKAKDGNCLDGD 201
+ A N +D +
Sbjct: 109 ENTQFDA--ANGIDDE 122
>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 = 115 bits (290), Expect = 5e-33
Identities = 20/68 (29%), Positives = 37/68 (54%)
Query: 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKE 259
KRPRT IT QL L+ ++ + P+ ++++ +GL +V++ WF+N KE
Sbjct: 3 SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKE 62
Query: 260 KRLKKDAG 267
++ +G
Sbjct: 63 RQSGPSSG 70
>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 = 115 bits (290), Expect = 6e-33
Identities = 31/79 (39%), Positives = 46/79 (58%)
Query: 189 AAKAKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVV 248
++ + G + Q +KR RTTIT +QLE L Y P R + + ++ + GL RVV
Sbjct: 2 SSGSSGGTGGEEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVV 61
Query: 249 QVWFQNRRAKEKRLKKDAG 267
QVWFQN RA+E++ +G
Sbjct: 62 QVWFQNTRARERKSGPSSG 80
>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 = 116 bits (291), Expect = 3e-32
Identities = 34/154 (22%), Positives = 59/154 (38%), Gaps = 17/154 (11%)
Query: 122 EDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKL 181
E F K F K ++G V L + N F+ +R F M K
Sbjct: 10 EQFAKTF--KQRRIKLGFTQGDVGLAMGKL--YGNDFSQTTISRFEALNLSFKNMSKLKP 65
Query: 182 VCKPDYEAAKAKDGNCLDGDQPN-------------KRPRTTITAKQLETLKMAYNTSPK 228
+ + A+A + P+ ++ RT+I L+ ++ + K
Sbjct: 66 LLEKWLNDAEANLSSDSSLSSPSALNSPGIEGLSRRRKKRTSIETNIRVALEKSFMENQK 125
Query: 229 PARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262
P +++ ++ V++VWF NRR KEKR+
Sbjct: 126 PTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI 159
>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA
complex, SOX; 2.05A {Mus musculus}
Length = 164
Score = 115 bits (288), Expect = 9e-32
Identities = 39/149 (26%), Positives = 62/149 (41%), Gaps = 5/149 (3%)
Query: 122 EDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHL--NCFACVMCARQLNTGDEFYLM-ED 178
E F K+F K ++G V L ++ C A QL+ + L
Sbjct: 16 EQFAKQF--KQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLL 73
Query: 179 RKLVCKPDYEAAKAKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLS 238
K + + D + + + + ++ RT+I L+ + PKP+ H L+
Sbjct: 74 NKWLEETDSSSGSPTNLDKIAAQGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLA 133
Query: 239 QDTGLDMRVVQVWFQNRRAKEKRLKKDAG 267
L+ VV+VWF NRR KEKR+ AG
Sbjct: 134 DSLQLEKEVVRVWFCNRRQKEKRMTPAAG 162
>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 = 109 bits (274), Expect = 3e-30
Identities = 32/137 (23%), Positives = 53/137 (38%), Gaps = 26/137 (18%)
Query: 68 ASIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE---KCFARNGLLFCKEDF 124
S+ CGGC I DR+ LK +++ WH CL C CG L E + + + G C+ D+
Sbjct: 1 GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 60
Query: 125 FKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCK 184
+ G+ + ++ G EF ED +L+ +
Sbjct: 61 LRLGGSGGHMG--------------------SGGDVMVVGEPTLMGGEFGD-EDERLITR 99
Query: 185 PDYEAAKAKDGNCLDGD 201
+ A N +D +
Sbjct: 100 LENTQFDA--ANGIDDE 114
>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 = 103 bits (260), Expect = 1e-28
Identities = 27/61 (44%), Positives = 39/61 (63%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263
R RT + KQL TL+ Y +P+P ++EQL + TGL RV++VWFQN+R K+K+
Sbjct: 3 TTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS 62
Query: 264 K 264
Sbjct: 63 I 63
>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 (262), Expect = 2e-28
Identities = 29/127 (22%), Positives = 45/127 (35%), Gaps = 12/127 (9%)
Query: 124 FFKRFGTK--CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKL 181
+ + FG CA C+ I ++ R +D VYHL CF C C + + GD + L+ +
Sbjct: 1 YLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINS-DI 59
Query: 182 VCKPDYEAAKAKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHV----REQL 237
VC+ D +G E M + R + Q
Sbjct: 60 VCEQDIYEWTKINGGSGGSGGSGGDVMVV-----GEPTLMGGEFGDEDERLITRLENTQF 114
Query: 238 SQDTGLD 244
G+D
Sbjct: 115 DAANGID 121
Score = 63.2 bits (153), Expect = 8e-13
Identities = 14/83 (16%), Positives = 29/83 (34%), Gaps = 3/83 (3%)
Query: 71 PKCGGCGDLIL-DRFILKVLERTWHARCLKCHECGAPLA--EKCFARNGLLFCKEDFFKR 127
C C I ++V ++ +H C KC C + ++ N + C++D ++
Sbjct: 9 GLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIVCEQDIYEW 68
Query: 128 FGTKCAGCEMGIPPTQVVRRAQD 150
G V+ +
Sbjct: 69 TKINGGSGGSGGSGGDVMVVGEP 91
>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 = 102 bits (257), Expect = 4e-28
Identities = 19/68 (27%), Positives = 33/68 (48%)
Query: 66 PIASIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFF 125
I C GC + I L L++ WH C KC C L + +++G+ +C+ D+
Sbjct: 11 KIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEYISKDGVPYCESDYH 70
Query: 126 KRFGTKCA 133
+FG+ +
Sbjct: 71 AQFGSGPS 78
Score = 49.7 bits (119), Expect = 2e-08
Identities = 21/67 (31%), Positives = 31/67 (46%), Gaps = 4/67 (5%)
Query: 123 DFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLV 182
R + CAGC+ I Q + A D +H++CF C C+ L E+ +D
Sbjct: 9 PIKIRGPSHCAGCKEEIKHGQSLL-ALDKQWHVSCFKCQTCSVILT--GEYI-SKDGVPY 64
Query: 183 CKPDYEA 189
C+ DY A
Sbjct: 65 CESDYHA 71
>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 = 94.8 bits (236), Expect = 4e-25
Identities = 27/65 (41%), Positives = 35/65 (53%)
Query: 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKE 259
KR RT+ QL T+K + + P +QL+Q TGL RV+QVWFQN RAK
Sbjct: 3 SGSSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKF 62
Query: 260 KRLKK 264
+R
Sbjct: 63 RRNLL 67
>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 = 96.0 bits (238), Expect = 8e-25
Identities = 26/84 (30%), Positives = 41/84 (48%), Gaps = 3/84 (3%)
Query: 49 SSSFNDVDYEGIMPVYMPIASIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLA 108
S + S +C GCG I DRF+L ++ WH+RCLKC C A L
Sbjct: 40 GSQSKLGGGGSGGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLG 99
Query: 109 E---KCFARNGLLFCKEDFFKRFG 129
+ + ++G++ C+ D+ + FG
Sbjct: 100 DIGTSSYTKSGMILCRNDYIRLFG 123
Score = 48.6 bits (115), Expect = 1e-07
Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 1/58 (1%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
+CAGC I ++ A D +H C C C QL + ++C+ DY
Sbjct: 63 RCAGCGGKIADRFLLY-AMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 119
>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 = 95.2 bits (236), Expect = 3e-24
Identities = 25/77 (32%), Positives = 36/77 (46%)
Query: 185 PDYEAAKAKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLD 244
D + Q KR RT+I + +L+ + SPKP+ ++ GL+
Sbjct: 77 ADNNENLQEISKSETLVQARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLE 136
Query: 245 MRVVQVWFQNRRAKEKR 261
VV+VWF NRR K KR
Sbjct: 137 KDVVRVWFSNRRQKGKR 153
>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 = 92.5 bits (230), Expect = 3e-24
Identities = 19/71 (26%), Positives = 32/71 (45%), Gaps = 2/71 (2%)
Query: 118 LFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLME 177
+D++ +FG C GC + + A + YH CFAC+ C + GD + L++
Sbjct: 4 GSSGKDYWGKFGEFCHGCSLLMTGP--FMVAGEFKYHPECFACMSCKVIIEDGDAYALVQ 61
Query: 178 DRKLVCKPDYE 188
L C +
Sbjct: 62 HATLYCGKCHN 72
Score = 59.4 bits (144), Expect = 7e-12
Identities = 13/67 (19%), Positives = 24/67 (35%), Gaps = 4/67 (5%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEK---CFARNGLLFCKEDFFKR 127
C GC L+ F+ E +H C C C + + ++ L+C + +
Sbjct: 16 EFCHGCSLLMTGPFM-VAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEV 74
Query: 128 FGTKCAG 134
+G
Sbjct: 75 VSGPSSG 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 = 87.8 bits (218), Expect = 2e-22
Identities = 21/68 (30%), Positives = 32/68 (47%), Gaps = 3/68 (4%)
Query: 68 ASIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA--RNGLLFCKEDFF 125
A++ KC C ILDR IL+ + + +H C C C L F + C EDF
Sbjct: 13 ATLEKCATCSQPILDR-ILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFH 71
Query: 126 KRFGTKCA 133
++F + +
Sbjct: 72 RKFASGPS 79
Score = 56.6 bits (137), Expect = 6e-11
Identities = 21/69 (30%), Positives = 28/69 (40%), Gaps = 3/69 (4%)
Query: 120 CKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDR 179
E + KCA C I + RA YH CF CV+C R L G F +
Sbjct: 6 SGEGCYVATLEKCATCSQPI--LDRILRAMGKAYHPGCFTCVVCHRGL-DGIPFTVDATS 62
Query: 180 KLVCKPDYE 188
++ C D+
Sbjct: 63 QIHCIEDFH 71
>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 = 87.4 bits (217), Expect = 2e-22
Identities = 22/63 (34%), Positives = 31/63 (49%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
+ RT T QL L+ ++ + P EQLS L RV+ VWFQN R K ++
Sbjct: 8 RSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGP 67
Query: 265 DAG 267
+G
Sbjct: 68 SSG 70
>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 = 86.0 bits (213), Expect = 1e-21
Identities = 19/67 (28%), Positives = 32/67 (47%), Gaps = 2/67 (2%)
Query: 69 SIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKC-FARNGLLFCKEDFFKR 127
+P C CG I+ F+ K+ +R H C C +CG L +K F ++C++ +R
Sbjct: 14 KLPMCDKCGTGIVGVFV-KLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARER 72
