Psyllid ID: psy284

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------14
Protein Sequence
MSNEIGLEHLKINRMSMDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccccccccccccccccccccccccEEEEEccccccccccccccccccccccccEEEEEccEEEcHHHHHHHHccccccccccccccccccEEEEcccEEccccccccccccc
Secondary Structure Prediction (SSPRO)
cccHHcccccEEEEcccccccccccccccccccccccccHcccccccccccEEEEEccccHHHHHHEHHHHcccccccccEEEEccccEEEHHHHHHHHcccccHHHccccccHHHHHHHHccccEEcccEEHHHHccc
Coil and Loop (DISEMBL)
msneigleHLKINRMSMDvktqqgaqqtkavpnnaqgpqecagcgkhitDRFLLKALDMywhedclkcgccdcrlgevgstlyTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR
Flexible Loop (DISEMBL)
msneigleHLKINRMSMDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFacqqcnhr
Low Complexity Region (SEG)
MSNEIGLEHLKINRMSMDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR
Disordered region (IsUnstruct)
****************************************CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC***
Disordered Region (DISOPRED)
******************************************GCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH*
Disordered Region (DISEMBL)
MSNEIGLEHLKINRMSM*********************QECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR
Disordered Region (DISPRO)
****************************K*****AQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH*
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MSNEIGLEHLKINRMSMDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR
Positional Conservation
no confident homologs detected

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Close Homologs for Annotation Transfer

Close Homologs in SWISS-PROT Database Detected by BLAST

Original result of BLAST against SWISS-PROT Database

ID	Length	Definition	RBH(Q2H)	RBH(H2Q)	Q cover	H cover	Identity	E-value
Query	139	2.2.26 [Sep-21-2011]
Q8JFQ2	155	Rhombotin-1 OS=Danio reri	yes	N/A	0.870	0.780	0.715	5e-47
Q3B8H4	156	Rhombotin-1 OS=Xenopus la	N/A	N/A	0.870	0.775	0.715	6e-47
Q0P5B3	156	Rhombotin-1 OS=Bos taurus	yes	N/A	0.870	0.775	0.715	9e-47
P25800	156	Rhombotin-1 OS=Homo sapie	yes	N/A	0.870	0.775	0.715	9e-47
Q924W9	156	Rhombotin-1 OS=Mus muscul	yes	N/A	0.870	0.775	0.715	1e-46
Q9YH16	156	LIM domain only protein 3	N/A	N/A	0.820	0.730	0.75	1e-46
Q5RBW7	145	LIM domain only protein 3	no	N/A	0.719	0.689	0.823	4e-46
Q8BZL8	145	LIM domain only protein 3	no	N/A	0.719	0.689	0.823	4e-46
Q8TAP4	145	LIM domain only protein 3	no	N/A	0.719	0.689	0.823	4e-46
Q2KIA3	145	LIM domain only protein 3	no	N/A	0.719	0.689	0.823	4e-46

>sp|Q8JFQ2|RBTN1_DANRE Rhombotin-1 OS=Danio rerio GN=lmo1 PE=2 SV=1

 Score =  186 bits (471), Expect = 5e-47,   Method: Compositional matrix adjust.
 Identities = 88/123 (71%), Positives = 99/123 (80%), Gaps = 2/123 (1%)

Query: 17  MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
           M +  ++G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct: 1   MVLDKEEGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLG 58

Query: 77  EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
           EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct: 59  EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 118

Query: 137 NHR 139
           N R
Sbjct: 119 NQR 121

May be involved in gene regulation within neural lineage cells potentially by direct DNA binding or by binding to other transcription factors.
Danio rerio (taxid: 7955)

>sp|Q3B8H4|RBTN1_XENLA Rhombotin-1 OS=Xenopus laevis GN=lmo1 PE=2 SV=1

 Score =  185 bits (470), Expect = 6e-47,   Method: Compositional matrix adjust.
 Identities = 88/123 (71%), Positives = 99/123 (80%), Gaps = 2/123 (1%)

Query: 17  MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
           M ++ + G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct: 2   MVLEKEDGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLG 59

Query: 77  EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
           EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct: 60  EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 119

Query: 137 NHR 139
           N R
Sbjct: 120 NQR 122

May be involved in gene regulation within neural lineage cells potentially by direct DNA binding or by binding to other transcription factors.

Xenopus laevis (taxid: 8355)

>sp|Q0P5B3|RBTN1_BOVIN Rhombotin-1 OS=Bos taurus GN=LMO1 PE=2 SV=1

 Score =  185 bits (469), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 88/123 (71%), Positives = 98/123 (79%), Gaps = 2/123 (1%)

Query: 17  MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
           M +  + G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct: 2   MVLDKEDGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLG 59

Query: 77  EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
           EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct: 60  EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 119

Query: 137 NHR 139
           N R
Sbjct: 120 NQR 122

May be involved in gene regulation within neural lineage cells potentially by direct DNA binding or by binding to other transcription factors.

Bos taurus (taxid: 9913)

>sp|P25800|RBTN1_HUMAN Rhombotin-1 OS=Homo sapiens GN=LMO1 PE=2 SV=1

 Score =  185 bits (469), Expect = 9e-47,   Method: Compositional matrix adjust.
 Identities = 88/123 (71%), Positives = 98/123 (79%), Gaps = 2/123 (1%)

Query: 17  MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
           M +  + G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct: 2   MVLDKEDGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLG 59

Query: 77  EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
           EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct: 60  EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 119

Query: 137 NHR 139
           N R
Sbjct: 120 NQR 122

May be involved in gene regulation within neural lineage cells potentially by direct DNA binding or by binding to other transcription factors.

Homo sapiens (taxid: 9606)

>sp|Q924W9|RBTN1_MOUSE Rhombotin-1 OS=Mus musculus GN=Lmo1 PE=2 SV=1

 Score =  184 bits (468), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 88/123 (71%), Positives = 98/123 (79%), Gaps = 2/123 (1%)

Query: 17  MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
           M +  + G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct: 2   MVLDKEDGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLG 59

Query: 77  EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
           EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct: 60  EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 119

Query: 137 NHR 139
           N R
Sbjct: 120 NQR 122

May be involved in gene regulation within neural lineage cells potentially by direct DNA binding or by binding to other transcription factors.

Mus musculus (taxid: 10090)

>sp|Q9YH16|LMO3_XENLA LIM domain only protein 3 OS=Xenopus laevis GN=lmo3 PE=2 SV=1

 Score =  184 bits (467), Expect = 1e-46,   Method: Compositional matrix adjust.
 Identities = 87/116 (75%), Positives = 95/116 (81%), Gaps = 2/116 (1%)

Query: 24  GAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLY 83
           G Q     P+    P+ CAGC + I DR+LLKALD YWHEDCLKC CCDCRLGEVGSTLY
Sbjct: 9   GIQMLSVQPDTK--PKGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLY 66

Query: 84  TKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           TKANLILC+RDYLRLFG TG CAACSK+IPAFEMVMRA+ NVYHL+CFACQ CN R
Sbjct: 67  TKANLILCRRDYLRLFGVTGNCAACSKLIPAFEMVMRAKENVYHLDCFACQLCNQR 122

Xenopus laevis (taxid: 8355)

>sp|Q5RBW7|LMO3_PONAB LIM domain only protein 3 OS=Pongo abelii GN=LMO3 PE=2 SV=1

 Score =  182 bits (463), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 84/102 (82%), Positives = 92/102 (90%)

Query: 38  PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLR 97
           P+ CAGC + I DR+LLKALD YWHEDCLKC CCDCRLGEVGSTLYTKANLILC+RDYLR
Sbjct: 10  PKGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLR 69

Query: 98  LFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           LFG TG CAACSK+IPAFEMVMRA++NVYHL+CFACQ CN R
Sbjct: 70  LFGVTGNCAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQR 111

Pongo abelii (taxid: 9601)

>sp|Q8BZL8|LMO3_MOUSE LIM domain only protein 3 OS=Mus musculus GN=Lmo3 PE=2 SV=1

 Score =  182 bits (463), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 84/102 (82%), Positives = 92/102 (90%)

Query: 38  PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLR 97
           P+ CAGC + I DR+LLKALD YWHEDCLKC CCDCRLGEVGSTLYTKANLILC+RDYLR
Sbjct: 10  PKGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLR 69

Query: 98  LFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           LFG TG CAACSK+IPAFEMVMRA++NVYHL+CFACQ CN R
Sbjct: 70  LFGVTGNCAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQR 111

Mus musculus (taxid: 10090)

>sp|Q8TAP4|LMO3_HUMAN LIM domain only protein 3 OS=Homo sapiens GN=LMO3 PE=2 SV=1

 Score =  182 bits (463), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 84/102 (82%), Positives = 92/102 (90%)

Query: 38  PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLR 97
           P+ CAGC + I DR+LLKALD YWHEDCLKC CCDCRLGEVGSTLYTKANLILC+RDYLR
Sbjct: 10  PKGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLR 69

Query: 98  LFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           LFG TG CAACSK+IPAFEMVMRA++NVYHL+CFACQ CN R
Sbjct: 70  LFGVTGNCAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQR 111

Homo sapiens (taxid: 9606)

>sp|Q2KIA3|LMO3_BOVIN LIM domain only protein 3 OS=Bos taurus GN=LMO3 PE=2 SV=1

 Score =  182 bits (463), Expect = 4e-46,   Method: Compositional matrix adjust.
 Identities = 84/102 (82%), Positives = 92/102 (90%)

Query: 38  PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLR 97
           P+ CAGC + I DR+LLKALD YWHEDCLKC CCDCRLGEVGSTLYTKANLILC+RDYLR
Sbjct: 10  PKGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLR 69

Query: 98  LFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           LFG TG CAACSK+IPAFEMVMRA++NVYHL+CFACQ CN R
Sbjct: 70  LFGVTGNCAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQR 111

Bos taurus (taxid: 9913)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	139
91080717	241	PREDICTED: similar to beadex/dLMO protei	0.863	0.497	0.824	2e-55
242005244	284	LIM-only protein, putative [Pediculus hu	0.784	0.383	0.855	1e-52
270005132	254	hypothetical protein TcasGA2_TC007141 [T	0.856	0.468	0.784	6e-52
322796207	127	hypothetical protein SINV_11229 [Solenop	0.877	0.960	0.778	2e-51
157116702	218	rhombotin [Aedes aegypti] gi|108876328|g	0.726	0.463	0.910	3e-51
307206044	118	Rhombotin-1 [Harpegnathos saltator]	0.805	0.949	0.867	4e-51
307170935	118	Rhombotin-1 [Camponotus floridanus]	0.848	1.0	0.792	4e-51
357622819	359	beadex/dLMO protein [Danaus plexippus]	0.892	0.345	0.757	4e-51
158289946	204	AGAP010391-PA [Anopheles gambiae str. PE	0.726	0.495	0.910	4e-51
198467349	407	GA22333 [Drosophila pseudoobscura pseudo	0.741	0.253	0.902	5e-51

>gi|91080717|ref|XP_975367.1| PREDICTED: similar to beadex/dLMO protein [Tribolium castaneum] gi|270005467|gb|EFA01915.1| hypothetical protein TcasGA2_TC007525 [Tribolium castaneum]

 Score =  219 bits (559), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 103/125 (82%), Positives = 113/125 (90%), Gaps = 5/125 (4%)

Query: 15  MSMDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCR 74
           M+MDV   + A+     P++ QGPQECAGC K IT+R+LLKALD+YWHEDCLKCGCCDCR
Sbjct: 15  MTMDVSKGEAAK-----PSSGQGPQECAGCCKTITERYLLKALDLYWHEDCLKCGCCDCR 69

Query: 75  LGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQ 134
           LGEVGSTLYTKANLILCKRDYLRLFG+TGYCAACSKVIPAFEMVMRAR+NVYHLECFACQ
Sbjct: 70  LGEVGSTLYTKANLILCKRDYLRLFGNTGYCAACSKVIPAFEMVMRARSNVYHLECFACQ 129

Query: 135 QCNHR 139
           QCNHR
Sbjct: 130 QCNHR 134

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242005244|ref|XP_002423481.1| LIM-only protein, putative [Pediculus humanus corporis] gi|212506569|gb|EEB10743.1| LIM-only protein, putative [Pediculus humanus corporis]

 Score =  210 bits (535), Expect = 1e-52,   Method: Compositional matrix adjust.
 Identities = 95/111 (85%), Positives = 107/111 (96%), Gaps = 2/111 (1%)

Query: 29  KAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANL 88
           +A+P  + GP+ECAGCGK IT+RFLLKA+D++WHEDCLKCGCCDCRLGEVGSTLYTKANL
Sbjct: 39  QALP--SSGPRECAGCGKRITERFLLKAIDLFWHEDCLKCGCCDCRLGEVGSTLYTKANL 96

Query: 89  ILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           ILCKRDYLRLFG+TGYCAAC+KVIPAFEMVMRA++NVYHLECFACQQCNHR
Sbjct: 97  ILCKRDYLRLFGTTGYCAACNKVIPAFEMVMRAKSNVYHLECFACQQCNHR 147

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270005132|gb|EFA01580.1| hypothetical protein TcasGA2_TC007141 [Tribolium castaneum]

 Score =  208 bits (529), Expect = 6e-52,   Method: Compositional matrix adjust.
 Identities = 98/125 (78%), Positives = 108/125 (86%), Gaps = 6/125 (4%)

Query: 15  MSMDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCR 74
           + + V T   +  T A      G +ECAGCGK IT+RFLLKALD+YWHEDCLKCGCCDCR
Sbjct: 28  VPVSVSTAANSTATGA------GVRECAGCGKRITERFLLKALDLYWHEDCLKCGCCDCR 81

Query: 75  LGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQ 134
           LGEVGSTLYTKANLILCKRDYLRLFG+TGYCAAC+KVIPAFEMVMRA++NVYHLECFACQ
Sbjct: 82  LGEVGSTLYTKANLILCKRDYLRLFGTTGYCAACNKVIPAFEMVMRAKSNVYHLECFACQ 141

Query: 135 QCNHR 139
           QCNHR
Sbjct: 142 QCNHR 146

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|322796207|gb|EFZ18783.1| hypothetical protein SINV_11229 [Solenopsis invicta]

 Score =  207 bits (526), Expect = 2e-51,   Method: Compositional matrix adjust.
 Identities = 102/131 (77%), Positives = 111/131 (84%), Gaps = 9/131 (6%)

Query: 10  LKINRMSMDVKTQQGAQQTKAVPN-NAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKC 68
           L  ++M+MD         +K+ P  N    QECAGCGK IT+R+LLKALDMYWHEDCLKC
Sbjct: 5   LAGDKMTMD--------GSKSEPGKNGATQQECAGCGKAITERYLLKALDMYWHEDCLKC 56

Query: 69  GCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHL 128
           GCCDCRLGEVGSTLYTKANLILCKRDYLRLFG+TG+CAACSKVIPAFEMVMRAR NVYHL
Sbjct: 57  GCCDCRLGEVGSTLYTKANLILCKRDYLRLFGNTGHCAACSKVIPAFEMVMRARTNVYHL 116

Query: 129 ECFACQQCNHR 139
           ECFACQQCNHR
Sbjct: 117 ECFACQQCNHR 127

Source: Solenopsis invicta

Species: Solenopsis invicta

Genus: Solenopsis

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|157116702|ref|XP_001652842.1| rhombotin [Aedes aegypti] gi|108876328|gb|EAT40553.1| AAEL007719-PA [Aedes aegypti]

 Score =  206 bits (523), Expect = 3e-51,   Method: Compositional matrix adjust.
 Identities = 92/101 (91%), Positives = 100/101 (99%)

Query: 39  QECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 98
           ++CAGCGK IT+RFLLKALD++WHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL
Sbjct: 65  KDCAGCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 124

Query: 99  FGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           FG+TGYCAAC+KVIPAFEMVMRA+NNVYHLECFACQQCNHR
Sbjct: 125 FGTTGYCAACNKVIPAFEMVMRAKNNVYHLECFACQQCNHR 165

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307206044|gb|EFN84137.1| Rhombotin-1 [Harpegnathos saltator]

 Score =  206 bits (523), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 98/113 (86%), Positives = 104/113 (92%), Gaps = 1/113 (0%)

Query: 28  TKAVPN-NAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKA 86
           +K+ P  N    QECAGCGK IT+R+LLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKA
Sbjct: 6   SKSEPGKNGATQQECAGCGKAITERYLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKA 65

Query: 87  NLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           NLILCKRDYLRLFG+TG+CAACSKVIPAFEMVMRAR NVYHLECFACQQCNHR
Sbjct: 66  NLILCKRDYLRLFGNTGHCAACSKVIPAFEMVMRARTNVYHLECFACQQCNHR 118

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307170935|gb|EFN63035.1| Rhombotin-1 [Camponotus floridanus]

 Score =  205 bits (522), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 99/125 (79%), Positives = 106/125 (84%), Gaps = 7/125 (5%)

Query: 15  MSMDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCR 74
           M+MD    +  +       N    QECAGCGK IT+R+LLKALDMYWHEDCLKCGCCDCR
Sbjct: 1   MTMDGSKSESGK-------NGATQQECAGCGKAITERYLLKALDMYWHEDCLKCGCCDCR 53

Query: 75  LGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQ 134
           LGEVGSTLYTKANLILCKRDYLRLFG+TG+CAACSKVIPAFEMVMRAR NVYHLECFACQ
Sbjct: 54  LGEVGSTLYTKANLILCKRDYLRLFGNTGHCAACSKVIPAFEMVMRARTNVYHLECFACQ 113

Query: 135 QCNHR 139
           QCNHR
Sbjct: 114 QCNHR 118

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357622819|gb|EHJ74198.1| beadex/dLMO protein [Danaus plexippus]

 Score =  205 bits (522), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 97/128 (75%), Positives = 106/128 (82%), Gaps = 4/128 (3%)

Query: 15  MSMDVKTQQGAQ---QTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCC 71
           ++MDV  +  A     T   P   Q PQ CAGC K IT+R+LLKALD  WHEDCLKCGCC
Sbjct: 139 LAMDVTKEARASPLPSTTGAPAQPQ-PQICAGCSKVITERYLLKALDQLWHEDCLKCGCC 197

Query: 72  DCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECF 131
           DCRLGEVG TLYT+ANLILCKRDYLRLFG+TGYCAAC+KVIPAFEMVMRAR+NVYHLECF
Sbjct: 198 DCRLGEVGHTLYTRANLILCKRDYLRLFGNTGYCAACNKVIPAFEMVMRARSNVYHLECF 257

Query: 132 ACQQCNHR 139
           ACQQCNHR
Sbjct: 258 ACQQCNHR 265

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|158289946|ref|XP_311556.4| AGAP010391-PA [Anopheles gambiae str. PEST] gi|157018403|gb|EAA07238.4| AGAP010391-PA [Anopheles gambiae str. PEST]

 Score =  205 bits (522), Expect = 4e-51,   Method: Compositional matrix adjust.
 Identities = 92/101 (91%), Positives = 100/101 (99%)

Query: 39  QECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 98
           ++CAGCGK IT+RFLLKALD++WHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL
Sbjct: 51  KDCAGCGKRITERFLLKALDIFWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 110

Query: 99  FGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           FG+TGYCAAC+KVIPAFEMVMRA+NNVYHLECFACQQCNHR
Sbjct: 111 FGTTGYCAACNKVIPAFEMVMRAKNNVYHLECFACQQCNHR 151

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198467349|ref|XP_002134510.1| GA22333 [Drosophila pseudoobscura pseudoobscura] gi|198149202|gb|EDY73137.1| GA22333 [Drosophila pseudoobscura pseudoobscura]

 Score =  205 bits (522), Expect = 5e-51,   Method: Compositional matrix adjust.
 Identities = 93/103 (90%), Positives = 97/103 (94%)

Query: 37  GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYL 96
           G Q CAGCGKHI DR+LL+ALDM WHEDCLKCGCCDCRLGEVGSTLYTK NL+LCKRDYL
Sbjct: 182 GSQLCAGCGKHIQDRYLLRALDMLWHEDCLKCGCCDCRLGEVGSTLYTKGNLMLCKRDYL 241

Query: 97  RLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           RLFG+TGYCAACSKVIPAFEMVMRAR NVYHLECFACQQCNHR
Sbjct: 242 RLFGNTGYCAACSKVIPAFEMVMRARTNVYHLECFACQQCNHR 284

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	139
UNIPROTKB|P91608	266	Bx "Dttg protein" [Drosophila	0.769	0.402	0.887	4.9e-53
UNIPROTKB|Q3B8H4	156	lmo1 "Rhombotin-1" [Xenopus la	0.870	0.775	0.715	3.3e-47
ZFIN|ZDB-GENE-021115-6	155	lmo1 "LIM domain only 1" [Dani	0.870	0.780	0.715	3.3e-47
UNIPROTKB|Q0P5B3	156	LMO1 "Rhombotin-1" [Bos taurus	0.870	0.775	0.715	4.2e-47
UNIPROTKB|E2RLZ2	156	LMO1 "Uncharacterized protein"	0.870	0.775	0.715	5.4e-47
UNIPROTKB|E9PSF5	155	LMO1 "Rhombotin-1" [Homo sapie	0.870	0.780	0.715	5.4e-47
UNIPROTKB|P25800	156	LMO1 "Rhombotin-1" [Homo sapie	0.870	0.775	0.715	5.4e-47
UNIPROTKB|A9ED79	156	LMO1 "Uncharacterized protein"	0.870	0.775	0.715	5.4e-47
MGI|MGI:102812	156	Lmo1 "LIM domain only 1" [Mus	0.870	0.775	0.715	5.4e-47
UNIPROTKB|E2RHK8	156	LMO3 "Uncharacterized protein"	0.820	0.730	0.75	6.9e-47

UNIPROTKB|P91608 Bx "Dttg protein" [Drosophila sp. (taxid:7242)]

 Score = 549 (198.3 bits), Expect = 4.9e-53, P = 4.9e-53
 Identities = 95/107 (88%), Positives = 99/107 (92%)

Query:    33 NNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCK 92
             NN  G Q CAGCGKHI DR+LL+ALDM WHEDCLKCGCCDCRLGEVGSTLYTK NL+LCK
Sbjct:    37 NNNNGSQLCAGCGKHIQDRYLLRALDMLWHEDCLKCGCCDCRLGEVGSTLYTKGNLMLCK 96

Query:    93 RDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
             RDYLRLFG+TGYCAACSKVIPAFEMVMRAR NVYHLECFACQQCNHR
Sbjct:    97 RDYLRLFGNTGYCAACSKVIPAFEMVMRARTNVYHLECFACQQCNHR 143

GO:0002121 "inter-male aggressive behavior" evidence=IMP

GO:0005634 "nucleus" evidence=NAS

GO:0006911 "phagocytosis, engulfment" evidence=IMP

GO:0007476 "imaginal disc-derived wing morphogenesis" evidence=IGI;IMP

GO:0035218 "leg disc development" evidence=IMP

GO:0036011 "imaginal disc-derived leg segmentation" evidence=IMP

GO:0042220 "response to cocaine" evidence=IMP

GO:0045475 "locomotor rhythm" evidence=IMP

UNIPROTKB|Q3B8H4 lmo1 "Rhombotin-1" [Xenopus laevis (taxid:8355)]

 Score = 494 (179.0 bits), Expect = 3.3e-47, P = 3.3e-47
 Identities = 88/123 (71%), Positives = 99/123 (80%)

Query:    17 MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
             M ++ + G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct:     2 MVLEKEDGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLG 59

Query:    77 EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
             EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct:    60 EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 119

Query:   137 NHR 139
             N R
Sbjct:   120 NQR 122

GO:0003674 "molecular_function" evidence=ND

GO:0005634 "nucleus" evidence=ISS

GO:0008150 "biological_process" evidence=ND

ZFIN|ZDB-GENE-021115-6 lmo1 "LIM domain only 1" [Danio rerio (taxid:7955)]

 Score = 494 (179.0 bits), Expect = 3.3e-47, P = 3.3e-47
 Identities = 88/123 (71%), Positives = 99/123 (80%)

Query:    17 MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
             M +  ++G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct:     1 MVLDKEEGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLG 58

Query:    77 EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
             EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct:    59 EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 118

Query:   137 NHR 139
             N R
Sbjct:   119 NQR 121

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISS

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|Q0P5B3 LMO1 "Rhombotin-1" [Bos taurus (taxid:9913)]

 Score = 493 (178.6 bits), Expect = 4.2e-47, P = 4.2e-47
 Identities = 88/123 (71%), Positives = 98/123 (79%)

Query:    17 MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
             M +  + G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct:     2 MVLDKEDGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLG 59

Query:    77 EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
             EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct:    60 EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 119

Query:   137 NHR 139
             N R
Sbjct:   120 NQR 122

GO:0005634 "nucleus" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E2RLZ2 LMO1 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 492 (178.3 bits), Expect = 5.4e-47, P = 5.4e-47
 Identities = 88/123 (71%), Positives = 98/123 (79%)

Query:    17 MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
             M +  + G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct:     2 MVLDKEDGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLG 59

Query:    77 EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
             EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct:    60 EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 119

Query:   137 NHR 139
             N R
Sbjct:   120 NQR 122

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E9PSF5 LMO1 "Rhombotin-1" [Homo sapiens (taxid:9606)]

 Score = 492 (178.3 bits), Expect = 5.4e-47, P = 5.4e-47
 Identities = 88/123 (71%), Positives = 98/123 (79%)

Query:    17 MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
             M +  + G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct:     1 MVLDQEDGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLG 58

Query:    77 EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
             EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct:    59 EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 118

Query:   137 NHR 139
             N R
Sbjct:   119 NQR 121

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|P25800 LMO1 "Rhombotin-1" [Homo sapiens (taxid:9606)]

 Score = 492 (178.3 bits), Expect = 5.4e-47, P = 5.4e-47
 Identities = 88/123 (71%), Positives = 98/123 (79%)

Query:    17 MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
             M +  + G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct:     2 MVLDKEDGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLG 59

Query:    77 EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
             EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct:    60 EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 119

Query:   137 NHR 139
             N R
Sbjct:   120 NQR 122

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0005634 "nucleus" evidence=ISS

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IMP

UNIPROTKB|A9ED79 LMO1 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 492 (178.3 bits), Expect = 5.4e-47, P = 5.4e-47
 Identities = 88/123 (71%), Positives = 98/123 (79%)

Query:    17 MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
             M +  + G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct:     2 MVLDKEDGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLG 59

Query:    77 EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
             EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct:    60 EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 119

Query:   137 NHR 139
             N R
Sbjct:   120 NQR 122

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

MGI|MGI:102812 Lmo1 "LIM domain only 1" [Mus musculus (taxid:10090)]

 Score = 492 (178.3 bits), Expect = 5.4e-47, P = 5.4e-47
 Identities = 88/123 (71%), Positives = 98/123 (79%)

Query:    17 MDVKTQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG 76
             M +  + G       P   Q  + CAGC + I DR+LLKALD YWHEDCLKC CCDCRLG
Sbjct:     2 MVLDKEDGVPMLSVQPKGKQ--KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLG 59

Query:    77 EVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
             EVGSTLYTKANLILC+RDYLRLFG+TG CAACSK+IPAFEMVMRAR+NVYHL+CFACQ C
Sbjct:    60 EVGSTLYTKANLILCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLC 119

Query:   137 NHR 139
             N R
Sbjct:   120 NQR 122

GO:0000122 "negative regulation of transcription from RNA polymerase II promoter" evidence=IGI

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005730 "nucleolus" evidence=IDA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0045944 "positive regulation of transcription from RNA polymerase II promoter" evidence=ISO;IGI

GO:0046872 "metal ion binding" evidence=IEA

UNIPROTKB|E2RHK8 LMO3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 491 (177.9 bits), Expect = 6.9e-47, P = 6.9e-47
 Identities = 87/116 (75%), Positives = 96/116 (82%)

Query:    24 GAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLY 83
             G Q     P+    P+ CAGC + I DR+LLKALD YWHEDCLKC CCDCRLGEVGSTLY
Sbjct:     9 GIQMLSVQPDTK--PKGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLY 66

Query:    84 TKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
             TKANLILC+RDYLRLFG TG CAACSK+IPAFEMVMRA++NVYHL+CFACQ CN R
Sbjct:    67 TKANLILCRRDYLRLFGVTGNCAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQR 122

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q5FVB2	LMO41_XENTR	No assigned EC number	0.5371	0.8705	0.7245	yes	N/A
Q8BZL8	LMO3_MOUSE	No assigned EC number	0.8235	0.7194	0.6896	no	N/A
Q9YH16	LMO3_XENLA	No assigned EC number	0.75	0.8201	0.7307	N/A	N/A
Q503U0	LMO3_DANRE	No assigned EC number	0.8235	0.7194	0.6896	no	N/A
Q5RBW7	LMO3_PONAB	No assigned EC number	0.8235	0.7194	0.6896	no	N/A
Q3B8H4	RBTN1_XENLA	No assigned EC number	0.7154	0.8705	0.7756	N/A	N/A
Q924W9	RBTN1_MOUSE	No assigned EC number	0.7154	0.8705	0.7756	yes	N/A
Q8TAP4	LMO3_HUMAN	No assigned EC number	0.8235	0.7194	0.6896	no	N/A
Q8JFQ2	RBTN1_DANRE	No assigned EC number	0.7154	0.8705	0.7806	yes	N/A
Q99MB5	LMO3_RAT	No assigned EC number	0.8190	0.7482	0.7172	no	N/A
P25800	RBTN1_HUMAN	No assigned EC number	0.7154	0.8705	0.7756	yes	N/A
Q0P5B3	RBTN1_BOVIN	No assigned EC number	0.7154	0.8705	0.7756	yes	N/A
Q2KIA3	LMO3_BOVIN	No assigned EC number	0.8235	0.7194	0.6896	no	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	139
cd09388	55	cd09388, LIM1_LMO1_LMO3, The first LIM domain of L	9e-30
cd09386	55	cd09386, LIM1_LMO4, The first LIM domain of LMO4 (	2e-21
cd09384	56	cd09384, LIM1_LMO2, The first LIM domain of LMO2 (	1e-18
cd09390	55	cd09390, LIM2_dLMO, The second LIM domain of dLMO	3e-17
cd09389	55	cd09389, LIM2_LMO1_LMO3, The second LIM domain of	6e-14
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	7e-13
cd09467	55	cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b	7e-11
cd09466	56	cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a	1e-10
cd09387	55	cd09387, LIM2_LMO4, The second LIM domain of LMO4	1e-10
pfam00412	58	pfam00412, LIM, LIM domain	1e-09
cd09373	54	cd09373, LIM1_AWH, The first LIM domain of Arrowhe	2e-09
cd09468	52	cd09468, LIM1_Lhx4, The first LIM domain of Lhx4	3e-09
cd09371	53	cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b	5e-09
cd09377	59	cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of	8e-09
cd09369	54	cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of L	1e-08
cd09469	64	cd09469, LIM1_Lhx2, The first LIM domain of Lhx2	1e-08
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	2e-08
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	2e-08
cd09368	52	cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of L	2e-08
cd09366	55	cd09366, LIM1_Isl, The first LIM domain of Isl, a	1e-07
cd09381	56	cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of L	1e-07
cd09379	55	cd09379, LIM2_AWH, The second LIM domain of Arrowh	1e-07
cd09470	54	cd09470, LIM1_Lhx9, The first LIM domain of Lhx9	2e-07
cd09376	56	cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of	2e-07
cd09385	56	cd09385, LIM2_LMO2, The second LIM domain of LMO2	2e-07
cd09370	52	cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a	2e-07
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	2e-07
cd09380	54	cd09380, LIM1_Lhx6, The first LIM domain of Lhx6	5e-07
cd09475	59	cd09475, LIM2_Lhx9, The second LIM domain of Lhx9	6e-07
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	9e-07
cd09378	55	cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain o	2e-06
cd09474	59	cd09474, LIM2_Lhx2, The second LIM domain of Lhx2	4e-06
pfam00412	58	pfam00412, LIM, LIM domain	5e-06
cd09374	55	cd09374, LIM2_Isl, The second LIM domain of Isl, a	5e-06
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	5e-06
cd09375	56	cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of	2e-05
cd09471	55	cd09471, LIM2_Isl2, The second LIM domain of Isl2	2e-05
cd09473	56	cd09473, LIM2_Lhx4, The second LIM domain of Lhx4	4e-05
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	7e-05
cd09472	57	cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3	1e-04
cd09382	55	cd09382, LIM2_Lhx6, The second LIM domain of Lhx6	1e-04
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	1e-04
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	2e-04
cd09353	60	cd09353, LIM2_Zyxin, The second LIM domain of Zyxi	5e-04
cd09383	55	cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of	6e-04
cd09391	57	cd09391, LIM1_Lrg1p_like, The first LIM domain of	9e-04
cd09389	55	cd09389, LIM2_LMO1_LMO3, The second LIM domain of	0.001
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	0.001
cd09391	57	cd09391, LIM1_Lrg1p_like, The first LIM domain of	0.002
cd09332	52	cd09332, LIM2_PINCH, The second LIM domain of prot	0.004

>gnl|CDD|188774 cd09388, LIM1_LMO1_LMO3, The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

 Score =  101 bits (254), Expect = 9e-30
 Identities = 47/55 (85%), Positives = 50/55 (90%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          CAGC + I DR+LLKALD YWHEDCLKC CCDCRLGEVGSTLYTKANLILC+RDY
Sbjct: 1  CAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDY 55

The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188772 cd09386, LIM1_LMO4, The first LIM domain of LMO4 (LIM domain only protein 4)

 Score = 80.5 bits (199), Expect = 2e-21
 Identities = 37/55 (67%), Positives = 41/55 (74%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          CAGCG  I DRFLL ALD YWH  CLKC CC  +LGE+GS+ YTK  +ILCK DY
Sbjct: 1  CAGCGGKIVDRFLLHALDRYWHNGCLKCSCCQAQLGEIGSSCYTKGGMILCKNDY 55