Query: 128 FGTKCAG 134
+G
Sbjct: 73 VSGPSSG 79
Score = 44.4 bits (105), Expect = 2e-06
Identities = 12/65 (18%), Positives = 22/65 (33%), Gaps = 4/65 (6%)
Query: 128 FGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C C GI V + +D H C+ C C L + + + ++ C+
Sbjct: 14 KLPMCDKCGTGI--VGVFVKLRDRHRHPECYVCTDCGTNL--KQKGHFFVEDQIYCEKHA 69
Query: 188 EAAKA 192
+
Sbjct: 70 RERVS 74
>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein,
KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo
sapiens}
Length = 76
Score = 83.2 bits (206), Expect = 9e-21
Identities = 19/66 (28%), Positives = 31/66 (46%)
Query: 199 DGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258
G + + +QL LK ++ + P + E L++ TGL R V+ WF +RR
Sbjct: 3 SGSSGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYH 62
Query: 259 EKRLKK 264
+ LK
Sbjct: 63 CRNLKG 68
>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 = 82.6 bits (204), Expect = 2e-20
Identities = 16/69 (23%), Positives = 25/69 (36%), Gaps = 1/69 (1%)
Query: 200 GDQPNKRPRTTITAKQLETLKMAY-NTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258
R RT I+ + L L+ + P + LS L + +FQN+R
Sbjct: 3 SGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYH 62
Query: 259 EKRLKKDAG 267
K +G
Sbjct: 63 VKHSGPSSG 71
>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 = 82.2 bits (203), Expect = 4e-20
Identities = 17/70 (24%), Positives = 28/70 (40%), Gaps = 2/70 (2%)
Query: 66 PIASIPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDF 124
+P C CG I+ + K ++ H C C +C L +K + G L+C+
Sbjct: 21 SAQRMPLCDKCGSGIVGAVV-KARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHA 79
Query: 125 FKRFGTKCAG 134
R +G
Sbjct: 80 RARTSGPSSG 89
Score = 43.6 bits (103), Expect = 3e-06
Identities = 17/62 (27%), Positives = 24/62 (38%), Gaps = 4/62 (6%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAA 190
C C GI V +A+D H CF C C L + Y + +L C+ A
Sbjct: 27 LCDKCGSGI--VGAVVKARDKYRHPECFVCADCNLNL--KQKGYFFVEGELYCETHARAR 82
Query: 191 KA 192
+
Sbjct: 83 TS 84
>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 = 78.2 bits (193), Expect = 8e-19
Identities = 18/64 (28%), Positives = 31/64 (48%), Gaps = 2/64 (3%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRFG 129
PKCGGC +L+ ++ ++ WH C C +C + F +G FC+ + R G
Sbjct: 16 PKCGGCNRPVLENYL-SAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRG 74
Query: 130 TKCA 133
+ +
Sbjct: 75 SGPS 78
Score = 60.4 bits (147), Expect = 3e-12
Identities = 19/78 (24%), Positives = 28/78 (35%), Gaps = 4/78 (5%)
Query: 116 GLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYL 175
+DF F KC GC + + A D V+H CF C C + F+
Sbjct: 2 SSGSSGKDFLAMFSPKCGGCNRPV--LENYLSAMDTVWHPECFVCGDCFTSF-STGSFF- 57
Query: 176 MEDRKLVCKPDYEAAKAK 193
D + C+ Y +
Sbjct: 58 ELDGRPFCELHYHHRRGS 75
>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 89
Score = 78.1 bits (192), Expect = 1e-18
Identities = 15/73 (20%), Positives = 29/73 (39%), Gaps = 2/73 (2%)
Query: 192 AKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVW 251
+ P K T Q++ L+ ++ S P + ++L +T L R + W
Sbjct: 3 SGSSGAYPDFAPQKFKEKT--QGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSW 60
Query: 252 FQNRRAKEKRLKK 264
F RR +++
Sbjct: 61 FSERRKLRDSMEQ 73
>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 = 79.3 bits (195), Expect = 2e-18
Identities = 17/60 (28%), Positives = 30/60 (50%)
Query: 202 QPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
++ RT+ T + +E L + +P P +++++ D VV+VWF NRR K
Sbjct: 91 SKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN 150
>2d5v_A Hepatocyte nuclear factor 6; transcription factor,
transcription-DNA complex; 2.00A {Rattus norvegicus}
PDB: 1s7e_A
Length = 164
Score = 79.5 bits (195), Expect = 3e-18
Identities = 27/148 (18%), Positives = 54/148 (36%), Gaps = 10/148 (6%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYL--------MEDRKLV 182
K I +V+ R+Q + L +L +G E + E +++
Sbjct: 18 KRYSIPQAIFAQRVLCRSQGTLSDL--LRNPKPWSKLKSGRETFRRMWKWLQEPEFQRMS 75
Query: 183 CKPDYEAAKAKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTG 242
+ + + D K+PR T Q TL + + +P++ ++ +SQ G
Sbjct: 76 ALRLAACKRKEQEHGKDRGNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLG 135
Query: 243 LDMRVVQVWFQNRRAKEKRLKKDAGRTR 270
L++ V +F N R + +
Sbjct: 136 LELSTVSNFFMNARRRSLDKWLEHHHHH 163
>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 = 75.9 bits (187), Expect = 6e-18
Identities = 19/69 (27%), Positives = 30/69 (43%), Gaps = 1/69 (1%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRFG 129
KCG CG + ++ R++H C C C L A + ++CK + K++G
Sbjct: 8 NKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG 67
Query: 130 TKCAGCEMG 138
K G G
Sbjct: 68 PKGYGYGQG 76
Score = 45.5 bits (108), Expect = 6e-07
Identities = 15/61 (24%), Positives = 27/61 (44%), Gaps = 3/61 (4%)
Query: 129 GTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
G KC C + + V+ +H CF C++C + L++ + D ++ CK Y
Sbjct: 7 GNKCGACGRTVYHAEEVQ-CDGRSFHRCCFLCMVCRKNLDSTT--VAIHDAEVYCKSCYG 63
Query: 189 A 189
Sbjct: 64 K 64
>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 = 75.2 bits (185), Expect = 2e-17
Identities = 21/92 (22%), Positives = 32/92 (34%), Gaps = 5/92 (5%)
Query: 43 GSSSSFSSSFNDVDYEGIMPVYMPIASIPKCGGCGDLILDRFILKVLERTWHARCLKCHE 102
GSS S + P C C +I F+ L ++WH C
Sbjct: 1 GSSGSS---GDQDTLVQRAEHIPAGKRTPMCAHCNQVIRGPFL-VALGKSWHPEEFNCAH 56
Query: 103 CGAPLAEKCF-ARNGLLFCKEDFFKRFGTKCA 133
C +A F G L+C+ + K F + +
Sbjct: 57 CKNTMAYIGFVEEKGALYCELCYEKFFASGPS 88
Score = 49.0 bits (117), Expect = 4e-08
Identities = 16/78 (20%), Positives = 25/78 (32%), Gaps = 5/78 (6%)
Query: 112 FARNGLLFCKEDFF-KRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTG 170
++ L+ E + CA C I A +H F C C +
Sbjct: 7 GDQDTLVQRAEHIPAGKRTPMCAHCNQVI--RGPFLVALGKSWHPEEFNCAHCKNTM--A 62
Query: 171 DEFYLMEDRKLVCKPDYE 188
++ E L C+ YE
Sbjct: 63 YIGFVEEKGALYCELCYE 80
>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain,
transcription factor, structural genomics, NPPSFA; NMR
{Homo sapiens} SCOP: a.4.1.1
Length = 89
Score = 74.3 bits (182), Expect = 4e-17
Identities = 15/73 (20%), Positives = 27/73 (36%), Gaps = 2/73 (2%)
Query: 192 AKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVW 251
G+ P K T A+QL L+ ++ S +L T L R + W
Sbjct: 1 GSSGSSGPDFTPQKFKEKT--AEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAW 58
Query: 252 FQNRRAKEKRLKK 264
F ++ + ++
Sbjct: 59 FTEKKKSKALKEE 71
>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 = 71.8 bits (176), Expect = 2e-16
Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 2/65 (3%)
Query: 71 PKCGGCGDLI-LDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRF 128
C C LI D L +R +H C +C C LA++ F ++ L C + + F
Sbjct: 16 NTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAF 75
Query: 129 GTKCA 133
+ +
Sbjct: 76 SSGPS 80
Score = 58.3 bits (141), Expect = 2e-11
Identities = 20/75 (26%), Positives = 30/75 (40%), Gaps = 2/75 (2%)
Query: 119 FCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMED 178
+ F CA C+ I +D +H CF C C R L DE + +D
Sbjct: 5 SSGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSL--ADEPFTCQD 62
Query: 179 RKLVCKPDYEAAKAK 193
+L+C Y +A +
Sbjct: 63 SELLCNDCYCSAFSS 77
>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 = 70.4 bits (173), Expect = 5e-16
Identities = 14/64 (21%), Positives = 23/64 (35%), Gaps = 2/64 (3%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRFG 129
C C I + E+ WH C C C L+ + F R+ +C F +
Sbjct: 6 SGCVQCKKPITTGGV-TYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYA 64
Query: 130 TKCA 133
+ +
Sbjct: 65 SGPS 68
Score = 45.0 bits (107), Expect = 8e-07
Identities = 15/63 (23%), Positives = 23/63 (36%), Gaps = 4/63 (6%)
Query: 126 KRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKP 185
+ C C+ I V ++ +H CF C C +QL +G F D C
Sbjct: 2 SSGSSGCVQCKKPITTGGV--TYREQPWHKECFVCTACRKQL-SGQRFT-ARDDFAYCLN 57
Query: 186 DYE 188
+
Sbjct: 58 CFC 60
>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor,
homeodomain, domain swapping, structural oxford protein
production facility, OPPF; 2.70A {Homo sapiens}
Length = 66
Score = 70.2 bits (172), Expect = 6e-16
Identities = 14/58 (24%), Positives = 26/58 (44%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+ T +Q+ LK ++ S P +L + TGL ++ WF + R + +R
Sbjct: 4 HHHHHRKKTKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQR 61
>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 = 70.4 bits (173), Expect = 7e-16
Identities = 17/64 (26%), Positives = 29/64 (45%), Gaps = 2/64 (3%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRFG 129
P+C C + + ++ WH CL C C PLA + F +R+ +C F + F
Sbjct: 16 PRCARCSKTLTQGGV-TYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFA 74
Query: 130 TKCA 133
+ +
Sbjct: 75 SGPS 78
Score = 57.3 bits (139), Expect = 3e-11
Identities = 13/72 (18%), Positives = 22/72 (30%), Gaps = 4/72 (5%)
Query: 118 LFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLME 177