The first LIM domain of LMO4 (LIM domain only protein 4): LMO4 is a nuclear protein that plays important roles in transcriptional regulation and development. LMO4 is involved in various functions in tumorigenesis and cellular differentiation. LMO4 proteins regulate gene expression by interacting with a wide variety of transcription factors and cofactors to form large transcription complexes. It can interact with Smad proteins, and associate with the promoter of the PAI-1 (plasminogen activator inhibitor-1) gene in a TGFbeta (transforming growth factor beta)-dependent manner. LMO4 can also form a complex with transcription regulator CREB (cAMP response element-binding protein) and interact with CLIM1 and CLIM2. In breast tissue, LMO4 interacts with multiple proteins, including the cofactor CtIP [CtBP (C-terminal binding protein)-interacting protein], the breast and ovarian tumor suppressor BRCA1 (breast-cancer susceptibility gene 1) and the LIM-domain-binding protein LDB1. Functionally, LMO4 is shown to repress BRCA1-mediated transcription activation, thus invoking a potential role for LMO4 as a negative regulator of BRCA1 in sporadic breast cancer. LMO4 also forms complex to both ERa (oestrogen receptor alpha), MTA1 (metastasis tumor antigen 1), and HDACs (histone deacetylases), implying that LMO4 is also a component of the MTA1 corepressor complex. Over-expressed LMO4 represses ERa transactivation functions in an HDAC-dependent manner, and contributes to the process of breast cancer progression by allowing the development of Era-negative phenotypes. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188770 cd09384, LIM1_LMO2, The first LIM domain of LMO2 (LIM domain only protein 2)

 Score = 73.3 bits (180), Expect = 1e-18
 Identities = 35/56 (62%), Positives = 40/56 (71%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYL 96
          C GC ++I DR+ LKA+D YWHEDCL C  C CRLGEVG  LY K    LC+RDYL
Sbjct: 1  CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 56

The first LIM domain of LMO2 (LIM domain only protein 2): LMO2 is a nuclear protein that plays important roles in transcriptional regulation and development. The two tandem LIM domains of LMO2 support the assembly of a crucial cell-regulatory complex by interacting with both the TAL1-E47 and GATA1 transcription factors to form a DNA-binding complex that is capable of transcriptional activation. LMOs have also been shown to be involved in oncogenesis. LMO1 and LMO2 are activated in T-cell acute lymphoblastic leukemia by distinct chromosomal translocations. LMO2 was also shown to be involved in erythropoiesis and is required for the hematopoiesis in the adult animals. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188776 cd09390, LIM2_dLMO, The second LIM domain of dLMO (Beaderx)

 Score = 69.9 bits (171), Expect = 3e-17
 Identities = 32/35 (91%), Positives = 33/35 (94%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           CAACSK IPAFEMVMRAR NVYHLECFACQ+CNHR
Sbjct: 1   CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHR 35

The second LIM domain of dLMO (Beaderx): dLMO is a nuclear protein that plays important roles in transcriptional regulation and development. In Drosophila dLMO modulates the activity of LIM-homeodomain protein Apterous (Ap), which regulates the formation of the dorsal-ventral axis of the Drosophila wing. Biochemical analysis shows that dLMO protein influences the activity of Apterous by binding of its cofactor Chip. Further studies shown that dLMO proteins might function in an evolutionarily conserved mechanism involved in patterning the appendages. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188775 cd09389, LIM2_LMO1_LMO3, The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

 Score = 61.6 bits (149), Expect = 6e-14
 Identities = 29/35 (82%), Positives = 33/35 (94%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           CAACSK+IPAFEMVMRA++NVYHL+CFACQ CN R
Sbjct: 1   CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQR 35

The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain, containing two zinc fingers

 Score = 58.9 bits (143), Expect = 7e-13
 Identities = 25/55 (45%), Positives = 30/55 (54%), Gaps = 2/55 (3%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          CAGCGK I  R LL+AL   WH +C KC  C   LG  G + Y K     C++ Y
Sbjct: 1  CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLG--GDSFYEKDGKPYCEKCY 53

LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16, 21)-C-x(2,3)-[CHD] (where X denotes any amino acid). Length = 53

>gnl|CDD|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b

 Score = 53.8 bits (129), Expect = 7e-11
 Identities = 25/55 (45%), Positives = 35/55 (63%), Gaps = 3/55 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          CAGC +HI DRF+LK LD +WH  CLKC  C  +L E     +++ + + CK D+
Sbjct: 4  CAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAE---KCFSRGDSVYCKDDF 55

The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|188850 cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a

 Score = 53.2 bits (128), Expect = 1e-10
 Identities = 22/55 (40%), Positives = 30/55 (54%), Gaps = 3/55 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          CAGC   I DRF+LK  D  WH  CLKC  C  +L +     +++   + CK D+
Sbjct: 4  CAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTD---KCFSRGGQVYCKEDF 55

The first LIM domain of Lhx3a: Lhx3a is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3a is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

>gnl|CDD|188773 cd09387, LIM2_LMO4, The second LIM domain of LMO4 (LIM domain only protein 4)

 Score = 52.9 bits (127), Expect = 1e-10
 Identities = 20/35 (57%), Positives = 28/35 (80%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           C+AC + IPA E+VMRA+ NVYHL+CF C  C+++
Sbjct: 1   CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQ 35

The second LIM domain of LMO4 (LIM domain only protein 4): LMO4 is a nuclear protein that plays important roles in transcriptional regulation and development. LMO4 is involved in various functions in tumorigenesis and cellular differentiation. LMO4 proteins regulate gene expression by interacting with a wide variety of transcription factors and cofactors to form large transcription complexes. It can interact with Smad proteins, and associate with the promoter of the PAI-1 (plasminogen activator inhibitor-1) gene in a TGFbeta (transforming growth factor beta)-dependent manner. LMO4 can also form a complex with transcription regulator CREB (cAMP response element-binding protein) and interact with CLIM1 and CLIM2. In breast tissue, LMO4 interacts with multiple proteins, including the cofactor CtIP [CtBP (C-terminal binding protein)-interacting protein], the breast and ovarian tumor suppressor BRCA1 (breast-cancer susceptibility gene 1) and the LIM-domain-binding protein LDB1. Functionally, LMO4 is shown to repress BRCA1-mediated transcription activation, thus invoking a potential role for LMO4 as a negative regulator of BRCA1 in sporadic breast cancer. LMO4 also forms complex to both ERa (oestrogen receptor alpha), MTA1 (metastasis tumor antigen 1), and HDACs (histone deacetylases), implying that LMO4 is also a component of the MTA1 corepressor complex. Over-expressed LMO4 represses ERa transactivation functions in an HDAC-dependent manner, and contributes to the process of breast cancer progression by allowing the development of Era-negative phenotypes. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|215907 pfam00412, LIM, LIM domain

 Score = 50.4 bits (121), Expect = 1e-09
 Identities = 26/60 (43%), Positives = 33/60 (55%), Gaps = 3/60 (5%)

Query: 41 CAGCGKHITDRFLLK-ALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99
          CAGCGK I DR L++ AL   WH +C +C  C   LG      + K   + CK DY +LF
Sbjct: 1  CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGP--GDFFEKDGKLYCKHDYFKLF 58

This family represents two copies of the LIM structural domain. Length = 58

>gnl|CDD|188759 cd09373, LIM1_AWH, The first LIM domain of Arrowhead (AWH)

 Score = 50.1 bits (120), Expect = 2e-09
 Identities = 26/55 (47%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          C GCG+ ITDRFLLK     WH  CL+C  C   L    S  +T+   I CK DY
Sbjct: 1  CTGCGEPITDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSC-FTRDRQIYCKADY 54

The first LIM domain of Arrowhead (AWH): Arrowhead belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. During embryogenesis of Drosophila, Arrowhead is expressed in each abdominal segment and in the labial segment. Late in embryonic development, expression of arrowhead is refined to the abdominal histoblasts and salivary gland imaginal ring cells themselves. The Arrowhead gene required for establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4

 Score = 49.6 bits (118), Expect = 3e-09
 Identities = 25/55 (45%), Positives = 35/55 (63%), Gaps = 3/55 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          CAGC +HI D+F+LK LD +WH  CLKC  C  +L E     +++A  + CK D+
Sbjct: 1  CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAE---RCFSRAGNVYCKEDF 52

The first LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 52

>gnl|CDD|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b

 Score = 48.9 bits (117), Expect = 5e-09
 Identities = 22/55 (40%), Positives = 33/55 (60%), Gaps = 3/55 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          CAGC + I+DR+LL+  +  WHE+CL+C  C   L     + Y +   + CK+DY
Sbjct: 1  CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPLTT---SCYFRDRKLYCKQDY 52

The first LIM domain of Lmx1b: Lmx1b belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188763 cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of Lhx2 and Lhx9 family

 Score = 48.4 bits (116), Expect = 8e-09
 Identities = 19/33 (57%), Positives = 22/33 (66%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           CA C   I A E+VMRAR+ V+HL CF C  CN
Sbjct: 5   CARCHLGISASELVMRARDLVFHLNCFTCATCN 37

The second LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 59

>gnl|CDD|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9 family

 Score = 48.1 bits (115), Expect = 1e-08
 Identities = 25/55 (45%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          CAGCG+ I DRF L A+D  WH  CLKC  C   L +   + +++   I CK DY
Sbjct: 1  CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPL-DSELSCFSRDGNIYCKEDY 54

The first LIM domain of Lhx2 and Lhx9 family: Lhx2 and Lhx9 are highly homologous LHX regulatory proteins. They belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Although Lhx2 and Lhx9 are highly homologous, they seems to play regulatory roles in different organs. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. Lhx9 is expressed in several regions of the developing mouse brain , the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188853 cd09469, LIM1_Lhx2, The first LIM domain of Lhx2

 Score = 48.1 bits (114), Expect = 1e-08
 Identities = 28/56 (50%), Positives = 35/56 (62%), Gaps = 3/56 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG-EVGSTLYTKANLILCKRDY 95
          CAGCG  I+DR+ L A+D  WH  CLK  CC+C+L  E   T ++K   I CK DY
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLK--CCECKLNLESELTCFSKDGSIYCKEDY 64

The first LIM domain of Lhx2: Lhx2 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. The Lhx2 protein has been shown to bind to the mouse M71 olfactory receptor promoter. Similar to other LIM domains, this domain family is 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 64

>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 47.4 bits (113), Expect = 2e-08
 Identities = 22/55 (40%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 41 CAGCGKHITDR-FLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRD 94
          CAGCGK I     +L+AL   WH +C KC  C   L   G T + K   + CK  
Sbjct: 2  CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPL--SGDTFFEKDGKLYCKDC 54

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways. Length = 54

>gnl|CDD|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known as Lim1) and Lhx5

 Score = 47.4 bits (113), Expect = 2e-08
 Identities = 21/55 (38%), Positives = 31/55 (56%), Gaps = 3/55 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          CAGC + I D+FLL  LD  WH  C++C  C C L E     +++   + C+ D+
Sbjct: 1  CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTE---KCFSREGKLYCRNDF 52

The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4 family

 Score = 47.0 bits (112), Expect = 2e-08
 Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 3/55 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          C GC +HI DRF+LK LD  WH  CLKC  C  +L +     + +   + CK D+
Sbjct: 1  CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTD---KCFARNGHVYCKDDF 52

The first LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription. Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 52

>gnl|CDD|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX protein family

 Score = 45.4 bits (108), Expect = 1e-07
 Identities = 24/56 (42%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 41 CAGCGKHITDRFLLK-ALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          C GCG  I D+++L+ A D+ WH  CLKC  C   L E   T + +     CKRDY
Sbjct: 1  CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYLDE-TCTCFVRDGKTYCKRDY 55

The first LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Is l2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188767 cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of Lhx7 and Lhx8

 Score = 45.4 bits (107), Expect = 1e-07
 Identities = 24/56 (42%), Positives = 30/56 (53%), Gaps = 1/56 (1%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYL 96
          C+ CG  I D++LLK  D+ WH  CL C  C   LG   ++ Y K   I CK DY 
Sbjct: 2  CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGR-HTSCYIKDKDIFCKLDYF 56

The first LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

>gnl|CDD|188765 cd09379, LIM2_AWH, The second LIM domain of Arrowhead (AWH)

 Score = 45.1 bits (107), Expect = 1e-07
 Identities = 19/32 (59%), Positives = 23/32 (71%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
           CA CS+ I A + V RAR++VYHL CFAC  C
Sbjct: 1   CAKCSRNISASDWVRRARDHVYHLACFACDAC 32

The second LIM domain of Arrowhead (AWH): Arrowhead belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. During embryogenesis of Drosophila, Arrowhead is expressed in each abdominal segment and in the labial segment. Late in embryonic development, expression of arrowhead is refined to the abdominal histoblasts and salivary gland imaginal ring cells themselves. The Arrowhead gene required for establishment of a subset of imaginal tissues: the abdominal histoblasts and the salivary gland imaginal rings. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|188854 cd09470, LIM1_Lhx9, The first LIM domain of Lhx9

 Score = 45.0 bits (106), Expect = 2e-07
 Identities = 28/56 (50%), Positives = 34/56 (60%), Gaps = 3/56 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLG-EVGSTLYTKANLILCKRDY 95
          CAGCG  I+DR+ L A+D  WH  CLK  CC+C+L  E   T + K   I CK DY
Sbjct: 1  CAGCGGKISDRYYLLAVDKQWHLRCLK--CCECKLALESELTCFAKDGSIYCKEDY 54

The first LIM domain of Lhx9: Lhx9 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx9 is highly homologous to Lhx2. It is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice have reduced levels of the Sf1 nuclear receptor that is required for gonadogenesis, and recent studies have shown that Lhx9 is able to activate the Sf1/FtzF1 gene. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188762 cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of Lhx3-Lhx4 family

 Score = 44.6 bits (106), Expect = 2e-07
 Identities = 19/35 (54%), Positives = 25/35 (71%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           CA C + IP  ++V RA++NVYHLECFAC  C  +
Sbjct: 1   CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQ 35

The second LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription.Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

>gnl|CDD|188771 cd09385, LIM2_LMO2, The second LIM domain of LMO2 (LIM domain only protein 2)

 Score = 45.0 bits (106), Expect = 2e-07
 Identities = 19/32 (59%), Positives = 23/32 (71%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
           CA+C K I A+EM MR ++ VYHLECF C  C
Sbjct: 1   CASCDKRIRAYEMTMRVKDKVYHLECFKCAAC 32

The second LIM domain of LMO2 (LIM domain only protein 2): LMO2 is a nuclear protein that plays important roles in transcriptional regulation and development. The two tandem LIM domains of LMO2 support the assembly of a crucial cell-regulatory complex by interacting with both the TAL1-E47 and GATA1 transcription factors to form a DNA-binding complex that is capable of transcriptional activation. LMOs have also been shown to be involved in oncogenesis. LMO1 and LMO2 are activated in T-cell acute lymphoblastic leukemia by distinct chromosomal translocations. LMO2 was also shown to be involved in erythropoiesis and is required for the hematopoiesis in the adult animals. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a

 Score = 44.4 bits (105), Expect = 2e-07
 Identities = 23/55 (41%), Positives = 30/55 (54%), Gaps = 3/55 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          C GC + I DRFLL+  D  WHE CL+C  C   L    +T + +   + CK DY
Sbjct: 1  CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPL---ETTCFYRDKKLYCKEDY 52

The first LIM domain of Lmx1a: Lmx1a belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. Human Lmx1a can be found in pancreas, skeletal muscle, adipose tissue, developing brain, mammary glands, and pituitary. The functions of Lmx1a in the developing nervous system were revealed by studies of mutant mouse. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp 6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility; skeletal defects; and behavioral abnormalities. Within pancreatic cells, the Lmx1a protein interacts synergistically with the bHLH transcription factor E47 to activate the insulin gene enhancer/promoter. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 52

>gnl|CDD|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase )

 Score = 44.4 bits (105), Expect = 2e-07
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          CAGC   I D   ++AL+  WH DC +C  C   L    +  + K   + C++DY
Sbjct: 1  CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSL---SNWYFEKDGKLYCRKDY 52

The first LIM domain of LIMK (LIM domain Kinase ): LIMK protein family is comprised of two members LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerisation. LIMKs can function in both cytoplasm and nucleus and are expressed in all tissues. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. However, LIMK1 and LIMk2 have different cellular locations. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The LIM domains of LIMK have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6

 Score = 43.5 bits (102), Expect = 5e-07
 Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          C+ CG  I DR+LLK  ++ WH  CL+C  C   L +  ++ Y K   I CK DY
Sbjct: 1  CSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQ-HNSCYIKNKEIFCKMDY 54

The first LIM domain of Lhx6. Lhx6 is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Lhx6 functions in the brain and nervous system. It is expressed at high levels in several regions of the embryonic mouse CNS, including the telencephalon and hypothalamus, and the first branchial arch. Lhx6 is proposed to have a role in patterning of the mandible and maxilla, and in signaling during odontogenesis. In brain sections, knockdown of Lhx6 gene blocks the normal migration of neurons to the cortex. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188859 cd09475, LIM2_Lhx9, The second LIM domain of Lhx9

 Score = 43.5 bits (102), Expect = 6e-07
 Identities = 22/37 (59%), Positives = 23/37 (62%)

Query: 101 STGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           S   CA C   I A EMVMRAR +VYHL CF C  CN
Sbjct: 1   SVQRCARCHLGISASEMVMRARESVYHLSCFTCTTCN 37

The second LIM domain of Lhx9: Lhx9 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx9 is highly homologous to Lhx2. It is expressed in several regions of the developing mouse brain, the spinal cord, the pancreas, in limb mesenchyme, and in the urogenital region. Lhx9 plays critical roles in gonad development. Homozygous mice lacking functional Lhx9 alleles exhibit numerous urogenital defects, such as gonadal agenesis, infertility, and undetectable levels of testosterone and estradiol coupled with high FSH levels. Lhx9 null mice have reduced levels of the Sf1 nuclear receptor that is required for gonadogenesis, and recent studies have shown that Lhx9 is able to activate the Sf1/FtzF1 gene. Lhx9 null mice are phenotypically female, even those that are genotypically male. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 59

>gnl|CDD|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 43.1 bits (102), Expect = 9e-07
 Identities = 16/35 (45%), Positives = 18/35 (51%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           CA C K I   E V+RA   V+H ECF C  C   
Sbjct: 2   CAGCGKPIYGTERVLRALGKVWHPECFKCATCGKP 36

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways. Length = 54

>gnl|CDD|188764 cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain of Lmx1a and Lmx1b

 Score = 42.0 bits (99), Expect = 2e-06
 Identities = 17/35 (48%), Positives = 21/35 (60%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           C+ C + I   E+VMRA  NVYHL CF C  C  +
Sbjct: 1   CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQ 35

The second LIM domain of Lmx1a and Lmx1b: Lmx1a and Lmx1b belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Mouse Lmx1a is expressed in multiple tissues, including the roof plate of the neural tube, the developing brain, the otic vesicles, the notochord, and the pancreas. In mouse, mutations in Lmx1a result in failure of the roof plate to develop. Lmx1a may act upstream of other roof plate markers such as MafB, Gdf7, Bmp6, and Bmp7. Further characterization of these mice reveals numerous defects including disorganized cerebellum, hippocampus, and cortex; altered pigmentation; female sterility, skeletal defects, and behavioral abnormalities. In the mouse, Lmx1b functions in the developing limbs and eyes, the kidneys, the brain, and in cranial mesenchyme. The disruption of Lmx1b gene results kidney and limb defects. In the brain, Lmx1b is important for generation of mesencephalic dopamine neurons and the differentiation of serotonergic neurons. In the mouse eye, Lmx1b regulates anterior segment (cornea, iris, ciliary body, trabecular meshwork, and lens) development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|188858 cd09474, LIM2_Lhx2, The second LIM domain of Lhx2

 Score = 41.6 bits (97), Expect = 4e-06
 Identities = 22/37 (59%), Positives = 23/37 (62%)

Query: 101 STGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           S   CA C   I A EMVMRAR+ VYHL CF C  CN
Sbjct: 1   SVQRCARCHLGISASEMVMRARDLVYHLNCFTCTTCN 37

The second LIM domain of Lhx2: Lhx2 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. In animals, Lhx2 plays important roles in eye, cerebral cortex, limb, the olfactory organs, and erythrocyte development. Lhx2 gene knockout mice exhibit impaired patterning of the cortical hem and the telencephalon of the developing brain, and a lack of development in olfactory structures. The Lhx2 protein has been shown to bind to the mouse M71 olfactory receptor promoter. Similar to other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 59

>gnl|CDD|215907 pfam00412, LIM, LIM domain

 Score = 41.2 bits (97), Expect = 5e-06
 Identities = 16/34 (47%), Positives = 18/34 (52%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNH 138
           CA C K I   E+V RA   V+H ECF C  C  
Sbjct: 1   CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGK 34

This family represents two copies of the LIM structural domain. Length = 58

>gnl|CDD|188760 cd09374, LIM2_Isl, The second LIM domain of Isl, a member of LHX protein family

 Score = 40.9 bits (96), Expect = 5e-06
 Identities = 15/35 (42%), Positives = 21/35 (60%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           CA C +     + VMRAR  +YH+ECF C  C+ +
Sbjct: 1   CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQ 35

The second LIM domain of Isl: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Isl1 and Isl2 are the two conserved members of this family. Proteins in this group are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl-1 is one of the LHX proteins isolated originally by virtue of its ability to bind DNA sequences from the 5'-flanking region of the rat insulin gene in pancreatic insulin-producing cells. Mice deficient in Isl-1 fail to form the dorsal exocrine pancreas and islet cells fail to differentiate. On the other hand, Isl-1 takes part in the pituitary development by activating the gonadotropin-releasing hormone receptor gene together with LHX3 and steroidogenic factor 1. Mouse Isl2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Same as Isl1, Isl2 may also be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain Kinase 1)

 Score = 41.4 bits (97), Expect = 5e-06
 Identities = 22/55 (40%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          CA CG+ I D   L+AL+  WH DC +C  C   L       Y K   + CK+DY
Sbjct: 22 CASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSH---WYYEKDGRLFCKKDY 73

The first LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 74

>gnl|CDD|188761 cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of Lhx1 (also known as Lim1) and Lhx5

 Score = 39.7 bits (93), Expect = 2e-05
 Identities = 15/33 (45%), Positives = 20/33 (60%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           CA C + I   ++V RAR+ V+HL CF C  C 
Sbjct: 1   CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCR 33

The second LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188855 cd09471, LIM2_Isl2, The second LIM domain of Isl2

 Score = 39.5 bits (92), Expect = 2e-05
 Identities = 16/35 (45%), Positives = 24/35 (68%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           CA C     + ++VMRAR++VYH+ECF C  C+ +
Sbjct: 1   CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQ 35

The second LIM domain of Isl2: Isl is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Isl proteins are found in the nucleus and act as transcription factors or cofactors. Isl1 and Isl2 are the two conserved members of this family. Mouse Isl2 is expressed in the retinal ganglion cells and the developing spinal cord where it plays a role in motor neuron development. Isl2 may be able to bind to the insulin gene enhancer to promote gene activation. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188857 cd09473, LIM2_Lhx4, The second LIM domain of Lhx4

 Score = 38.8 bits (90), Expect = 4e-05
 Identities = 16/35 (45%), Positives = 24/35 (68%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           C AC + IP  ++V +A++ VYHL CFAC  C+ +
Sbjct: 1   CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQ 35

The second LIM domain of Lhx4. Lhx4 belongs to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

>gnl|CDD|188711 cd08368, LIM, LIM is a small protein-protein interaction domain, containing two zinc fingers

 Score = 38.1 bits (89), Expect = 7e-05
 Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 1/35 (2%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           CA C K I     ++RA    +H ECF C  C   
Sbjct: 1   CAGCGKPIEG-RELLRALGKKWHPECFKCSVCGKP 34

LIM domains are identified in a diverse group of proteins with wide variety of biological functions, including gene expression regulation, cell fate determination, cytoskeleton organization, tumor formation and development. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. They perform their functions through interactions with other protein partners. LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. The consensus sequence of LIM domain has been defined as C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16, 21)-C-x(2,3)-[CHD] (where X denotes any amino acid). Length = 53

>gnl|CDD|188856 cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3b

 Score = 37.4 bits (86), Expect = 1e-04
 Identities = 18/35 (51%), Positives = 24/35 (68%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           CAAC + IP  ++V RA++ VYHL CFAC  C  +
Sbjct: 2   CAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQ 36

The second LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 57

>gnl|CDD|188768 cd09382, LIM2_Lhx6, The second LIM domain of Lhx6

 Score = 37.4 bits (86), Expect = 1e-04
 Identities = 18/35 (51%), Positives = 21/35 (60%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           CA C + I A + V RAR N YHL CFAC  C  +
Sbjct: 1   CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQ 35

The second LIM domain of Lhx6. Lhx6 is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Lhx6 functions in brain and nervous system. It is expressed at high levels in several regions of the embryonic mouse CNS, including the telencephalon and hypothalamus, and the first branchial arch. Lhx6 is proposed to have a role in patterning of the mandible and maxilla, and in signaling during odontogenesis. In brain sections, knockdown of Lhx6 gene blocks the normal migration of neurons to the cortex. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain Kinase 2)

 Score = 37.2 bits (86), Expect = 1e-04
 Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 3/55 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          C GCG  I D F  + +   WH  C +C  C   L    +  Y K   + C + Y
Sbjct: 1  CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLL---TNWYYEKDGKLYCHKHY 52

The first LIM domain of LIMK2 (LIM domain Kinase 2): LIMK2 is a member of the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, altering the rate of actin depolymerization. LIMK activity is activated by phosphorylation of a threonine residue within the activation loop of the kinase by p21-activated kinases 1 and 4 and by Rho kinase. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK2 is expressed in all tissues. While LIMK1 localizes mainly at focal adhesions, LIMK2 is found in cytoplasmic punctae, suggesting that they may have different cellular functions. The activity of LIM kinase 2 to regulate cofilin phosphorylation is inhibited by the direct binding of Par-3. LIMK2 activation promotes cell cycle progression. The phenotype of Limk2 knockout mice shows a defect in spermatogenesis. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM (abLIM) proteins

 Score = 36.9 bits (86), Expect = 2e-04
 Identities = 24/56 (42%), Positives = 27/56 (48%), Gaps = 5/56 (8%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRL-GEVGSTLYTKANLILCKRDY 95
          CAGCG+ I +   L ALD  WH  C KC  C   L GE       K     C+RDY
Sbjct: 1  CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLTGEYMG----KDGKPYCERDY 52

The third LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188739 cd09353, LIM2_Zyxin, The second LIM domain of Zyxin

 Score = 36.1 bits (83), Expect = 5e-04
 Identities = 24/59 (40%), Positives = 30/59 (50%), Gaps = 2/59 (3%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99
          CA C + ITDR +LKA    +H  C  C  C C L E  S +  +AN   C  DY R +
Sbjct: 1  CAVCDQKITDR-MLKATGKSYHPQCFTCVVCKCPL-EGESFIVDQANQPHCVNDYHRRY 57

The second LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cellsubstratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors o r scaffolds to support the assembly of multimeric protein. Length = 60

>gnl|CDD|188769 cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of Lhx7 and Lhx8

 Score = 35.4 bits (81), Expect = 6e-04
 Identities = 16/35 (45%), Positives = 22/35 (62%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           C+ C + I + + V RA+ NVYHL CFAC  C  +
Sbjct: 1   CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQ 35

The second LIM domain of Lhx7 and Lhx8: Lhx7 and Lhx8 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs such as the pituitary gland and the pancreas. Studies using mutant mice have revealed roles for Lhx7 and Lhx8 in the development of cholinergic neurons in the telencephalon and in basal forebrain development. Mice lacking alleles of the LIM-homeobox gene Lhx7 or Lhx8 display dramatically reduced number of forebrain cholinergic neurons. In addition, Lhx7 mutation affects male and female mice differently, with females appearing more affected than males. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 35.4 bits (82), Expect = 9e-04
 Identities = 15/33 (45%), Positives = 18/33 (54%), Gaps = 2/33 (6%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           CA C K I      +RA  +VYHL+CF C  C 
Sbjct: 1   CAKCGKPITG--QFVRALGDVYHLDCFTCHDCG 31

The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 57

>gnl|CDD|188775 cd09389, LIM2_LMO1_LMO3, The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

 Score = 35.0 bits (80), Expect = 0.001
 Identities = 22/56 (39%), Positives = 30/56 (53%), Gaps = 2/56 (3%)

Query: 41 CAGCGKHITD-RFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          CA C K I     +++A D  +H DC  C  C+ R   VG   + K N+ILC+ DY
Sbjct: 1  CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFC-VGDKFFLKNNMILCQMDY 55

The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3): LMO1 and LMO3 are highly homologous and belong to the LMO protein family. LMO1 and LMO3 are nuclear protein that plays important roles in transcriptional regulation and development. As LIM domains lack intrinsic DNA-binding activity, nuclear LMOs are involved in transcriptional regulation by forming complexes with other transcription factors or cofactors. For example, LMO1 interacts with the the bHLH domain of bHLH transcription factor, TAL1 (T-cell acute leukemia1)/SCL (stem cell leukemia) . LMO1 inhibits the expression of TAL1/SCL target genes. LMO3 facilitates p53 binding to its response elements, which suggests that LMO3 acts as a co-repressor of p53, suppressing p53-dependent transcriptional regulation. In addition, LMO3 interacts with neuronal transcription factor, HEN2, and acts as an oncogene in neuroblastoma. Another binding partner of LMO3 is calcium- and integrin-binding protein CIB, which binds via the second LIM domain (LIM2) of LMO3. One role of the CIB/LMO3 complex is to inhibit cell proliferation. Although LMO1 and LMO3 are highly homologous proteins, they play different roles in the regulation of the pituitary glycoprotein hormone alpha-subunit (alpha GSU) gene. Alpha GSU promoter activity was markedly repressed by LMO1 but activated by LMO3. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin like protein family

 Score = 35.0 bits (81), Expect = 0.001
 Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
          C GC K I + ++  AL+  WH +C  C   +C    +  + +    L  C+  Y
Sbjct: 1  CGGCNKPILENYI-SALNTQWHPECFVCR--ECHKPFINGSFFEHEGLPYCETHY 52

The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 15/31 (48%), Positives = 19/31 (61%), Gaps = 1/31 (3%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCC 71
          CA CGK IT +F+ +AL   +H DC  C  C
Sbjct: 1  CAKCGKPITGQFV-RALGDVYHLDCFTCHDC 30

The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 57

>gnl|CDD|188718 cd09332, LIM2_PINCH, The second LIM domain of protein PINCH

 Score = 33.5 bits (77), Expect = 0.004
 Identities = 14/39 (35%), Positives = 24/39 (61%), Gaps = 1/39 (2%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVG 79
          C  CG+ +  R ++KA++  WH DC +C  C+  L ++G
Sbjct: 1  CGKCGEFVIGR-VIKAMNNNWHPDCFRCEICNKELADIG 38

The second LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	139
KOG1701|consensus	468		99.86
KOG1044|consensus	670		99.86
KOG1701|consensus	468		99.82
KOG4577|consensus	383		99.82
KOG2272|consensus	332		99.76
KOG2272|consensus	332		99.74
KOG1703|consensus	479		99.63
KOG1703|consensus	479		99.56
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.51
KOG1044|consensus	670		99.27
KOG1700|consensus	200		99.16
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	99.0
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.0
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.63
KOG4577|consensus	383		98.29
KOG0490|consensus	235		98.01
KOG1700|consensus	200		97.85
KOG1702|consensus	264		97.56
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	93.43
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	91.83
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	89.49
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	87.31
PF07754	24	DUF1610: Domain of unknown function (DUF1610); Int	87.13
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	86.9
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	84.54
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	83.55
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	83.2
KOG0320|consensus	187		81.99
KOG1813|consensus	313		81.27
PF10235	90	Cript: Microtubule-associated protein CRIPT; Inter	80.52

>KOG1701|consensus

Probab=99.86  E-value=6.5e-23  Score=151.30  Aligned_cols=99  Identities=27%  Similarity=0.674  Sum_probs=87.9

Q ss_pred             CCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeE-eeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLY-TKANLILCKRDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      .+..+|..|++.|.+. ++.++++.||+.||+|..|.+.|+  +..|. ..++++||..||+++|++  +|+.|+++|++
T Consensus       332 ~tlekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ld--gipFtvd~~n~v~Cv~dfh~kfAP--rCs~C~~PI~P  406 (468)
T KOG1701|consen  332 DTLEKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLD--GIPFTVDSQNNVYCVPDFHKKFAP--RCSVCGNPILP  406 (468)
T ss_pred             HHHHHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccC--CccccccCCCceeeehhhhhhcCc--chhhccCCccC
Confidence            4567899999999998 789999999999999999999994  44555 578899999999999999  99999999988


Q ss_pred             Cce-----EEEeCCccccccccccccCCCC
Q psy284          115 FEM-----VMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       115 ~~~-----~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      .+.     .|+++++.||.+||+|+.|+.+
T Consensus       407 ~~G~~etvRvvamdr~fHv~CY~CEDCg~~  436 (468)
T KOG1701|consen  407 RDGKDETVRVVAMDRDFHVNCYKCEDCGLL  436 (468)
T ss_pred             CCCCcceEEEEEccccccccceehhhcCcc
Confidence            542     6789999999999999999863

>KOG1044|consensus

Probab=99.86  E-value=1.4e-22  Score=154.15  Aligned_cols=123  Identities=31%  Similarity=0.706  Sum_probs=111.5

Q ss_pred             cCccccccccccc---ccCCCCCCCCCCCCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEee
Q psy284            9 HLKINRMSMDVKT---QQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTK   85 (139)
Q Consensus         9 ~~~~~~~~~~~~~---~~~~~~~~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~   85 (139)
                      -..+++++++++.   |+.+.+.+..+....+...|++|++.|.....+.++++.||..||+|..|+..|.   ..|+.+
T Consensus       101 f~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~---gey~sk  177 (670)
T KOG1044|consen  101 FKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN---GEYMSK  177 (670)
T ss_pred             CCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhccccc---ceeecc
Confidence            4567888888877   7777777777888888999999999999987788999999999999999999884   569999


Q ss_pred             CCccccHhhHHHHhCCCccccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284           86 ANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus        86 ~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      ++.+||+.||...||.  +|..|.+.|.|  .++.|.|++|||.|-+|++|++
T Consensus       178 dg~pyce~dy~~~fgv--kc~~c~~fisg--kvLqag~kh~HPtCARCsRCgq  226 (670)
T KOG1044|consen  178 DGVPYCEKDYQAKFGV--KCEECEKFISG--KVLQAGDKHFHPTCARCSRCGQ  226 (670)
T ss_pred             CCCcchhhhhhhhcCe--ehHHhhhhhhh--hhhhccCcccCcchhhhhhhcc
Confidence            9999999999999999  99999999988  8999999999999999999985

>KOG1701|consensus

Probab=99.82  E-value=2.8e-22  Score=147.92  Aligned_cols=95  Identities=27%  Similarity=0.645  Sum_probs=86.0

Q ss_pred             CCCcccccccccccc-eeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCC
Q psy284           37 GPQECAGCGKHITDR-FLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAF  115 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~  115 (139)
                      ...+|.+|++.|.++ ..+.++++.||..||+|..|.+.|  .++.||..++++||+.||....   ++|..|+++|++ 
T Consensus       273 ~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L--~Gq~FY~v~~k~~CE~cyq~tl---ekC~~Cg~~I~d-  346 (468)
T KOG1701|consen  273 YFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQL--AGQSFYQVDGKPYCEGCYQDTL---EKCNKCGEPIMD-  346 (468)
T ss_pred             hhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhh--ccccccccCCcccchHHHHHHH---HHHhhhhhHHHH-
Confidence            344999999999985 447899999999999999999999  6789999999999999998754   389999999965 


Q ss_pred             ceEEEeCCccccccccccccCCC
Q psy284          116 EMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       116 ~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                       .+++|.|+.||+.||+|..|++
T Consensus       347 -~iLrA~GkayHp~CF~Cv~C~r  368 (468)
T KOG1701|consen  347 -RILRALGKAYHPGCFTCVVCAR  368 (468)
T ss_pred             -HHHHhcccccCCCceEEEEecc
Confidence             9999999999999999999986

>KOG4577|consensus

Probab=99.82  E-value=3.3e-22  Score=141.21  Aligned_cols=101  Identities=42%  Similarity=0.950  Sum_probs=92.8

Q ss_pred             CCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCC
Q psy284           34 NAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIP  113 (139)
Q Consensus        34 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~  113 (139)
                      .....++|++|.+.|.+.+++.++++.||..|++|+.|..+|+   ..++.+++.+||+++|.++||.  +|..|+..|.
T Consensus        29 ~~~eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~---drCFsR~~s~yCkedFfKrfGT--KCsaC~~GIp  103 (383)
T KOG4577|consen   29 SNVEIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLA---DRCFSREGSVYCKEDFFKRFGT--KCSACQEGIP  103 (383)
T ss_pred             cccccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHH---HHHhhcCCceeehHHHHHHhCC--cchhhcCCCC
Confidence            3446889999999999999999999999999999999999995   4689999999999999999999  9999999999


Q ss_pred             CCceEEEeCCccccccccccccCCCC
Q psy284          114 AFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       114 ~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +...+..|.+..||.+||.|..|+++
T Consensus       104 PtqVVRkAqd~VYHl~CF~C~iC~R~  129 (383)
T KOG4577|consen  104 PTQVVRKAQDFVYHLHCFACFICKRQ  129 (383)
T ss_pred             hHHHHHHhhcceeehhhhhhHhhhcc
Confidence            96556679999999999999999875

>KOG2272|consensus

Probab=99.76  E-value=3.7e-20  Score=128.82  Aligned_cols=97  Identities=32%  Similarity=0.789  Sum_probs=90.8

Q ss_pred             CCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284           35 AQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        35 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      ..+.++|+.|.++|.+. +|.++++.||.+.|+|..|.+++  .+.+.|.+.|..||+.+|.++||.  .|..|+..|.|
T Consensus       192 ~mgipiCgaC~rpIeer-vi~amgKhWHveHFvCa~CekPF--lGHrHYEkkGlaYCe~h~~qLfG~--~CF~C~~~i~G  266 (332)
T KOG2272|consen  192 KMGIPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEKPF--LGHRHYEKKGLAYCETHYHQLFGN--LCFICNRVIGG  266 (332)
T ss_pred             ccCCcccccccCchHHH-HHHHhccccchhheeehhcCCcc--cchhhhhhcCchhHHHHHHHHhhh--hheecCCccCc
Confidence            36788999999999986 68899999999999999999998  778899999999999999999999  99999999977


Q ss_pred             CceEEEeCCccccccccccccCCC
Q psy284          115 FEMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       115 ~~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                        .++.++++.|.++||.|+.|++
T Consensus       267 --~vv~al~KawCv~cf~Cs~Cdk  288 (332)
T KOG2272|consen  267 --DVVSALNKAWCVECFSCSTCDK  288 (332)
T ss_pred             --cHHHHhhhhhcccccccccccc
Confidence              7999999999999999999986

>KOG2272|consensus

Probab=99.74  E-value=6.5e-20  Score=127.60  Aligned_cols=96  Identities=27%  Similarity=0.662  Sum_probs=86.9

Q ss_pred             CCCcccccccccccce-eeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCC
Q psy284           37 GPQECAGCGKHITDRF-LLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAF  115 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~  115 (139)
                      ....|.+|.......+ ++..++..||..||.|..|-.++  ++..||..+++.||+.++..+|+|  .|..|++.|.| 
T Consensus        11 ~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf--~~g~~~efEgRkYCEhDF~~LfaP--cC~kC~EFiiG-   85 (332)
T KOG2272|consen   11 ANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPF--PDGIFYEFEGRKYCEHDFHVLFAP--CCGKCGEFIIG-   85 (332)
T ss_pred             HHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcC--CCceeEEecCcccccccchhhhch--hhcccccchhh-
Confidence            3557999998887753 45678899999999999999999  678899999999999999999999  99999999988 


Q ss_pred             ceEEEeCCccccccccccccCCC
Q psy284          116 EMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       116 ~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                       ++|.+++..|||.||+|..|++
T Consensus        86 -rVikamnnSwHp~CF~Cd~Cn~  107 (332)
T KOG2272|consen   86 -RVIKAMNNSWHPACFRCDLCNK  107 (332)
T ss_pred             -HHHHhhccccCcccchhHHHHH
Confidence             8999999999999999999875

>KOG1703|consensus

Probab=99.63  E-value=4.4e-17  Score=126.11  Aligned_cols=98  Identities=26%  Similarity=0.582  Sum_probs=89.0

Q ss_pred             CCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCC
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAF  115 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~  115 (139)
                      ...+.|.+|+.+|.+. .|.+++..||++||.|..|...+  ....++..++.+||..||..++.+  +|..|.++|...
T Consensus       361 ~~~p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~--~~~~~~~~~~~pyce~~~~~~~~~--~~~~~~~p~~~~  435 (479)
T KOG1703|consen  361 PFRPNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPL--KNSSFFESDGEPYCEDHYKKLFTT--KCDYCKKPVEFG  435 (479)
T ss_pred             hhCccccccCCchHHh-HhhhccCeechhceeeecccCCC--CCCcccccCCccchhhhHhhhccc--cchhccchhHhh
Confidence            5567999999999997 57777999999999999998888  567899999999999999999998  999999998765


Q ss_pred             ceEEEeCCccccccccccccCCC
Q psy284          116 EMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       116 ~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      +..+.+++..||..||+|+.|.+
T Consensus       436 ~~~ie~~~~~~h~~~F~c~~c~~  458 (479)
T KOG1703|consen  436 SRQIEADGSPFHGDCFRCANCMK  458 (479)
T ss_pred             hhHhhccCccccccceehhhhhc
Confidence            68899999999999999999975

>KOG1703|consensus

Probab=99.56  E-value=1.4e-15  Score=117.75  Aligned_cols=97  Identities=24%  Similarity=0.502  Sum_probs=87.0

Q ss_pred             CCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCC
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAF  115 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~  115 (139)
                      ...++|..|...|.+...+.+++..||..+|.|..|...+.  ...+...++++||..||.+.+.+  .|.+|+++|.+ 
T Consensus       301 ~~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~--~~~~~~~~g~~~c~~~~~~~~~p--~C~~C~~~i~~-  375 (479)
T KOG1703|consen  301 VTRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVIL--DGGPRELDGKILCHECFHAPFRP--NCKRCLLPILE-  375 (479)
T ss_pred             cccccccccccCcccceeEeeccccccccceeecccccccc--CCCccccCCCccHHHHHHHhhCc--cccccCCchHH-
Confidence            44589999999999944788999999999999999999985  34568899999999999999999  99999999976 


Q ss_pred             ceEEEeCCccccccccccccCCC
Q psy284          116 EMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       116 ~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                       .+|.+.++.||++||.|..|++
T Consensus       376 -~~v~a~~~~wH~~cf~C~~C~~  397 (479)
T KOG1703|consen  376 -EGVCALGRLWHPECFVCADCGK  397 (479)
T ss_pred             -hHhhhccCeechhceeeecccC
Confidence             8899999999999999999954

>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.51  E-value=2.4e-14  Score=80.42  Aligned_cols=57  Identities=37%  Similarity=0.831  Sum_probs=50.3

Q ss_pred             ccccccccccceee-eecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHh
Q psy284           41 CAGCGKHITDRFLL-KALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF   99 (139)
Q Consensus        41 C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~   99 (139)
                      |.+|+++|.+...+ .++++.||++||+|..|+..|.  +..++..++++||..||.++|
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLN--DGDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTT--TSSEEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccC--CCeeEeECCEEECHHHHhhhC
Confidence            78999999986554 6999999999999999999995  345899999999999999875

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....

>KOG1044|consensus

Probab=99.27  E-value=4.7e-12  Score=97.34  Aligned_cols=92  Identities=27%  Similarity=0.677  Sum_probs=72.7

Q ss_pred             CCCCCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCC
Q psy284           31 VPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSK  110 (139)
Q Consensus        31 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~  110 (139)
                      ++........|..|.+.-... ++.+.++.||..||+|..|++.|++.  .|+.+++.        +++++    ..|..
T Consensus         9 s~~~~~~~i~c~~c~~kc~ge-vlrv~d~~fhi~cf~c~~cg~~la~~--gff~k~~~--------~~ygt----~~c~~   73 (670)
T KOG1044|consen    9 SPQTGKQGIKCDKCRKKCSGE-VLRVNDNHFHINCFQCKKCGRNLAEG--GFFTKPEN--------RLYGT----DDCRA   73 (670)
T ss_pred             CccccccceehhhhCCccccc-eeEeeccccceeeeeccccCCCcccc--cceecccc--------eeecc----cchhh
Confidence            344455567899999988886 78999999999999999999999743  36665554        33332    55777


Q ss_pred             CCCCCceEEEeCCccccccccccccCCCC
Q psy284          111 VIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       111 ~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      .|.+  .+|.++|+.||++||.|+.|+++
T Consensus        74 ~~~g--evvsa~gktyh~~cf~cs~ck~p  100 (670)
T KOG1044|consen   74 FVEG--EVVSTLGKTYHPKCFSCSTCKSP  100 (670)
T ss_pred             hccc--eeEecccceeccccceecccCCC
Confidence            7766  89999999999999999999763

>KOG1700|consensus

Probab=99.16  E-value=5e-12  Score=87.65  Aligned_cols=99  Identities=26%  Similarity=0.591  Sum_probs=81.9

Q ss_pred             CCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCc-------------
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTG-------------  103 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~-------------  103 (139)
                      ....|..|++.++..+.+...+..||+.||.|..|...|.  ...+..+++.+||+.+|...+++.+             
T Consensus         6 ~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~--~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~   83 (200)
T KOG1700|consen    6 TTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLT--LSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGL   83 (200)
T ss_pred             ccchhhhccCcchHHHHHhccCcchhhhHHhccccccccc--cccccccccccccccchHhhhCcccccccccccccCCC
Confidence            3458999999999976677889999999999999999994  4567889999999997766554422             


Q ss_pred             --------------------------cccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284          104 --------------------------YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       104 --------------------------~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                                                .|..|++.+.+.| .+...+..||..||+|+.|+.
T Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~E-k~~~~~~~~hk~cfrc~~~~~  143 (200)
T KOG1700|consen   84 GKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLE-KVTGNGLEFHKSCFRCTHCGK  143 (200)
T ss_pred             CcccccccccccccchhHHhhhccccccccccceeeehH-HHhhhhhhhhhhheeeccccc
Confidence                                      1999999998754 556789999999999999975

>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3

Probab=99.00  E-value=3.2e-10  Score=58.17  Aligned_cols=36  Identities=44%  Similarity=0.929  Sum_probs=32.3

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|.+|+++|.+.+..+.+.++.||++||+|..|+++
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~   36 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKP   36 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCc
Confidence            588999999886678899999999999999999864

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

>PF00412 LIM: LIM domain; InterPro: IPR001781 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=99.00  E-value=3e-10  Score=63.58  Aligned_cols=35  Identities=40%  Similarity=0.921  Sum_probs=31.7

Q ss_pred             ccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       105 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      |..|+++|.+.+.++.+.++.||++||+|+.|+++
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~   35 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKP   35 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCB
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCc
Confidence            78999999987777789999999999999999863

Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....

>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3

Probab=98.63  E-value=2.6e-08  Score=50.87  Aligned_cols=36  Identities=47%  Similarity=1.104  Sum_probs=32.3

Q ss_pred             cccccccccccc-eeeeecCccccccCcccccCCCCc
Q psy284           40 ECAGCGKHITDR-FLLKALDMYWHEDCLKCGCCDCRL   75 (139)
Q Consensus        40 ~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l   75 (139)
                      +|.+|++.|.+. ..+.+.+..||..||+|..|+..|
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L   37 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPL   37 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcC
Confidence            588999999986 567889999999999999999887

Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.

>KOG4577|consensus

Probab=98.29  E-value=2e-07  Score=66.91  Aligned_cols=64  Identities=23%  Similarity=0.489  Sum_probs=51.2

Q ss_pred             CCcccccccccccceee-eecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCC
Q psy284           38 PQECAGCGKHITDRFLL-KALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGS  101 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~  101 (139)
                      ..+|..|+..|-+..++ .+.+..||..||.|..|.+.|..++..|...+.++.|+++|+..-..
T Consensus        92 GTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k  156 (383)
T KOG4577|consen   92 GTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQK  156 (383)
T ss_pred             CCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhc
Confidence            45899999999886544 56788999999999999999985444444688999999999865433

>KOG0490|consensus

Probab=98.01  E-value=3.4e-07  Score=64.75  Aligned_cols=91  Identities=47%  Similarity=0.998  Sum_probs=74.7

Q ss_pred             cccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHH--HhCCCccccccCCCCCCCceEEEe
Q psy284           44 CGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLR--LFGSTGYCAACSKVIPAFEMVMRA  121 (139)
Q Consensus        44 C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~--~~~~~~~C~~C~~~I~~~~~~~~~  121 (139)
                      |+..|.+.+.+.+.+..||..|..|..|...+..... .+..++..||..+|.+  .+..  +|.+|.+.|...|.+..+
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~g~~~~~~d~~~~~~~~~--rr~rt~~~~~ql~~ler~   78 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDT-CFSKDGSIYCKRDYQREFKFSK--RCARCKFTISQLDELERA   78 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCC-cccCCCcccccccchhhhhccc--cccCCCCCcCHHHHHHHh
Confidence            6677788766677799999999999999999963334 4444999999999998  6666  999999999877778888


Q ss_pred             CCccccccccccccCCC
Q psy284          122 RNNVYHLECFACQQCNH  138 (139)
Q Consensus       122 ~~~~~H~~Cf~C~~C~~  138 (139)
                      ..+. |.-||.|..|..
T Consensus        79 f~~~-h~Pd~~~r~~la   94 (235)
T KOG0490|consen   79 FEKV-HLPCFACRECLA   94 (235)
T ss_pred             hcCC-CcCccchHHHHh
Confidence            8888 999999988753

>KOG1700|consensus

Probab=97.85  E-value=3.8e-06  Score=58.41  Aligned_cols=65  Identities=22%  Similarity=0.517  Sum_probs=54.8

Q ss_pred             CCCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHh
Q psy284           33 NNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF   99 (139)
Q Consensus        33 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~   99 (139)
                      ........|..|++.+++.+.+...+..||..||+|..|+..|.  ...+....+.+||...+..++
T Consensus       103 ~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls--~~~~~~~~g~l~~~~~~~~~~  167 (200)
T KOG1700|consen  103 VFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLS--PKNYAALEGVLYCKHHFAQLF  167 (200)
T ss_pred             hhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccC--CcchhhcCCccccchhhheee
Confidence            45566789999999999987788899999999999999999995  456788889999987766544

>KOG1702|consensus

Probab=97.56  E-value=6.9e-06  Score=56.47  Aligned_cols=59  Identities=25%  Similarity=0.523  Sum_probs=50.0

Q ss_pred             CCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHH
Q psy284           38 PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL   98 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~   98 (139)
                      ...|..|++.+++.+.+.-+++.||..||+|..|+..|++  ..+-..+.++||..+|.+.
T Consensus         4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnm--KnyKgy~kkpycn~hYpkq   62 (264)
T KOG1702|consen    4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNM--KNYKGYDKKPYCNPHYPKQ   62 (264)
T ss_pred             cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhh--hhccccccCCCcCcccccc
Confidence            3457789999999777888999999999999999999963  4566789999999999653

>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators

Probab=93.43  E-value=0.06  Score=27.03  Aligned_cols=29  Identities=31%  Similarity=0.677  Sum_probs=22.5

Q ss_pred             ccccCCCCCCCceEEEeCCcccccccccc
Q psy284          105 CAACSKVIPAFEMVMRARNNVYHLECFAC  133 (139)
Q Consensus       105 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C  133 (139)
                      |.-|++.|.+.-.++...++.||--|-+|
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC   29 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYYFCCPTC   29 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEEEECHHH
Confidence            67899999986568889999999544443

It is thought to function as a metal-sensing regulatory module [].

>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=91.83  E-value=0.13  Score=31.67  Aligned_cols=29  Identities=24%  Similarity=0.504  Sum_probs=22.7

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFA  132 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~  132 (139)
                      .|..|+++|...-.++...|..+|..|+.
T Consensus        80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   80 KCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            79999999977545666777889988863

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=89.49  E-value=0.25  Score=26.98  Aligned_cols=28  Identities=21%  Similarity=0.548  Sum_probs=22.1

Q ss_pred             cccccCCCCCCCceEEE--eCCcccccccc
Q psy284          104 YCAACSKVIPAFEMVMR--ARNNVYHLECF  131 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~--~~~~~~H~~Cf  131 (139)
                      +|..|+++|.+++.++.  .=+..||.+|+
T Consensus         7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~   36 (54)
T PF14446_consen    7 KCPVCGKKFKDGDDIVVCPECGAPYHRDCW   36 (54)
T ss_pred             cChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence            89999999976555555  45688999998

>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function

Probab=87.31  E-value=0.25  Score=30.53  Aligned_cols=29  Identities=28%  Similarity=0.521  Sum_probs=22.2

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFA  132 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~  132 (139)
                      +|..|+++|...+..-...+..-|..||+
T Consensus         4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~   32 (101)
T PF09943_consen    4 KCYICGKPIYEGQLFTFTKKGPVHYECFR   32 (101)
T ss_pred             EEEecCCeeeecceEEEecCCcEeHHHHH
Confidence            79999999987544444566888988886

>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species

Probab=87.13  E-value=0.43  Score=21.53  Aligned_cols=15  Identities=27%  Similarity=0.705  Sum_probs=9.7

Q ss_pred             ccccCCCCCCCceEE
Q psy284          105 CAACSKVIPAFEMVM  119 (139)
Q Consensus       105 C~~C~~~I~~~~~~~  119 (139)
                      |..|+..|.+.+..+
T Consensus         1 C~sC~~~i~~r~~~v   15 (24)
T PF07754_consen    1 CTSCGRPIAPREQAV   15 (24)
T ss_pred             CccCCCcccCcccCc
Confidence            667888887754333

It is likely to bind zinc via its four well-conserved cysteine residues.

>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A

Probab=86.90  E-value=1.5  Score=23.18  Aligned_cols=44  Identities=18%  Similarity=0.394  Sum_probs=29.3

Q ss_pred             ccccCCCCcccCCCeeEeeCCcc-ccHhhHHHHhCCCccccccCCCCC
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLI-LCKRDYLRLFGSTGYCAACSKVIP  113 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~-~C~~cy~~~~~~~~~C~~C~~~I~  113 (139)
                      .|..|.....   ...+..=+.. +|..|+.+.+....+|..|.++|.
T Consensus         4 ~C~iC~~~~~---~~~~~pCgH~~~C~~C~~~~~~~~~~CP~Cr~~i~   48 (50)
T PF13920_consen    4 ECPICFENPR---DVVLLPCGHLCFCEECAERLLKRKKKCPICRQPIE   48 (50)
T ss_dssp             B-TTTSSSBS---SEEEETTCEEEEEHHHHHHHHHTTSBBTTTTBB-S
T ss_pred             CCccCCccCC---ceEEeCCCChHHHHHHhHHhcccCCCCCcCChhhc
Confidence            4555655542   3455667777 999999877544449999999985

...

>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function

Probab=84.54  E-value=0.35  Score=29.86  Aligned_cols=31  Identities=26%  Similarity=0.420  Sum_probs=23.4

Q ss_pred             cccccccccccceeeee-cCccccccCccccc
Q psy284           40 ECAGCGKHITDRFLLKA-LDMYWHEDCLKCGC   70 (139)
Q Consensus        40 ~C~~C~~~i~~~~~~~~-~~~~~H~~Cf~C~~   70 (139)
                      .|..|+++|+.++...+ .+...|..||+=..
T Consensus         4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~   35 (101)
T PF09943_consen    4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKA   35 (101)
T ss_pred             EEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence            69999999998766554 44678999998443

>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1

Probab=83.55  E-value=0.94  Score=27.77  Aligned_cols=32  Identities=25%  Similarity=0.589  Sum_probs=21.4

Q ss_pred             CCCCcccccccccccc-eeeeecCccccccCcc
Q psy284           36 QGPQECAGCGKHITDR-FLLKALDMYWHEDCLK   67 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~   67 (139)
                      .....|..|++.|... ..+.-.+..+|..|++
T Consensus        76 ~~~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   76 TESTKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            4456799999988875 3334456677877753

Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].

>smart00504 Ubox Modified RING finger domain

Probab=83.20  E-value=2.1  Score=23.43  Aligned_cols=46  Identities=9%  Similarity=0.048  Sum_probs=33.1

Q ss_pred             cccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284           66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      |.|..|...+.   ..+....|..||..+..+.+.....|..|++++..
T Consensus         2 ~~Cpi~~~~~~---~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMK---DPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCC---CCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence            56777877774   23566778999999977655434489999988854

Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.

>KOG0320|consensus

Probab=81.99  E-value=1.2  Score=30.51  Aligned_cols=52  Identities=25%  Similarity=0.446  Sum_probs=37.8

Q ss_pred             cccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284           62 HEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        62 H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      -..+++|..|-....+. ..+..+-|.+||..|-........+|..|++.|.-
T Consensus       128 ~~~~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~  179 (187)
T KOG0320|consen  128 KEGTYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH  179 (187)
T ss_pred             cccccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence            34578998887776422 22446889999999987665444599999998864

>KOG1813|consensus

Probab=81.27  E-value=0.79  Score=33.76  Aligned_cols=46  Identities=22%  Similarity=0.388  Sum_probs=36.8

Q ss_pred             cccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284           66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      |.|..|.....   ..+...-+..+|..|..+.|...++|..|++.+.+
T Consensus       242 f~c~icr~~f~---~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g  287 (313)
T KOG1813|consen  242 FKCFICRKYFY---RPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG  287 (313)
T ss_pred             ccccccccccc---cchhhcCCceeehhhhccccccCCcceeccccccc
Confidence            77888887773   34566778899999999888665699999999976

>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production

Probab=80.52  E-value=1  Score=27.33  Aligned_cols=43  Identities=23%  Similarity=0.505  Sum_probs=29.5

Q ss_pred             cccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284           60 YWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        60 ~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      .|-..--.|..|...+.        ..+..||..|..+    ++.|+-|++.|.+
T Consensus        39 Py~~~~~~C~~CK~~v~--------q~g~~YCq~CAYk----kGiCamCGKki~d   81 (90)
T PF10235_consen   39 PYAPYSSKCKICKTKVH--------QPGAKYCQTCAYK----KGICAMCGKKILD   81 (90)
T ss_pred             cccccCccccccccccc--------cCCCccChhhhcc----cCcccccCCeecc
Confidence            34443346777876663        2256799999655    4599999999965

This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	139
2dfy_X	195	Crystal Structure Of A Cyclized Protein Fusion Of L		3e-33
1rut_X	188	Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 L		3e-33
2xjy_A	131	Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21		9e-31
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		3e-20
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		5e-20
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		6e-20
2l4z_A	123	Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-L		2e-18
1m3v_A	122	Flin4: Fusion Of The Lim Binding Domain Of Ldb1 And		1e-17
1j2o_A	114	Structure Of Flin2, A Complex Containing The N-Term		1e-16
2lxd_A	125	Backbone 1h, 13c, And 15n Chemical Shift Assignment		1e-10
2l6y_B	96	Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid Length =		2e-10
2dj7_A	80	Solution Structure Of 3rd Lim Domain Of Actin-Bindi		3e-06
2cup_A	101	Solution Structure Of The Skeletal Muscle Lim-Prote		7e-04

>pdb|2DFY|X Chain X, Crystal Structure Of A Cyclized Protein Fusion Of Lmo4 Lim Domains 1 And 2 With The Lim Interacting Domain Of Ldb1 Length = 195

Iteration: 1
 Score =  137 bits (344), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 58/101 (57%), Positives = 77/101 (76%)
Query: 39  QECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 98
           + CAGCG  I DRFLL A+D YWH  CLKC  C  +LG++G++ YTK+ +ILC+ DY+RL
Sbjct: 4   KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 63
Query: 99  FGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           FG++G C+AC + IPA E+VMRA+ NVYHL+CF C  C +R
Sbjct: 64  FGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNR 104

>pdb|1RUT|X Chain X, Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 Lid Domain Length = 188

Iteration: 1
 Score =  136 bits (343), Expect = 3e-33,   Method: Compositional matrix adjust.
 Identities = 58/101 (57%), Positives = 77/101 (76%)
Query: 39  QECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 98
           + CAGCG  I DRFLL A+D YWH  CLKC  C  +LG++G++ YTK+ +ILC+ DY+RL
Sbjct: 6   KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 65
Query: 99  FGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           FG++G C+AC + IPA E+VMRA+ NVYHL+CF C  C +R
Sbjct: 66  FGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNR 106

>pdb|2XJY|A Chain A, Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21 Crystal Form Length = 131

Iteration: 1
 Score =  128 bits (322), Expect = 9e-31,   Method: Compositional matrix adjust.
 Identities = 59/97 (60%), Positives = 68/97 (70%)
Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           C GC ++I DR+ LKA+D YWHEDCL C  C CRLGEVG  LY K    LC+RDYLRLFG
Sbjct: 5   CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFG 64
Query: 101 STGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
             G CA+C K I A+EM MR ++ VYHLECF C  C 
Sbjct: 65  QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQ 101

>pdb|3MMK|A Chain A, The Structural Basis For Partial Redundancy In A Class Of Transcription Factors, The Lim-Homeodomain Proteins, In Neural Cell Type Specification Length = 169

Iteration: 1
 Score = 94.0 bits (232), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 46/104 (44%), Positives = 68/104 (65%), Gaps = 6/104 (5%)
Query: 36  QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
           Q PQ CAGC +HI D+F+LK LD +WH  CLKC   DC++ ++    +++A  + CK D+
Sbjct: 5   QIPQ-CAGCNQHILDKFILKVLDRHWHSSCLKCA--DCQM-QLADRCFSRAGSVYCKEDF 60
Query: 96  LRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
            + FG+   C AC + IP  ++V +A++ VYHL CFAC  CN +
Sbjct: 61  FKRFGTK--CTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQ 102

>pdb|2RGT|A Chain A, Crystal Structure Of Lhx3 Lim Domains 1 And 2 With The Binding Domain Of Isl1 Length = 169

Iteration: 1
 Score = 92.8 bits (229), Expect = 5e-20,   Method: Compositional matrix adjust.
 Identities = 46/97 (47%), Positives = 60/97 (61%), Gaps = 5/97 (5%)
Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           CAGC +HI DRF+LKALD +WH  CLKC  C   L E     +++   + CK D+ + FG
Sbjct: 9   CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE---RCFSRGESVYCKDDFFKRFG 65
Query: 101 STGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           +   CAAC   IP  ++V RA++ VYHL CFAC  C 
Sbjct: 66  TK--CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCK 100

>pdb|2JTN|A Chain A, Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Complex Length = 182

Iteration: 1
 Score = 92.8 bits (229), Expect = 6e-20,   Method: Compositional matrix adjust.
 Identities = 46/99 (46%), Positives = 61/99 (61%), Gaps = 5/99 (5%)
Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           CAGC +HI DRF+LKALD +WH  CLKC  C   L E     +++   + CK D+ + FG
Sbjct: 63  CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE---RCFSRGESVYCKDDFFKRFG 119
Query: 101 STGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           +   CAAC   IP  ++V RA++ VYHL CFAC  C  +
Sbjct: 120 TK--CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQ 156

>pdb|2L4Z|A Chain A, Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-Lim1 (18-82) Length = 123

Iteration: 1
 Score = 87.8 bits (216), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 36/62 (58%), Positives = 47/62 (75%)
Query: 39  QECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 98
           + CAGCG  I DRFLL A+D YWH  CLKC  C  +LG++G++ YTK+ +ILC+ DY+RL
Sbjct: 62  KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 121
Query: 99  FG 100
           FG
Sbjct: 122 FG 123

>pdb|1M3V|A Chain A, Flin4: Fusion Of The Lim Binding Domain Of Ldb1 And The N- Terminal Lim Domain Of Lmo4 Length = 122

Iteration: 1
 Score = 85.1 bits (209), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 35/61 (57%), Positives = 46/61 (75%)
Query: 39 QECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 98
          + CAGCG  I DRFLL A+D YWH  CLKC  C  +LG++G++ YTK+ +ILC+ DY+RL
Sbjct: 6  KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 65
Query: 99 F 99
          F
Sbjct: 66 F 66

>pdb|1J2O|A Chain A, Structure Of Flin2, A Complex Containing The N-Terminal Lim Domain Of Lmo2 And Ldb1-Lid Length = 114

Iteration: 1
 Score = 82.0 bits (201), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 37/58 (63%), Positives = 42/58 (72%)
Query: 41 CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 98
          C GC ++I DR+ LKA+D YWHEDCL C  C CRLGEVG  LY K    LC+RDYLRL
Sbjct: 6  CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL 63

>pdb|2LXD|A Chain A, Backbone 1h, 13c, And 15n Chemical Shift Assignments For Lmo2(Lim2)- Ldb1(Lid) Length = 125

Iteration: 1
 Score = 62.0 bits (149), Expect = 1e-10,   Method: Compositional matrix adjust.
 Identities = 26/42 (61%), Positives = 30/42 (71%)
Query: 95  YLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
           YLRLFG  G CA+C K I A+EM MR ++ VYHLECF C  C
Sbjct: 3   YLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAAC 44

>pdb|2L6Y|B Chain B, Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid Length = 96

Iteration: 1
 Score = 60.8 bits (146), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 26/43 (60%), Positives = 30/43 (69%)
Query: 95  YLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           YLRLFG  G CA+C K I A+EM MR ++ VYHLECF C  C 
Sbjct: 1   YLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQ 43

>pdb|2DJ7|A Chain A, Solution Structure Of 3rd Lim Domain Of Actin-Binding Lim Protein 3 Length = 80

Iteration: 1
 Score = 47.4 bits (111), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 29/79 (36%), Positives = 36/79 (45%), Gaps = 5/79 (6%)
Query: 24  GAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRL-GEVGSTL 82
           G+  +   P   +GP  CAGC + I     L ALD  WH  C KC  C   L GE     
Sbjct: 1   GSSGSSGKPIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGE----Y 56
Query: 83  YTKANLILCKRDYLRLFGS 101
            +K  +  C+ DY   FGS
Sbjct: 57  ISKDGVPYCESDYHAQFGS 75

>pdb|2CUP|A Chain A, Solution Structure Of The Skeletal Muscle Lim-Protein 1 Length = 101

Iteration: 1
 Score = 39.3 bits (90), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 28/99 (28%), Positives = 42/99 (42%), Gaps = 5/99 (5%)
Query: 35  AQGPQECAGCGKHI-TDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKR 93
           + G   C  C K I  D   +   + +WH+ C +C  C   L     T   K N ILC +
Sbjct: 2   SSGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPL--ANETFVAKDNKILCNK 59
Query: 94  DYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFA 132
              R    +  C  C K I A +  +  +  V+H +CF+
Sbjct: 60  CTTRE--DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFS 96

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	139
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	1e-42
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	3e-07
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	1e-39
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	4e-08
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	2e-38
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	2e-05
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	7e-36
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	2e-13
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	2e-29
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	3e-28
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	1e-25
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	3e-25
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-24
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	6e-06
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	9e-21
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	2e-15
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	4e-12
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	5e-13
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	2e-12
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	4e-12
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	2e-11
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	8e-11
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	5e-05
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	1e-10
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	1e-10
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	4e-04
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	2e-10
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	2e-10
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	2e-06
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	3e-10
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	6e-06
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	4e-10
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	6e-09
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	4e-10
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	1e-07
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	5e-10
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	4e-04
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	6e-10
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	1e-07
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	8e-10
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	1e-05
2cuq_A	80	Four and A half LIM domains 3; structural genomics	1e-09
2cuq_A	80	Four and A half LIM domains 3; structural genomics	4e-06
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	2e-09
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	9e-06
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	3e-09
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	7e-09
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	8e-09
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	6e-08
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	3e-08
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	4e-07
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	7e-08
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	7e-08
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	6e-04
2co8_A	82	NEDD9 interacting protein with calponin homology a	9e-08
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	2e-07
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	2e-07
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	3e-07
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	6e-07
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	6e-07
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	4e-06
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	6e-06
2cor_A	79	Pinch protein; LIM domain, particularly interestin	1e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	4e-04

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A Length = 131

 Score =  136 bits (343), Expect = 1e-42
 Identities = 59/99 (59%), Positives = 68/99 (68%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           C GC ++I DR+ LKA+D YWHEDCL C  C CRLGEVG  LY K    LC+RDYLRLFG
Sbjct: 5   CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFG 64