+ +F +CA C + V +D +H C C C L + +
Sbjct: 4 GSSGPCYENKFAPRCARCSKTLTQGGV--TYRDQPWHRECLVCTGCQTPL--AGQQFTSR 59
Query: 178 DRKLVCKPDYEA 189
D C +
Sbjct: 60 DEDPYCVACFGE 71
>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant,
DNA binding protein, developmental protein, disease
mutation, DNA-binding; NMR {Homo sapiens}
Length = 67
Score = 70.0 bits (172), Expect = 7e-16
Identities = 24/62 (38%), Positives = 38/62 (61%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
+RPRT T Q+E L+ + + P + E L+Q L++ +Q+WFQNRRAK KR +
Sbjct: 2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHR 61
Query: 265 DA 266
++
Sbjct: 62 ES 63
>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 = 69.7 bits (171), Expect = 9e-16
Identities = 15/65 (23%), Positives = 22/65 (33%), Gaps = 2/65 (3%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRFG 129
C C I I ++ WHA C C C LA + F +C + +
Sbjct: 6 SGCVKCNKAITSGGI-TYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVS 64
Query: 130 TKCAG 134
+G
Sbjct: 65 GPSSG 69
Score = 44.7 bits (106), Expect = 1e-06
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 4/66 (6%)
Query: 128 FGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
+ C C I + QD +H +CF CV C+++L G F + + C Y
Sbjct: 4 GSSGCVKCNKAITSGGIT--YQDQPWHADCFVCVTCSKKL-AGQRFT-AVEDQYYCVDCY 59
Query: 188 EAAKAK 193
+ +
Sbjct: 60 KNFVSG 65
>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three
helices with the DNA binding helix- turn-helix motif,
structural genomics, NPPSFA; NMR {Homo sapiens}
Length = 75
Score = 69.9 bits (171), Expect = 9e-16
Identities = 15/63 (23%), Positives = 26/63 (41%), Gaps = 2/63 (3%)
Query: 202 QPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
P K +QL L+ ++ +P P ++L +T + R + WF RR K
Sbjct: 7 GPTKYKERA--PEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNA 64
Query: 262 LKK 264
+
Sbjct: 65 EET 67
>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 = 69.8 bits (171), Expect = 1e-15
Identities = 22/60 (36%), Positives = 36/60 (60%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
+R RTT T QL+ L+ + + P +RE+++ L VQVWF+NRRAK ++ ++
Sbjct: 8 RRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQ 67
>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 = 72.4 bits (177), Expect = 2e-15
Identities = 20/114 (17%), Positives = 36/114 (31%), Gaps = 1/114 (0%)
Query: 27 GICASKLHDLLHEAHAGSSSSFSSSFNDVDYEGIMPVYMPIASIPKCGGCGDLILDRFIL 86
G + + + + + C CG + +
Sbjct: 72 GKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAEKV 131
Query: 87 KVLERTWHARCLKCHECGAPLA-EKCFARNGLLFCKEDFFKRFGTKCAGCEMGI 139
++WH C +C +CG L ++G ++CK + K FG K G G
Sbjct: 132 IGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQGA 185
Score = 65.8 bits (160), Expect = 4e-13
Identities = 22/168 (13%), Positives = 40/168 (23%), Gaps = 52/168 (30%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHEC-------------GAPLAEKCFAR--- 114
KCG C + ++ ++H C C C + C+ +
Sbjct: 8 KKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYG 67
Query: 115 ---------------------------------NGLLFCKEDFFKRFGTKCAGCEMGIPP 141
+ C C +
Sbjct: 68 PKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYA 127
Query: 142 TQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEA 189
+ V +H +CF C C + L + +D ++ CK Y
Sbjct: 128 AEKV-IGAGKSWHKSCFRCAKCGKSLESTT--LADKDGEIYCKGCYAK 172
Score = 44.6 bits (105), Expect = 8e-06
Identities = 15/69 (21%), Positives = 30/69 (43%), Gaps = 3/69 (4%)
Query: 129 GTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
G KC C+ + + V+ + +H +CF C++C + L++ + ++ CK Y
Sbjct: 7 GKKCGVCQKAVYFAEEVQ-CEGSSFHKSCFLCMVCKKNLDSTT--VAVHGDEIYCKSCYG 63
Query: 189 AAKAKDGNC 197
G
Sbjct: 64 KKYGPKGKG 72
>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 73
Score = 68.6 bits (168), Expect = 3e-15
Identities = 15/68 (22%), Positives = 29/68 (42%), Gaps = 1/68 (1%)
Query: 204 NKRPRTTITAKQLETLKMAYN-TSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262
+ + + T Q+E L+ +N + P ++ + GL Q WF+ R A+ +R
Sbjct: 2 SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRS 61
Query: 263 KKDAGRTR 270
+ R
Sbjct: 62 EGLPSECR 69
>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices
with the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 80
Score = 68.8 bits (167), Expect = 3e-15
Identities = 15/71 (21%), Positives = 29/71 (40%), Gaps = 4/71 (5%)
Query: 205 KRPRTTITAKQLETLKMAY----NTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260
+ RT + + L TLK + + R E ++ + +D +V+ W NRR K +
Sbjct: 9 LQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYR 68
Query: 261 RLKKDAGRTRW 271
+ +
Sbjct: 69 LMGIEVSGPSS 79
>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 = 68.6 bits (168), Expect = 3e-15
Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 2/65 (3%)
Query: 71 PKCGGCGDLIL-DRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRF 128
C CG+ ++ L+ +TWH C C C PL + F G +C + +F
Sbjct: 6 SGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKF 65
Query: 129 GTKCA 133
+ +
Sbjct: 66 ASGPS 70
Score = 52.4 bits (126), Expect = 2e-09
Identities = 14/66 (21%), Positives = 24/66 (36%), Gaps = 2/66 (3%)
Query: 128 FGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
+ C+ C + P +H +CF C C + L + ++ + C P Y
Sbjct: 4 GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRS--FVPDKGAHYCVPCY 61
Query: 188 EAAKAK 193
E A
Sbjct: 62 ENKFAS 67
>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor,
homeodomain, structural genomics, oxford production
facility, OPPF, transcription; 2.60A {Homo sapiens}
Length = 96
Score = 68.3 bits (166), Expect = 7e-15
Identities = 18/77 (23%), Positives = 34/77 (44%), Gaps = 5/77 (6%)
Query: 201 DQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260
+ T +QL LK A+ + P+ ++L++++GL + WF + R K
Sbjct: 22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWK 81
Query: 261 RLKKDAGRTRWSQYFRS 277
G +W Y++S
Sbjct: 82 N-----GNLKWYYYYQS 93
>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 = 67.4 bits (165), Expect = 8e-15
Identities = 15/65 (23%), Positives = 26/65 (40%), Gaps = 2/65 (3%)
Query: 71 PKCGGCGDLIL-DRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRF 128
C C I+ ++ +WH C CH C P+ K F ++ FC + K+
Sbjct: 6 SGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQH 65
Query: 129 GTKCA 133
+ +
Sbjct: 66 ASGPS 70
Score = 53.6 bits (129), Expect = 8e-10
Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 2/66 (3%)
Query: 128 FGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
+ C C+ I P + +H CF C C + + G + ++ +D + C P Y
Sbjct: 4 GSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPI--GTKSFIPKDNQNFCVPCY 61
Query: 188 EAAKAK 193
E A
Sbjct: 62 EKQHAS 67
>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the
DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 70
Score = 67.0 bits (164), Expect = 1e-14
Identities = 26/70 (37%), Positives = 37/70 (52%), Gaps = 2/70 (2%)
Query: 200 GDQPNK--RPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257
G + R RT T +QLE L+ + + P REQL++ L V+VWF+NRRA
Sbjct: 1 GSSGSSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRA 60
Query: 258 KEKRLKKDAG 267
K +R +G
Sbjct: 61 KWRRSGPSSG 70
>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 = 66.7 bits (163), Expect = 1e-14
Identities = 17/65 (26%), Positives = 27/65 (41%), Gaps = 2/65 (3%)
Query: 70 IPKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRF 128
C CG+ I+ R I K + +WH C +C C LA+ F G C+ +
Sbjct: 5 SSGCHQCGEFIIGRVI-KAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREK 63
Query: 129 GTKCA 133
+ +
Sbjct: 64 ASGPS 68
Score = 45.5 bits (108), Expect = 5e-07
Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 4/67 (5%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAA 190
C C I + +A + +H CF C +C L D ++ + +C+P +
Sbjct: 7 GCHQCGEFIIGRVI--KAMNNSWHPECFRCDLCQEVL--ADIGFVKNAGRHLCRPCHNRE 62
Query: 191 KAKDGNC 197
KA +
Sbjct: 63 KASGPSS 69
>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 = 66.1 bits (162), Expect = 1e-14
Identities = 11/60 (18%), Positives = 30/60 (50%)
Query: 201 DQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260
+ + + +++I+ + L+ + +E++++ G+ V+VWF N+R + K
Sbjct: 2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK 61
>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 = 66.3 bits (162), Expect = 2e-14
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 3/71 (4%)
Query: 123 DFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLV 182
D+ + +GT+C C+ I V A YH +CF C +C GD ++ +
Sbjct: 9 DYQRLYGTRCFSCDQFI--EGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTF-NGKECM 65
Query: 183 CKPDYEAAKAK 193
C+
Sbjct: 66 CQKCSLPVSVS 76
Score = 47.1 bits (112), Expect = 2e-07
Identities = 11/54 (20%), Positives = 17/54 (31%), Gaps = 3/54 (5%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF--ARNGLLFCKE 122
+C C I + L +T+H C C C P C++
Sbjct: 16 TRCFSCDQFIEGEVV-SALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQK 68
>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA
complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P
2lkx_A* 2l7m_P
Length = 68
Score = 65.8 bits (161), Expect = 2e-14
Identities = 21/60 (35%), Positives = 37/60 (61%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
+R RT T++QL+ L+ + + P RE+++ T L V+VWF+NRRAK ++ ++
Sbjct: 4 RRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREE 63
>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 = 65.4 bits (160), Expect = 3e-14
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 2/61 (3%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKRFG 129
P CG C I R + + + WH C +C P R GL +C+ + + FG
Sbjct: 6 PICGACRRPIEGRVV-NAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFG 64
Query: 130 T 130
Sbjct: 65 D 65
Score = 43.8 bits (104), Expect = 2e-06
Identities = 13/62 (20%), Positives = 17/62 (27%), Gaps = 4/62 (6%)
Query: 128 FGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
C C I V A +H+ F C C + G Y C+ Y
Sbjct: 4 GVPICGACRRPIEGRVVN--AMGKQWHVEHFVCAKCEKPF-LGHRHY-ERKGLAYCETHY 59
Query: 188 EA 189
Sbjct: 60 NQ 61
>2cue_A Paired box protein PAX6; homeobox domain, transcription factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 80
Score = 65.9 bits (161), Expect = 3e-14
Identities = 24/67 (35%), Positives = 36/67 (53%), Gaps = 2/67 (2%)
Query: 200 GDQPNK--RPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257
G + R RT+ T +Q+E L+ + + P RE+L+ L +QVWF NRRA
Sbjct: 1 GSSGSSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRA 60
Query: 258 KEKRLKK 264
K +R +K
Sbjct: 61 KWRREEK 67
>3a02_A Homeobox protein aristaless; homeodomain, developmental protein,
DNA-binding, N gene regulation; 1.00A {Drosophila
melanogaster} PDB: 3lnq_A 3cmy_A
Length = 60
Score = 64.9 bits (159), Expect = 4e-14
Identities = 24/57 (42%), Positives = 35/57 (61%)
Query: 208 RTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
T T+ QLE L+ A++ + P RE+L+ GL +QVWFQNRRAK ++ +K
Sbjct: 3 HMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK 59
>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription
regulation; HET: DNA; 2.00A {Drosophila melanogaster}
SCOP: a.4.1.1 PDB: 3a01_B
Length = 81
Score = 64.7 bits (158), Expect = 7e-14
Identities = 25/60 (41%), Positives = 38/60 (63%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
+R RTT +A QL+ L+ A+ + P + RE+L+Q T L +QVWFQNRRA+ ++
Sbjct: 19 RRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT 78
>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac
development, riken structural genomics/proteomics
initiative, RSGI, transcription; NMR {Mus musculus}
SCOP: a.4.1.1
Length = 72
Score = 64.3 bits (157), Expect = 9e-14
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 1/66 (1%)
Query: 206 RPRTTITAKQLETLKMAYNTSPK-PARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
T+T Q+E L+ +N K P ++ + GL Q WF+ R A+ +R +
Sbjct: 3 EGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEG 62
Query: 265 DAGRTR 270
R
Sbjct: 63 LPSECR 68
>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 = 64.0 bits (156), Expect = 1e-13
Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 3/70 (4%)
Query: 68 ASIPKCGGCGDLILDR-FILKVLERTWHARCLKCHECGAPLA-EKCFARNGLLFCKEDFF 125
+ CGGCG+ ++ + L+R +H C C C A L + +A +C+ +
Sbjct: 3 SGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYV 62
Query: 126 KRFGTKCAGC 135
Sbjct: 63 ATL-ESGPSS 71
Score = 60.5 bits (147), Expect = 2e-12
Identities = 20/67 (29%), Positives = 27/67 (40%), Gaps = 2/67 (2%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAA 190
C GC + A D V+H+ CF C C QL G FY +E + C+ Y A
Sbjct: 7 GCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLR-GQHFYAVER-RAYCEGCYVAT 64
Query: 191 KAKDGNC 197
+
Sbjct: 65 LESGPSS 71
>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 = 64.3 bits (157), Expect = 1e-13
Identities = 14/65 (21%), Positives = 23/65 (35%), Gaps = 2/65 (3%)
Query: 71 PKCGGCGDLIL-DRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRF 128
PKC GC I+ ++ WH C C C + F + +C +F
Sbjct: 16 PKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKF 75
Query: 129 GTKCA 133
+ +
Sbjct: 76 ASGPS 80
Score = 60.8 bits (148), Expect = 2e-12
Identities = 16/78 (20%), Positives = 26/78 (33%), Gaps = 2/78 (2%)
Query: 116 GLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYL 175
+ + KC GC I + V+H +CF C C + + TG +
Sbjct: 2 SSGSSGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGS--FF 59
Query: 176 MEDRKLVCKPDYEAAKAK 193
+ C +E A
Sbjct: 60 PKGEDFYCVTCHETKFAS 77
>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 = 63.1 bits (154), Expect = 3e-13
Identities = 21/67 (31%), Positives = 27/67 (40%), Gaps = 2/67 (2%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKED-FFKRF 128
PKC C + + L + WH CLKC +CG L A G +C + F
Sbjct: 1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMF 60
Query: 129 GTKCAGC 135
G K G
Sbjct: 61 GPKGFGR 67
Score = 41.6 bits (98), Expect = 1e-05
Identities = 12/57 (21%), Positives = 21/57 (36%), Gaps = 3/57 (5%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
KC C+ + + V + +H C C C + L +G + + K C
Sbjct: 2 KCPKCDKEVYFAERVT-SLGKDWHRPCLKCEKCGKTLTSGG--HAEHEGKPYCNHPC 55
>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain,
transcription factor, leucine zipper- containing factor,
structural genomics, NPPSFA; NMR {Homo sapiens} SCOP:
a.4.1.1
Length = 76
Score = 60.4 bits (146), Expect = 3e-12
Identities = 20/78 (25%), Positives = 30/78 (38%), Gaps = 7/78 (8%)
Query: 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKE 259
G + R T +QL LK + R ++L Q TGL + WF + R
Sbjct: 1 GSSGSSGKRKT--KEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYAL 58
Query: 260 KRLKKDAGRTRWSQYFRS 277
K G+ +W + S
Sbjct: 59 KH-----GQLKWFRDNAS 71
>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 = 59.1 bits (143), Expect = 6e-12
Identities = 16/67 (23%), Positives = 21/67 (31%), Gaps = 4/67 (5%)
Query: 71 PKCGGCGDLILDRFILKV---LERTWHARCLKCHECGAPLAEKCF-ARNGLLFCKEDFFK 126
C GC + I K ER WH C C +C L + F + C +
Sbjct: 6 SGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKD 65
Query: 127 RFGTKCA 133
G
Sbjct: 66 ISGPSSG 72
Score = 46.4 bits (110), Expect = 3e-07
Identities = 15/64 (23%), Positives = 25/64 (39%), Gaps = 4/64 (6%)
Query: 127 RFGTKCAGCEMGIPPTQVVR--RAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCK 184
+ CAGC I + ++ +H +CF C C+ L G F D ++C
Sbjct: 3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL-VGRGFLTERD-DILCP 60
Query: 185 PDYE 188
+
Sbjct: 61 DCGK 64
>2e19_A Transcription factor 8; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens}
Length = 64
Score = 58.1 bits (140), Expect = 1e-11
Identities = 11/51 (21%), Positives = 24/51 (47%)
Query: 214 KQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
L LK Y + +P+ +++ L + VV+ WF+ +A + ++
Sbjct: 13 NLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISVQS 63
>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 = 58.6 bits (142), Expect = 1e-11
Identities = 14/76 (18%), Positives = 25/76 (32%), Gaps = 5/76 (6%)
Query: 116 GLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRR---AQDLVYHLNCFACVMCARQLNTGDE 172
+ + KCAGC+ I + +H CF C C+ L
Sbjct: 2 SSGSSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNL-ANKR 60
Query: 173 FYLMEDRKLVCKPDYE 188
F ++ ++ C +
Sbjct: 61 FVFHQE-QVYCPDCAK 75
Score = 50.6 bits (121), Expect = 9e-09
Identities = 14/59 (23%), Positives = 23/59 (38%), Gaps = 5/59 (8%)
Query: 71 PKCGGCGDLIL----DRFILKVLERTWHARCLKCHECGAPLAEK-CFARNGLLFCKEDF 124
KC GC + I ++ ++WH C C +C LA K ++C +
Sbjct: 16 KKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCA 74
>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national
project on protein structural and functional analyses;
NMR {Homo sapiens}
Length = 70
Score = 57.4 bits (139), Expect = 3e-11
Identities = 20/68 (29%), Positives = 35/68 (51%)
Query: 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKE 259
++PRT ++ QL L+ + + A R +L+ GL V++WFQN+R+K
Sbjct: 3 SGSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKI 62
Query: 260 KRLKKDAG 267
K+ +G
Sbjct: 63 KKSGPSSG 70
>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA
binding protein/DNA), transcription/DNA complex; HET:
DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB:
1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A
1du0_A* 1ztr_A 1enh_A 2p81_A
Length = 61
Score = 56.2 bits (136), Expect = 5e-11
Identities = 23/58 (39%), Positives = 37/58 (63%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
KRPRT +++QL LK +N + R+QLS + GL+ +++WF+N+RAK K+
Sbjct: 3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK 60
>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor,
structural genomics, loop insertion, NPPSFA; NMR {Homo
sapiens} SCOP: a.4.1.1
Length = 95
Score = 57.0 bits (137), Expect = 8e-11
Identities = 17/76 (22%), Positives = 26/76 (34%), Gaps = 15/76 (19%)