Query: 101 STGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
             G CA+C K I A+EM MR ++ VYHLECF C  C   
Sbjct: 65  QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKH 103

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A Length = 131

 Score = 45.5 bits (108), Expect = 3e-07
 Identities = 16/64 (25%), Positives = 24/64 (37%), Gaps = 2/64 (3%)

Query: 41  CAGCGKHIT-DRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99
           CA C K I      ++  D  +H +C KC  C       G       + I+C++D     
Sbjct: 69  CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCV-GDRYLLINSDIVCEQDIYEWT 127

Query: 100 GSTG 103
              G
Sbjct: 128 KING 131

>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 =  130 bits (329), Expect = 1e-39
 Identities = 58/103 (56%), Positives = 77/103 (74%)

Query: 37  GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYL 96
             + CAGCG  I DRFLL A+D YWH  CLKC  C  +LG++G++ YTK+ +ILC+ DY+
Sbjct: 4   SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

Query: 97  RLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           RLFG++G C+AC + IPA E+VMRA+ NVYHL+CF C  C +R
Sbjct: 64  RLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNR 106

>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 = 48.9 bits (116), Expect = 4e-08
 Identities = 14/80 (17%), Positives = 25/80 (31%), Gaps = 4/80 (5%)

Query: 41  CAGCGKHIT-DRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99
           C+ CG+ I     +++A    +H  C  C  C  RL   G   +     + C+ D     
Sbjct: 72  CSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVP-GDRFHYINGSLFCEHDRPTAL 130

Query: 100 GSTGYCAACSKVIPAFEMVM 119
            +            +     
Sbjct: 131 ING--HLNSGGSGGSGGSGG 148

>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 =  127 bits (321), Expect = 2e-38
 Identities = 50/144 (34%), Positives = 69/144 (47%), Gaps = 15/144 (10%)

Query: 6   GLEHLKINRMSMDVKTQQGAQQTKAVPNNAQGPQE----------CAGCGKHITDRFLLK 55
           G    +  R+   ++  Q             G             CAGC +HI DRF+LK
Sbjct: 18  GEFGDEDERLITRLENTQFDAANGIDDEGGSGGHMGSGGTPEIPMCAGCDQHILDRFILK 77

Query: 56  ALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAF 115
           ALD +WH  CLKC  C   L E     +++   + CK D+ + FG+   CAAC   IP  
Sbjct: 78  ALDRHWHSKCLKCSDCHVPLAE---RCFSRGESVYCKDDFFKRFGTK--CAACQLGIPPT 132

Query: 116 EMVMRARNNVYHLECFACQQCNHR 139
           ++V RA++ VYHL CFAC  C  +
Sbjct: 133 QVVRRAQDFVYHLHCFACVVCKRQ 156

>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 = 41.4 bits (97), Expect = 2e-05
 Identities = 16/57 (28%), Positives = 23/57 (40%), Gaps = 3/57 (5%)

Query: 41  CAGCGKHI--TDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
           CA C   I  T     +A D  +H  C  C  C  +L         + + ++CK DY
Sbjct: 122 CAACQLGIPPTQVVR-RAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY 177

>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 =  120 bits (303), Expect = 7e-36
 Identities = 46/99 (46%), Positives = 61/99 (61%), Gaps = 5/99 (5%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           CAGC +HI DRF+LKALD +WH  CLKC  C   L E     +++   + CK D+ + FG
Sbjct: 9   CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE---RCFSRGESVYCKDDFFKRFG 65

Query: 101 STGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           +   CAAC   IP  ++V RA++ VYHL CFAC  C  +
Sbjct: 66  TK--CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQ 102

>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 = 62.6 bits (152), Expect = 2e-13
 Identities = 18/100 (18%), Positives = 29/100 (29%), Gaps = 5/100 (5%)

Query: 41  CAGCGKHIT-DRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99
           CA C   I   + + +A D  +H  C  C  C  +L         + + ++CK DY    
Sbjct: 68  CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK 127

Query: 100 GSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
                              M A +   H           +
Sbjct: 128 QGG--SGGSGGSGG--GTPMVAASPERHDGGLQANPVEVQ 163

>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 =  102 bits (255), Expect = 2e-29
 Identities = 44/99 (44%), Positives = 55/99 (55%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           C GC ++I DR+ LKA+D YWHEDCL C  C CRLGEVG  LY K    LC+RDYLRL G
Sbjct: 6   CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGG 65

Query: 101 STGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           S G+  +   V+   E  +         E    +  N +
Sbjct: 66  SGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQ 104

>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 = 98.6 bits (246), Expect = 3e-28
 Identities = 27/97 (27%), Positives = 39/97 (40%), Gaps = 5/97 (5%)

Query: 41  CAGCGKHIT-DRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99
           C  C K I  D   +   + +WH+ C +C  C   L     T   K N ILC +   R  
Sbjct: 8   CVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLA--NETFVAKDNKILCNKCTTRED 65

Query: 100 GSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQC 136
                C  C K I A +  +  +  V+H +CF+    
Sbjct: 66  SPK--CKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100

>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 = 93.3 bits (231), Expect = 1e-25
 Identities = 37/79 (46%), Positives = 50/79 (63%)

Query: 22  QQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGST 81
             G      + +     + CAGCG  I DRFLL A+D YWH  CLKC  C  +LG++G++
Sbjct: 45  LGGGGSGGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTS 104

Query: 82  LYTKANLILCKRDYLRLFG 100
            YTK+ +ILC+ DY+RLFG
Sbjct: 105 SYTKSGMILCRNDYIRLFG 123

>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 = 92.0 bits (228), Expect = 3e-25
 Identities = 39/107 (36%), Positives = 60/107 (56%), Gaps = 6/107 (5%)

Query: 37  GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYL 96
             + CAGCG  I DRFLL A+D YWH  CLKC  C  +LG++G++ YTK+ +ILC+ DY+
Sbjct: 4   SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

Query: 97  RLFGSTGYCAACSKVIPAFEMVMRARNNV------YHLECFACQQCN 137
           RLFG++G   +   +    ++++     +         E    +  N
Sbjct: 64  RLFGNSGAGGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLEN 110

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens} Length = 126

 Score = 90.5 bits (225), Expect = 1e-24
 Identities = 26/99 (26%), Positives = 36/99 (36%), Gaps = 6/99 (6%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           CAGC + I      +A +  WH     C  CD  L   G       +  +CK  Y++   
Sbjct: 6   CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILA--GEIYVMVNDKPVCKPCYVKNHA 63

Query: 101 STGYCAACSKVIPAFEMVMRARNNVYHL--ECFACQQCN 137
               C  C   I      +   N  +H   ECF C  C+
Sbjct: 64  V--VCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCS 100

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens} Length = 126

 Score = 41.6 bits (98), Expect = 6e-06
 Identities = 13/62 (20%), Positives = 20/62 (32%), Gaps = 5/62 (8%)

Query: 41  CAGCGKHITDRFL-LKALDMYWH--EDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLR 97
           C GC   I      +   +  WH   +C  C CC   L   G        ++ C  +  +
Sbjct: 66  CQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI--GQKFMPVEGMVFCSVECKK 123

Query: 98  LF 99
             
Sbjct: 124 RM 125

>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 = 79.0 bits (195), Expect = 9e-21
 Identities = 27/84 (32%), Positives = 36/84 (42%), Gaps = 5/84 (5%)

Query: 24  GAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLY 83
           G+  +   P   +GP  CAGC + I     L ALD  WH  C KC  C   L        
Sbjct: 1   GSSGSSGKPIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG---EYI 57

Query: 84  TKANLILCKRDYLRLFGSTGYCAA 107
           +K  +  C+ DY   FGS    ++
Sbjct: 58  SKDGVPYCESDYHAQFGSG--PSS 79

>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 = 59.3 bits (144), Expect = 5e-13
 Identities = 20/67 (29%), Positives = 29/67 (43%), Gaps = 4/67 (5%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           CA C + I DR L +A+   +H  C  C  C   L  +  T     + I C  D+ R F 
Sbjct: 18  CATCSQPILDRIL-RAMGKAYHPGCFTCVVCHRGLDGIPFT-VDATSQIHCIEDFHRKFA 75

Query: 101 STGYCAA 107
           S    ++
Sbjct: 76  S--GPSS 80

>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 = 57.8 bits (140), Expect = 2e-12
 Identities = 19/78 (24%), Positives = 29/78 (37%), Gaps = 3/78 (3%)

Query: 24  GAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLY 83
           G+  +     NAQ    C  CG  I   F+ K  D + H +C  C  C   L + G   +
Sbjct: 1   GSSGSSGSIGNAQKLPMCDKCGTGIVGVFV-KLRDRHRHPECYVCTDCGTNLKQKGH--F 57

Query: 84  TKANLILCKRDYLRLFGS 101
              + I C++        
Sbjct: 58  FVEDQIYCEKHARERVSG 75

>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 = 57.1 bits (138), Expect = 4e-12
 Identities = 17/87 (19%), Positives = 28/87 (32%), Gaps = 5/87 (5%)

Query: 21  TQQGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGS 80
            +    +      +AQ    C  CG  I    + KA D Y H +C  C  C+  L + G 
Sbjct: 8   VRAPVTKVHGGAGSAQRMPLCDKCGSGIVGAVV-KARDKYRHPECFVCADCNLNLKQKGY 66

Query: 81  TLYTKANLILCKRDYLRLFGSTGYCAA 107
             +     + C+             + 
Sbjct: 67  --FFVEGELYCETHARARTSGP--SSG 89

>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 = 55.5 bits (134), Expect = 2e-11
 Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 2/71 (2%)

Query: 34  NAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKR 93
           N  G  +C  CG+ +     ++     +H  C  C  C   L    +T+      + CK 
Sbjct: 3   NWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLD--STTVAIHDAEVYCKS 60

Query: 94  DYLRLFGSTGY 104
            Y + +G  GY
Sbjct: 61  CYGKKYGPKGY 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 = 54.0 bits (130), Expect = 8e-11
 Identities = 17/67 (25%), Positives = 27/67 (40%), Gaps = 5/67 (7%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           CA C + I   FL  AL   WH +   C  C   +  +G     +   + C+  Y + F 
Sbjct: 28  CAHCNQVIRGPFL-VALGKSWHPEEFNCAHCKNTMAYIGF--VEEKGALYCELCYEKFFA 84

Query: 101 STGYCAA 107
           S    ++
Sbjct: 85  SG--PSS 89

>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 = 38.6 bits (90), Expect = 5e-05
 Identities = 13/58 (22%), Positives = 20/58 (34%), Gaps = 3/58 (5%)

Query: 80  STLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
            +   +  L+            T  CA C++VI      + A    +H E F C  C 
Sbjct: 4   GSSGDQDTLVQRAEHIPAG-KRTPMCAHCNQVI--RGPFLVALGKSWHPEEFNCAHCK 58

>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 = 53.1 bits (128), Expect = 1e-10
 Identities = 16/71 (22%), Positives = 27/71 (38%), Gaps = 5/71 (7%)

Query: 37  GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYL 96
           G   C  C K IT   +    +  WH++C  C  C  +L   G     + +   C   + 
Sbjct: 4   GSSGCVQCKKPITTGGV-TYREQPWHKECFVCTACRKQLS--GQRFTARDDFAYCLNCFC 60

Query: 97  RLFGSTGYCAA 107
            L+ S    ++
Sbjct: 61  DLYAS--GPSS 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 = 53.3 bits (128), Expect = 1e-10
 Identities = 20/80 (25%), Positives = 32/80 (40%), Gaps = 2/80 (2%)

Query: 24  GAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLY 83
           G+  +  +   A   + C  C K +     L A    +H  C +C  C+ +L     T  
Sbjct: 1   GSSGSSGMKFQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLS--LGTYA 58

Query: 84  TKANLILCKRDYLRLFGSTG 103
           +    I CK  + +LF S G
Sbjct: 59  SLHGRIYCKPHFNQLFKSKG 78

>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 = 36.4 bits (84), Expect = 4e-04
 Identities = 12/39 (30%), Positives = 18/39 (46%), Gaps = 1/39 (2%)

Query: 99  FGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
             +   C  C K +   E ++ A   V+H+ CF C  CN
Sbjct: 12  APARETCVECQKTVYPMERLL-ANQQVFHISCFRCSYCN 49

>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 = 52.3 bits (126), Expect = 2e-10
 Identities = 17/61 (27%), Positives = 25/61 (40%), Gaps = 3/61 (4%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           C  C + I  R +  A+   WH +   C  C+      G   Y +  L  C+  Y +LFG
Sbjct: 8   CGACRRPIEGRVV-NAMGKQWHVEHFVCAKCEKPFL--GHRHYERKGLAYCETHYNQLFG 64

Query: 101 S 101
            
Sbjct: 65  D 65

>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 = 52.3 bits (126), Expect = 2e-10
 Identities = 16/67 (23%), Positives = 27/67 (40%), Gaps = 5/67 (7%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           C GC + + + +L  A+D  WH +C  CG C         + +       C+  Y    G
Sbjct: 18  CGGCNRPVLENYL-SAMDTVWHPECFVCGDCFTSFS--TGSFFELDGRPFCELHYHHRRG 74

Query: 101 STGYCAA 107
           S    ++
Sbjct: 75  SG--PSS 79

>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 = 42.3 bits (100), Expect = 2e-06
 Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 4/47 (8%)

Query: 91  CKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
             +D+L +F     C  C++ +   E  + A + V+H ECF C  C 
Sbjct: 6   SGKDFLAMFSPK--CGGCNRPV--LENYLSAMDTVWHPECFVCGDCF 48

>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 = 52.1 bits (125), Expect = 3e-10
 Identities = 18/68 (26%), Positives = 27/68 (39%), Gaps = 5/68 (7%)

Query: 41  CAGCGKHIT-DRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99
           CA C + I  D   L   D ++HE C +C  C   L         + + +LC   Y   F
Sbjct: 18  CAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSL--ADEPFTCQDSELLCNDCYCSAF 75

Query: 100 GSTGYCAA 107
            S    ++
Sbjct: 76  SS--GPSS 81

>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 = 40.9 bits (96), Expect = 6e-06
 Identities = 12/47 (25%), Positives = 19/47 (40%), Gaps = 2/47 (4%)

Query: 91  CKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
               Y   F +T  CA C ++I      +   +  +H  CF C +C 
Sbjct: 6   SGPCYDNTFANT--CAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQ 50

>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 = 54.3 bits (130), Expect = 4e-10
 Identities = 27/150 (18%), Positives = 44/150 (29%), Gaps = 49/150 (32%)

Query: 34  NAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKR 93
           N  G ++C  C K +     ++     +H+ C  C  C   L    +T+    + I CK 
Sbjct: 3   NWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNL--DSTTVAVHGDEIYCKS 60

Query: 94  DYLRLFGSTGY----------------------------------------------CAA 107
            Y + +G  G                                               C  
Sbjct: 61  CYGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPR 120

Query: 108 CSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           C + + A E V+      +H  CF C +C 
Sbjct: 121 CGQAVYAAEKVI-GAGKSWHKSCFRCAKCG 149

>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 = 50.8 bits (121), Expect = 6e-09
 Identities = 19/77 (24%), Positives = 27/77 (35%), Gaps = 4/77 (5%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           C  CG+ +     +      WH+ C +C  C   L    +TL  K   I CK  Y + FG
Sbjct: 118 CPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLE--STTLADKDGEIYCKGCYAKNFG 175

Query: 101 STGYCAACSKVIPAFEM 117
                    +   A   
Sbjct: 176 PK--GFGFGQGAGALIH 190

>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 = 51.7 bits (124), Expect = 4e-10
 Identities = 17/53 (32%), Positives = 21/53 (39%), Gaps = 4/53 (7%)

Query: 87  NLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
           +     +DY   FG    C  CS ++      M A    YH ECFAC  C   
Sbjct: 2   SSGSSGKDYWGKFGEF--CHGCSLLMT--GPFMVAGEFKYHPECFACMSCKVI 50

>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 = 45.2 bits (107), Expect = 1e-07
 Identities = 11/61 (18%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           C GC   +T  F+  A +  +H +C  C  C   + +  +    +   + C + +  +  
Sbjct: 18  CHGCSLLMTGPFM-VAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVS 76

Query: 101 S 101
            
Sbjct: 77  G 77

>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 = 51.3 bits (123), Expect = 5e-10
 Identities = 20/70 (28%), Positives = 30/70 (42%), Gaps = 3/70 (4%)

Query: 36  QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 95
            G   C  CG+ I  R + KA++  WH +C +C  C   L ++G      A   LC+  +
Sbjct: 3   SGSSGCHQCGEFIIGRVI-KAMNNSWHPECFRCDLCQEVLADIG--FVKNAGRHLCRPCH 59

Query: 96  LRLFGSTGYC 105
            R   S    
Sbjct: 60  NREKASGPSS 69

>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 = 35.9 bits (83), Expect = 4e-04
 Identities = 13/33 (39%), Positives = 17/33 (51%), Gaps = 2/33 (6%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           C  C + I     V++A NN +H ECF C  C 
Sbjct: 8   CHQCGEFI--IGRVIKAMNNSWHPECFRCDLCQ 38

>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 = 51.3 bits (123), Expect = 6e-10
 Identities = 18/73 (24%), Positives = 26/73 (35%), Gaps = 3/73 (4%)

Query: 35  AQGPQECAGCGKHITDR-FLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKR 93
           + G   C GCG+ +      + ALD  +H  C  C  C  +L   G   Y       C+ 
Sbjct: 2   SSGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLR--GQHFYAVERRAYCEG 59

Query: 94  DYLRLFGSTGYCA 106
            Y+    S     
Sbjct: 60  CYVATLESGPSSG 72

>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 = 45.1 bits (107), Expect = 1e-07
 Identities = 9/39 (23%), Positives = 17/39 (43%)

Query: 101 STGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR 139
            +  C  C + +      + A + V+H+ CF C  C  +
Sbjct: 4   GSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQ 42

>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 = 50.8 bits (122), Expect = 8e-10
 Identities = 16/68 (23%), Positives = 24/68 (35%), Gaps = 5/68 (7%)

Query: 41  CAGCGKHIT-DRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99
           C+ CG+ +      L+     WHE C  C  C+  LG    +         C   Y   F
Sbjct: 8   CSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLG--SRSFVPDKGAHYCVPCYENKF 65

Query: 100 GSTGYCAA 107
            S    ++
Sbjct: 66  ASG--PSS 71

>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 = 40.0 bits (94), Expect = 1e-05
 Identities = 8/33 (24%), Positives = 13/33 (39%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           C+AC + +      +      +H  CF C  C 
Sbjct: 8   CSACGETVMPGSRKLEYGGQTWHEHCFLCSGCE 40

>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 = 50.4 bits (121), Expect = 1e-09
 Identities = 18/67 (26%), Positives = 26/67 (38%), Gaps = 5/67 (7%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           CA C K +T   +    D  WH +CL C  C   L   G    ++     C   +  LF 
Sbjct: 18  CARCSKTLTQGGV-TYRDQPWHRECLVCTGCQTPLA--GQQFTSRDEDPYCVACFGELFA 74

Query: 101 STGYCAA 107
           S    ++
Sbjct: 75  S--GPSS 79

>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 = 41.2 bits (97), Expect = 4e-06
 Identities = 13/47 (27%), Positives = 18/47 (38%), Gaps = 4/47 (8%)

Query: 91  CKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
               Y   F     CA CSK +   +  +  R+  +H EC  C  C 
Sbjct: 6   SGPCYENKFAPR--CARCSKTL--TQGGVTYRDQPWHRECLVCTGCQ 48

>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 = 49.7 bits (119), Expect = 2e-09
 Identities = 16/68 (23%), Positives = 23/68 (33%), Gaps = 5/68 (7%)

Query: 41  CAGCGKHIT-DRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99
           C  C K I      ++     WHE C  C  C   +G    +   K N   C   Y +  
Sbjct: 8   CQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIG--TKSFIPKDNQNFCVPCYEKQH 65

Query: 100 GSTGYCAA 107
            S    ++
Sbjct: 66  ASG--PSS 71

>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 = 40.1 bits (94), Expect = 9e-06
 Identities = 10/33 (30%), Positives = 14/33 (42%)

Query: 105 CAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           C  C K I      M  + + +H  CF C +C 
Sbjct: 8   CQECKKTIMPGTRKMEYKGSSWHETCFICHRCQ 40

>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 = 49.3 bits (118), Expect = 3e-09
 Identities = 17/65 (26%), Positives = 20/65 (30%), Gaps = 3/65 (4%)

Query: 37  GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYL 96
           G   C  C K IT   +    D  WH DC  C  C  +L   G       +   C   Y 
Sbjct: 4   GSSGCVKCNKAITSGGI-TYQDQPWHADCFVCVTCSKKLA--GQRFTAVEDQYYCVDCYK 60

Query: 97  RLFGS 101
                
Sbjct: 61  NFVSG 65

>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 = 48.3 bits (115), Expect = 7e-09
 Identities = 19/63 (30%), Positives = 25/63 (39%), Gaps = 5/63 (7%)

Query: 41  CAGCGKHITDRF---LLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLR 97
           CAGC   I+       +   +  WH DC  C  C   L  VG    T+ + ILC      
Sbjct: 8   CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL--VGRGFLTERDDILCPDCGKD 65

Query: 98  LFG 100
           + G
Sbjct: 66  ISG 68

>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 = 48.5 bits (116), Expect = 8e-09
 Identities = 16/68 (23%), Positives = 25/68 (36%), Gaps = 5/68 (7%)

Query: 41  CAGCGKHIT-DRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99
           C GC K I      ++     WH+DC  C  C   +G    + + K     C   +   F
Sbjct: 18  CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIG--TGSFFPKGEDFYCVTCHETKF 75

Query: 100 GSTGYCAA 107
            S    ++
Sbjct: 76  ASG--PSS 81

>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 = 46.2 bits (110), Expect = 6e-08
 Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 2/47 (4%)

Query: 91  CKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
             +   R       C  C K I A +  +  +  V+H +CF C  C 
Sbjct: 6   SGKCTTREDSPK--CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCK 50

>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 = 47.1 bits (112), Expect = 3e-08
 Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 4/44 (9%)

Query: 94  DYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           DY RL+G+   C +C + I     V+ A    YH +CF C  C 
Sbjct: 9   DYQRLYGTR--CFSCDQFIE--GEVVSALGKTYHPDCFVCAVCR 48

>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 = 44.0 bits (104), Expect = 4e-07
 Identities = 14/62 (22%), Positives = 22/62 (35%), Gaps = 2/62 (3%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           C  C + I    +  AL   +H DC  C  C       G  +       +C++  L +  
Sbjct: 18  CFSCDQFIEGEVV-SALGKTYHPDCFVCAVCRLPFPP-GDRVTFNGKECMCQKCSLPVSV 75

Query: 101 ST 102
           S 
Sbjct: 76  SG 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 = 45.8 bits (109), Expect = 7e-08
 Identities = 17/65 (26%), Positives = 22/65 (33%), Gaps = 3/65 (4%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRD-YLRLF 99
           C  C K +     + +L   WH  CLKC  C   L               C    Y  +F
Sbjct: 3   CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLT--SGGHAEHEGKPYCNHPCYSAMF 60

Query: 100 GSTGY 104
           G  G+
Sbjct: 61  GPKGF 65

>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 = 45.9 bits (109), Expect = 7e-08
 Identities = 18/74 (24%), Positives = 26/74 (35%), Gaps = 3/74 (4%)

Query: 32  PNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILC 91
             ++    +C  C K +     + +L   WH+ CLKC  C   L               C
Sbjct: 3   SGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLT--PGGHAEHDGKPFC 60

Query: 92  KRD-YLRLFGSTGY 104
            +  Y  LFGS   
Sbjct: 61  HKPCYATLFGSGPS 74

>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 = 35.5 bits (82), Expect = 6e-04
 Identities = 10/39 (25%), Positives = 16/39 (41%), Gaps = 1/39 (2%)

Query: 99  FGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
            G    C  C K +   E V  +    +H  C  C++C+
Sbjct: 6   SGMASKCPKCDKTVYFAEKVS-SLGKDWHKFCLKCERCS 43

>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 = 45.7 bits (108), Expect = 9e-08
 Identities = 15/80 (18%), Positives = 26/80 (32%)

Query: 24  GAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLY 83
           G+  +      A     CA CG+H+     L     ++H  C +C  C+  L   G   +
Sbjct: 1   GSSGSSGQHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQH 60

Query: 84  TKANLILCKRDYLRLFGSTG 103
                  C +   +      
Sbjct: 61  PGDGHFYCLQHLPQTDSGPS 80

>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 = 44.5 bits (105), Expect = 2e-07
 Identities = 17/65 (26%), Positives = 24/65 (36%), Gaps = 5/65 (7%)

Query: 41  CAGCGKHITDRF---LLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLR 97
           C  C K I+       +   D  WH +C  CG C   L  VG    T+   I C++    
Sbjct: 8   CVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSL--VGKGFLTQNKEIFCQKCGSG 65

Query: 98  LFGST 102
           +    
Sbjct: 66  MDTDI 70

>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 = 44.3 bits (105), Expect = 2e-07
 Identities = 12/61 (19%), Positives = 19/61 (31%), Gaps = 3/61 (4%)

Query: 41  CAGCGKHIT-DRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99
           C  C         ++ +    +HE C  C  C  +        Y       C+ D+  LF
Sbjct: 14  CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP--EGLFYEFEGRKYCEHDFQMLF 71

Query: 100 G 100
            
Sbjct: 72  A 72

>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 = 43.9 bits (104), Expect = 3e-07
 Identities = 10/37 (27%), Positives = 17/37 (45%)

Query: 101 STGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           ++  C  C       E ++ +   +YH +CF C QC 
Sbjct: 10  ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCF 46

>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 = 43.5 bits (103), Expect = 6e-07
 Identities = 12/61 (19%), Positives = 19/61 (31%), Gaps = 3/61 (4%)

Query: 41  CAGCGKHIT-DRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF 99
           C  C         ++ +    +HE C  C  C  +        Y       C+ D+  LF
Sbjct: 14  CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP--EGLFYEFEGRKYCEHDFQMLF 71

Query: 100 G 100
            
Sbjct: 72  A 72

>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 = 43.5 bits (103), Expect = 6e-07
 Identities = 12/48 (25%), Positives = 20/48 (41%), Gaps = 2/48 (4%)

Query: 90  LCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCN 137
           + +     L  +T  C  C       E ++ +   +YH +CF C QC 
Sbjct: 1   ISEFMANALASAT--CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCF 46

>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 = 41.3 bits (97), Expect = 4e-06
 Identities = 12/52 (23%), Positives = 17/52 (32%), Gaps = 5/52 (9%)

Query: 89  ILCKRDYLRLFGSTGYCAACSKVIPAF---EMVMRARNNVYHLECFACQQCN 137
                 Y         CA C   I  F     V+      +H  CF C++C+
Sbjct: 4   GSSGDCYKNFVAKK--CAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCS 53

>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 = 40.9 bits (96), Expect = 6e-06
 Identities = 14/62 (22%), Positives = 19/62 (30%), Gaps = 6/62 (9%)

Query: 41 CAGCGKHIT----DRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYL 96
          CAGC   IT       ++      WH+ C  C  C   L             + C     
Sbjct: 18 CAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLA--NKRFVFHQEQVYCPDCAK 75

Query: 97 RL 98
          +L
Sbjct: 76 KL 77

>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 = 40.2 bits (94), Expect = 1e-05
 Identities = 11/62 (17%), Positives = 19/62 (30%), Gaps = 4/62 (6%)

Query: 41  CAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           C  C   I ++ L    +  +H D   C  C   L             + C   + ++  
Sbjct: 18  CQKCHAIIDEQPL-IFKNDPYHPDHFNCANCGKELTADA---RELKGELYCLPCHDKMGV 73

Query: 101 ST 102
           S 
Sbjct: 74  SG 75

>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 = 38.3 bits (88), Expect = 4e-04
 Identities = 23/140 (16%), Positives = 40/140 (28%), Gaps = 42/140 (30%)

Query: 12  INRMSMDVKTQQGAQQTKAVPNNA-QGPQECAGCGKHI------TDRFLLKALD--MYWH 62
           ++R+   +K +Q   + +   N    G     G GK            +   +D  ++W 
Sbjct: 131 VSRLQPYLKLRQALLELRPAKNVLIDGV---LGSGKTWVALDVCLSYKVQCKMDFKIFW- 186

Query: 63  EDCLKCGCCDC--RLGEVGSTLYTKANLILCKR---------------DYLR-LFGSTGY 104
              L    C+    + E+   L  + +     R                 LR L  S  Y
Sbjct: 187 ---LNLKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSIQAELRRLLKSKPY 243

Query: 105 CAAC--------SKVIPAFE 116
                       +K   AF 
Sbjct: 244 ENCLLVLLNVQNAKAWNAFN 263

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	139
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.95
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.95
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.95
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.94
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.93
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.93
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.91
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.79
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.74
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.73
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.71
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.7
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.69
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.68
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.68
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.67
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.67
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.67
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.65
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.65
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.65
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.65
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.65
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.64
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.64
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.63
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.62
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.6
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.6
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.6
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.59
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.59
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.59
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.56
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.56
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.56
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.55
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.54
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.54
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.53
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.52
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.52
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.5
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.48
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.47
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.47
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.46
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.45
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.45
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.44
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.28
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.28
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.22
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.17
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.15
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.14
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.11
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.09
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.08
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.07
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.06
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.06
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.03
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.03
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.02
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.0
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.0
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	98.98
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	98.96
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	98.95
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	98.94
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	98.92
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	98.91
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	98.88
2cor_A	79	Pinch protein; LIM domain, particularly interestin	98.87
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	98.85
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	98.85
2co8_A	82	NEDD9 interacting protein with calponin homology a	98.84
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	98.82
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	98.81
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	98.81
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	98.78
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	98.72
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	98.69
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.26
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.09
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	92.29
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	85.17
2ect_A	78	Ring finger protein 126; metal binding protein, st	84.64
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	83.45
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	82.95
2y43_A	99	E3 ubiquitin-protein ligase RAD18; DNA repair, met	80.87
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	80.55
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	80.49

>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

Probab=99.95  E-value=9.8e-29  Score=153.52  Aligned_cols=97  Identities=28%  Similarity=0.576  Sum_probs=89.3

Q ss_pred             CCCccccccccccc-ceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCC
Q psy284           37 GPQECAGCGKHITD-RFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAF  115 (139)
Q Consensus        37 ~~~~C~~C~~~i~~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~  115 (139)
                      ..++|..|+++|.. .+++.++++.||.+||+|..|+.+|  .+..|+.+++++||..||.++|++  +|..|+++|.+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L--~~~~~~~~~g~~yC~~cy~~~~~~--~C~~C~~~I~~~   79 (101)
T 2cup_A            4 GSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPL--ANETFVAKDNKILCNKCTTREDSP--KCKGCFKAIVAG   79 (101)
T ss_dssp             CCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCT--TSSCCEEETTEEECHHHHTTCCCC--BCSSSCCBCCSS
T ss_pred             CCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCC--CcCeeECcCCEEEChhHhhhhcCC--ccccCCCccccC
Confidence            46799999999984 6678999999999999999999999  456789999999999999999999  999999999966


Q ss_pred             ceEEEeCCccccccccccccCC
Q psy284          116 EMVMRARNNVYHLECFACQQCN  137 (139)
Q Consensus       116 ~~~~~~~~~~~H~~Cf~C~~C~  137 (139)
                      |.+|.++++.||++||+|..|+
T Consensus        80 ~~~~~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           80 DQNVEYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             SCEEESSSCEEETTTCCCTTCC
T ss_pred             CeEEEeCCcchHHhCCCCCCCC
Confidence            6899999999999999999995

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A

Probab=99.95  E-value=5.2e-28  Score=156.76  Aligned_cols=101  Identities=58%  Similarity=1.258  Sum_probs=92.6

Q ss_pred             CCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCCce
Q psy284           38 PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEM  117 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~  117 (139)
                      .++|..|+++|.+.+++.++++.||++||+|..|+.+|++.+..|+.+++++||..||.++|++.++|..|+++|.+.|.
T Consensus         2 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~~e~   81 (131)
T 2xjy_A            2 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEM   81 (131)
T ss_dssp             CCBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECTTSE
T ss_pred             cccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCccce
Confidence            46899999999998778999999999999999999999633467999999999999999999876689999999998778


Q ss_pred             EEEeCCccccccccccccCCC
Q psy284          118 VMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       118 ~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      +|.+.++.||++||+|..|++
T Consensus        82 ~~~a~~~~~H~~CF~C~~C~~  102 (131)
T 2xjy_A           82 TMRVKDKVYHLECFKCAACQK  102 (131)
T ss_dssp             EEEETTEEEEGGGCBCTTTCC
T ss_pred             eEeeCCceECccCcccCCCCC
Confidence            999999999999999999986

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens}

Probab=99.95  E-value=1.4e-27  Score=153.80  Aligned_cols=98  Identities=27%  Similarity=0.524  Sum_probs=91.1

Q ss_pred             CCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCCce
Q psy284           38 PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEM  117 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~  117 (139)
                      .++|.+|+++|.+.+++.++++.||++||+|..|+.+|  .+..|+.+++++||..||.++|++  +|..|+++|.+.+.
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L--~~~~f~~~~g~~yC~~cy~~~~~~--~C~~C~~~I~~~~~   78 (126)
T 2xqn_T            3 KPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSIL--AGEIYVMVNDKPVCKPCYVKNHAV--VCQGCHNAIDPEVQ   78 (126)
T ss_dssp             CCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBC--TTSEEEEETTEEEEHHHHHHHSCC--BCTTTCSBCCTTSC
T ss_pred             CCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCC--CcCEEEeECCEEechHHhCcCcCc--cCcccCCcCCcCce
Confidence            46899999999987778999999999999999999999  456899999999999999999999  99999999998678


Q ss_pred             EEEeCCcccc--ccccccccCCCC
Q psy284          118 VMRARNNVYH--LECFACQQCNHR  139 (139)
Q Consensus       118 ~~~~~~~~~H--~~Cf~C~~C~~~  139 (139)
                      +|.++++.||  ++||+|..|+++
T Consensus        79 ~~~a~~~~~H~~~~CF~C~~C~~~  102 (126)
T 2xqn_T           79 RVTYNNFSWHASTECFLCSCCSKC  102 (126)
T ss_dssp             EEEETTEEEESSTTTSBCTTTCCB
T ss_pred             EEECCCCEeeCCCCCcCcCCCCCc
Confidence            9999999999  999999999863