Query: 206 RPRTTITAKQLETLKMAYNTSPKPARHVREQL---------------SQDTGLDMRVVQV 250
R T + L ++ +N + P RE++ S + V
Sbjct: 9 GSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYN 68
Query: 251 WFQNRRAKEKRLKKDA 266
WF NRR + KR A
Sbjct: 69 WFANRRKEIKRRANIA 84
>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 = 56.3 bits (136), Expect = 8e-11
Identities = 15/65 (23%), Positives = 21/65 (32%), Gaps = 3/65 (4%)
Query: 71 PKCGGCGDLIL-DRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRF 128
C C I+ +H +C C +C E F G +C+ DF F
Sbjct: 12 ATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF 71
Query: 129 GTKCA 133
C
Sbjct: 72 A-PCW 75
Score = 55.9 bits (135), Expect = 1e-10
Identities = 16/70 (22%), Positives = 28/70 (40%), Gaps = 2/70 (2%)
Query: 120 CKEDFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDR 179
+ C C+ G P + + + +YH CF C C +Q G FY +
Sbjct: 2 SEFMANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFY-EFEG 59
Query: 180 KLVCKPDYEA 189
+ C+ D++
Sbjct: 60 RKYCEHDFQM 69
>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 = 56.8 bits (137), Expect = 8e-11
Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 1/67 (1%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRFG 129
C C + L ++ +H C +C C L+ +A +G ++CK F + F
Sbjct: 16 ETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFK 75
Query: 130 TKCAGCE 136
+K E
Sbjct: 76 SKGNYDE 82
Score = 51.0 bits (122), Expect = 1e-08
Identities = 20/77 (25%), Positives = 33/77 (42%), Gaps = 3/77 (3%)
Query: 124 FFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
F C C+ + P + + A V+H++CF C C +L+ G Y ++ C
Sbjct: 10 FQAPARETCVECQKTVYPMERLL-ANQQVFHISCFRCSYCNNKLSLGT--YASLHGRIYC 66
Query: 184 KPDYEAAKAKDGNCLDG 200
KP + GN +G
Sbjct: 67 KPHFNQLFKSKGNYDEG 83
>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics,
protein structure initiative, PSI, center for eukaryotic
structural genomics; NMR {Homo sapiens}
Length = 84
Score = 56.4 bits (136), Expect = 1e-10
Identities = 18/62 (29%), Positives = 31/62 (50%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263
++ RT ++ QL L + + ++LS L + V+ WFQN+R K KR +
Sbjct: 22 KQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQ 81
Query: 264 KD 265
K+
Sbjct: 82 KN 83
>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 = 55.9 bits (135), Expect = 1e-10
Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 2/61 (3%)
Query: 71 PKCGGCGDLI-LDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKEDFFKRF 128
C C I+ +H +C C +C E F G +C+ DF F
Sbjct: 12 ATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF 71
Query: 129 G 129
Sbjct: 72 A 72
Score = 55.9 bits (135), Expect = 1e-10
Identities = 17/66 (25%), Positives = 28/66 (42%), Gaps = 2/66 (3%)
Query: 123 DFFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLV 182
F C C+ G P + + + +YH CF C C +Q G FY + +
Sbjct: 5 YFQGSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFY-EFEGRKY 62
Query: 183 CKPDYE 188
C+ D++
Sbjct: 63 CEHDFQ 68
>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding
domain, transcription, structural genomics, NPPSFA; NMR
{Mus musculus} SCOP: a.4.1.1
Length = 72
Score = 55.2 bits (133), Expect = 2e-10
Identities = 14/63 (22%), Positives = 29/63 (46%), Gaps = 1/63 (1%)
Query: 206 RPRTTITAKQLETLKMAYNTSPK-PARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
+ + +TL+ + + K P + LS+ +R +Q WF++RR ++K
Sbjct: 10 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSGP 69
Query: 265 DAG 267
+G
Sbjct: 70 SSG 72
>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 = 54.4 bits (131), Expect = 4e-10
Identities = 12/63 (19%), Positives = 20/63 (31%), Gaps = 1/63 (1%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFARNGLLFCKEDFFKRFGT 130
C C +I ++ + +H C CG L G L+C K +
Sbjct: 16 YICQKCHAIIDEQPL-IFKNDPYHPDHFNCANCGKELTADARELKGELYCLPCHDKMGVS 74
Query: 131 KCA 133
+
Sbjct: 75 GPS 77
Score = 34.4 bits (79), Expect = 0.005
Identities = 12/57 (21%), Positives = 22/57 (38%), Gaps = 5/57 (8%)
Query: 132 CAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYE 188
C C I ++ ++ YH + F C C ++L +L C P ++
Sbjct: 18 CQKCHAIIDEQPLI--FKNDPYHPDHFNCANCGKEL---TADARELKGELYCLPCHD 69
>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA
complex; 2.20A {Mus musculus} SCOP: a.4.1.1
Length = 58
Score = 52.3 bits (126), Expect = 1e-09
Identities = 22/58 (37%), Positives = 30/58 (51%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262
++PRT T QL L+ + + R + S L V++WFQNRRAK KRL
Sbjct: 1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL 58
>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices
with the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 71
Score = 52.9 bits (126), Expect = 1e-09
Identities = 12/66 (18%), Positives = 23/66 (34%)
Query: 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKE 259
G + + LK Y + +P ++S GL V+ WF+ R+ +
Sbjct: 1 GSSGSSGSPINPYKDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVYQ 60
Query: 260 KRLKKD 265
+
Sbjct: 61 YSNSRS 66
>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 = 52.4 bits (126), Expect = 2e-09
Identities = 18/64 (28%), Positives = 25/64 (39%), Gaps = 2/64 (3%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA-RNGLLFCKED-FFKRF 128
KC C + + L + WH CLKC C L A +G FC + + F
Sbjct: 10 SKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLF 69
Query: 129 GTKC 132
G+
Sbjct: 70 GSGP 73
Score = 42.4 bits (100), Expect = 7e-06
Identities = 16/73 (21%), Positives = 26/73 (35%), Gaps = 4/73 (5%)
Query: 125 FKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC- 183
+KC C+ + + V + +H C C C++ L G + D K C
Sbjct: 5 SSGMASKCPKCDKTVYFAEKVS-SLGKDWHKFCLKCERCSKTLTPGG--HAEHDGKPFCH 61
Query: 184 KPDYEAAKAKDGN 196
KP Y +
Sbjct: 62 KPCYATLFGSGPS 74
>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural
genomics consortiu PSI-biology, protein structure
initiative; NMR {Homo sapiens}
Length = 69
Score = 52.0 bits (125), Expect = 2e-09
Identities = 15/63 (23%), Positives = 31/63 (49%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263
+ + ++ Q+ L+ ++ + R L+++ L V++WFQNRR K KR +
Sbjct: 4 HHHHHSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQ 63
Query: 264 KDA 266
+
Sbjct: 64 LSS 66
>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 = 52.5 bits (126), Expect = 2e-09
Identities = 21/79 (26%), Positives = 35/79 (44%)
Query: 189 AAKAKDGNCLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVV 248
++ + G + +R RT T QL L+ + + R L++ GL V
Sbjct: 2 SSGSSGGEPGTKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQV 61
Query: 249 QVWFQNRRAKEKRLKKDAG 267
+ W+QNRR K K+ +G
Sbjct: 62 KTWYQNRRMKWKKSGPSSG 80
>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex,
DNA-binding protein, protein/DNA complex; HET: DNA;
2.35A {Homo sapiens} SCOP: a.4.1.1
Length = 97
Score = 53.0 bits (127), Expect = 2e-09
Identities = 20/68 (29%), Positives = 37/68 (54%)
Query: 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKE 259
G RT T +QL L+ ++ + +R R +++ L+ V++WFQNRR K+
Sbjct: 30 GLGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQ 89
Query: 260 KRLKKDAG 267
K+ +++ G
Sbjct: 90 KKREREGG 97
>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription,
transcription facto developmental protein, transcription
regulation, NUC homeobox; 2.6A {Mus musculus}
Length = 62
Score = 51.5 bits (124), Expect = 3e-09
Identities = 18/60 (30%), Positives = 29/60 (48%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263
++ RT + QL LK + + ++LS L + V+ WFQN+R K KR +
Sbjct: 3 KQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRWQ 62
>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 = 52.2 bits (125), Expect = 3e-09
Identities = 15/56 (26%), Positives = 22/56 (39%), Gaps = 4/56 (7%)
Query: 71 PKCGGCGDLILDRFILKVLE---RTWHARCLKCHECGAPLAEKCF-ARNGLLFCKE 122
C C I K + WH+ C C +C L K F +N +FC++
Sbjct: 6 SGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQK 61
Score = 44.1 bits (104), Expect = 2e-06
Identities = 14/68 (20%), Positives = 21/68 (30%), Gaps = 4/68 (5%)
Query: 127 RFGTKCAGCEMGIPPTQVVR--RAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCK 184
+ C C I + QD +H CF C C+ L G F ++ C+
Sbjct: 3 SGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSL-VGKGFLTQNK-EIFCQ 60
Query: 185 PDYEAAKA 192
Sbjct: 61 KCGSGMDT 68
>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic
development, complex (homeodomain/DNA); HET: DNA; NMR
{Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P*
1vnd_A 1qry_A
Length = 77
Score = 52.1 bits (125), Expect = 3e-09
Identities = 18/64 (28%), Positives = 28/64 (43%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263
++ R T Q L+ + + RE L+ L V++WFQN R K KR +
Sbjct: 9 KRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQ 68
Query: 264 KDAG 267
+ G
Sbjct: 69 NEKG 72
>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation,
helix-turn-helix, structural genomics, NPPSFA; NMR {Homo
sapiens} SCOP: a.4.1.1
Length = 70
Score = 51.8 bits (124), Expect = 3e-09
Identities = 20/68 (29%), Positives = 32/68 (47%)
Query: 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKE 259
++ R + QL L+ Y + + R ++S T L R + +WFQNRR KE
Sbjct: 3 SGSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKE 62
Query: 260 KRLKKDAG 267
K+ +G
Sbjct: 63 KKSGPSSG 70
>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding
protein; NMR {Rattus norvegicus} SCOP: a.4.1.1
Length = 68
Score = 51.6 bits (124), Expect = 3e-09
Identities = 18/63 (28%), Positives = 28/63 (44%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
++ R + Q+ L+ + + RE L+ L V++WFQN R K KR K
Sbjct: 3 RKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAK 62
Query: 265 DAG 267
D
Sbjct: 63 DKA 65
>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex,
DNA-binding, homeobox, NUC developmental protein; 2.70A
{Drosophila melanogaster}
Length = 93
Score = 51.4 bits (123), Expect = 7e-09
Identities = 19/62 (30%), Positives = 31/62 (50%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263
K+PRT+ T Q+ L+ ++ A R L++ + V+ WFQNRR K +R
Sbjct: 17 RKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQT 76
Query: 264 KD 265
+
Sbjct: 77 AE 78
>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 70
Score = 50.5 bits (121), Expect = 7e-09
Identities = 19/64 (29%), Positives = 31/64 (48%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263
K + + Q L+ + T + R++L++ L R V+ WFQNRRAK +R
Sbjct: 7 GKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSG 66
Query: 264 KDAG 267
+G
Sbjct: 67 PSSG 70
>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 = 53.0 bits (126), Expect = 1e-08
Identities = 21/124 (16%), Positives = 37/124 (29%), Gaps = 24/124 (19%)
Query: 162 MCARQLNTGDEFYLMEDRKLVCKPDYEAAKAKDGNCLDGDQPNK---RPRTTITAKQLET 218
M ++ +Y+ + R++ + + + P K R R +
Sbjct: 70 MKTQKRAALYTWYVRKQREVAQQFTHAGQGGLIEEPTGDELPTKKGRRNRFKWGPASQQI 129
Query: 219 LKMAYNTSPKPARHVREQLSQ---------------------DTGLDMRVVQVWFQNRRA 257
L AY P++ RE L + + V WF NRR
Sbjct: 130 LFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRK 189
Query: 258 KEKR 261
+E
Sbjct: 190 EEAF 193
>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 = 50.3 bits (120), Expect = 1e-08
Identities = 13/64 (20%), Positives = 18/64 (28%), Gaps = 1/64 (1%)
Query: 124 FFKRFGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVC 183
G CA C + + + +H +CF C C L G D C
Sbjct: 10 QEAGAGDLCALCGEHLYVLERLC-VNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYC 68
Query: 184 KPDY 187
Sbjct: 69 LQHL 72
Score = 47.6 bits (113), Expect = 1e-07
Identities = 15/67 (22%), Positives = 25/67 (37%), Gaps = 3/67 (4%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAEKCFA---RNGLLFCKEDFFKR 127
C CG+ + L V +H C +CH C A L + +G +C + +
Sbjct: 16 DLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQT 75
Query: 128 FGTKCAG 134
+G
Sbjct: 76 DSGPSSG 82
>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB:
2ld5_A*
Length = 73
Score = 48.7 bits (116), Expect = 3e-08
Identities = 22/61 (36%), Positives = 33/61 (54%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263
++ R T QL+ L+ Y T+ + R ++S T L R V +WFQNRR KEK++
Sbjct: 7 GRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVI 66
Query: 264 K 264
Sbjct: 67 N 67
>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA
complex, transcription/DNA complex; 2.00A {Drosophila
melanogaster} SCOP: a.4.1.1
Length = 60
Score = 48.5 bits (116), Expect = 3e-08
Identities = 21/57 (36%), Positives = 30/57 (52%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R RT T QL L+ + +R R +L+ L ++VWFQNRR K+KR
Sbjct: 2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKR 58
>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix,
helix-turn-helix; NMR {Drosophila melanogaster} SCOP:
a.4.1.1
Length = 68
Score = 48.6 bits (116), Expect = 4e-08
Identities = 17/61 (27%), Positives = 26/61 (42%)
Query: 205 KRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
+R RTT T+ Q+ L+ + LS L V++WF+NRR + K
Sbjct: 3 RRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSD 62
Query: 265 D 265
Sbjct: 63 Q 63
>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex,
HOX hexapeptide, TALE homeodomain, homeodomain
interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB:
1san_A
Length = 77
Score = 48.7 bits (116), Expect = 4e-08
Identities = 19/67 (28%), Positives = 34/67 (50%)
Query: 202 QPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+ ++ R T Q L+ + + R R ++++ L R V++WFQNRR K K+
Sbjct: 11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKK 70
Query: 262 LKKDAGR 268
+ KD +
Sbjct: 71 INKDRAK 77
>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus,
transcription-DNA CO; 1.70A {Homo sapiens}
Length = 58
Score = 48.0 bits (115), Expect = 4e-08
Identities = 17/57 (29%), Positives = 28/57 (49%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260
++PR + Q+ L+ + + R+QL+ L V++WFQNRR K K
Sbjct: 2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK 58
>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A
{Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A
Length = 99
Score = 49.1 bits (116), Expect = 7e-08
Identities = 18/89 (20%), Positives = 27/89 (30%), Gaps = 21/89 (23%)
Query: 197 CLDGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQ----------------- 239
+D + +R R + L AY P++ RE L +
Sbjct: 2 RIDPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQA 61
Query: 240 ----DTGLDMRVVQVWFQNRRAKEKRLKK 264
+ V WF NRR +E K
Sbjct: 62 QGLGSNLVTEVRVYNWFANRRKEEAFRHK 90
>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo,
protein-DNA, human disease; 3.20A {Homo sapiens}
Length = 221
Score = 51.2 bits (121), Expect = 7e-08
Identities = 16/83 (19%), Positives = 26/83 (31%), Gaps = 21/83 (25%)
Query: 200 GDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQ-------------------- 239
++ +R R + L AY+ P++ RE L +
Sbjct: 138 TNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGL 197
Query: 240 -DTGLDMRVVQVWFQNRRAKEKR 261
+ V WF NRR +E
Sbjct: 198 GSNLVTEVRVYNWFANRRKEEAF 220
>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA
complex, transcription/DNA complex; 2.42A {Mesocricetus
auratus}
Length = 63
Score = 47.0 bits (112), Expect = 1e-07
Identities = 22/59 (37%), Positives = 32/59 (54%)
Query: 203 PNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
NKR RT T QL L+ + + +R R +L+ L R +++WFQNRR K K+
Sbjct: 2 SNKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKK 60
>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR
{Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A
1hom_A 1ftz_A
Length = 68
Score = 46.6 bits (111), Expect = 2e-07
Identities = 21/64 (32%), Positives = 32/64 (50%)
Query: 204 NKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLK 263
KR R T T Q L+ ++ + R R +++ L R +++WFQNRR K K+
Sbjct: 2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEN 61
Query: 264 KDAG 267
K G
Sbjct: 62 KTKG 65
>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A
{Drosophila melanogaster} PDB: 2r5z_A*
Length = 88
Score = 47.2 bits (112), Expect = 2e-07
Identities = 20/66 (30%), Positives = 34/66 (51%)
Query: 199 DGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258
+ + KR RT+ T Q L+ ++ + R R +++ L R +++WFQNRR K
Sbjct: 23 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMK 82
Query: 259 EKRLKK 264
K+ K
Sbjct: 83 WKKEHK 88
>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Mus musculus} SCOP:
a.4.1.1
Length = 64
Score = 46.3 bits (110), Expect = 2e-07
Identities = 16/50 (32%), Positives = 25/50 (50%), Gaps = 1/50 (2%)
Query: 212 TAKQLETLKMAY-NTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEK 260
TA+ L+ + + P E LS+ D+R +Q WF+ RR +EK
Sbjct: 8 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEK 57
>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA
binding, homeodomain, homeotic proteins, development,
specificity; HET: DNA; 2.40A {Drosophila melanogaster}
SCOP: a.4.1.1 PDB: 9ant_A*
Length = 81
Score = 46.7 bits (111), Expect = 3e-07
Identities = 19/66 (28%), Positives = 33/66 (50%)
Query: 199 DGDQPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAK 258
+ +R R T T Q L+ ++T+ R R +++ L R +++WFQNRR K
Sbjct: 15 GTNGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMK 74
Query: 259 EKRLKK 264
K+ +
Sbjct: 75 LKKEIQ 80
>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental
protein, DNA-binding, N gene regulation; 1.54A {Homo
sapiens}
Length = 56
Score = 41.9 bits (99), Expect = 6e-06
Identities = 15/53 (28%), Positives = 25/53 (47%)
Query: 209 TTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
T+ + Q+ L+ + A R L++ + V+ WFQNRR K +R
Sbjct: 2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRR 54
>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 = 39.5 bits (92), Expect = 6e-05
Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 4/61 (6%)
Query: 72 KCGGCGDLI-LDRFILKVLERTWHA--RCLKCHECGAPLAEKCF-ARNGLLFCKEDFFKR 127