>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

Probab=99.94  E-value=5e-27  Score=160.73  Aligned_cols=101  Identities=56%  Similarity=1.265  Sum_probs=92.1

Q ss_pred             CCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCCce
Q psy284           38 PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFEM  117 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~  117 (139)
                      .++|..|+++|.+.+++.++++.||++||+|..|+..|...+..|+.+++++||..||.++|+++++|..|+++|.+.+.
T Consensus         5 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~~e~   84 (188)
T 1rut_X            5 WKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASEL   84 (188)
T ss_dssp             CCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECTTSE
T ss_pred             CCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCccccCcE
Confidence            56899999999998778999999999999999999999532467999999999999999999985569999999998778


Q ss_pred             EEEeCCccccccccccccCCC
Q psy284          118 VMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       118 ~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      +|.+.++.||++||+|..|++
T Consensus        85 ~i~a~~~~~H~~CF~C~~C~~  105 (188)
T 1rut_X           85 VMRAQGNVYHLKCFTCSTCRN  105 (188)
T ss_dssp             EEEETTEEECGGGCBCTTTCC
T ss_pred             EEEcCCCEEeCCCCeECCCCC
Confidence            999999999999999999976

>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

Probab=99.93  E-value=1.3e-26  Score=156.20  Aligned_cols=97  Identities=46%  Similarity=1.006  Sum_probs=87.9

Q ss_pred             CCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCCc
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFE  116 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~  116 (139)
                      +.++|..|+++|.+.+++.++++.||.+||+|..|+..|.  +.. +.+++++||..||.++|++  +|..|+++|.+.+
T Consensus         5 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~--~~~-f~~~g~~yC~~~y~~~f~~--~C~~C~~~I~~~~   79 (169)
T 2rgt_A            5 EIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLA--ERC-FSRGESVYCKDDFFKRFGT--KCAACQLGIPPTQ   79 (169)
T ss_dssp             --CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCC--SCC-EESSSCEECHHHHHHHHSC--BCTTTCCBCCTTS
T ss_pred             CCCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCC--CCC-cccCCeeeecccccccccc--cccccccccCCCc
Confidence            4579999999999987788999999999999999999995  333 5899999999999999999  9999999999877


Q ss_pred             eEEEeCCccccccccccccCCC
Q psy284          117 MVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       117 ~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      .++.++++.||++||+|..|++
T Consensus        80 ~v~~a~~~~~H~~CF~C~~C~~  101 (169)
T 2rgt_A           80 VVRRAQDFVYHLHCFACVVCKR  101 (169)
T ss_dssp             EEEEETTEEEEGGGCBCTTTCC
T ss_pred             EEEEcCCceEeeCCCcCCCCCC
Confidence            7889999999999999999986

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus}

Probab=99.93  E-value=4.3e-26  Score=155.35  Aligned_cols=100  Identities=45%  Similarity=0.982  Sum_probs=90.6

Q ss_pred             CCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284           35 AQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        35 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      ....++|..|+++|.+.+++.++++.||++||+|..|+.+|.  +.. +.+++++||..||.++|++  +|..|+++|.+
T Consensus        57 ~~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~--~~~-f~~~g~~yC~~~y~~~f~~--kC~~C~~~I~~  131 (182)
T 2jtn_A           57 TPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLA--ERC-FSRGESVYCKDDFFKRFGT--KCAACQLGIPP  131 (182)
T ss_dssp             CCSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCS--SCC-EEETTEEECHHHHHHTTSC--CCTTTCCCCCS
T ss_pred             CCCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccC--CCc-eeECCEeeecCcccccccc--ccccCCCccCC
Confidence            455789999999999987788999999999999999999995  333 5799999999999999999  99999999998


Q ss_pred             CceEEEeCCccccccccccccCCCC
Q psy284          115 FEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       115 ~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      .+.++.+.++.||++||+|..|+++
T Consensus       132 ~~~v~~a~~~~~H~~CF~C~~C~~~  156 (182)
T 2jtn_A          132 TQVVRRAQDFVYHLHCFACVVCKRQ  156 (182)
T ss_dssp             SCCCCEETTEECCTTTCCCTTTCCC
T ss_pred             CceEEecCCCCEEeCCCcCCCCCCC
Confidence            7778899999999999999999863

>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

Probab=99.91  E-value=1.1e-24  Score=149.59  Aligned_cols=101  Identities=23%  Similarity=0.540  Sum_probs=87.7

Q ss_pred             CCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCC-------------
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGST-------------  102 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~-------------  102 (139)
                      .+.++|..|+++|.+.+.+.++++.||++||+|..|+.+|.  +..|+.+++++||..||.++|++.             
T Consensus         5 ~~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~cy~~~f~~~c~~c~~~~g~~~~   82 (192)
T 1b8t_A            5 GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLD--STTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGTLST   82 (192)
T ss_dssp             CCCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCC--SSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCCCCC
T ss_pred             CCCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCC--CCeeEecCCEeeChhhhHhhcCccccccccccccEec
Confidence            34679999999998766788999999999999999999995  456899999999999999999872             


Q ss_pred             ---------------------------------ccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          103 ---------------------------------GYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       103 ---------------------------------~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                                                       .+|.+|+++|.+. ..|.++++.||++||+|..|+++
T Consensus        83 ~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~C~~C~~~I~~~-~~v~a~~~~~H~~CF~C~~C~~~  151 (192)
T 1b8t_A           83 DKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAA-EKVIGAGKSWHKSCFRCAKCGKS  151 (192)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECTTTSCEECSS-SCEEETTEEECTTTCBCTTTCCB
T ss_pred             CCCcccccccccccccCCCCcCccccccccCCCCcCCCCCCEecCc-EEEecCCCccchhcCCccccCCC
Confidence                                             1388999999864 45679999999999999999863

>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

Probab=99.79  E-value=6.1e-20  Score=117.37  Aligned_cols=85  Identities=44%  Similarity=0.944  Sum_probs=73.2

Q ss_pred             CCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCCCc
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPAFE  116 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~  116 (139)
                      ..++|..|+++|.+.+++.++++.||++||+|..|+.+|.+.+..|+.+++++||..||.++|+++++|..|+++|.+  
T Consensus         4 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~--   81 (122)
T 1m3v_A            4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSG--   81 (122)
T ss_dssp             CCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCC--
T ss_pred             CCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCc--
Confidence            357899999999998778899999999999999999999522356899999999999999999988899999999987  


Q ss_pred             eEEEeCC
Q psy284          117 MVMRARN  123 (139)
Q Consensus       117 ~~~~~~~  123 (139)
                      ..+.+.+
T Consensus        82 ~~~~~~g   88 (122)
T 1m3v_A           82 GDVMVVG   88 (122)
T ss_dssp             EESSSSS
T ss_pred             hheEEcC
Confidence            3334444

>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

Probab=99.74  E-value=4e-18  Score=101.22  Aligned_cols=72  Identities=38%  Similarity=0.742  Sum_probs=63.2

Q ss_pred             CCCCCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccc
Q psy284           31 VPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAA  107 (139)
Q Consensus        31 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~  107 (139)
                      .+....+.++|..|+++|.+.+.+.++++.||++||+|..|+..|.  + .|+.+++++||+.||.++|++  +|.+
T Consensus         8 ~~~~~~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~--~-~~~~~~g~~yC~~~y~~~fg~--~C~~   79 (80)
T 2dj7_A            8 KPIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILT--G-EYISKDGVPYCESDYHAQFGS--GPSS   79 (80)
T ss_dssp             CCCCCSSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCS--S-CCEEETTEEECTTHHHHHTTC--CSTT
T ss_pred             CCcCCCCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcC--C-CeEEECCEEECHHHHHHHcCC--CCCC
Confidence            3455567889999999999776789999999999999999999994  3 589999999999999999999  8864

>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

Probab=99.73  E-value=5e-18  Score=99.83  Aligned_cols=72  Identities=22%  Similarity=0.408  Sum_probs=64.3

Q ss_pred             CcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccH-hhHHHHhCCCccccccCCCCCC
Q psy284           39 QECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCK-RDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        39 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~-~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      ++|..|+++|.+.+.+.++++.||.+||+|..|+.+|.  +..|+.+++++||. .||.++|++  +|.+|++.+..
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~~cy~~~f~~--~C~~C~~~~~~   73 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLT--SGGHAEHEGKPYCNHPCYSAMFGP--KGFGRGGAESH   73 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCC--TTTEEEETTEEEETTTHHHHHSSC--CCSSCCCSSSC
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCC--CCceECcCCeEeeCHHHHHHHhCc--cCCCcCCceee
Confidence            47999999999766788999999999999999999995  44689999999999 699999999  99999987653

>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

Probab=99.71  E-value=5e-18  Score=101.01  Aligned_cols=72  Identities=19%  Similarity=0.427  Sum_probs=55.3

Q ss_pred             CCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCC
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVI  112 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I  112 (139)
                      +.++|..|+++|.+.+.+.++++.||++||+|..|+.+|.  +..|+.+++++||..||.++|++  +|.+|++..
T Consensus         6 ~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~~~~yC~~cy~~~f~~--~c~gcg~g~   77 (81)
T 1a7i_A            6 GGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLD--STTVAIHDAEVYCKSCYGKKYGP--KGYGYGQGA   77 (81)
T ss_dssp             --CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEEC--SSCCEEETTEEECSHHHHHHCC------------
T ss_pred             CCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCC--CCCeEeeCCEEECHHHHHHHhCC--cccccCCcc
Confidence            4678999999998766789999999999999999999994  45688999999999999999999  999999754

>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

Probab=99.70  E-value=2e-17  Score=104.49  Aligned_cols=70  Identities=57%  Similarity=1.091  Sum_probs=62.3

Q ss_pred             CCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccC
Q psy284           38 PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACS  109 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~  109 (139)
                      .++|.+|+++|.+.+++.++++.||++||+|..|+.+|.+.+..|+.+++++||..||.++|++  +|..|.
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~--~c~~c~   72 (114)
T 1j2o_A            3 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGS--GGHMGS   72 (114)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTS--CCSSCB
T ss_pred             CCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCc--ccCcCC
Confidence            5689999999999878899999999999999999999953235789999999999999999999  876664

>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

Probab=99.69  E-value=6.1e-17  Score=97.92  Aligned_cols=68  Identities=24%  Similarity=0.455  Sum_probs=59.8

Q ss_pred             CCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCcccc
Q psy284           34 NAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCA  106 (139)
Q Consensus        34 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~  106 (139)
                      ......+|..|++.|.+. .+.++++.||.+||+|..|+..|.  +..|+.+++++||..||.++|++  ++.
T Consensus        21 ~~~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~~y~~~f~p--~~~   88 (89)
T 1x64_A           21 SAQRMPLCDKCGSGIVGA-VVKARDKYRHPECFVCADCNLNLK--QKGYFFVEGELYCETHARARTSG--PSS   88 (89)
T ss_dssp             CCCSCCBCTTTCCBCCSC-CEESSSCEECTTTCCCSSSCCCTT--TSCCEEETTEEECHHHHHHHSSS--CCC
T ss_pred             CCCcCCCcccCCCEeccc-EEEECCceECccCCEecCCCCCCC--CCCeEeECCEEECHHHHHHHhCC--CCC
Confidence            445678999999999985 688999999999999999999994  45688999999999999999998  664

>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

Probab=99.68  E-value=4.9e-17  Score=95.54  Aligned_cols=68  Identities=26%  Similarity=0.453  Sum_probs=60.4

Q ss_pred             CCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccH-hhHHHHhCCCccccc
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCK-RDYLRLFGSTGYCAA  107 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~-~cy~~~~~~~~~C~~  107 (139)
                      ...++|..|+++|.+.+.+.++++.||++||+|..|+.+|.  +..|+.+++++||. .||.++|++  +|.+
T Consensus         7 ~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~~cy~~~f~~--kc~g   75 (76)
T 2cu8_A            7 GMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLT--PGGHAEHDGKPFCHKPCYATLFGS--GPSS   75 (76)
T ss_dssp             CCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCC--TTSCEEETTEEECTTTHHHHHSCS--SCSC
T ss_pred             CCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccC--CCceEeECCEEecchHHHHHhccc--ccCC
Confidence            34679999999999766788999999999999999999994  45689999999999 799999999  8863

>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

Probab=99.68  E-value=8.3e-17  Score=97.71  Aligned_cols=71  Identities=25%  Similarity=0.434  Sum_probs=62.1

Q ss_pred             CCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCcccccc
Q psy284           34 NAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAAC  108 (139)
Q Consensus        34 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C  108 (139)
                      ......+|..|++.|.+.+.+.++++.||.+||+|..|+..|.  +..|+.+++++||..||.++|++  +|.-+
T Consensus        11 ~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~~y~~~f~~--kc~~~   81 (91)
T 2d8y_A           11 QAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLS--LGTYASLHGRIYCKPHFNQLFKS--KGNYD   81 (91)
T ss_dssp             CSSSSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCC--TTTCCCSSSCCCCHHHHHHHSCC--CSCCC
T ss_pred             CCCCCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCC--CCCcEeECCEEECHHHHHHHhCC--CcCcc
Confidence            3456789999999999866788999999999999999999995  34588999999999999999999  88733

>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

Probab=99.67  E-value=1.1e-16  Score=96.99  Aligned_cols=68  Identities=22%  Similarity=0.481  Sum_probs=59.9

Q ss_pred             CCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccc
Q psy284           35 AQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAA  107 (139)
Q Consensus        35 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~  107 (139)
                      ....++|..|+++|.+. .+.++++.||++||+|..|+..|.  +..|+.+++++||..||.++|++  +|..
T Consensus        22 ~~~~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~~f~~--~c~s   89 (90)
T 2dar_A           22 GKRTPMCAHCNQVIRGP-FLVALGKSWHPEEFNCAHCKNTMA--YIGFVEEKGALYCELCYEKFFAS--GPSS   89 (90)
T ss_dssp             TTCCCBBSSSCCBCCSC-EEEETTEEECTTTCBCSSSCCBCS--SSCBEESSSCEECHHHHHHHTSC--CCCC
T ss_pred             CCCCCCCccCCCEecce-EEEECCccccccCCccCCCCCCCC--CCEeEeECCEEECHHHHHHHcCC--CCCC
Confidence            34577999999999765 678999999999999999999994  45688999999999999999999  8863

>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

Probab=99.67  E-value=1e-16  Score=92.41  Aligned_cols=66  Identities=26%  Similarity=0.569  Sum_probs=59.5

Q ss_pred             CCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccc
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAA  107 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~  107 (139)
                      ..++|..|+++|.+. .+.++++.||.+||+|..|+.+|.  +..|+.+++++||..||.++|++  +|.+
T Consensus         4 ~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~~~~yC~~cy~~~f~~--~C~g   69 (69)
T 2cur_A            4 GSSGCVKCNKAITSG-GITYQDQPWHADCFVCVTCSKKLA--GQRFTAVEDQYYCVDCYKNFVSG--PSSG   69 (69)
T ss_dssp             CCCCCSSSCCCCCTT-CEEETTEEECTTTTBCTTTCCBCT--TSCEEECSSCEEEHHHHHHHHTC--SCCC
T ss_pred             CcCCCcccCCEeCcc-eEEECccccccCcCEECCCCCCCC--CCccEeECCEEECHHHhHHHhcC--CCCC
Confidence            457999999999876 588999999999999999999994  56799999999999999999999  8864

>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

Probab=99.67  E-value=5.4e-17  Score=96.06  Aligned_cols=67  Identities=22%  Similarity=0.406  Sum_probs=59.0

Q ss_pred             CCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCcccc
Q psy284           35 AQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCA  106 (139)
Q Consensus        35 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~  106 (139)
                      ....++|..|++.|.+. .+.++++.||.+||+|..|+..|.  +..|+.+++++||..||.++|++  ++.
T Consensus        12 ~~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~cy~~~~~p--~g~   78 (79)
T 1x62_A           12 AQKLPMCDKCGTGIVGV-FVKLRDRHRHPECYVCTDCGTNLK--QKGHFFVEDQIYCEKHARERVSG--PSS   78 (79)
T ss_dssp             CCCCCCCSSSCCCCCSS-CEECSSCEECTTTTSCSSSCCCHH--HHCCEESSSCEECHHHHHHHHSS--CCC
T ss_pred             CCCCCccccCCCCccCc-EEEECcceeCcCcCeeCCCCCCCC--CCCeEeECCEEECHHHHHHHhCC--CCC
Confidence            35578999999999986 688999999999999999999994  35688999999999999999998  643

>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

Probab=99.65  E-value=4.3e-17  Score=95.78  Aligned_cols=68  Identities=26%  Similarity=0.589  Sum_probs=61.4

Q ss_pred             CCccccccccccc---ceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccC
Q psy284           38 PQECAGCGKHITD---RFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACS  109 (139)
Q Consensus        38 ~~~C~~C~~~i~~---~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~  109 (139)
                      .++|..|+++|.+   .+.+.++++.||++||+|..|+.+|  .+..|+.+++++||..||.++|++  +|..++
T Consensus         5 ~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L--~~~~f~~~~g~~yC~~cy~~~f~~--~C~~~s   75 (76)
T 1x68_A            5 SSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSL--VGKGFLTQNKEIFCQKCGSGMDTD--ISGPSS   75 (76)
T ss_dssp             CCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBC--SSSCEEEETTEEEETTTTCCCCCC--SSSSSC
T ss_pred             CCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcC--CCCceEeECCEEECHHHhhhhhCC--cCCCCC
Confidence            5689999999995   3578999999999999999999999  456799999999999999999999  998875

>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

Probab=99.65  E-value=2.2e-16  Score=91.69  Aligned_cols=67  Identities=25%  Similarity=0.549  Sum_probs=59.5

Q ss_pred             CCCcccccccccccc-eeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccc
Q psy284           37 GPQECAGCGKHITDR-FLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAA  107 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~  107 (139)
                      ..++|..|+++|.+. +++.++++.||.+||+|..|+.+|.  +..|+.+++++||..||.++|++  +|.+
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~~~~yC~~cy~~~f~~--~C~~   71 (72)
T 1wyh_A            4 GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLG--SRSFVPDKGAHYCVPCYENKFAS--GPSS   71 (72)
T ss_dssp             CCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTT--TSCEEEETTEEEEHHHHHHHTSC--CCCC
T ss_pred             cCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCC--CCccCCcCCeEECHHHHHHHccC--cCCC
Confidence            356899999999974 6788999999999999999999994  45689999999999999999999  8863

>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}

Probab=99.65  E-value=3.6e-16  Score=99.90  Aligned_cols=67  Identities=54%  Similarity=1.217  Sum_probs=58.9

Q ss_pred             CCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           34 NAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        34 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      .....++|.+|+++|.+.+++.++++.||.+||+|..|+..|.+.+..|+.+++++||+.||.++||
T Consensus        57 ~~~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           57 GGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             SCSSCSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             cCccCCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            3455689999999999987789999999999999999999995334578999999999999999885

>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

Probab=99.65  E-value=2.3e-16  Score=91.19  Aligned_cols=66  Identities=24%  Similarity=0.587  Sum_probs=59.0

Q ss_pred             CCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccc
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAA  107 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~  107 (139)
                      ..++|..|+++|.+. .+.++++.||++||+|..|+.+|  .+..|+.+++++||..||.++|++  +|.+
T Consensus         4 ~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L--~~~~~~~~~~~~yC~~cy~~~f~~--~c~~   69 (70)
T 2d8z_A            4 GSSGCVQCKKPITTG-GVTYREQPWHKECFVCTACRKQL--SGQRFTARDDFAYCLNCFCDLYAS--GPSS   69 (70)
T ss_dssp             CCCBCSSSCCBCCSS-EEESSSSEEETTTSBCSSSCCBC--TTSCCEESSSSEECHHHHHHHTCC--CCTT
T ss_pred             CCCCCcccCCeeccc-eEEECccccCCCCCccCCCCCcC--CcCceEeeCCeEECHHHHHHHhcc--ccCC
Confidence            456899999999976 48899999999999999999999  456788999999999999999999  8863

>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

Probab=99.65  E-value=2.3e-16  Score=91.66  Aligned_cols=66  Identities=24%  Similarity=0.475  Sum_probs=59.2

Q ss_pred             CCcccccccccccc-eeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccc
Q psy284           38 PQECAGCGKHITDR-FLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAA  107 (139)
Q Consensus        38 ~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~  107 (139)
                      .++|..|+++|.+. .++.++++.||.+||+|..|+..|.  +..|+.+++++||..||.++|++  +|..
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~~~~yC~~cy~~~f~~--~C~~   71 (72)
T 1x4k_A            5 SSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIG--TKSFIPKDNQNFCVPCYEKQHAS--GPSS   71 (72)
T ss_dssp             CCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCC--SSSEEEETTEEEEHHHHHHHTSS--CCCC
T ss_pred             CCCCccCCCcccCCceEEEECcCeecccCCcccccCCccC--CCccCccCCeEECHHHHhHHhCC--CCCC
Confidence            46899999999985 5788999999999999999999994  45789999999999999999999  8863

>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

Probab=99.64  E-value=7.9e-17  Score=96.00  Aligned_cols=71  Identities=18%  Similarity=0.350  Sum_probs=59.1

Q ss_pred             CCCCCCCCCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeE--eeCCccccHhhHHHHhCC
Q psy284           29 KAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLY--TKANLILCKRDYLRLFGS  101 (139)
Q Consensus        29 ~~~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~--~~~~~~~C~~cy~~~~~~  101 (139)
                      +..+....+..+|.+|++.|++.+.+.++++.||.+||+|..|+..|.  ...|+  .+++++||+.||.++|+.
T Consensus         6 ~~~~~~~~~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~--~~~~~~~~~~g~~yC~~~y~~~~~~   78 (82)
T 2co8_A            6 SGQHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLW--PGGYEQHPGDGHFYCLQHLPQTDSG   78 (82)
T ss_dssp             CCCCCCCCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCC--TTSEECCTTTCCCEETTTCCCCCCC
T ss_pred             CCCCcCCCCCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcC--CCceeEeCcCCEEEChHHHHhhhcC
Confidence            344455567789999999999876788999999999999999999995  34455  479999999999988765

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.64  E-value=2.2e-16  Score=92.89  Aligned_cols=67  Identities=18%  Similarity=0.447  Sum_probs=57.5

Q ss_pred             CCCCccccccccccc-ceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCcccc
Q psy284           36 QGPQECAGCGKHITD-RFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCA  106 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~  106 (139)
                      ....+|.+|+++|.+ ..++.++++.||.+||+|..|+.+|.  +..|+.+++++||..||.++|++  +|.
T Consensus         9 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~~y~~~f~~--~C~   76 (77)
T 1g47_A            9 LASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP--EGLFYEFEGRKYCEHDFQMLFAP--CWI   76 (77)
T ss_dssp             CCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCG--GGCSEEETTEEECHHHHHHHCCC--C--
T ss_pred             CCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCC--CCCeEeECCeEeCHHHHHHHhhc--ccC
Confidence            346799999999986 44578999999999999999999995  34689999999999999999999  885

>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

Probab=99.63  E-value=3.6e-16  Score=90.86  Aligned_cols=63  Identities=32%  Similarity=0.668  Sum_probs=56.7

Q ss_pred             CCCccccccccccc---ceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCC
Q psy284           37 GPQECAGCGKHITD---RFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGS  101 (139)
Q Consensus        37 ~~~~C~~C~~~i~~---~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~  101 (139)
                      ..++|..|+++|.+   ..++.++++.||++||+|..|+..|  .+..|+.+++++||..||.++|+|
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L--~~~~f~~~~g~~yC~~c~~~~~~p   69 (72)
T 1x4l_A            4 GSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL--VGRGFLTERDDILCPDCGKDISGP   69 (72)
T ss_dssp             CSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBC--TTSCCEECSSSEECHHHHHTCCCS
T ss_pred             CCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcC--CCCccEeECCEEEChhHcCcccCC
Confidence            46799999999996   3578889999999999999999999  456788899999999999999988

>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

Probab=99.62  E-value=4.2e-16  Score=89.06  Aligned_cols=61  Identities=28%  Similarity=0.698  Sum_probs=55.5

Q ss_pred             CCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCC
Q psy284           38 PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGS  101 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~  101 (139)
                      .++|.+|+++|.+. .+.++++.||++||+|..|+.+|.  +..|+.+++++||..||.++|++
T Consensus         5 ~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~~y~~~f~~   65 (66)
T 1nyp_A            5 VPICGACRRPIEGR-VVNAMGKQWHVEHFVCAKCEKPFL--GHRHYERKGLAYCETHYNQLFGD   65 (66)
T ss_dssp             CCEETTTTEECCSC-EECCTTSBEETTTCBCTTTCCBCS--SSCCEEETTEEECHHHHHHHCSC
T ss_pred             CCCCcccCCEecce-EEEECccccccCcCEECCCCCCCC--CCceEeECCcEECHHHHHHHhCC
Confidence            56899999999954 688999999999999999999994  56789999999999999999987

>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

Probab=99.60  E-value=9.8e-16  Score=90.73  Aligned_cols=65  Identities=25%  Similarity=0.653  Sum_probs=58.6

Q ss_pred             CCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccc
Q psy284           38 PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAA  107 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~  107 (139)
                      .++|..|+++|.+. .+.++++.||++||+|..|+.+|.  +..++.+++++||..||.++|++  +|.+
T Consensus        15 ~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~~~~yC~~~y~~~f~~--~C~~   79 (80)
T 1x3h_A           15 SPKCGGCNRPVLEN-YLSAMDTVWHPECFVCGDCFTSFS--TGSFFELDGRPFCELHYHHRRGS--GPSS   79 (80)
T ss_dssp             SCBCTTTCCBCCSS-CEEETTEEECTTTCBCSSSCCBSC--SSCCEESSSCEECHHHHHHHHSS--SCCC
T ss_pred             CCccccCCCeecce-eEEECCCeEecCcCChhhCCCCCC--CCcEEeECCEEECHHHHHHHcCC--CCCC
Confidence            56899999999985 688999999999999999999994  45688999999999999999999  8864

>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

Probab=99.60  E-value=1.1e-15  Score=104.56  Aligned_cols=73  Identities=26%  Similarity=0.537  Sum_probs=66.0

Q ss_pred             CCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCC
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVI  112 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I  112 (139)
                      .+.++|..|+++|.+.+.+.++++.||.+||+|..|+..|.  +..|+.+++++||+.||.++|++  +|.+|+++|
T Consensus       113 ~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~cy~~~f~~--kc~~C~~~~  185 (192)
T 1b8t_A          113 GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLE--STTLADKDGEIYCKGCYAKNFGP--KGFGFGQGA  185 (192)
T ss_dssp             CCCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCC--SSSEEEETTEEEEHHHHHHHTCC--CCCCCCCCC
T ss_pred             CCCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCC--CCcccccCCEEeCHHHHHHhcCC--cCCCCCCcc
Confidence            34678999999999866788999999999999999999994  45689999999999999999999  999999986

>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

Probab=99.60  E-value=2e-15  Score=87.24  Aligned_cols=63  Identities=30%  Similarity=0.651  Sum_probs=56.2

Q ss_pred             CCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCC
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGS  101 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~  101 (139)
                      .+..+|..|+++|.+. .+.++++.||++||+|..|+..|.  +..|+.+++++||..||.++|++
T Consensus         3 ~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~c~~~~~~~   65 (70)
T 2d8x_A            3 SGSSGCHQCGEFIIGR-VIKAMNNSWHPECFRCDLCQEVLA--DIGFVKNAGRHLCRPCHNREKAS   65 (70)
T ss_dssp             CCSSBCSSSCCBCCSC-CEEETTEEECTTTSBCSSSCCBCS--SSCCEEETTEEECHHHHHHHHCC
T ss_pred             CCCCcCccCCCEecce-EEEECcccccccCCEeCCCCCcCC--CCccEeECCeEECHHHhhhhcCC
Confidence            3467999999999975 688999999999999999999995  44688899999999999999987

>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

Probab=99.59  E-value=1.6e-15  Score=88.01  Aligned_cols=62  Identities=27%  Similarity=0.674  Sum_probs=55.8

Q ss_pred             CCCcccccccccccc-eeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           37 GPQECAGCGKHITDR-FLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      ..++|.+|+++|.+. ..+.++++.||.+||+|..|+..|  .+..|+.+++++||..||.++|.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L--~~~~~~~~~~~~yC~~cy~~~~~   66 (72)
T 1x61_A            4 GSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQL--RGQHFYAVERRAYCEGCYVATLE   66 (72)
T ss_dssp             CCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBC--TTSCEEESSSCEEEHHHHHHHHH
T ss_pred             CCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcC--CcCcCEeeCCeEECHHHHHHHHc
Confidence            467999999999974 578899999999999999999999  45679999999999999999986

>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

Probab=99.59  E-value=1.8e-15  Score=89.62  Aligned_cols=66  Identities=27%  Similarity=0.523  Sum_probs=59.1

Q ss_pred             CCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccc
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAA  107 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~  107 (139)
                      ..++|..|+++|.+. .+.++++.||.+||+|..|+.+|  .+..|+.+++++||..||.++|++  +|..
T Consensus        14 ~~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L--~~~~~~~~~~~~yC~~cy~~~f~~--~c~s   79 (80)
T 2cuq_A           14 FAPRCARCSKTLTQG-GVTYRDQPWHRECLVCTGCQTPL--AGQQFTSRDEDPYCVACFGELFAS--GPSS   79 (80)
T ss_dssp             SSCCCTTTCCCCCSC-CEESSSSEECTTTCBCSSSCCBC--TTCCEEECSSSEEEHHHHHHHTTC--STTC
T ss_pred             cCCcCCCCCCEecCc-EEEECCchhhhhhCCcccCCCcC--CCCeeEeECCEEECHHHHHHHcCC--CCCC
Confidence            357899999999886 68899999999999999999999  456789999999999999999999  8853

>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

Probab=99.59  E-value=1.9e-15  Score=89.75  Aligned_cols=66  Identities=30%  Similarity=0.631  Sum_probs=57.8

Q ss_pred             CCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEee-CCccccHhhHHHHhCCCccccc
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTK-ANLILCKRDYLRLFGSTGYCAA  107 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~-~~~~~C~~cy~~~~~~~~~C~~  107 (139)
                      ..++|..|+++|.+. ++.++++.||++||+|..|+.+|.  +..|+.. ++++||..||.++|++  +|.+
T Consensus        14 ~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~--~~~f~~~~~g~~yC~~cy~~~f~~--~C~~   80 (81)
T 2dlo_A           14 TLEKCATCSQPILDR-ILRAMGKAYHPGCFTCVVCHRGLD--GIPFTVDATSQIHCIEDFHRKFAS--GPSS   80 (81)
T ss_dssp             SCCBCTTTCCBCCSC-CEEETTEEECTTTCBCSSSCCBCT--TSCEECCTTCCCEEHHHHHHHTTS--SSCC
T ss_pred             CCCccccCCCeecce-eEEECCccccHHhcCcccCCCccC--CCeeEECCCCEEECHHHHHHHhcC--cCCC
Confidence            467999999999975 789999999999999999999994  4556665 7899999999999999  8864

>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}

Probab=99.56  E-value=7.7e-16  Score=91.62  Aligned_cols=65  Identities=26%  Similarity=0.475  Sum_probs=58.1

Q ss_pred             CCccccccccccc-ceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCcccc
Q psy284           38 PQECAGCGKHITD-RFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCA  106 (139)
Q Consensus        38 ~~~C~~C~~~i~~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~  106 (139)
                      .++|..|+++|.+ ..++.++++.||++||+|..|+.+|.  +..|+.+++++||..||.++|++  +|.
T Consensus        15 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~--~~~f~~~~~~~~C~~c~~~~~~~--~C~   80 (82)
T 2ehe_A           15 ANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLA--DEPFTCQDSELLCNDCYCSAFSS--GPS   80 (82)
T ss_dssp             SCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCS--SCCEEEETTEEEETTTSSCCGGG--SSC
T ss_pred             CCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccC--CCccEeeCCEEECHHHHhhhcCC--CCC
Confidence            5689999999994 55688899999999999999999994  56789999999999999999998  875

>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

Probab=99.56  E-value=5.1e-15  Score=87.48  Aligned_cols=62  Identities=19%  Similarity=0.267  Sum_probs=54.7

Q ss_pred             CCCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCC
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGS  101 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~  101 (139)
                      ...++|..|+++|.+. .+.++++.||++||+|..|+.+|.  +. ++.+++++||..||.++|++
T Consensus        13 ~~~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~--~~-~f~~~g~~yC~~cy~~~f~p   74 (79)
T 2cor_A           13 LGKYICQKCHAIIDEQ-PLIFKNDPYHPDHFNCANCGKELT--AD-ARELKGELYCLPCHDKMGVS   74 (79)
T ss_dssp             CCCCBCTTTCCBCCSC-CCCCSSSCCCTTTSBCSSSCCBCC--TT-CEEETTEEECHHHHHTTSCC
T ss_pred             cCCCCCccCCCEecce-EEEECcceeCCCCCEeCCCCCccC--CC-CEeECCEEeCHHHHHHhCCC
Confidence            4467999999999965 588999999999999999999995  34 45999999999999999988

>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

Probab=99.56  E-value=5.5e-15  Score=87.84  Aligned_cols=66  Identities=24%  Similarity=0.512  Sum_probs=57.8

Q ss_pred             CCCcccccccccccc-eeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCcccc
Q psy284           37 GPQECAGCGKHITDR-FLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCA  106 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~  106 (139)
                      ..++|..|+++|.+. .++.++++.||++||+|..|+..|.  +..++.+++++||..||.++|++  +|.
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~~~~yC~~cy~~~f~~--~~~   80 (82)
T 1x63_A           14 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIG--TGSFFPKGEDFYCVTCHETKFAS--GPS   80 (82)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCT--TSCEEEETTEEEEHHHHHHHTSC--CCS
T ss_pred             cCCcCccCCcccccCceEEEECccccccccCchhhCCCccC--CCccEeeCCEEECHHHHHHHhCC--CCC
Confidence            357999999999964 3588999999999999999999994  45789999999999999999998  653