C GC + I + + +WHA C C C L + F G++FC + KR
Sbjct: 4 VCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKR 63
Query: 128 F 128
Sbjct: 64 M 64
Score = 31.0 bits (70), Expect = 0.057
Identities = 12/61 (19%), Positives = 23/61 (37%), Gaps = 4/61 (6%)
Query: 128 FGTKCAGCEMGIPPTQVVRRAQDLVYHLN--CFACVMCARQLNTGDEFYLMEDRKLVCKP 185
C GC I P + +H + CF C C++ L + ++ + + C
Sbjct: 1 HAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL--IGQKFMPVEGMVFCSV 58
Query: 186 D 186
+
Sbjct: 59 E 59
>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 = 39.7 bits (92), Expect = 7e-05
Identities = 19/67 (28%), Positives = 30/67 (44%), Gaps = 3/67 (4%)
Query: 128 FGTKCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDY 187
+ C CE I T V A + YH +C CV C + G+E Y ++ +
Sbjct: 4 GSSGCDSCEKYI--TGRVLEAGEKHYHPSCALCVRCGQMFAEGEEMY-LQGSSIWHPACR 60
Query: 188 EAAKAKD 194
+AA+ +D
Sbjct: 61 QAARTED 67
Score = 37.8 bits (87), Expect = 3e-04
Identities = 13/54 (24%), Positives = 21/54 (38%), Gaps = 3/54 (5%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARCLKCHECGAPLAE--KCFARNGLLFCKE 122
C C I R L+ E+ +H C C CG AE + + + ++
Sbjct: 6 SGCDSCEKYITGRV-LEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPA 58
>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein,
protein/DNA complex; HET: DNA; 2.35A {Homo sapiens}
SCOP: a.4.1.1 PDB: 1lfu_P
Length = 87
Score = 37.1 bits (86), Expect = 8e-04
Identities = 19/85 (22%), Positives = 39/85 (45%), Gaps = 6/85 (7%)
Query: 205 KRPRTTITAKQLETLK---MAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R R + E L ++ ++P P+ +E+L++ G+ + V WF N+R R
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKR---IR 58
Query: 262 LKKDAGRTRWSQYFRSMKGGTSPKD 286
KK+ G+ + + K + +
Sbjct: 59 YKKNIGKFQEEANIYAAKTAVTATN 83
>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 = 39.5 bits (91), Expect = 0.001
Identities = 44/323 (13%), Positives = 90/323 (27%), Gaps = 90/323 (27%)
Query: 1 MSDVKAKSFLYQRIGLAVQ-------RGNGLTVGICASKLHD-------LLHEAHAGSSS 46
++ + KS L + + Q N + I A + D H ++
Sbjct: 298 LTPDEVKSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTT 357
Query: 47 SFSSSFNDVDYEGIMPVYMPIASIPKCGGCGDLILDRFI-LKVLERTWHA---RCL---- 98
SS N ++ ++ ++ P I +L W +
Sbjct: 358 IIESSLNVLEPAEYRKMFDRLSVFPP---------SAHIPTILLSLIWFDVIKSDVMVVV 408
Query: 99 -KCHECGAPLAEKCFARN-----GLLF---CKED--------FFKRFGTKCAGCEMGIPP 141
K H+ L EK + + K + + + P
Sbjct: 409 NKLHKYS--LVEKQPKESTISIPSIYLELKVKLENEYALHRSIVDHYNIPKTFDSDDLIP 466
Query: 142 TQVVRRAQD------LVYHLNCFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAKAKDG 195
+ D + +HL + + + L L D+ + K
Sbjct: 467 PYL-----DQYFYSHIGHHL---------KNIEHPERMTLFRMVFL----DFRFLEQK-- 506
Query: 196 NCLDGDQPNKRPRTTITAKQLETLKMAY--NTSPKPARHVREQL----SQDTGL----DM 245
D N T +QL+ K Y + PK R V L + L
Sbjct: 507 IRHDSTAWNASGSILNTLQQLKFYK-PYICDNDPKYERLVNAILDFLPKIEENLICSKYT 565
Query: 246 RVVQVWFQNRRAKEKRLKKDAGR 268
++++ +++ + ++A +
Sbjct: 566 DLLRIALMA---EDEAIFEEAHK 585
Score = 38.3 bits (88), Expect = 0.003
Identities = 28/188 (14%), Positives = 58/188 (30%), Gaps = 47/188 (25%)
Query: 141 PTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLMED--RKLVCKPDY----------- 187
P V+ Q L+Y ++ N + ++ R+L+ Y
Sbjct: 195 PETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPYENCLLVLLNVQ 254
Query: 188 --EAAKAKDGNCLDGDQPNKRPRTTITA--KQLETLKMAYNTSPKPARHVREQLSQDTGL 243
+A A + +C + +T KQ+ A T+ H L+ D
Sbjct: 255 NAKAWNAFNLSC----------KILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVK 304
Query: 244 DM--RVVQVWFQN--RRAKE---------KRLKKDAGRTRWSQYFRSMKGGTSPKDELKI 290
+ + + Q+ R +D G W ++ + D+L
Sbjct: 305 SLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRD-GLATW-DNWKHVN-----CDKLTT 357
Query: 291 DLDSNFSH 298
++S+ +
Sbjct: 358 IIESSLNV 365
>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription
regulation, transcriptional repression, DNA- binding
protein; HET: DNA; 2.25A {Saccharomyces cerevisiae}
SCOP: a.4.1.1
Length = 87
Score = 36.4 bits (84), Expect = 0.001
Identities = 16/79 (20%), Positives = 27/79 (34%), Gaps = 4/79 (5%)
Query: 185 PDYEAAKAKDGNCLDGDQPNKRPRTTITAKQLETLK---MAYNTSPKPARHVREQLSQDT 241
D + ++ R T + + L+ +P E L ++T
Sbjct: 9 ADGLVFNVVTQDMINKSTKPYR-GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNT 67
Query: 242 GLDMRVVQVWFQNRRAKEK 260
L ++ W NRR KEK
Sbjct: 68 SLSRIQIKNWVSNRRRKEK 86
>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration
calorimetry, protein-DNA complex, transcription/DNA
complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1
PDB: 1akh_B* 1apl_C* 1yrn_B*
Length = 83
Score = 35.2 bits (81), Expect = 0.003
Identities = 11/60 (18%), Positives = 18/60 (30%), Gaps = 4/60 (6%)
Query: 227 PKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWSQYFRSMKGGTSPKD 286
P E L ++T L ++ W RR +K S + K+
Sbjct: 28 PYLDTKGLENLMKNTSLSRIQIKNWVAARR----AKEKTITIAPELADLLSGEPLAKKKE 83
>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain,
hoogsteen base PAIR, transcription/DNA complex; HET:
5IU; 2.10A {Synthetic} SCOP: a.4.1.1
Length = 60
Score = 34.2 bits (79), Expect = 0.004
Identities = 12/36 (33%), Positives = 17/36 (47%)
Query: 227 PKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262
P E L ++T L ++ W NRR KEK +
Sbjct: 24 PYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI 59
>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 = 37.0 bits (85), Expect = 0.009
Identities = 56/340 (16%), Positives = 93/340 (27%), Gaps = 134/340 (39%)
Query: 10 LYQRIGLAVQRGNGLTVGICASKLHDLLHEAHAGSSSSFSSSFN------------DVDY 57
LYQ + V + A L +L+ + F+ N D DY
Sbjct: 176 LYQTYHVLVGD----LIKFSAETLSELIRTTLD-AEKVFTQGLNILEWLENPSNTPDKDY 230
Query: 58 EGIMPVYMPIASIPKCGGCGDLI----LDRFI--LKVLERT-----WHARCLKCHECG-- 104
+P+ S P LI L ++ K+L T + + H G
Sbjct: 231 LLSIPI-----SCP-------LIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLV 278
Query: 105 --APLAE----KCFARNGLLFCKEDFFKRFGTKC--AGCEMGIPPTQVVRRAQDLVYHLN 156
+AE + F + FF G +C A +PP+ + +D + +
Sbjct: 279 TAVAIAETDSWESFFVSVRKAITVLFF--IGVRCYEAYPNTSLPPSIL----EDSLENNE 332
Query: 157 CFACVMCARQLNTGDEFYLMEDRKLVCKPDYEAAKAKDGNCLDGDQPNKRPRTTITAKQL 216
M L +T +Q+
Sbjct: 333 GVPSPM------------------LSIS---------------N----------LTQEQV 349
Query: 217 ETLKMAYNTSPKPARHVREQLSQDTGLDMRVV----------QVWFQNRRAKEKRLKKDA 266
+ N+ + V ++S G VV + + +A D
Sbjct: 350 QDYVNKTNSHLPAGKQV--EISLVNGAKNLVVSGPPQSLYGLNLTLRKAKAPS---GLDQ 404
Query: 267 GRTRWSQYFRSMKGG------TSPKDELKIDLDSNFSHSH 300
R +S+ R +K SP F HSH
Sbjct: 405 SRIPFSE--RKLKFSNRFLPVASP-----------F-HSH 430
>2ys9_A Homeobox and leucine zipper protein homez; homeodomain, structural
genomics, NPPSFA, national project on protein structural
and functional analyses; NMR {Homo sapiens}
Length = 70
Score = 33.7 bits (76), Expect = 0.009
Identities = 10/57 (17%), Positives = 21/57 (36%)
Query: 211 ITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAG 267
++ L+ + + QLSQ + L + V WF +R + + +
Sbjct: 13 PPPPDIQPLERYWAAHQQLRETDIPQLSQASRLSTQQVLDWFDSRLPQPAEVSGPSS 69
>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger
homeobox family protein, riken structural
genomics/proteomics initiative; NMR {Arabidopsis
thaliana} SCOP: a.4.1.1
Length = 80
Score = 33.8 bits (77), Expect = 0.010
Identities = 17/72 (23%), Positives = 32/72 (44%), Gaps = 4/72 (5%)
Query: 189 AAKAKDGNCLDGDQPNKRPRTTITAKQLETLKMAYN----TSPKPARHVREQLSQDTGLD 244
++ + + G KR RT TA+Q E + + V ++ Q+TG+
Sbjct: 2 SSGSSGSSAEAGGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVP 61
Query: 245 MRVVQVWFQNRR 256
+V++VW N +
Sbjct: 62 RQVLKVWLHNNK 73
>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian,
protein-DNA complex, HOX hexapeptide, TALE homeodomain,
homeodomain interaction; 1.90A {Homo sapiens} SCOP:
a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*
Length = 73
Score = 32.3 bits (74), Expect = 0.021
Identities = 18/69 (26%), Positives = 35/69 (50%), Gaps = 6/69 (8%)
Query: 205 KRPRTTITAKQLETLK---MAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKR 261
+R R + E L ++ ++P P+ +E+L++ G+ + V WF N+R R
Sbjct: 2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKR---IR 58
Query: 262 LKKDAGRTR 270
KK+ G+ +
Sbjct: 59 YKKNIGKFQ 67
>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding,
transcription, nucleus, phosphoprotein, DNA bindi
protein; 1.95A {Homo sapiens}
Length = 67
Score = 32.3 bits (74), Expect = 0.021
Identities = 16/43 (37%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 227 PKPARHVREQLSQDTGLDMRVVQVWFQN-RRAKEKRLKKDAGR 268
P P+ ++QL+QDTGL + V WF N RR + + + R
Sbjct: 24 PYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQSNR 66
>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus
musculus} SCOP: a.4.1.1
Length = 64
Score = 31.5 bits (72), Expect = 0.037
Identities = 13/39 (33%), Positives = 22/39 (56%), Gaps = 3/39 (7%)
Query: 227 PKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKD 265
P P+ +E+L++ G+ + V WF N+R R KK+