>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}

Probab=99.54  E-value=5e-16  Score=92.45  Aligned_cols=52  Identities=21%  Similarity=0.427  Sum_probs=47.7

Q ss_pred             CCccccHhhHHHHhCCCccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284           86 ANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        86 ~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      ++++||+.||.++|++  +|.+|+++|.+.+.+|.++++.||++||+|+.|+++
T Consensus         1 ~g~~yC~~~y~~~~~~--~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~   52 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFAN--TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRS   52 (82)
T ss_dssp             CCCCCCCCCCCCCCSC--BCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCB
T ss_pred             CCceechhHhCcccCC--cCccCCCccccCcEEEEeCCccccccCCeecCCCCc
Confidence            4789999999999999  999999999965689999999999999999999863

>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}

Probab=99.54  E-value=1.2e-15  Score=89.70  Aligned_cols=51  Identities=22%  Similarity=0.436  Sum_probs=46.9

Q ss_pred             CccccHhhHHHHhCCCccccccCCCCCC---CceEEEeCCccccccccccccCCCC
Q psy284           87 NLILCKRDYLRLFGSTGYCAACSKVIPA---FEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        87 ~~~~C~~cy~~~~~~~~~C~~C~~~I~~---~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +++||+.||.++|++  +|.+|+++|.+   .+.+|.++++.||++||+|..|+++
T Consensus         2 ~~~yC~~cy~~~~~~--~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~   55 (77)
T 2egq_A            2 SSGSSGDCYKNFVAK--KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVN   55 (77)
T ss_dssp             CSSCCTTCCCSCCCC--CCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCB
T ss_pred             CCeEchhHhchhhCc--cCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCC
Confidence            679999999999998  99999999996   4589999999999999999999863

>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

Probab=99.53  E-value=8.8e-15  Score=84.72  Aligned_cols=63  Identities=19%  Similarity=0.487  Sum_probs=54.8

Q ss_pred             CCCCcccccccccccce-eeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           36 QGPQECAGCGKHITDRF-LLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      ....+|..|+++|.+.+ ++.++++.||++||+|..|+.+|.  +..++.+++++||..||.++|+
T Consensus         9 ~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B            9 SASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP--EGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             CTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCG--GGCCEEETTEEECHHHHHHHTC
T ss_pred             cCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCC--CCCeEeECCeEeCHHHHHHhhC
Confidence            34669999999999754 467999999999999999999995  3468899999999999999885

>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

Probab=99.52  E-value=1.5e-14  Score=85.84  Aligned_cols=66  Identities=17%  Similarity=0.401  Sum_probs=56.4

Q ss_pred             CCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeE-eeCCccccHhhHHHHhCCCcccc
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLY-TKANLILCKRDYLRLFGSTGYCA  106 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~~~C~~cy~~~~~~~~~C~  106 (139)
                      ..++|..|+++|.+. .+.++++.||++||+|..|+..|. .+..|+ .+++++||..||.++|++  .|.
T Consensus        14 ~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~-~g~~f~~~~~~~~~C~~c~~~~~~~--~~s   80 (81)
T 1x6a_A           14 FGEFCHGCSLLMTGP-FMVAGEFKYHPECFACMSCKVIIE-DGDAYALVQHATLYCGKCHNEVVSG--PSS   80 (81)
T ss_dssp             SSCBCTTTCCBCCSC-CBCCTTCCBCTTSCBCTTTCCBCC-TTSCEEECSSSCEEEHHHHHHHHCT--TSC
T ss_pred             cCCcCccCCCCcCce-EEEECCceeccccCCccCCCCccC-CCCcEEEeeCCEEECHHHHHHHhcC--CCC
Confidence            356899999999954 688999999999999999999995 235566 589999999999999988  654

>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

Probab=99.52  E-value=2.2e-15  Score=89.58  Aligned_cols=51  Identities=24%  Similarity=0.436  Sum_probs=47.2

Q ss_pred             CccccHhhHHHHhCCCccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284           87 NLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        87 ~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +.+||+.||.+++++  +|.+|+++|.+.+.+|.++++.||++||+|..|+++
T Consensus         2 ~~~yC~~cy~~~~~~--~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~   52 (82)
T 1x63_A            2 SSGSSGKCTTREDSP--KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQV   52 (82)
T ss_dssp             CSCCCCCCCSCCCSC--BCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCC
T ss_pred             CCcCchhHHccccCC--cCccCCcccccCceEEEECccccccccCchhhCCCc
Confidence            578999999999998  999999999976789999999999999999999863

>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

Probab=99.50  E-value=1.8e-14  Score=83.87  Aligned_cols=63  Identities=25%  Similarity=0.438  Sum_probs=55.4

Q ss_pred             CCCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCC
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGS  101 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~  101 (139)
                      ..++|..|+++|.+. .+.++++.||++||+|..|+.+|. .+..|+.+++++||..||.+++..
T Consensus         4 ~~~~C~~C~~~I~~~-~v~a~~~~wH~~CF~C~~C~~~L~-~~~~f~~~~~~~yC~~C~~~~~~~   66 (73)
T 1wig_A            4 GSSGCDSCEKYITGR-VLEAGEKHYHPSCALCVRCGQMFA-EGEEMYLQGSSIWHPACRQAARTE   66 (73)
T ss_dssp             SCCSCSSSCCCCSSC-CBCCSSCCBCTTTSCCSSSCCCCC-SSCCCEEETTEEECTTHHHHTSSS
T ss_pred             CcCCcccCCCEecCe-eEEeCCCCCCCCcCEeCCCCCCCC-CCCeeEeeCCEEEChHHChHhhcc
Confidence            356899999999985 688999999999999999999995 256789999999999999987764

>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

Probab=99.48  E-value=9.6e-15  Score=86.65  Aligned_cols=49  Identities=33%  Similarity=0.705  Sum_probs=45.1

Q ss_pred             CccccHhhHHHHhCCCccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284           87 NLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        87 ~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      ..+||..||.++|++  +|..|+++|.+  .+|.++++.||++||+|..|+++
T Consensus         2 ~~~yC~~dy~~~~~~--~C~~C~~~I~~--~~v~a~~~~wH~~CF~C~~C~~~   50 (81)
T 1v6g_A            2 SSGSSGLDYQRLYGT--RCFSCDQFIEG--EVVSALGKTYHPDCFVCAVCRLP   50 (81)
T ss_dssp             CCCCCCSCGGGSCCC--BCTTTCCBCCS--CCEEETTEEECTTTSSCSSSCCC
T ss_pred             CCCcchHHHHhHhCC--cCccccCEecc--ceEEECCceeCccCCccccCCCC
Confidence            358999999999999  99999999985  68999999999999999999864

>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

Probab=99.47  E-value=5.6e-15  Score=87.41  Aligned_cols=50  Identities=26%  Similarity=0.498  Sum_probs=45.8

Q ss_pred             CCccccHhhHHHHhCCCccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284           86 ANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        86 ~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      ++++||+.||.+++++  +|..|+++|.+  ..|.++++.||++||+|..|+++
T Consensus         1 gg~~yC~~cy~~~~~~--~C~~C~~~I~~--~~v~a~~~~~H~~CF~C~~C~~~   50 (80)
T 2cuq_A            1 GSSGSSGPCYENKFAP--RCARCSKTLTQ--GGVTYRDQPWHRECLVCTGCQTP   50 (80)
T ss_dssp             CCCCSCCCCCCCCSSC--CCTTTCCCCCS--CCEESSSSEECTTTCBCSSSCCB
T ss_pred             CCcEEcHHHHccccCC--cCCCCCCEecC--cEEEECCchhhhhhCCcccCCCc
Confidence            4789999999999998  99999999987  57899999999999999999863

>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

Probab=99.47  E-value=6.2e-15  Score=87.24  Aligned_cols=50  Identities=26%  Similarity=0.654  Sum_probs=45.8

Q ss_pred             CCccccHhhHHHHhCCCccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284           86 ANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        86 ~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      ++++||+.||.++|++  +|.+|+++|.+  .+|.++++.||++||+|..|+++
T Consensus         1 gg~~yC~~~y~~~~~~--~C~~C~~~I~~--~~v~a~~~~~H~~CF~C~~C~~~   50 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFSP--KCGGCNRPVLE--NYLSAMDTVWHPECFVCGDCFTS   50 (80)
T ss_dssp             CCCCCCCCCCCCCCSC--BCTTTCCBCCS--SCEEETTEEECTTTCBCSSSCCB
T ss_pred             CCCccchhHHhhhcCC--ccccCCCeecc--eeEEECCCeEecCcCChhhCCCC
Confidence            3689999999999998  99999999987  67899999999999999999863

>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}

Probab=99.46  E-value=5.5e-14  Score=82.51  Aligned_cols=58  Identities=22%  Similarity=0.566  Sum_probs=51.9

Q ss_pred             CCccccccccccc----ceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHH
Q psy284           38 PQECAGCGKHITD----RFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLR   97 (139)
Q Consensus        38 ~~~C~~C~~~i~~----~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~   97 (139)
                      .++|.+|+++|.+    .+.+.++++.||++||+|..|+.+|  .+..|+.+++++||..||.+
T Consensus        15 ~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L--~~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A           15 AKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNL--ANKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBC--TTSCCCEETTEECCHHHHHH
T ss_pred             CccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCC--CCCccEeECCEEEChHHhcc
Confidence            5789999999995    4678999999999999999999999  45678899999999999975

>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

Probab=99.45  E-value=7.3e-15  Score=87.14  Aligned_cols=49  Identities=35%  Similarity=0.689  Sum_probs=45.2

Q ss_pred             CccccHhhHHHHhCCCccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284           87 NLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        87 ~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +.+||+.||.++|++  +|..|+++|.+  .+|.++++.||++||+|..|+++
T Consensus         2 ~~~yC~~~y~~~~~~--~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~   50 (81)
T 1x6a_A            2 SSGSSGKDYWGKFGE--FCHGCSLLMTG--PFMVAGEFKYHPECFACMSCKVI   50 (81)
T ss_dssp             CCCCCCCCSSCCSSC--BCTTTCCBCCS--CCBCCTTCCBCTTSCBCTTTCCB
T ss_pred             CCccchhHHhhhcCC--cCccCCCCcCc--eEEEECCceeccccCCccCCCCc
Confidence            578999999999999  99999999984  78999999999999999999863

>2iyb_E Testin, TESS, TES; LIM domain, SH3-binding, tumour supressor LIM domain EVH1 DO cell motility, phosphorylation, cytoskeleton; 2.35A {Homo sapiens}

Probab=99.45  E-value=5.6e-14  Score=79.96  Aligned_cols=59  Identities=24%  Similarity=0.663  Sum_probs=51.7

Q ss_pred             CCccccccccccc-ceeeeecCcccc--ccCcccccCCCCcccCCCeeEeeCCcccc-HhhHHHH
Q psy284           38 PQECAGCGKHITD-RFLLKALDMYWH--EDCLKCGCCDCRLGEVGSTLYTKANLILC-KRDYLRL   98 (139)
Q Consensus        38 ~~~C~~C~~~i~~-~~~~~~~~~~~H--~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C-~~cy~~~   98 (139)
                      .++|.+|+++|.+ .+.+.++++.||  ++||+|..|+.+|  .+..|+.+++++|| .+||.++
T Consensus         2 a~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L--~~~~f~~~~g~~yC~~~C~~k~   64 (65)
T 2iyb_E            2 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL--IGQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBC--TTSCCEEETTEEESSHHHHHTT
T ss_pred             cCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcC--CCCceEEECCEEecCHHHhhhh
Confidence            3589999999996 357899999999  9999999999999  56679999999999 8888653

>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

Probab=99.44  E-value=1.8e-14  Score=85.47  Aligned_cols=48  Identities=29%  Similarity=0.559  Sum_probs=44.1

Q ss_pred             CCccccHhhHHHHhCCCccccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284           86 ANLILCKRDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus        86 ~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      ++++||+.||. ++++  +|..|+++|.+  .+|.++++.||++||+|..|++
T Consensus         2 ~g~~yC~~~y~-~~~~--~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~   49 (81)
T 2dlo_A            2 SSGSSGEGCYV-ATLE--KCATCSQPILD--RILRAMGKAYHPGCFTCVVCHR   49 (81)
T ss_dssp             CCCCCCCCCCC-SSCC--BCTTTCCBCCS--CCEEETTEEECTTTCBCSSSCC
T ss_pred             cCCEECHHHhh-cCCC--ccccCCCeecc--eeEEECCccccHHhcCcccCCC
Confidence            57899999998 6777  99999999985  6899999999999999999986

>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

Probab=99.28  E-value=2.1e-12  Score=88.01  Aligned_cols=91  Identities=16%  Similarity=0.292  Sum_probs=64.8

Q ss_pred             cccccccccccc-eeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCC----C
Q psy284           40 ECAGCGKHITDR-FLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIP----A  114 (139)
Q Consensus        40 ~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~----~  114 (139)
                      +|..|+++|... .++.++++.||+.||+|..|++.|. .+..|+..++++||..||.+++++  +|...+....    .
T Consensus        71 ~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~-~g~~f~~~~g~~yC~~c~~~~~~~--~~~~~g~~~~~~~~~  147 (188)
T 1rut_X           71 ACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLV-PGDRFHYINGSLFCEHDRPTALIN--GHLNSGGSGGSGGSG  147 (188)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCC-TTCEEEEETTEEEEGGGCCTTTC------------------
T ss_pred             ccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCC-CCCeEEEECCeEECHHHHHHHhcc--cccccCCCCcccccC
Confidence            799999999974 4678999999999999999999995 345788999999999999999988  8877765210    1


Q ss_pred             CceE----EEeCCcccccccccc
Q psy284          115 FEMV----MRARNNVYHLECFAC  133 (139)
Q Consensus       115 ~~~~----~~~~~~~~H~~Cf~C  133 (139)
                      .+..    ...++..||++..+.
T Consensus       148 ~~v~vvgep~l~g~~~~~~~~r~  170 (188)
T 1rut_X          148 GDVMVVGEPTLMGGEFGDEDERL  170 (188)
T ss_dssp             CCCEECCCCEETTCCCCCTTEEE
T ss_pred             CcccccCCCcccCCCCCCCCCce
Confidence            1111    246778888887764

>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

Probab=99.28  E-value=2.6e-12  Score=76.03  Aligned_cols=62  Identities=23%  Similarity=0.514  Sum_probs=49.3

Q ss_pred             CCcccccccccccceeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCC
Q psy284           38 PQECAGCGKHITDRFLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGS  101 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~  101 (139)
                      .++|..|+++|.+. .+.++++.||++||+|..|+.+|. .+..+...++.+||..||.++++.
T Consensus        15 ~~~C~~C~~~I~~~-~v~a~~~~wH~~CF~C~~C~~~L~-~~~~~~~~~~~~~C~~C~~~~~~~   76 (81)
T 1v6g_A           15 GTRCFSCDQFIEGE-VVSALGKTYHPDCFVCAVCRLPFP-PGDRVTFNGKECMCQKCSLPVSVS   76 (81)
T ss_dssp             CCBCTTTCCBCCSC-CEEETTEEECTTTSSCSSSCCCCC-SSSCEEEETTEEEEHHHHSCCSSC
T ss_pred             CCcCccccCEeccc-eEEECCceeCccCCccccCCCCCC-CCCEEEeCCCCEEChhhhcccCCC
Confidence            45899999999964 789999999999999999999995 233344445457999999766543

>2xjy_A Rhombotin-2; oncoprotein, T-cell leukemia, proto-oncogene, transcription, developmental protein; 2.40A {Homo sapiens} PDB: 2xjz_A

Probab=99.22  E-value=1.1e-11  Score=79.72  Aligned_cols=61  Identities=26%  Similarity=0.580  Sum_probs=54.1

Q ss_pred             cccccccccccc-eeeeecCccccccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCC
Q psy284           40 ECAGCGKHITDR-FLLKALDMYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGS  101 (139)
Q Consensus        40 ~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~  101 (139)
                      +|..|+++|.+. .++.++++.||++||+|..|++.|. .+..|+..++++||..||.++|++
T Consensus        68 ~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~-~g~~f~~~~~~~~C~~c~~~~~~~  129 (131)
T 2xjy_A           68 LCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFC-VGDRYLLINSDIVCEQDIYEWTKI  129 (131)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCC-TTCEEEEETTEEEEGGGHHHHHHH
T ss_pred             ChhhcCCccCccceeEeeCCceECccCcccCCCCCCCC-CCCEEEEECCEEEcHHHHHHHhhc
Confidence            899999999874 4678999999999999999999995 356789999999999999998864

>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

Probab=99.17  E-value=4.1e-11  Score=80.22  Aligned_cols=88  Identities=24%  Similarity=0.386  Sum_probs=63.5

Q ss_pred             CCcccccccccccce-eeeecCccccccCcccccCCCCcccCCCeeE-eeCCccccHhhHHHHhCCCccc--cccCCCCC
Q psy284           38 PQECAGCGKHITDRF-LLKALDMYWHEDCLKCGCCDCRLGEVGSTLY-TKANLILCKRDYLRLFGSTGYC--AACSKVIP  113 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~~~C~~cy~~~~~~~~~C--~~C~~~I~  113 (139)
                      .++|..|+++|.+.+ ++.+++..||.+||+|..|+..|. .+..++ ..++++||..||.+.+..  .+  .+...+. 
T Consensus        65 ~~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~-~g~~f~~~~~g~~~C~~c~~~~~~~--~~~~~~~~rpr-  140 (169)
T 2rgt_A           65 GTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLA-TGDEFYLMEDSRLVCKADYETAKQG--GSGGSGGSGGG-  140 (169)
T ss_dssp             SCBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCC-TTCEEEECTTSCEEEHHHHHHHHHC--C-----------
T ss_pred             cccccccccccCCCcEEEEcCCceEeeCCCcCCCCCCCCC-CCCceEEccCCeEECHHHHHHHhhc--cCCCCCCcCCC-
Confidence            358999999998853 467899999999999999999995 245565 468899999999988765  33  2333332 


Q ss_pred             CCceEEEeCCccccccccc
Q psy284          114 AFEMVMRARNNVYHLECFA  132 (139)
Q Consensus       114 ~~~~~~~~~~~~~H~~Cf~  132 (139)
                         ..+.+....+|...|.
T Consensus       141 ---t~~~~~q~~~l~~~f~  156 (169)
T 2rgt_A          141 ---TPMVAASPERHDGGLQ  156 (169)
T ss_dssp             ---EEEECCCCEECCSSCC
T ss_pred             ---CcccHHHHHHHHHHHh
Confidence               3566777777777664

>2xqn_T Testin, TESS; metal-binding protein, cytoskeleton, focal adhesion, acrosom; 2.62A {Homo sapiens}

Probab=99.15  E-value=3.7e-11  Score=76.67  Aligned_cols=60  Identities=22%  Similarity=0.674  Sum_probs=52.9

Q ss_pred             CCcccccccccccc-eeeeecCcccc--ccCcccccCCCCcccCCCeeEeeCCccccHhhHHHHh
Q psy284           38 PQECAGCGKHITDR-FLLKALDMYWH--EDCLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLF   99 (139)
Q Consensus        38 ~~~C~~C~~~i~~~-~~~~~~~~~~H--~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~   99 (139)
                      .++|..|+++|.+. ..+.++++.||  ++||+|..|+++|  .+..|+..++++||..+|.++|
T Consensus        63 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l--~~~~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           63 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL--IGQKFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             CCBCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBC--TTSEEEEETTEEESSHHHHHSC
T ss_pred             CccCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCCCCcc--CCCeeEeECCEEcchHHhhhhc
Confidence            46899999999973 56889999999  9999999999999  4677889999999998887765

>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

Probab=99.14  E-value=2e-11  Score=70.48  Aligned_cols=40  Identities=28%  Similarity=0.565  Sum_probs=35.9

Q ss_pred             HhCCCccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284           98 LFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        98 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|++  +|..|+++|.+.+.+|.++++.||++||+|..|+++
T Consensus         3 ~~~~--~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~   42 (72)
T 1x4k_A            3 SGSS--GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQP   42 (72)
T ss_dssp             SCCC--CBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCC
T ss_pred             ccCC--CCccCCCcccCCceEEEECcCeecccCCcccccCCc
Confidence            4666  999999999986789999999999999999999863

>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

Probab=99.11  E-value=3.2e-11  Score=70.45  Aligned_cols=40  Identities=33%  Similarity=0.600  Sum_probs=35.3

Q ss_pred             HhCCCccccccCCCCCC--CceEEEeCCccccccccccccCCCC
Q psy284           98 LFGSTGYCAACSKVIPA--FEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        98 ~~~~~~~C~~C~~~I~~--~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|++  +|..|+++|.+  .+.+|.++++.||++||+|..|+++
T Consensus         3 ~~~~--~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~   44 (76)
T 1x68_A            3 SGSS--GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVS   44 (76)
T ss_dssp             TCCC--CCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCB
T ss_pred             ccCC--CCccCCCcccCCCCceeEEECCcccCcccCChhhCCCc
Confidence            5667  99999999986  5578999999999999999999863

>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

Probab=99.09  E-value=2.5e-11  Score=70.43  Aligned_cols=38  Identities=32%  Similarity=0.620  Sum_probs=33.9

Q ss_pred             HhCCCccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284           98 LFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        98 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|++  +|.+|+++|.+  .+|.++++.||++||+|..|+++
T Consensus         3 ~~~~--~C~~C~~~I~~--~~v~a~~~~wH~~CF~C~~C~~~   40 (73)
T 1wig_A            3 SGSS--GCDSCEKYITG--RVLEAGEKHYHPSCALCVRCGQM   40 (73)
T ss_dssp             CSCC--SCSSSCCCCSS--CCBCCSSCCBCTTTSCCSSSCCC
T ss_pred             cCcC--CcccCCCEecC--eeEEeCCCCCCCCcCEeCCCCCC
Confidence            3566  99999999987  78899999999999999999863

>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

Probab=99.08  E-value=3e-11  Score=69.60  Aligned_cols=40  Identities=25%  Similarity=0.673  Sum_probs=35.5

Q ss_pred             HhCCCccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284           98 LFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        98 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      .+++  +|.+|+++|.+.+.++.+.++.||++||+|..|+++
T Consensus         9 ~~~~--~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~   48 (72)
T 3f6q_B            9 SASA--TCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQ   48 (72)
T ss_dssp             CTTC--BCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCC
T ss_pred             cCCc--cchhcCccccCCceEEEeCcCeeCcCCCcccCCCCC
Confidence            3455  999999999987778899999999999999999864

>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

Probab=99.07  E-value=3.7e-11  Score=69.31  Aligned_cols=40  Identities=23%  Similarity=0.513  Sum_probs=35.3

Q ss_pred             HhCCCccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284           98 LFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        98 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      ++++  +|..|+++|.+.+.+|.++++.||++||+|..|+++
T Consensus         3 ~~~~--~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~   42 (72)
T 1wyh_A            3 SGSS--GCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQP   42 (72)
T ss_dssp             CCCC--BCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCB
T ss_pred             ccCC--CCccCCCccccCccEEEECccccCcccCeECCCCCc
Confidence            4566  999999999976689999999999999999999863

>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

Probab=99.06  E-value=7e-11  Score=68.17  Aligned_cols=36  Identities=25%  Similarity=0.665  Sum_probs=33.2

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|.+|+++|.+.+.+|.++++.||++||+|..|+++
T Consensus         7 ~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~   42 (72)
T 1x61_A            7 GCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQ   42 (72)
T ss_dssp             CCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCB
T ss_pred             CCccCCCccCCCceEEEECCCeEcccCCcccccCCc
Confidence            999999999976679999999999999999999863

>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

Probab=99.06  E-value=6.4e-11  Score=68.35  Aligned_cols=36  Identities=25%  Similarity=0.671  Sum_probs=32.8

Q ss_pred             cccccCCCCCC--CceEEEeCCccccccccccccCCCC
Q psy284          104 YCAACSKVIPA--FEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       104 ~C~~C~~~I~~--~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|.+|+++|.+  .+.+|.++++.||++||+|..|+++
T Consensus         7 ~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~   44 (72)
T 1x4l_A            7 GCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLS   44 (72)
T ss_dssp             SBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCB
T ss_pred             CCcCCCccccCCCCcceEEECCcccCcccCEeccCCCc
Confidence            99999999986  5678999999999999999999863

>2iyb_E Testin, TESS, TES; LIM domain, SH3-binding, tumour supressor LIM domain EVH1 DO cell motility, phosphorylation, cytoskeleton; 2.35A {Homo sapiens}

Probab=99.03  E-value=7.3e-11  Score=66.85  Aligned_cols=36  Identities=28%  Similarity=0.618  Sum_probs=32.8

Q ss_pred             cccccCCCCCCCceEEEeCCcccc--ccccccccCCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYH--LECFACQQCNHR  139 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H--~~Cf~C~~C~~~  139 (139)
                      +|.+|+++|.+.+..|.++++.||  ++||+|+.|+++
T Consensus         4 ~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~   41 (65)
T 2iyb_E            4 VCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKC   41 (65)
T ss_dssp             ECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCB
T ss_pred             CCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCc
Confidence            899999999865579999999999  999999999863

>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

Probab=99.02  E-value=7.7e-11  Score=70.99  Aligned_cols=40  Identities=28%  Similarity=0.521  Sum_probs=34.8

Q ss_pred             HHHHhCCCccccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284           95 YLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus        95 y~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      +...+++  +|..|+++|.+  .+|.++++.||++||+|..|++
T Consensus        20 ~~~~~~~--~C~~C~~~I~~--~~v~a~~~~~H~~CF~C~~C~~   59 (90)
T 2dar_A           20 PAGKRTP--MCAHCNQVIRG--PFLVALGKSWHPEEFNCAHCKN   59 (90)
T ss_dssp             CTTTCCC--BBSSSCCBCCS--CEEEETTEEECTTTCBCSSSCC
T ss_pred             CCCCCCC--CCccCCCEecc--eEEEECCccccccCCccCCCCC
Confidence            3455666  99999999965  7899999999999999999986

>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

Probab=99.00  E-value=7.3e-11  Score=66.98  Aligned_cols=36  Identities=31%  Similarity=0.675  Sum_probs=32.5

Q ss_pred             hCCCccccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284           99 FGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus        99 ~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      +++  +|.+|+++|.+  .+|.++++.||++||+|..|++
T Consensus         4 ~~~--~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~   39 (66)
T 1nyp_A            4 GVP--ICGACRRPIEG--RVVNAMGKQWHVEHFVCAKCEK   39 (66)
T ss_dssp             CCC--EETTTTEECCS--CEECCTTSBEETTTCBCTTTCC
T ss_pred             CCC--CCcccCCEecc--eEEEECccccccCcCEECCCCC
Confidence            455  99999999984  6899999999999999999986

>1g47_A Pinch protein; LIM domain, Zn finger, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.00  E-value=1.9e-10  Score=67.15  Aligned_cols=36  Identities=28%  Similarity=0.774  Sum_probs=33.3

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|.+|+++|.+.+.++.+.++.||++||+|..|+++
T Consensus        13 ~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~   48 (77)
T 1g47_A           13 TCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQ   48 (77)
T ss_dssp             BCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCC
T ss_pred             CchhcCCccCCCceEEEeCccEeccccCeECCCCCC
Confidence            999999999876789999999999999999999864

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus}

Probab=98.98  E-value=4.3e-10  Score=76.09  Aligned_cols=60  Identities=28%  Similarity=0.653  Sum_probs=49.7

Q ss_pred             CCcccccccccccce-eeeecCccccccCcccccCCCCcccCCCeeE-eeCCccccHhhHHHH
Q psy284           38 PQECAGCGKHITDRF-LLKALDMYWHEDCLKCGCCDCRLGEVGSTLY-TKANLILCKRDYLRL   98 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~~~C~~cy~~~   98 (139)
                      .++|..|+++|.+.+ ++.+.+..||+.||+|..|++.|. .+..|+ ..++++||..||.+.
T Consensus       119 ~~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~-~g~~f~~~~~g~~yC~~cy~~~  180 (182)
T 2jtn_A          119 GTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLA-TGDEFYLMEDSRLVCKADYETA  180 (182)
T ss_dssp             SCCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTCCCCC-TTCEEEECTTSCEECHHHHHHH
T ss_pred             ccccccCCCccCCCceEEecCCCCEEeCCCcCCCCCCCCC-CCCceEEccCCEEECHHHHHHh
Confidence            468999999998753 457899999999999999999995 345555 468899999999864

>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

Probab=98.96  E-value=3e-10  Score=65.15  Aligned_cols=33  Identities=39%  Similarity=0.893  Sum_probs=31.0

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      +|..|+++|.+  .+|.++++.||++||+|..|++
T Consensus         7 ~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~   39 (70)
T 2d8x_A            7 GCHQCGEFIIG--RVIKAMNNSWHPECFRCDLCQE   39 (70)
T ss_dssp             BCSSSCCBCCS--CCEEETTEEECTTTSBCSSSCC
T ss_pred             cCccCCCEecc--eEEEECcccccccCCEeCCCCC
Confidence            89999999986  6899999999999999999986

>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

Probab=98.95  E-value=2.8e-10  Score=65.21  Aligned_cols=37  Identities=32%  Similarity=0.674  Sum_probs=32.6

Q ss_pred             hCCCccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284           99 FGSTGYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus        99 ~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +++  +|..|+++|.+  ..|.++++.||++||+|..|+++
T Consensus         4 ~~~--~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~   40 (70)
T 2d8z_A            4 GSS--GCVQCKKPITT--GGVTYREQPWHKECFVCTACRKQ   40 (70)
T ss_dssp             CCC--BCSSSCCBCCS--SEEESSSSEEETTTSBCSSSCCB
T ss_pred             CCC--CCcccCCeecc--ceEEECccccCCCCCccCCCCCc
Confidence            445  99999999986  57999999999999999999863

>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

Probab=98.94  E-value=3.2e-10  Score=64.84  Aligned_cols=34  Identities=26%  Similarity=0.783  Sum_probs=31.1

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|..|+++|.+  ..|.++++.||++||+|..|+++
T Consensus         7 ~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~   40 (69)
T 2cur_A            7 GCVKCNKAITS--GGITYQDQPWHADCFVCVTCSKK   40 (69)
T ss_dssp             CCSSSCCCCCT--TCEEETTEEECTTTTBCTTTCCB
T ss_pred             CCcccCCEeCc--ceEEECccccccCcCEECCCCCC
Confidence            99999999986  57899999999999999999863

>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

Probab=98.92  E-value=4.9e-10  Score=65.80  Aligned_cols=34  Identities=26%  Similarity=0.769  Sum_probs=31.5

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|..|+++|.+  .+|.++++.||++||+|..|+++
T Consensus        17 ~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~   50 (79)
T 1x62_A           17 MCDKCGTGIVG--VFVKLRDRHRHPECYVCTDCGTN   50 (79)
T ss_dssp             CCSSSCCCCCS--SCEECSSCEECTTTTSCSSSCCC
T ss_pred             ccccCCCCccC--cEEEECcceeCcCcCeeCCCCCC
Confidence            89999999987  58999999999999999999864

>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

Probab=98.91  E-value=6.1e-10  Score=64.86  Aligned_cols=35  Identities=20%  Similarity=0.567  Sum_probs=31.2

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|..|+++|.+. ..|.++++.||++||+|..|+++
T Consensus        11 ~C~~C~~~I~~~-~~v~a~~~~~H~~CF~C~~C~~~   45 (76)
T 2cu8_A           11 KCPKCDKTVYFA-EKVSSLGKDWHKFCLKCERCSKT   45 (76)
T ss_dssp             BCTTTCCBCCTT-TEEEETTEEEETTTCBCSSSCCB
T ss_pred             CCcCCCCEeECC-eEEEECCeEeeCCCCCCCCCCCc
Confidence            999999999864 46789999999999999999863

>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

Probab=98.88  E-value=9.4e-10  Score=64.78  Aligned_cols=35  Identities=31%  Similarity=0.724  Sum_probs=31.2

Q ss_pred             ccccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284          103 GYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       103 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      ++|..|+++|... .+|.++++.||++||+|..|++
T Consensus        16 ~~C~~C~~~I~~~-~~v~a~~~~wH~~CF~C~~C~~   50 (80)
T 2dj7_A           16 SHCAGCKEEIKHG-QSLLALDKQWHVSCFKCQTCSV   50 (80)
T ss_dssp             SCCTTTCCCCSSS-CCEEETTEEECTTTCBCSSSCC
T ss_pred             CCCcCcCCeeCCC-eEEEECCcccccccCCcCcCCC
Confidence            3899999999853 5788999999999999999976

>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

Probab=98.87  E-value=5.8e-10  Score=65.52  Aligned_cols=33  Identities=27%  Similarity=0.745  Sum_probs=30.8

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      +|..|+++|.+  .+|.++++.||++||+|..|++
T Consensus        17 ~C~~C~~~I~~--~~v~a~~~~~H~~CF~C~~C~~   49 (79)
T 2cor_A           17 ICQKCHAIIDE--QPLIFKNDPYHPDHFNCANCGK   49 (79)
T ss_dssp             BCTTTCCBCCS--CCCCCSSSCCCTTTSBCSSSCC
T ss_pred             CCccCCCEecc--eEEEECcceeCCCCCEeCCCCC
Confidence            89999999985  7789999999999999999986

>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

Probab=98.85  E-value=1.2e-09  Score=63.65  Aligned_cols=35  Identities=20%  Similarity=0.573  Sum_probs=31.0

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|.+|+++|... ..|.++++.||++||+|..|+++
T Consensus         2 ~C~~C~~~I~~~-~~v~a~~~~~H~~CF~C~~C~~~   36 (76)
T 1iml_A            2 KCPKCDKEVYFA-ERVTSLGKDWHRPCLKCEKCGKT   36 (76)
T ss_dssp             BCTTTSSBCCGG-GEEEETTEEEETTTCBCTTTCCB
T ss_pred             cCCCCCCEEECc-eEEEECCccccCCCCCccccCcc
Confidence            899999999853 57899999999999999999863

>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

Probab=98.85  E-value=1.2e-09  Score=65.50  Aligned_cols=34  Identities=38%  Similarity=0.864  Sum_probs=31.4

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|..|+++|.+  .+|.++++.||++||+|..|++.
T Consensus        27 ~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~   60 (89)
T 1x64_A           27 LCDKCGSGIVG--AVVKARDKYRHPECFVCADCNLN   60 (89)
T ss_dssp             BCTTTCCBCCS--CCEESSSCEECTTTCCCSSSCCC
T ss_pred             CcccCCCEecc--cEEEECCceECccCCEecCCCCC
Confidence            89999999987  68999999999999999999863

>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

Probab=98.84  E-value=1.2e-09  Score=64.64  Aligned_cols=36  Identities=25%  Similarity=0.751  Sum_probs=31.0

Q ss_pred             ccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          103 GYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       103 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      .+|.+|+++|...+ .|.++++.||++||+|..|+++
T Consensus        16 ~~C~~C~~~I~~~e-~v~a~~~~wH~~CF~C~~C~~~   51 (82)
T 2co8_A           16 DLCALCGEHLYVLE-RLCVNGHFFHRSCFRCHTCEAT   51 (82)
T ss_dssp             CBCSSSCCBCCTTT-BCCBTTBCCBTTTCBCSSSCCB
T ss_pred             CCCcccCCCcccce-EEEECCCeeCCCcCEEcCCCCC
Confidence            38999999997644 4569999999999999999863

>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}

Probab=98.82  E-value=1.8e-09  Score=68.60  Aligned_cols=34  Identities=26%  Similarity=0.765  Sum_probs=31.1

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      +|.+|+++|.+ ..+|.++++.||++||+|..|++
T Consensus        63 ~C~~C~~~I~~-~~~v~a~~~~wH~~CF~C~~C~~   96 (123)
T 2l4z_A           63 RCAGCGGKIAD-RFLLYAMDSYWHSRCLKCSSCQA   96 (123)
T ss_dssp             BBSSSSSBCCS-SSEEEETTEEEETTTSBCTTTCC
T ss_pred             cCcCCCCCcCC-cEEEEeCCcEEcccccCcCcCCC
Confidence            99999999987 34789999999999999999986

>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

Probab=98.81  E-value=3e-09  Score=66.68  Aligned_cols=36  Identities=25%  Similarity=0.719  Sum_probs=32.0

Q ss_pred             ccccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          103 GYCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       103 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      ++|.+|+++|.+ ..++.++++.||++||+|+.|+++
T Consensus         4 ~~C~~C~~~I~~-~~~~~a~~~~wH~~CF~C~~C~~~   39 (114)
T 1j2o_A            4 LTCGGCQQNIGD-RYFLKAIDQYWHEDCLSCDLCGCR   39 (114)
T ss_dssp             BCBSSSCSCBCS-SEEEECSSSEECTTTCCCSSSCSC
T ss_pred             CCCcCCCCeeCC-cEEEEECchhHHHhcCcccccCCc
Confidence            489999999986 348899999999999999999864

>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

Probab=98.81  E-value=2.7e-09  Score=65.32  Aligned_cols=36  Identities=33%  Similarity=0.692  Sum_probs=32.7

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|..|+++|.+.+.+|.++++.||++||+|..|+++
T Consensus         7 ~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~   42 (101)
T 2cup_A            7 GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHP   42 (101)
T ss_dssp             BCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCC
T ss_pred             cCcccCCcccCCceEEEECccChhhcCCcccccCCC
Confidence            999999999854589999999999999999999864

>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

Probab=98.78  E-value=2.3e-09  Score=63.14  Aligned_cols=34  Identities=24%  Similarity=0.662  Sum_probs=30.9

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      +|..|+++|... ..+.+.++.||++||+|..|++
T Consensus         9 ~C~~C~~~I~~~-~~~~a~~~~~H~~CF~C~~C~~   42 (81)
T 1a7i_A            9 KCGACGRTVYHA-EEVQCDGRSFHRCCFLCMVCRK   42 (81)
T ss_dssp             BCSSSCCBCSST-TEEEETTEEEESSSEECSSSCC
T ss_pred             cCcCcCccccCc-eeEEeCCcccccccCccCCCCC
Confidence            999999999754 4789999999999999999986

>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

Probab=98.72  E-value=6.6e-09  Score=62.51  Aligned_cols=34  Identities=35%  Similarity=0.928  Sum_probs=30.9

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNH  138 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~  138 (139)
                      +|..|+++|.+.+ .|.++++.||++||+|..|++
T Consensus        17 ~C~~C~~~I~~~~-~v~a~~~~~H~~CF~C~~C~~   50 (91)
T 2d8y_A           17 TCVECQKTVYPME-RLLANQQVFHISCFRCSYCNN   50 (91)
T ss_dssp             BCTTTCCBCCTTS-EEECSSSEEETTTCBCTTTCC
T ss_pred             cCccCCCccCCce-eEEECCCEECCCCCeeCCCCC
Confidence            8999999998754 578999999999999999976

>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

Probab=98.69  E-value=3.9e-09  Score=66.91  Aligned_cols=35  Identities=26%  Similarity=0.723  Sum_probs=31.3

Q ss_pred             cccccCCCCCCCceEEEeCCccccccccccccCCCC
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECFACQQCNHR  139 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~  139 (139)
                      +|..|+++|.+. .+|.++++.||++||+|..|+++
T Consensus         7 ~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~   41 (122)
T 1m3v_A            7 RCAGCGGKIADR-FLLYAMDSYWHSRCLKCSSCQAQ   41 (122)
T ss_dssp             CBSSSSSCCCSS-CCEEETTEEECHHHHCCSSSCCC
T ss_pred             CCcccCCEeCCc-EEEEECCceeHhhCCCcCCCCCc
Confidence            999999999873 36889999999999999999864

>1zfo_A LAsp-1; LIM domain, zinc-finger, metal-binding protein; NMR {Sus scrofa} SCOP: g.39.1.4

Probab=98.26  E-value=3.3e-07  Score=43.96  Aligned_cols=29  Identities=34%  Similarity=0.875  Sum_probs=26.6

Q ss_pred             CCcccccccccccceeeeecCccccccCc
Q psy284           38 PQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      .++|..|++.++..+.+.++++.||..||
T Consensus         3 ~~~C~~C~k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            3 NPNCARCGKIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             CCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCcCCccCCEEecceeEEECCeEecccCC
Confidence            45899999999998889999999999997

>1zfo_A LAsp-1; LIM domain, zinc-finger, metal-binding protein; NMR {Sus scrofa} SCOP: g.39.1.4

Probab=98.09  E-value=7.7e-07  Score=42.63  Aligned_cols=27  Identities=30%  Similarity=0.739  Sum_probs=24.0

Q ss_pred             cccccCCCCCCCceEEEeCCcccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      +|..|++.+.+.| .+.+.|+.||..||
T Consensus         5 ~C~~C~k~Vy~~E-k~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            5 NCARCGKIVYPTE-KVNCLDKFWHKACF   31 (31)
T ss_dssp             BCSSSCSBCCGGG-CCCSSSSCCCGGGC
T ss_pred             cCCccCCEEecce-eEEECCeEecccCC
Confidence            8999999999875 55689999999998

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=92.29  E-value=0.11  Score=29.82  Aligned_cols=35  Identities=23%  Similarity=0.598  Sum_probs=29.2

Q ss_pred             CCCCCcccccccccccceeeeecCccccccCcccc
Q psy284           35 AQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCG   69 (139)
Q Consensus        35 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~   69 (139)
                      ....-.|..|.+.+.+...+.--...-|+-||-|.
T Consensus        12 ~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCs   46 (93)
T 2cs3_A           12 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCS   46 (93)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHH
T ss_pred             CCCeeEeecchhhhccCceeeCCCccCCeeecccc
Confidence            45567899999999997667777888899999976

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=85.17  E-value=2.2  Score=23.62  Aligned_cols=47  Identities=4%  Similarity=0.133  Sum_probs=34.3

Q ss_pred             CcccccCCCCcccCCCeeEeeCCccccHhhHHHHhCC-CccccccCCCCCC
Q psy284           65 CLKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGS-TGYCAACSKVIPA  114 (139)
Q Consensus        65 Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~-~~~C~~C~~~I~~  114 (139)
                      -|.|..|...+.   ......-|..||..|..+.+.. ...|..|..++..
T Consensus         8 ~~~C~IC~~~~~---~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            8 YFRCPISLELMK---DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSCTTTSCCCS---SEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             cCCCCCcccccc---CCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            467888877663   2355678889999998766543 3479999999865

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=84.64  E-value=1.3  Score=24.64  Aligned_cols=11  Identities=27%  Similarity=0.815  Sum_probs=8.5

Q ss_pred             cccccCCCCCC
Q psy284          104 YCAACSKVIPA  114 (139)
Q Consensus       104 ~C~~C~~~I~~  114 (139)
                      .|..|...|..
T Consensus        54 ~CP~Cr~~~~~   64 (78)
T 2ect_A           54 SCPVCRKSLTG   64 (78)
T ss_dssp             SCTTTCCCCCC
T ss_pred             cCcCcCCccCC
Confidence            78888887765

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1

Probab=83.45  E-value=2.1  Score=21.85  Aligned_cols=27  Identities=15%  Similarity=0.204  Sum_probs=14.4

Q ss_pred             CCccccHhhHHHHhCCCccccccCCCC
Q psy284           86 ANLILCKRDYLRLFGSTGYCAACSKVI  112 (139)
Q Consensus        86 ~~~~~C~~cy~~~~~~~~~C~~C~~~I  112 (139)
                      -+..||..|..+.+.....|..|...|
T Consensus        27 C~H~f~~~Ci~~w~~~~~~CP~Cr~~~   53 (55)
T 1iym_A           27 CGHGFHAECVDMWLGSHSTCPLCRLTV   53 (55)
T ss_dssp             SCCEECTTHHHHTTTTCCSCSSSCCCS
T ss_pred             CCCcccHHHHHHHHHcCCcCcCCCCEe
Confidence            344455555544333333677777665

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=82.95  E-value=1.3  Score=24.30  Aligned_cols=46  Identities=22%  Similarity=0.418  Sum_probs=29.7

Q ss_pred             cccccCCCCcccCCCeeEe-eCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284           66 LKCGCCDCRLGEVGSTLYT-KANLILCKRDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        66 f~C~~C~~~l~~~~~~~~~-~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      +.|..|...+.  . .... .-+..||..|..+.+.....|..|...|..
T Consensus        16 ~~C~IC~~~~~--~-p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   62 (72)
T 2djb_A           16 ILCSICKGYLI--D-ATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQ   62 (72)
T ss_dssp             GSCTTTSSCCS--S-CEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCS
T ss_pred             CCCCCCChHHH--C-cCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCc
Confidence            56667766652  1 2333 667788888876544222389999998865

>2y43_A E3 ubiquitin-protein ligase RAD18; DNA repair, metal-binding, translesion synthesis, UB conjugation pathway; 1.80A {Homo sapiens}

Probab=80.87  E-value=1.6  Score=25.52  Aligned_cols=46  Identities=15%  Similarity=0.422  Sum_probs=32.6

Q ss_pred             cccccCCCCcccCCCeeEe-eCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284           66 LKCGCCDCRLGEVGSTLYT-KANLILCKRDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        66 f~C~~C~~~l~~~~~~~~~-~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      +.|..|...+.   ..... .-|..||..|..+.+.....|..|...+..
T Consensus        23 ~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   69 (99)
T 2y43_A           23 LRCGICFEYFN---IAMIIPQCSHNYCSLCIRKFLSYKTQCPTCCVTVTE   69 (99)
T ss_dssp             TBCTTTCSBCS---SEEECTTTCCEEEHHHHHHHHTTCCBCTTTCCBCCG
T ss_pred             CCcccCChhhC---CcCEECCCCCHhhHHHHHHHHHCCCCCCCCCCcCCh
Confidence            67777876663   23344 677889999987666544489999998865

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=80.55  E-value=2.6  Score=22.88  Aligned_cols=30  Identities=20%  Similarity=0.277  Sum_probs=18.2

Q ss_pred             eCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284           85 KANLILCKRDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        85 ~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      .-+..||..|..+.+.....|..|...|..
T Consensus        32 ~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   61 (71)
T 2d8t_A           32 PCKHVFCYLCVKGASWLGKRCALCRQEIPE   61 (71)
T ss_dssp             TTTEEEEHHHHHHCTTCSSBCSSSCCBCCH
T ss_pred             cCCCHHHHHHHHHHHHCCCcCcCcCchhCH
Confidence            445556666665544333378888887753

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=80.49  E-value=2.6  Score=26.31  Aligned_cols=46  Identities=17%  Similarity=0.275  Sum_probs=34.2

Q ss_pred             cccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284           66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      +.|..|...+.   ......-|..||..|..+.+.....|..|..+|..
T Consensus        54 ~~C~iC~~~~~---~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~   99 (138)
T 4ayc_A           54 LQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECPICRKDIKS   99 (138)
T ss_dssp             SBCTTTCSBCS---SEEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCCC
T ss_pred             CCCcccCcccC---CceECCCCCCccHHHHHHHHHcCCcCCCCCCcCCC
Confidence            56888877763   23556788899999987665544589999999864

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

ID	Length	Definition	E-value
Query	139
d1j2oa2	33	g.39.1.3 (A:31-63) Rhombotin-2 (Lmo2) {Mouse (Mus	8e-15
d1rutx2	34	g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus m	1e-14
d1rutx3	31	g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus	1e-12
d1rutx1	30	g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus m	1e-11
d1j2oa1	30	g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus m	6e-11
d2dj7a2	36	g.39.1.3 (A:8-43) Actin-binding LIM protein 3, abL	2e-04
d1x3ha1	35	g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [	0.001
d2dara2	45	g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, En	0.002

>d1j2oa2 g.39.1.3 (A:31-63) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]} Length = 33

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 61.8 bits (150), Expect = 8e-15
 Identities = 21/33 (63%), Positives = 22/33 (66%)

Query: 66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL 98
          L C  C CRLGEVG  LY K    LC+RDYLRL
Sbjct: 1  LSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL 33

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]} Length = 34

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 60.9 bits (148), Expect = 1e-14
 Identities = 18/34 (52%), Positives = 27/34 (79%)

Query: 67  KCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG 100
           KC  C  +LG++G++ YTK+ +ILC+ DY+RLFG
Sbjct: 1   KCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 34

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]} Length = 31

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 55.9 bits (135), Expect = 1e-12
 Identities = 19/31 (61%), Positives = 26/31 (83%)

Query: 101 STGYCAACSKVIPAFEMVMRARNNVYHLECF 131
           ++G C+AC + IPA E+VMRA+ NVYHL+CF
Sbjct: 1   NSGACSACGQSIPASELVMRAQGNVYHLKCF 31

>d1rutx1 g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]} Length = 30

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 53.2 bits (128), Expect = 1e-11
 Identities = 18/28 (64%), Positives = 20/28 (71%)

Query: 39 QECAGCGKHITDRFLLKALDMYWHEDCL 66
          + CAGCG  I DRFLL A+D YWH  CL
Sbjct: 3  KRCAGCGGKIADRFLLYAMDSYWHSRCL 30

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]} Length = 30

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 51.7 bits (124), Expect = 6e-11
 Identities = 16/25 (64%), Positives = 20/25 (80%)

Query: 41 CAGCGKHITDRFLLKALDMYWHEDC 65
          C GC ++I DR+ LKA+D YWHEDC
Sbjct: 6  CGGCQQNIGDRYFLKAIDQYWHEDC 30

>d2dj7a2 g.39.1.3 (A:8-43) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 34.8 bits (80), Expect = 2e-04
 Identities = 15/35 (42%), Positives = 17/35 (48%)

Query: 32 PNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCL 66
          P   +GP  CAGC + I     L ALD  WH  C 
Sbjct: 2  PIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCF 36

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.7 bits (75), Expect = 0.001
 Identities = 12/39 (30%), Positives = 21/39 (53%), Gaps = 4/39 (10%)

Query: 93  RDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECF 131
           +D+L +F     C  C++ +   E  + A + V+H ECF
Sbjct: 1   KDFLAMFSPK--CGGCNRPVL--ENYLSAMDTVWHPECF 35

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]} Length = 45

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 32.4 bits (74), Expect = 0.002
 Identities = 14/43 (32%), Positives = 20/43 (46%), Gaps = 5/43 (11%)

Query: 23 QGAQQTKAVPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDC 65
          Q A+    +P   + P  CA C + I   FL+ AL   WH + 
Sbjct: 7  QRAEH---IPAGKRTPM-CAHCNQVIRGPFLV-ALGKSWHPEE 44

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	139
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.45
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	99.12
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	99.04
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	99.01
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.98
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.97
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.83
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.83
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.76
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	98.71
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.7
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	98.69
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	98.65
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.63
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	98.59
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.57
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.51
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.48
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.47
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.44
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.43
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.41
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.38
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.38
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.35
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	98.32
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.3
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.3
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.28
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.27
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.27
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.27
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.25
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.22
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.17
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.15
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.14
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.13
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	98.12
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.09
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.07
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.07
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	98.06
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.01
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.99
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.97
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.94
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.93
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.92
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.91
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	97.9
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.87
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	97.84
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.83
d2co8a2	36	Nedd9 interacting protein with calponin homology,	97.8
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.78
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.78
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.77
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.77
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.73
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.72
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.71
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.67
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.63
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.63
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.62
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.6
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.49
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.49
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.48
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.48
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.47
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.44
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.37
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.35
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.3
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.19
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.11
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.11
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.02
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	96.92
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	96.87
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	96.76
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	96.63
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.43
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.08
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	95.99
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.81
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	95.73
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	95.64
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	95.26
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	95.05
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	94.95
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	94.92
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	93.81
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	93.22
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	91.91
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	90.17
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	90.17
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	88.22
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	87.28
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	86.63
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	86.58
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	86.16
d2co8a1	33	Nedd9 interacting protein with calponin homology,	84.0
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	83.86

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.45  E-value=2.7e-15  Score=73.03  Aligned_cols=34  Identities=32%  Similarity=0.826  Sum_probs=31.8

Q ss_pred             hHHHHhCCCccccccCCCCCCCceEEEeCCcccccccc
Q psy284           94 DYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus        94 cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      ||.++|++  +|.+|+++|.+  .+|+|+|++|||+||
T Consensus         2 DY~~~fap--kC~~C~~~I~g--~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           2 DFLAMFSP--KCGGCNRPVLE--NYLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCCCCSC--BCTTTCCBCCS--SCEEETTEEECTTTC
T ss_pred             cHHHHhCh--hhhhcCCcccc--hheeecCCccCcccC
Confidence            57789999  99999999987  899999999999998

>d1x63a1 g.39.1.3 (A:8-44) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.12  E-value=3.8e-12  Score=61.91  Aligned_cols=36  Identities=28%  Similarity=0.447  Sum_probs=33.5

Q ss_pred             hHHHHhCCCccccccCCCCCCCceEEEeCCcccccccc
Q psy284           94 DYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus        94 cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      ||.+.|++  +|.+|.++|.+.++.|.+.|+.||.+||
T Consensus         2 Cy~~~~a~--~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           2 CTTREDSP--KCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCSCCCSC--BCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             ccccccCc--ccccCCCccCCCCeEeEeCCccchhccC
Confidence            66778888  9999999999988999999999999998

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.04  E-value=5.1e-11  Score=59.71  Aligned_cols=26  Identities=35%  Similarity=0.617  Sum_probs=25.0

Q ss_pred             cccccCCCCCCCceEEEeCCcccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      .|..|+++|.+  .+|+|+|+.|||+||
T Consensus        20 ~C~~C~~pI~g--~~vtAlgk~WHPEhF   45 (45)
T d2dara2          20 MCAHCNQVIRG--PFLVALGKSWHPEEF   45 (45)
T ss_dssp             BBSSSCCBCCS--CEEEETTEEECTTTC
T ss_pred             eccccCCcccC--ceeeecCCccCcCCC
Confidence            89999999987  899999999999998

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.01  E-value=3.4e-11  Score=59.28  Aligned_cols=34  Identities=38%  Similarity=0.849  Sum_probs=31.8

Q ss_pred             hhHHHHhCCCccccccCCCCCCCceEEEeCCccccccc
Q psy284           93 RDYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLEC  130 (139)
Q Consensus        93 ~cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~C  130 (139)
                      .+|+++|+.  +|..|++.|++  .+|.|.+++|||+|
T Consensus         8 ~DYq~~fG~--~C~~C~~~ItG--~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1           8 LDYQRLYGT--RCFSCDQFIEG--EVVSALGKTYHPDC   41 (41)
T ss_dssp             SCGGGSCCC--BCTTTCCBCCS--CCEEETTEEECTTT
T ss_pred             ccHHHHhCc--ccccccCEeee--eeeEecCcccCCCC
Confidence            478999999  99999999987  89999999999998

>d2cuqa2 g.39.1.3 (A:8-42) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.98  E-value=2.7e-11  Score=57.12  Aligned_cols=34  Identities=32%  Similarity=0.610  Sum_probs=31.5

Q ss_pred             hHHHHhCCCccccccCCCCCCCceEEEeCCcccccccc
Q psy284           94 DYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus        94 cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      ||+++|++  +|..|+++|+.  ..|++.++.||.+||
T Consensus         2 CyE~kfa~--~C~~Ckk~It~--GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           2 CYENKFAP--RCARCSKTLTQ--GGVTYRDQPWHRECL   35 (35)
T ss_dssp             CCCCCSSC--CCTTTCCCCCS--CCEESSSSEECTTTC
T ss_pred             chHHHHHH--HHhhcCCcccc--CceeecCCcchhhhC
Confidence            78889999  99999999986  688999999999998

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.97  E-value=1.2e-10  Score=55.08  Aligned_cols=28  Identities=39%  Similarity=0.776  Sum_probs=25.8

Q ss_pred             CccccccCCCCCCCceEEEeCCcccccccc
Q psy284          102 TGYCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       102 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      .++|..|+++|+.  .+++|.|+.|||.||
T Consensus         8 lEkC~~C~~~I~d--riLrA~Gk~yHP~CF   35 (35)
T d2dloa1           8 LEKCATCSQPILD--RILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCBCTTTCCBCCS--CCEEETTEEECTTTC
T ss_pred             HHHHHHhchHHHH--HHHHHhCCCCCCCCC
Confidence            4599999999965  999999999999998

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.83  E-value=6.8e-10  Score=51.22  Aligned_cols=29  Identities=66%  Similarity=1.272  Sum_probs=27.9

Q ss_pred             ccccccCCCCCCCceEEEeCCcccccccc
Q psy284          103 GYCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       103 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      +.|.+|++.|.+.|.+++|.+..||.+||
T Consensus         3 g~Ca~C~~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEETTEEECGGGC
T ss_pred             cccccccCcCChhHhheecccceeeeccC
Confidence            48999999999999999999999999998

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.76  E-value=6e-10  Score=51.03  Aligned_cols=25  Identities=32%  Similarity=0.642  Sum_probs=23.5

Q ss_pred             cccccCCCCCCCceEEEeCCccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLEC  130 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~C  130 (139)
                      +|+.|.+||.+  +++.|+|+.||+++
T Consensus         7 ~C~~C~~PI~~--~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           7 ICGACRRPIEG--RVVNAMGKQWHVEH   31 (31)
T ss_dssp             EETTTTEECCS--CEECCTTSBEETTT
T ss_pred             chhhcCCchhh--hHhhhhccccCCCC
Confidence            99999999977  89999999999975

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.71  E-value=4.4e-10  Score=52.16  Aligned_cols=33  Identities=39%  Similarity=0.802  Sum_probs=30.4

Q ss_pred             hHHHHhCCCccccccCCCCCCCceEEEeCCccccccc
Q psy284           94 DYLRLFGSTGYCAACSKVIPAFEMVMRARNNVYHLEC  130 (139)
Q Consensus        94 cy~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~C  130 (139)
                      +|+.+|+.  .|.+|...|+|  .+|.|.+.+|||+|
T Consensus         2 dYw~kfge--~C~~C~~~itG--pvMvAG~~K~HPEC   34 (34)
T d1x6aa1           2 DYWGKFGE--FCHGCSLLMTG--PFMVAGEFKYHPEC   34 (34)
T ss_dssp             CSSCCSSC--BCTTTCCBCCS--CCBCCTTCCBCTTS
T ss_pred             cHHHHHHH--HhhhhHhhccc--ceeeecccccCCCC
Confidence            57888998  99999999987  89999999999998

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.70  E-value=3.8e-09  Score=50.74  Aligned_cols=34  Identities=21%  Similarity=0.480  Sum_probs=31.1

Q ss_pred             cccccCCCCcccCCCeeEeeCCccccHhhHHHHhCC
Q psy284           66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGS  101 (139)
Q Consensus        66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~  101 (139)
                      |+|..|+++++  +..|+.++|++||+.||.++|+|
T Consensus         1 F~C~~C~~~f~--~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFP--EGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCG--GGCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCC--CCCeEEECCEecChHhHHhhcCC
Confidence            78999999995  56799999999999999999987

>d1x4la1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.69  E-value=3.9e-09  Score=47.13  Aligned_cols=27  Identities=26%  Similarity=0.721  Sum_probs=24.3

Q ss_pred             ccccCCCCCCCc--eEEEeCCcccccccc
Q psy284          105 CAACSKVIPAFE--MVMRARNNVYHLECF  131 (139)
Q Consensus       105 C~~C~~~I~~~~--~~~~~~~~~~H~~Cf  131 (139)
                      |..|.+||++.+  .+|.+.++.||..||
T Consensus         1 C~~C~kPItg~gg~kyisFE~R~WH~~CF   29 (29)
T d1x4la1           1 CAGCTNPISGLGGTKYISFEERQWHNDCF   29 (29)
T ss_dssp             BTTTTBCCCCSSSCSCEECSSCEECTTTC
T ss_pred             CCccCCcccccCCceEEEeecccccccCC
Confidence            789999998754  599999999999998

>d1x68a1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.65  E-value=6.2e-09  Score=46.37  Aligned_cols=27  Identities=37%  Similarity=0.812  Sum_probs=24.2

Q ss_pred             ccccCCCCCCCc--eEEEeCCcccccccc
Q psy284          105 CAACSKVIPAFE--MVMRARNNVYHLECF  131 (139)
Q Consensus       105 C~~C~~~I~~~~--~~~~~~~~~~H~~Cf  131 (139)
                      |..|.+||++.+  .+|.+.++.||.+||
T Consensus         1 C~~C~kPItg~gG~k~isFedR~WH~~CF   29 (29)
T d1x68a1           1 CVACSKPISGLTGAKFICFQDSQWHSECF   29 (29)
T ss_dssp             CTTTCCCCCTTTTCCEEEETTEEEEGGGC
T ss_pred             CccccccccccCCceEEEeehhhcccccC
Confidence            788999998754  599999999999998

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=98.63  E-value=1.2e-08  Score=51.23  Aligned_cols=36  Identities=19%  Similarity=0.600  Sum_probs=31.2

Q ss_pred             CCCCCCCCCcccccccccccceeeeecCccccccCc
Q psy284           31 VPNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        31 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      ......+.++|..|++.++..+.+.+.+..||..||
T Consensus         8 ~~~~~g~~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3           8 MAQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCCCCCCCEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             cccccCCCCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            344456678999999999999899999999999998

>d1x4ka2 g.39.1.3 (A:8-34) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.59  E-value=1.5e-08  Score=44.18  Aligned_cols=27  Identities=30%  Similarity=0.624  Sum_probs=25.6

Q ss_pred             ccccCCCCCCCceEEEeCCcccccccc
Q psy284          105 CAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       105 C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      |..|.+.|.+..+.|.+.|..||..||
T Consensus         1 C~~C~ktiMPGsrKme~kG~~WHEtCF   27 (27)
T d1x4ka2           1 CQECKKTIMPGTRKMEYKGSSWHETCF   27 (27)
T ss_dssp             BSSSCCCCCSSSCEEEETTEEEETTTT
T ss_pred             CccccccccCCceeecccCCccccccC
Confidence            788999999988999999999999998

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.57  E-value=1.3e-08  Score=48.95  Aligned_cols=29  Identities=31%  Similarity=0.934  Sum_probs=26.3

Q ss_pred             CCCcccccccccccceeeeecCccccccCc
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      -.++|..|+++|.+. .|.++++.||++||
T Consensus         7 fapkC~~C~~~I~g~-~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           7 FSPKCGGCNRPVLEN-YLSAMDTVWHPECF   35 (35)
T ss_dssp             CSCBCTTTCCBCCSS-CEEETTEEECTTTC
T ss_pred             hChhhhhcCCcccch-heeecCCccCcccC
Confidence            367999999999987 78999999999998

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=98.51  E-value=6e-08  Score=49.55  Aligned_cols=39  Identities=31%  Similarity=0.504  Sum_probs=33.5

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCccccccC
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGYCAACS  109 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~C~~C~  109 (139)
                      +|..|++.|+  ......+++++||+.||.++|+|  +..+.+
T Consensus         1 KC~~C~k~Ld--s~t~~ehdg~~YCk~CY~k~fGP--KG~g~G   39 (49)
T d1b8ta4           1 RCAKCGKSLE--STTLADKDGEIYCKGCYAKNFGP--KGFGFG   39 (49)
T ss_dssp             BCTTTCCBCC--SSSEEEETTEEEEHHHHHHHTCC--CCCCCC
T ss_pred             ChhhcCCccC--CCcccccCCcccchhhhhhccCC--CccCcc
Confidence            5888999995  35688999999999999999999  766655

>d1wyha2 g.39.1.3 (A:8-34) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.48  E-value=2.9e-08  Score=43.15  Aligned_cols=27  Identities=22%  Similarity=0.593  Sum_probs=25.4

Q ss_pred             ccccCCCCCCCceEEEeCCcccccccc
Q psy284          105 CAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       105 C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      |..|.+.|.+..+.+.+.|..||..||
T Consensus         1 C~~C~ktiMPGsrKmey~G~sWHE~CF   27 (27)
T d1wyha2           1 CSACGETVMPGSRKLEYGGQTWHEHCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEECSTTCCEETTTC
T ss_pred             CccccceecCCcccccccCcccccccC
Confidence            778999999988899999999999998

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.47  E-value=5.8e-08  Score=48.39  Aligned_cols=31  Identities=29%  Similarity=0.589  Sum_probs=27.6

Q ss_pred             CCCCCcccccccccccceeeeecCccccccCc
Q psy284           35 AQGPQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        35 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      ....++|..|+++|.+. .+.++++.||+++|
T Consensus        15 ~~r~P~C~~C~~pI~g~-~vtAlgk~WHPEhF   45 (45)
T d2dara2          15 GKRTPMCAHCNQVIRGP-FLVALGKSWHPEEF   45 (45)
T ss_dssp             TTCCCBBSSSCCBCCSC-EEEETTEEECTTTC
T ss_pred             CCCCeeccccCCcccCc-eeeecCCccCcCCC
Confidence            35678999999999988 68999999999998

>d2dj7a2 g.39.1.3 (A:8-43) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.44  E-value=7.4e-08  Score=45.00  Aligned_cols=35  Identities=43%  Similarity=0.900  Sum_probs=30.4

Q ss_pred             CCCCCCCCcccccccccccceeeeecCccccccCc
Q psy284           32 PNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        32 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      |....++..|.+|++.|.....+.++++.||.+||
T Consensus         2 p~~~~g~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           2 PIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CCCCSSCSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             CccccCCccccccchhhhCCceeeeeecceeeeeC
Confidence            34556778999999999998788999999999998

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.41  E-value=7.6e-08  Score=45.30  Aligned_cols=31  Identities=32%  Similarity=0.763  Sum_probs=28.0

Q ss_pred             CCCCCcccccccccccceeeeecCccccccCc
Q psy284           35 AQGPQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        35 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      ..+..+|..|+++|.+. ++.+.|+.||+.||
T Consensus         5 ~~tlEkC~~C~~~I~dr-iLrA~Gk~yHP~CF   35 (35)
T d2dloa1           5 VATLEKCATCSQPILDR-ILRAMGKAYHPGCF   35 (35)
T ss_dssp             CSSCCBCTTTCCBCCSC-CEEETTEEECTTTC
T ss_pred             HHHHHHHHHhchHHHHH-HHHHhCCCCCCCCC
Confidence            35578999999999998 79999999999998

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LASP-1
domain: LASP-1
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=98.38  E-value=5.5e-08  Score=43.56  Aligned_cols=29  Identities=34%  Similarity=0.875  Sum_probs=26.5

Q ss_pred             CCcccccccccccceeeeecCccccccCc
Q psy284           38 PQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      .+.|++|++.+++.+.+.-+++.||..||
T Consensus         2 n~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           2 NPNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCcccccCCccccHHHhhhhHHHHhhccC
Confidence            35799999999998889999999999998

>d1rutx1 g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.38  E-value=9.3e-08  Score=43.63  Aligned_cols=28  Identities=64%  Similarity=1.412  Sum_probs=26.1

Q ss_pred             CcccccccccccceeeeecCccccccCc
Q psy284           39 QECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        39 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      ..|.+|+++|.+.+++.++++.||..|+
T Consensus         3 ~~CaGC~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           3 KRCAGCGGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CBBTTTCCBCCCSEEEEETTEEECGGGC
T ss_pred             cccCCCCCccchhhhhccchhhhhhhhC
Confidence            5799999999999999999999999885

>d2dj7a2 g.39.1.3 (A:8-43) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.35  E-value=9.6e-08  Score=44.61  Aligned_cols=27  Identities=30%  Similarity=0.689  Sum_probs=25.0

Q ss_pred             cccccCCCCCCCceEEEeCCcccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      .|++|++.|.. +..+.|+++.||.+||
T Consensus        10 ~CagCg~eik~-gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2          10 HCAGCKEEIKH-GQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CCTTTCCCCSS-SCCEEETTEEECTTTC
T ss_pred             cccccchhhhC-CceeeeeecceeeeeC
Confidence            79999999985 6899999999999998

>d2d8za2 g.39.1.3 (A:33-64) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.30  E-value=2.8e-07  Score=42.45  Aligned_cols=32  Identities=19%  Similarity=0.569  Sum_probs=28.6

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      .|..|..+|  .+++|..+++++||..||..+|+
T Consensus         1 ~C~~C~~~L--~GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQL--SGQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBC--TTSCCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCccc--cCceeeecCCCeehHHhhHhhcC
Confidence            377899999  78999999999999999999874