Sbjct: 29 PYPSEEAKEELAKKCGITVSQVSNWFGNKR---IRYKKN 64
>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural
genomics, riken structural genomics/proteomics
initiative, RSGI; NMR {Arabidopsis thaliana} SCOP:
a.4.1.1
Length = 80
Score = 31.9 bits (72), Expect = 0.037
Identities = 17/73 (23%), Positives = 32/73 (43%), Gaps = 6/73 (8%)
Query: 189 AAKAKDGNCLDGDQPNKRPRTTITAKQLETL-----KMAYNTSPKPARHVREQLSQDTGL 243
++ + N KR RT TA+Q E + ++ + K EQ +TG+
Sbjct: 2 SSGSSGSNPSSSGGTTKRFRTKFTAEQKEKMLAFAERLGW-RIQKHDDVAVEQFCAETGV 60
Query: 244 DMRVVQVWFQNRR 256
+V+++W N +
Sbjct: 61 RRQVLKIWMHNNK 73
>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics,
NPPSFA, national project on protein structural and
functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1
Length = 73
Score = 30.8 bits (70), Expect = 0.097
Identities = 11/38 (28%), Positives = 19/38 (50%), Gaps = 3/38 (7%)
Query: 227 PKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKK 264
P P ++Q++ T L + V WF N R +R+ +
Sbjct: 33 PYPTEDEKKQIAAQTNLTLLQVNNWFINAR---RRILQ 67
>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast
structural genomics CON PSI-biology, transcription; NMR
{Homo sapiens}
Length = 89
Score = 30.5 bits (69), Expect = 0.13
Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 6/71 (8%)
Query: 201 DQPNKRPRTTITAKQLETLK---MAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRA 257
+ + + ++ L+ + + P+ + LSQ T L V WF N R
Sbjct: 2 GHHHHHHSHMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINAR- 60
Query: 258 KEKRLKKDAGR 268
+RL D R
Sbjct: 61 --RRLLPDMLR 69
>1u5k_A Hypothetical protein; OBD-fold, Zn-binding,
recombination,replication; 2.00A {Deinococcus
radiodurans} SCOP: b.40.4.13 g.45.1.2 PDB: 1w3s_A 2v1c_C
Length = 244
Score = 31.4 bits (71), Expect = 0.32
Identities = 11/52 (21%), Positives = 17/52 (32%), Gaps = 1/52 (1%)
Query: 74 GGCGDLILDRFILKVLERT-WHARCLKCHECGAPLAEKCFARNGLLFCKEDF 124
+ + K+L + +C CGAP E G L C +
Sbjct: 126 QPDPEWVALVMSYKLLGLAGVIPQTARCARCGAPDPEHPDPLGGQLLCSKCA 177
>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices
with the DNA binding helix- turn-helix motif, structural
genomics, NPPSFA; NMR {Homo sapiens}
Length = 102
Score = 29.8 bits (66), Expect = 0.36
Identities = 21/86 (24%), Positives = 29/86 (33%), Gaps = 21/86 (24%)
Query: 202 QPNKRPRTTITAKQLETLKMAYNTSPKPARHVREQL----------------SQDTGLDM 245
+ R R + L AY+ P++ RE L S+ GL
Sbjct: 4 GSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGS 63
Query: 246 R-----VVQVWFQNRRAKEKRLKKDA 266
V WF NRR +E +K A
Sbjct: 64 NLVTEVRVYNWFANRRKEEAFRQKLA 89
>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein,
X-linked TGF(beta) induced transcription factor 2-like
protein, TGIF-like on the X; NMR {Homo sapiens}
Length = 83
Score = 28.9 bits (65), Expect = 0.41
Identities = 13/68 (19%), Positives = 29/68 (42%), Gaps = 6/68 (8%)
Query: 200 GDQPNKRPRTTITAKQLETLK---MAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRR 256
K+ + + A+ ++ L+ + P+ ++ LS+ T L + + WF N R
Sbjct: 3 SGSSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINAR 62
Query: 257 AKEKRLKK 264
+R+
Sbjct: 63 ---RRILP 67
>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational
analysis, G protein, GAS subunit, A2A adenosine
receptor, cell-penetrating peptides; NMR {Synthetic}
PDB: 2o00_A
Length = 37
Score = 26.2 bits (57), Expect = 1.6
Identities = 9/16 (56%), Positives = 13/16 (81%)
Query: 246 RVVQVWFQNRRAKEKR 261
R +++WFQNRR K K+
Sbjct: 1 RQIKIWFQNRRMKWKK 16
>2k0a_A PRE-mRNA-splicing factor RDS3; zinc finger, topological knot, mRNA
processing, nucleus, spliceosome, RNA binding protein;
NMR {Saccharomyces cerevisiae}
Length = 109
Score = 27.6 bits (61), Expect = 2.5
Identities = 12/47 (25%), Positives = 21/47 (44%)
Query: 131 KCAGCEMGIPPTQVVRRAQDLVYHLNCFACVMCARQLNTGDEFYLME 177
KC C+ + P + VR ++ + C++C + D FY E
Sbjct: 31 KCPICDSYVRPKRKVRVCENCSFGKQAKNCIICNLNVGVNDAFYCWE 77
>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-PR; fatty
acid synthase, acyl-carrier-protein, beta-ketoacyl RED
beta-ketoacyl synthase, dehydratase; 4.00A {Saccharomyces
cerevisiae}
Length = 1688
Score = 28.7 bits (64), Expect = 2.9
Identities = 18/126 (14%), Positives = 27/126 (21%), Gaps = 58/126 (46%)
Query: 22 NGLTVGICASKLH-----------------------DLLHEAHAGSSSSFS-----SSFN 53
VG CA+ + D E F S+
Sbjct: 1099 IKTPVGACATSVESVDIGVETILSGKARICIVGGYDDFQEEGSFE----FGNMKATSNTL 1154
Query: 54 DVDYEGIMPVYMPIASIP----KCG-----GCGDLILDRFILKVLERTWHARCLKCHECG 104
+ G P S P + G G G ++ + A + G
Sbjct: 1155 EEFEHGRTPAE---MSRPATTTRNGFMEAQGAGIQ--------IIMQADLAL-----KMG 1198
Query: 105 AP-LAE 109
P
Sbjct: 1199 VPIYGI 1204
>2btv_A T2A, T2B, protein (VP3 core protein); virus/viral protein,
icosahedral virus; 3.50A {Bluetongue virus} SCOP:
e.28.1.1
Length = 901
Score = 28.6 bits (63), Expect = 3.0
Identities = 13/69 (18%), Positives = 23/69 (33%), Gaps = 1/69 (1%)
Query: 203 PNKRPRTTITAKQLETLKMAYNTSPKPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRL 262
+ P I A+ K N SP+ + V +++R + W + + L
Sbjct: 621 QRRFPDVLIQARPSHFWKAVLNDSPEAVKAVMNLSHSHNFINIRDMMRWV-LLPSLQPSL 679
Query: 263 KKDAGRTRW 271
K W
Sbjct: 680 KLVLEEEAW 688
>3o9p_A Periplasmic murein peptide-binding protein; oligopeptide binding
proteins, murein tripeptide, periplasmi protein; HET:
MHI; 2.07A {Escherichia coli}
Length = 519
Score = 28.0 bits (63), Expect = 4.5
Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 218 TLKMAYNTSP---KPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWS 272
L + YNTS K A V ++ G+D+++ ++ D R W
Sbjct: 362 KLTLLYNTSENHQKIAIAVASMWKKNLGVDVKLQNQEWKTYIDSRNTGNFDVIRASWV 419
>1jet_A OPPA, oligo-peptide binding protein; complex (peptide
transport/peptide), peptide transport; 1.20A {Salmonella
typhimurium} SCOP: c.94.1.1 PDB: 1b05_A* 1b0h_A* 1b2h_A
1b1h_A 1b3f_A 1b3g_A 1b3h_A* 1b3l_A 1b40_A 1b46_A 1b4h_A
1b4z_A 1b51_A 1b52_A 1b58_A 1b5h_A 1b5i_A 1b5j_A 1b6h_A
1b7h_A ...
Length = 517
Score = 27.6 bits (62), Expect = 5.4
Identities = 12/58 (20%), Positives = 22/58 (37%), Gaps = 3/58 (5%)
Query: 218 TLKMAYNTSP---KPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWS 272
T + YNTS K A V ++ G+++ + ++ + D R W
Sbjct: 360 TFDLLYNTSDLHKKLAIAVASIWKKNLGVNVNLENQEWKTFLDTRHQGTFDVARAGWC 417
>1zfo_A LAsp-1; LIM domain, zinc-finger, metal-binding protein; NMR {Sus
scrofa} SCOP: g.39.1.4
Length = 31
Score = 24.6 bits (53), Expect = 5.7
Identities = 8/27 (29%), Positives = 13/27 (48%)
Query: 71 PKCGGCGDLILDRFILKVLERTWHARC 97
P C CG ++ + L++ WH C
Sbjct: 4 PNCARCGKIVYPTEKVNCLDKFWHKAC 30
>3zs6_A Periplasmic oligopeptide-binding protein; peptide binding protein,
ABC transport system; HET: GOL; 2.10A {Burkholderia
pseudomallei}
Length = 506
Score = 27.6 bits (62), Expect = 6.0
Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 3/58 (5%)
Query: 218 TLKMAYNTSP---KPARHVREQLSQDTGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWS 272
T + YNT+ K A + G+ ++ V F+ + K R W
Sbjct: 350 TFTLTYNTNDLHKKVALFAASEWRTKLGVTAKLENVEFKVLMKQRHDGKVQIARDGWF 407
>3cf4_A Acetyl-COA decarboxylase/synthase alpha subunit; methanomicrobia,
iron-nikel-sulfur, 4Fe-NI-4S, oxidoreductas; 2.00A
{Methanosarcina barkeri}
Length = 807
Score = 27.1 bits (59), Expect = 8.4
Identities = 10/74 (13%), Positives = 16/74 (21%), Gaps = 6/74 (8%)
Query: 97 CLKCHECGAPLAEKCFARNGLLFCKEDFFKRFGTKCAGCEMGIPPTQVVRRAQ--DL--- 151
++ + L G C I + + A+ D
Sbjct: 389 TMEMAPIRDAAGITALPTDEELVNMVAKCADCGACLLACPEEIDIPEAMGFAKKGDFSYF 448
Query: 152 -VYHLNCFACVMCA 164
H C C C
Sbjct: 449 EEIHDTCIGCRRCE 462
>2adr_A ADR1; transcription regulation, zinc finger,; NMR {Saccharomyces
cerevisiae} SCOP: g.37.1.1 g.37.1.1
Length = 60
Score = 24.8 bits (55), Expect = 9.3
Identities = 6/20 (30%), Positives = 7/20 (35%), Gaps = 5/20 (25%)
Query: 99 KCHECGAPLAEKCFARNGLL 118
C C + F R LL
Sbjct: 32 PCGLCN-----RAFTRRDLL 46
>3na7_A HP0958; flagellar biogenesis, flagellum export, C4 Zn-ribbon,
coiled post-transcriptional, gene regulation, chaperone;
HET: EPE; 2.20A {Helicobacter pylori}
Length = 256
Score = 26.6 bits (58), Expect = 9.9
Identities = 6/31 (19%), Positives = 11/31 (35%), Gaps = 2/31 (6%)
Query: 129 GTKCAGCEMGIPPTQV--VRRAQDLVYHLNC 157
C GC + + V + D++ C
Sbjct: 198 KQACGGCFIRLNDKIYTEVLTSGDMITCPYC 228
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
0.322 0.136 0.428
Gapped
Lambda K H
0.267 0.0782 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 27921
Number of Hits to DB: 4,690,882
Number of extensions: 276320
Number of successful extensions: 1035
Number of sequences better than 10.0: 1
Number of HSP's gapped: 862
Number of HSP's successfully gapped: 195
Length of query: 306
Length of database: 6,701,793
Length adjustment: 93
Effective length of query: 213
Effective length of database: 4,105,140
Effective search space: 874394820
Effective search space used: 874394820
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 (21.9 bits)
S2: 57 (25.6 bits)