>d1rutx1 g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.30  E-value=2.4e-07  Score=42.22  Aligned_cols=27  Identities=26%  Similarity=0.680  Sum_probs=24.1

Q ss_pred             cccccCCCCCCCceEEEeCCcccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      .|++|+++|.+ ...+.+.++.||..|.
T Consensus         4 ~CaGC~~~I~D-RflL~v~dr~WH~~CL   30 (30)
T d1rutx1           4 RCAGCGGKIAD-RFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             BBTTTCCBCCC-SEEEEETTEEECGGGC
T ss_pred             ccCCCCCccch-hhhhccchhhhhhhhC
Confidence            89999999987 4688899999999884

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.28  E-value=2.4e-07  Score=42.09  Aligned_cols=28  Identities=57%  Similarity=1.321  Sum_probs=25.7

Q ss_pred             CCcccccccccccceeeeecCccccccC
Q psy284           38 PQECAGCGKHITDRFLLKALDMYWHEDC   65 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~C   65 (139)
                      ...|++|+++|.+.+++.++++.||..|
T Consensus         3 ~~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           3 LLTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             CcccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            4579999999999999999999999876

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.27  E-value=3.9e-07  Score=41.34  Aligned_cols=26  Identities=23%  Similarity=0.677  Sum_probs=23.5

Q ss_pred             cccccCCCCCCCceEEEeCCccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLEC  130 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~C  130 (139)
                      .|++|+++|.+ ...+.+.++.||..|
T Consensus         5 ~CaGC~~~I~D-RflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           5 TCGGCQQNIGD-RYFLKAIDQYWHEDC   30 (30)
T ss_dssp             CBSSSCSCBCS-SEEEECSSSEECTTT
T ss_pred             ccCCCCCcchH-HHHHHHHHHHHhcCC
Confidence            79999999987 468899999999987

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.27  E-value=2.6e-07  Score=44.09  Aligned_cols=32  Identities=28%  Similarity=0.512  Sum_probs=28.8

Q ss_pred             CCCCCcccccccccccceeeeecCccccccCc
Q psy284           35 AQGPQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        35 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      ..+..+|..|++.++..+.+.+.++.||..||
T Consensus         5 ~g~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           5 AGAGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CCCCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            34567999999999998889999999999998

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.27  E-value=2.6e-07  Score=43.93  Aligned_cols=31  Identities=23%  Similarity=0.419  Sum_probs=28.3

Q ss_pred             CCCCcccccccccccceeeeecCccccccCc
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      +..+.|..|++.++..+.+.+.+..||..||
T Consensus         5 p~~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           5 PARETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SSSCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CCCcccccCCCEEeeeeeEecCCeehhhccC
Confidence            4467999999999998899999999999998

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.25  E-value=2.1e-07  Score=42.21  Aligned_cols=29  Identities=28%  Similarity=0.602  Sum_probs=26.4

Q ss_pred             CCcccccccccccceeeeecCccccccCc
Q psy284           38 PQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        38 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      .+.|++|+++++.++.+..+|+.||..|+
T Consensus         2 ~~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CCBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CCcCCCCCCceeeHHhhccCCcccccccC
Confidence            46899999999999899999999999885

>d1imla2 g.39.1.3 (A:29-76) Cysteine-rich (intestinal) protein, CRP, CRIP {Rat (Rattus rattus) [TaxId: 10117]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=98.17  E-value=7.4e-07  Score=44.89  Aligned_cols=34  Identities=24%  Similarity=0.436  Sum_probs=29.7

Q ss_pred             ccccCCCCcccCCCeeEeeCCcccc-HhhHHHHhCCC
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILC-KRDYLRLFGST  102 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C-~~cy~~~~~~~  102 (139)
                      +|..|++.|.  .....++++++|| +.||.++|+|+
T Consensus         1 kC~~C~K~L~--sg~~aeHdg~pYC~k~CY~~~FGPk   35 (48)
T d1imla2           1 KCEKCGKTLT--SGGHAEHEGKPYCNHPCYSAMFGPK   35 (48)
T ss_dssp             BCTTTCCBCC--TTTEEEETTEEEETTTHHHHHSSCC
T ss_pred             CchhcCcCcC--CCChhhcCCcccccccchhhccCCC
Confidence            5888999995  4668999999999 77999999993

>d2dj7a1 g.39.1.3 (A:44-74) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.15  E-value=8e-07  Score=40.30  Aligned_cols=31  Identities=32%  Similarity=0.686  Sum_probs=26.9

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      +|..|+..|.   ..|..+++.+||+.+|...||
T Consensus         1 kC~~C~~vL~---gEYm~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVILT---GEYISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBCS---SCCEEETTEEECTTHHHHHTT
T ss_pred             CccccCcccc---ceeecCCCCcccHHHHHHhcC
Confidence            5788998883   569999999999999999885

>d1wiga1 g.39.1.3 (A:1-32) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.14  E-value=2.8e-07  Score=41.42  Aligned_cols=25  Identities=36%  Similarity=0.745  Sum_probs=23.5

Q ss_pred             cccccCCCCCCCceEEEeCCccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLEC  130 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~C  130 (139)
                      -|..|.+.|++  .++.|.+++|||.|
T Consensus         7 gC~~C~~~ItG--kVLEAG~khYHP~C   31 (32)
T d1wiga1           7 GCDSCEKYITG--RVLEAGEKHYHPSC   31 (32)
T ss_dssp             SCSSSCCCCSS--CCBCCSSCCBCTTT
T ss_pred             hhhhhhhhhhh--hhhhccccccCCCC
Confidence            69999999988  89999999999988

>d1b8ta2 g.39.1.3 (A:36-100) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=98.13  E-value=1.1e-06  Score=47.24  Aligned_cols=35  Identities=29%  Similarity=0.592  Sum_probs=30.3

Q ss_pred             cccCCCCcccCCCeeEeeCCccccHhhHHHHhCCCcc
Q psy284           68 CGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGSTGY  104 (139)
Q Consensus        68 C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~~~  104 (139)
                      |..|.+.|+  ...+..+++++||+.||.++|+|++.
T Consensus         2 C~~C~K~Ld--S~~~~eh~~e~YCk~CY~k~fGPkG~   36 (65)
T d1b8ta2           2 CMVCKKNLD--STTVAVHGDEIYCKSCYGKKYGPKGK   36 (65)
T ss_dssp             CTTTCCBCC--SSSEEEETTEEEEHHHHHHHHSCCCC
T ss_pred             chhcCCccC--CCccccCCCcccchhhhccccCCCcc
Confidence            778999995  46689999999999999999999543

>d1x62a2 g.39.1.3 (A:8-42) PDZ and LIM domain protein 1 Elfin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 1 Elfin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.12  E-value=6.3e-07  Score=41.34  Aligned_cols=26  Identities=27%  Similarity=0.694  Sum_probs=24.8

Q ss_pred             cccccCCCCCCCceEEEeCCcccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      .|..|+..|.+  .++.+.++.+||+||
T Consensus        10 ~CdkCg~GIVG--~~VK~rDk~rHPeCf   35 (35)
T d1x62a2          10 MCDKCGTGIVG--VFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCSSSCCCCCS--SCEECSSCEECTTTT
T ss_pred             cccccCCCcEe--EEEEeccccCCCCCC
Confidence            89999999998  799999999999998

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=98.09  E-value=8.6e-07  Score=39.40  Aligned_cols=30  Identities=33%  Similarity=0.618  Sum_probs=26.5

Q ss_pred             cccccCCCCcccCCCeeEeeCCccccHhhHHH
Q psy284           66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLR   97 (139)
Q Consensus        66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~   97 (139)
                      |+|..|++.|  .+..+..+++.+||+.||.+
T Consensus         1 frca~cgk~l--estt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSL--ESTTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEE--CSSCSEEETTEEECHHHHHH
T ss_pred             CccccccCcc--ccceeeccCCcEEEeeeeec
Confidence            7899999999  45678999999999999975

>d1u5sb2 g.39.1.3 (B:103-137) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.07  E-value=1.9e-06  Score=39.63  Aligned_cols=34  Identities=29%  Similarity=0.774  Sum_probs=31.2

Q ss_pred             cccccCCCCcccCCCeeEeeCCccccHhhHHHHhCC
Q psy284           66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGS  101 (139)
Q Consensus        66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~  101 (139)
                      |.|..|.+++  .+.+.+.+.|..||+.+|.++|+.
T Consensus         1 FvCA~CekPF--~G~rhyE~~g~ayCe~Hy~qLfg~   34 (35)
T d1u5sb2           1 FVCAKCEKPF--LGHRHYERKGLAYCETHYNQLFGD   34 (35)
T ss_dssp             CBCTTTCCBC--SSSCCEEETTEEECHHHHHHHCSC
T ss_pred             CcccccCCcc--CCchhhhhcCchHHHHHHHHHhcc
Confidence            7899999998  778899999999999999999974

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.07  E-value=6.4e-07  Score=40.75  Aligned_cols=28  Identities=29%  Similarity=0.732  Sum_probs=25.0

Q ss_pred             CCCcccccccccccceeeeecCccccccC
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDC   65 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~C   65 (139)
                      +.++|+.|.++|.+. ++.++++.||++.
T Consensus         4 g~p~C~~C~~PI~~~-~vtAlgk~WHpEH   31 (31)
T d1u5sb1           4 GVPICGACRRPIEGR-VVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCEETTTTEECCSC-EECCTTSBEETTT
T ss_pred             CCcchhhcCCchhhh-HhhhhccccCCCC
Confidence            567999999999997 7999999999873

>d1x64a1 g.39.1.3 (A:8-52) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.06  E-value=9.1e-07  Score=43.50  Aligned_cols=26  Identities=38%  Similarity=0.797  Sum_probs=24.9

Q ss_pred             cccccCCCCCCCceEEEeCCcccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      .|..|+..|.|  .++.+.++.+||+||
T Consensus        20 ~CdkCg~GIVG--~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          20 LCDKCGSGIVG--AVVKARDKYRHPECF   45 (45)
T ss_dssp             BCTTTCCBCCS--CCEESSSCEECTTTC
T ss_pred             cccccCCCcEE--EEEEeccccCCCCCC
Confidence            89999999998  799999999999998

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.01  E-value=2.6e-06  Score=39.29  Aligned_cols=32  Identities=19%  Similarity=0.439  Sum_probs=27.4

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      .|..|..++  .+..|++.++++||+.+|.++.|
T Consensus         1 VC~~C~~PF--~~~~Fy~~~g~PyCe~HyH~~~G   32 (32)
T d1x3ha2           1 VCGDCFTSF--STGSFFELDGRPFCELHYHHRRG   32 (32)
T ss_dssp             BCSSSCCBS--CSSCCEESSSCEECHHHHHHHHS
T ss_pred             CcCccCCcC--CCCCeEeECCccchHHhhhhhcC
Confidence            477899999  56789999999999999998754

>d2cuqa1 g.39.1.3 (A:43-74) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.99  E-value=3.5e-06  Score=38.18  Aligned_cols=32  Identities=22%  Similarity=0.475  Sum_probs=28.4

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      .|..|..+|  .+++|..++.++||.+||-.+|+
T Consensus         1 vCt~Ck~~L--aGqrFTSrde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1           1 VCTGCQTPL--AGQQFTSRDEDPYCVACFGELFA   32 (32)
T ss_dssp             BCSSSCCBC--TTCCEEECSSSEEEHHHHHHHTT
T ss_pred             CccccCccc--cCCccccCCCCccHHHHhHhhcC
Confidence            378899999  67999999999999999988874

>d2cupa3 g.39.1.3 (A:8-34) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.97  E-value=2.3e-06  Score=36.89  Aligned_cols=27  Identities=33%  Similarity=0.653  Sum_probs=23.8

Q ss_pred             ccccCCCCCCCceEEEeCCcccccccc
Q psy284          105 CAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       105 C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      |..|.+||.....-+...++.||..||
T Consensus         1 c~ecrkpigad~ke~h~knr~wh~~cf   27 (27)
T d2cupa3           1 CVECRKPIGADSKEVHYKNRFWHDTCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEEEETTEEEETTTC
T ss_pred             CccccCCcCcchHHhhccccccccccC
Confidence            678999998766788999999999998

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.94  E-value=2.4e-06  Score=39.29  Aligned_cols=34  Identities=53%  Similarity=1.286  Sum_probs=31.2

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      +|..|+..|++.+...|.+.+-++|+.+|.++||
T Consensus         1 KCscC~~~LgeiG~s~ytk~~mILCk~DY~rlFG   34 (34)
T d1rutx2           1 KCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG   34 (34)
T ss_dssp             BCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHS
T ss_pred             CCcchhcChhhccchheecCCEEEEchhHHHhcC
Confidence            4788999999889999999999999999999986

>d2d8ya2 g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.93  E-value=3.1e-06  Score=41.63  Aligned_cols=34  Identities=29%  Similarity=0.591  Sum_probs=29.2

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHHHhCCC
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFGST  102 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~~~  102 (139)
                      +|..|++.|.  ...|...++.+||+.||.++|.++
T Consensus         1 rC~~C~~~Ls--~~~yas~~G~lYCkpHf~qLF~~k   34 (42)
T d2d8ya2           1 RCSYCNNKLS--LGTYASLHGRIYCKPHFNQLFKSK   34 (42)
T ss_dssp             BCTTTCCBCC--TTTCCCSSSCCCCHHHHHHHSCCC
T ss_pred             CcCcCCCCcc--CCcchhhCCEeccHHHHHHHHHhh
Confidence            5888999995  356889999999999999999873

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.92  E-value=3.1e-06  Score=40.09  Aligned_cols=28  Identities=32%  Similarity=0.809  Sum_probs=25.2

Q ss_pred             ccccccCCCCCCCceEEEeCCcccccccc
Q psy284          103 GYCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       103 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      .+|..|++.+.+.| .+.+.|+.||..||
T Consensus         8 ~kC~~C~K~VY~~E-~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           8 ETCVECQKTVYPME-RLLANQQVFHISCF   35 (35)
T ss_dssp             CBCTTTCCBCCTTS-EEECSSSEEETTTC
T ss_pred             cccccCCCEEeeee-eEecCCeehhhccC
Confidence            48999999999874 66899999999998

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=97.91  E-value=1.8e-06  Score=43.03  Aligned_cols=29  Identities=24%  Similarity=0.582  Sum_probs=25.3

Q ss_pred             CccccccCCCCCCCceEEEeCCcccccccc
Q psy284          102 TGYCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       102 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      .++|..|++.+...|+ +.+.|+.||..||
T Consensus        15 ~~kC~~C~k~VY~~E~-~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          15 SDGCPRCGQAVYAAEK-VIGAGKSWHKSCF   43 (43)
T ss_dssp             CEECTTTSCEECSSSC-EEETTEEECTTTC
T ss_pred             CCcCccCCCEeeHHHH-hhcCCCccccCCC
Confidence            3489999999999865 4789999999998

>d1x63a1 g.39.1.3 (A:8-44) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.90  E-value=3.9e-06  Score=40.23  Aligned_cols=31  Identities=29%  Similarity=0.682  Sum_probs=26.4

Q ss_pred             CCCCcccccccccccc-eeeeecCccccccCc
Q psy284           36 QGPQECAGCGKHITDR-FLLKALDMYWHEDCL   66 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf   66 (139)
                      ....+|..|+++|..+ ..+.+.+..||..||
T Consensus         6 ~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           6 EDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             ccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            3466899999999874 458999999999998

>d1x64a1 g.39.1.3 (A:8-52) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.87  E-value=9.9e-06  Score=39.71  Aligned_cols=34  Identities=35%  Similarity=0.676  Sum_probs=29.8

Q ss_pred             CCCCCCCCcccccccccccceeeeecCccccccCc
Q psy284           32 PNNAQGPQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        32 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      .......+.|.+|+..|.+. ++.++++.+|++||
T Consensus        12 ~~~~QkLP~CdkCg~GIVG~-~VK~rDK~rHPeCf   45 (45)
T d1x64a1          12 AGSAQRMPLCDKCGSGIVGA-VVKARDKYRHPECF   45 (45)
T ss_dssp             CSCCCSCCBCTTTCCBCCSC-CEESSSCEECTTTC
T ss_pred             CCccccCccccccCCCcEEE-EEEeccccCCCCCC
Confidence            34567788999999999998 68999999999998

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LASP-1
domain: LASP-1
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=97.84  E-value=1.8e-06  Score=38.54  Aligned_cols=27  Identities=30%  Similarity=0.739  Sum_probs=24.3

Q ss_pred             cccccCCCCCCCceEEEeCCcccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      .|++|++.+.+.| .+...++.||..||
T Consensus         4 ~CaRC~k~VYp~E-kl~ClDk~WHK~CF   30 (30)
T d1zfoa_           4 NCARCGKIVYPTE-KVNCLDKFWHKACF   30 (30)
T ss_dssp             BCSSSCSBCCGGG-CCCSSSSCCCGGGC
T ss_pred             cccccCCccccHH-HhhhhHHHHhhccC
Confidence            8999999999964 66899999999998

>d2cuqa2 g.39.1.3 (A:8-42) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.83  E-value=4.1e-06  Score=39.07  Aligned_cols=30  Identities=33%  Similarity=0.682  Sum_probs=26.0

Q ss_pred             CCCCcccccccccccceeeeecCccccccCc
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      .-..+|..|+++|..+. +...++.||.+||
T Consensus         6 kfa~~C~~Ckk~It~GG-vtY~dqpWHkeCF   35 (35)
T d2cuqa2           6 KFAPRCARCSKTLTQGG-VTYRDQPWHRECL   35 (35)
T ss_dssp             CSSCCCTTTCCCCCSCC-EESSSSEECTTTC
T ss_pred             HHHHHHhhcCCccccCc-eeecCCcchhhhC
Confidence            34679999999998873 7889999999998

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.80  E-value=3.9e-06  Score=39.89  Aligned_cols=29  Identities=24%  Similarity=0.650  Sum_probs=25.4

Q ss_pred             CccccccCCCCCCCceEEEeCCcccccccc
Q psy284          102 TGYCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       102 ~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      ..+|..|++.+.+.| .+.+.|+.||..||
T Consensus         8 ~~~C~~C~K~VY~~E-rl~a~g~~yHk~CF   36 (36)
T d2co8a2           8 GDLCALCGEHLYVLE-RLCVNGHFFHRSCF   36 (36)
T ss_dssp             SCBCSSSCCBCCTTT-BCCBTTBCCBTTTC
T ss_pred             CCcccccCCEEeeee-EEEecCcEeccccC
Confidence            348999999999975 45899999999998

>d1x62a2 g.39.1.3 (A:8-42) PDZ and LIM domain protein 1 Elfin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 1 Elfin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.78  E-value=1.1e-05  Score=37.14  Aligned_cols=32  Identities=34%  Similarity=0.571  Sum_probs=28.0

Q ss_pred             CCCCCCcccccccccccceeeeecCccccccCc
Q psy284           34 NAQGPQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        34 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      .....+.|.+|+..|.+. ++.+.++.+|++||
T Consensus         4 ~~qklp~CdkCg~GIVG~-~VK~rDk~rHPeCf   35 (35)
T d1x62a2           4 NAQKLPMCDKCGTGIVGV-FVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCCCCCSSSCCCCCSS-CEECSSCEECTTTT
T ss_pred             ccccCccccccCCCcEeE-EEEeccccCCCCCC
Confidence            345678999999999998 68999999999997

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.78  E-value=7.9e-06  Score=36.87  Aligned_cols=27  Identities=22%  Similarity=0.470  Sum_probs=23.4

Q ss_pred             cccccCCCCCCCceEEEeCCcccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      +|.+|++++...| .+...|+.||..|.
T Consensus         4 ~CprC~K~VYfaE-k~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           4 KCPKCDKTVYFAE-KVSSLGKDWHKFCL   30 (30)
T ss_dssp             BCTTTCCBCCTTT-EEEETTEEEETTTC
T ss_pred             cCCCCCCceeeHH-hhccCCcccccccC
Confidence            8999999999975 55788999999884

>d1a7ia2 g.39.1.3 (A:36-67) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.77  E-value=7e-06  Score=36.92  Aligned_cols=31  Identities=26%  Similarity=0.522  Sum_probs=26.7

Q ss_pred             cccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           68 CGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        68 C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      |..|.+.|  .+.....+++.+||+.||-++||
T Consensus         2 C~~C~K~L--dStTva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNL--DSTTVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEE--CSSCCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhcc--CcceeeeecceEEehhhccccCC
Confidence            66788999  45678999999999999999875

>d2dara1 g.39.1.3 (A:53-84) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.73  E-value=1.5e-05  Score=36.14  Aligned_cols=31  Identities=16%  Similarity=0.487  Sum_probs=26.4

Q ss_pred             cccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           68 CGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        68 C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      |..|..+|.  ...|...++.+||+.||.+.|+
T Consensus         2 Ca~C~~sL~--d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           2 CAHCKNTMA--YIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             CSSSCCBCS--SSCBEESSSCEECHHHHHHHTS
T ss_pred             cccccccHh--hcceeeecCcEeHHHHHHHhcC
Confidence            778999995  4569999999999999998764

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.71  E-value=5.5e-06  Score=36.25  Aligned_cols=27  Identities=22%  Similarity=0.703  Sum_probs=24.1

Q ss_pred             CcccccccccccceeeeecCccccccC
Q psy284           39 QECAGCGKHITDRFLLKALDMYWHEDC   65 (139)
Q Consensus        39 ~~C~~C~~~i~~~~~~~~~~~~~H~~C   65 (139)
                      .+|.+|++.++.++.+.-.++.||..|
T Consensus         2 d~CpRC~~~VyaAEkviGaG~~WHk~C   28 (28)
T d1ibia1           2 EKCSRCGDSVYAAEKVIGAGKPWHKNC   28 (28)
T ss_dssp             EECTTTSSEESSSSCEESSSSEECSSC
T ss_pred             CcCcccchhHHHHHHHhcCCCccccCC
Confidence            479999999999888888899999876

>d1x61a1 g.39.1.3 (A:8-34) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.67  E-value=1.3e-05  Score=33.94  Aligned_cols=27  Identities=26%  Similarity=0.636  Sum_probs=24.5

Q ss_pred             ccccCCCCCCCceEEEeCCcccccccc
Q psy284          105 CAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       105 C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      |.+|++-+.+.+..+.+.++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            788999999877788999999999998

>d1wyha1 g.39.1.3 (A:35-66) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.63  E-value=3.1e-05  Score=35.11  Aligned_cols=31  Identities=23%  Similarity=0.513  Sum_probs=26.7

Q ss_pred             cccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           68 CGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        68 C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      |..|..+++  ...|..+++..||..||+++|+
T Consensus         2 C~~C~qPIG--tkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           2 CSGCEQPLG--SRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             CTTTCCBTT--TSCEEEETTEEEEHHHHHHHTS
T ss_pred             cccccCccc--ccccccCCCcEEEEeccccccC
Confidence            677899995  4678999999999999999874

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.63  E-value=3.3e-05  Score=35.10  Aligned_cols=31  Identities=23%  Similarity=0.483  Sum_probs=26.8

Q ss_pred             cccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           68 CGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        68 C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      |..|..+++  ...|..+++..||..||++.|+
T Consensus         2 C~~C~qPIG--tksfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           2 CHRCQQPIG--TKSFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CSSSCCCCC--SSSEEEETTEEEEHHHHHHHTS
T ss_pred             cccccCccc--ccccccCCCCceEeecchhhcC
Confidence            678999995  4668999999999999999874

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.62  E-value=1.3e-05  Score=36.55  Aligned_cols=28  Identities=25%  Similarity=0.753  Sum_probs=24.4

Q ss_pred             Ccccccccccccc-eeeeecCccccccCc
Q psy284           39 QECAGCGKHITDR-FLLKALDMYWHEDCL   66 (139)
Q Consensus        39 ~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf   66 (139)
                      ..|.+|++.|... +++.+.+..||..||
T Consensus         3 g~Ca~C~~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEETTEEECGGGC
T ss_pred             cccccccCcCChhHhheecccceeeeccC
Confidence            3699999999884 567899999999998

>d1x4ka2 g.39.1.3 (A:8-34) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.60  E-value=1.4e-05  Score=34.54  Aligned_cols=26  Identities=31%  Similarity=0.692  Sum_probs=22.7

Q ss_pred             ccccccccccc-eeeeecCccccccCc
Q psy284           41 CAGCGKHITDR-FLLKALDMYWHEDCL   66 (139)
Q Consensus        41 C~~C~~~i~~~-~~~~~~~~~~H~~Cf   66 (139)
                      |..|.+.|.+. ..+...+..||..||
T Consensus         1 C~~C~ktiMPGsrKme~kG~~WHEtCF   27 (27)
T d1x4ka2           1 CQECKKTIMPGTRKMEYKGSSWHETCF   27 (27)
T ss_dssp             BSSSCCCCCSSSCEEEETTEEEETTTT
T ss_pred             CccccccccCCceeecccCCccccccC
Confidence            77899999985 568899999999998

>d2cu8a2 g.39.1.3 (A:38-70) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.49  E-value=4.4e-05  Score=34.70  Aligned_cols=32  Identities=28%  Similarity=0.491  Sum_probs=26.3

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccH-hhHHHHhC
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCK-RDYLRLFG  100 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~-~cy~~~~~  100 (139)
                      +|..|++.|.  .....++++++||. .||..+||
T Consensus         1 kCekC~ktL~--~G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLT--PGGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCC--TTSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccC--CCCccccCCCcCcCcchHHhhcC
Confidence            5788999995  35588999999996 59998875

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=97.49  E-value=2.3e-05  Score=35.74  Aligned_cols=31  Identities=19%  Similarity=0.434  Sum_probs=27.5

Q ss_pred             CCCCcccccccccccceeeeecCccccccCc
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      .+..+|+.|++.++.++-+...++.||..||
T Consensus         5 ggg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           5 GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CCCceeccccceEeeeeeeeecCcccccccC
Confidence            4567999999999998778899999999997

>d2cura1 g.39.1.3 (A:33-63) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.48  E-value=5.2e-05  Score=33.83  Aligned_cols=29  Identities=21%  Similarity=0.458  Sum_probs=25.6

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHH
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLR   97 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~   97 (139)
                      .|..|++.|  .+.+|...++++||-+||..
T Consensus         1 vC~~C~K~L--ag~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKL--AGQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBC--TTSCEEECSSCEEEHHHHHH
T ss_pred             Ccccccchh--cCceeEEecceEEEeeeecc
Confidence            377899999  67899999999999999975

>d1x61a2 g.39.1.3 (A:35-66) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.48  E-value=6.1e-05  Score=33.68  Aligned_cols=30  Identities=23%  Similarity=0.596  Sum_probs=26.0

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHHH
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRL   98 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~   98 (139)
                      .|..|+..|  .++.||..+.+.||+.||...
T Consensus         1 vC~tC~~kL--RGqpFYAvekkayCE~CYi~t   30 (32)
T d1x61a2           1 VCSTCRAQL--RGQHFYAVERRAYCEGCYVAT   30 (32)
T ss_dssp             BCSSSCCBC--TTSCEEESSSCEEEHHHHHHH
T ss_pred             CeeEeCcee--cCCcceEeeccccccceeeee
Confidence            367889999  788999999999999999763

>d1wyha2 g.39.1.3 (A:8-34) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.47  E-value=2.2e-05  Score=33.82  Aligned_cols=26  Identities=31%  Similarity=0.783  Sum_probs=22.3

Q ss_pred             ccccccccccc-eeeeecCccccccCc
Q psy284           41 CAGCGKHITDR-FLLKALDMYWHEDCL   66 (139)
Q Consensus        41 C~~C~~~i~~~-~~~~~~~~~~H~~Cf   66 (139)
                      |..|.+.|.+. ..+...+..||..||
T Consensus         1 C~~C~ktiMPGsrKmey~G~sWHE~CF   27 (27)
T d1wyha2           1 CSACGETVMPGSRKLEYGGQTWHEHCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEECSTTCCEETTTC
T ss_pred             CccccceecCCcccccccCcccccccC
Confidence            67899999885 458889999999998

>d1x4la1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.44  E-value=3e-05  Score=34.26  Aligned_cols=26  Identities=35%  Similarity=0.885  Sum_probs=21.6

Q ss_pred             cccccccccc---ceeeeecCccccccCc
Q psy284           41 CAGCGKHITD---RFLLKALDMYWHEDCL   66 (139)
Q Consensus        41 C~~C~~~i~~---~~~~~~~~~~~H~~Cf   66 (139)
                      |..|.++|.+   ...|...++.||.+||
T Consensus         1 C~~C~kPItg~gg~kyisFE~R~WH~~CF   29 (29)
T d1x4la1           1 CAGCTNPISGLGGTKYISFEERQWHNDCF   29 (29)
T ss_dssp             BTTTTBCCCCSSSCSCEECSSCEECTTTC
T ss_pred             CCccCCcccccCCceEEEeecccccccCC
Confidence            7789999866   3458899999999998

>d1j2oa2 g.39.1.3 (A:31-63) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.37  E-value=9.3e-05  Score=33.21  Aligned_cols=33  Identities=64%  Similarity=1.230  Sum_probs=29.3

Q ss_pred             cccccCCCCcccCCCeeEeeCCccccHhhHHHH
Q psy284           66 LKCGCCDCRLGEVGSTLYTKANLILCKRDYLRL   98 (139)
Q Consensus        66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~   98 (139)
                      ++|..|+.+|++.+...|.+.+.++|+.+|.++
T Consensus         1 LkC~cC~cRLGEVG~tlytk~nliLCkrDYlRl   33 (33)
T d1j2oa2           1 LSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL   33 (33)
T ss_dssp             CCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHH
T ss_pred             CccccccccccchhhHHHhhcceeeehhhhhcC
Confidence            368889999999999999999999999999863

>d1a7ia1 g.39.1.3 (A:8-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.35  E-value=4.4e-05  Score=32.98  Aligned_cols=27  Identities=19%  Similarity=0.557  Sum_probs=24.6

Q ss_pred             cccccccccccceeeeecCccccccCc
Q psy284           40 ECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        40 ~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      +|+.|++.++.++-+...++.||..||
T Consensus         2 kcg~c~ktvy~aeevqc~grsfhk~cf   28 (28)
T d1a7ia1           2 KCGACGRTVYHAEEVQCDGRSFHRCCF   28 (28)
T ss_dssp             BCSSSCCBCSSTTEEEETTEEEESSSE
T ss_pred             ccccccceEeeeeeeeecCceeccccC
Confidence            699999999998778999999999987

>d1x68a1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.30  E-value=5.6e-05  Score=33.30  Aligned_cols=26  Identities=31%  Similarity=0.822  Sum_probs=21.4

Q ss_pred             cccccccccc---ceeeeecCccccccCc
Q psy284           41 CAGCGKHITD---RFLLKALDMYWHEDCL   66 (139)
Q Consensus        41 C~~C~~~i~~---~~~~~~~~~~~H~~Cf   66 (139)
                      |..|.++|.+   ...|...++.||.+||
T Consensus         1 C~~C~kPItg~gG~k~isFedR~WH~~CF   29 (29)
T d1x68a1           1 CVACSKPISGLTGAKFICFQDSQWHSECF   29 (29)
T ss_dssp             CTTTCCCCCTTTTCCEEEETTEEEEGGGC
T ss_pred             CccccccccccCCceEEEeehhhcccccC
Confidence            6788898866   3458899999999998

>d2dloa2 g.39.1.3 (A:43-75) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.19  E-value=0.00018  Score=32.99  Aligned_cols=32  Identities=28%  Similarity=0.547  Sum_probs=25.4

Q ss_pred             ccccCCCCcccCCCeeE-eeCCccccHhhHHHHhC
Q psy284           67 KCGCCDCRLGEVGSTLY-TKANLILCKRDYLRLFG  100 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~-~~~~~~~C~~cy~~~~~  100 (139)
                      .|..|++.|  .+..|. ..++++||..+|.++|+
T Consensus         1 tCvvC~~~L--DGvPFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           1 TCVVCHRGL--DGIPFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             BCSSSCCBC--TTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             CeeEcCccc--CCCcEEEcCCCCEeehhhhhhhcC
Confidence            477889999  455555 47889999999999874

>d1a7ia1 g.39.1.3 (A:8-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.11  E-value=0.00017  Score=31.06  Aligned_cols=27  Identities=26%  Similarity=0.653  Sum_probs=23.4

Q ss_pred             cccccCCCCCCCceEEEeCCcccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      +|..|.+.+.-.| -|...|+.||..||
T Consensus         2 kcg~c~ktvy~ae-evqc~grsfhk~cf   28 (28)
T d1a7ia1           2 KCGACGRTVYHAE-EVQCDGRSFHRCCF   28 (28)
T ss_dssp             BCSSSCCBCSSTT-EEEETTEEEESSSE
T ss_pred             ccccccceEeeee-eeeecCceeccccC
Confidence            7999999998764 55789999999998

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.11  E-value=8.4e-05  Score=32.37  Aligned_cols=26  Identities=27%  Similarity=0.631  Sum_probs=22.0

Q ss_pred             cccccCCCCCCCceEEEeCCccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLEC  130 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~C  130 (139)
                      +|.+|++.+...|.+| -.|+.||..|
T Consensus         3 ~CpRC~~~VyaAEkvi-GaG~~WHk~C   28 (28)
T d1ibia1           3 KCSRCGDSVYAAEKVI-GAGKPWHKNC   28 (28)
T ss_dssp             ECTTTSSEESSSSCEE-SSSSEECSSC
T ss_pred             cCcccchhHHHHHHHh-cCCCccccCC
Confidence            7999999999877666 4688999877

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.02  E-value=0.00025  Score=34.24  Aligned_cols=29  Identities=28%  Similarity=0.608  Sum_probs=24.7

Q ss_pred             CCCCcccccccccccceeeeecCccccccC
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDC   65 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~C   65 (139)
                      .-..+|..|++.|.+. ++.+.++.||+.|
T Consensus        13 ~fG~~C~~C~~~ItG~-V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          13 LYGTRCFSCDQFIEGE-VVSALGKTYHPDC   41 (41)
T ss_dssp             SCCCBCTTTCCBCCSC-CEEETTEEECTTT
T ss_pred             HhCcccccccCEeeee-eeEecCcccCCCC
Confidence            3456999999999765 8999999999987

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=96.92  E-value=0.00017  Score=32.73  Aligned_cols=28  Identities=25%  Similarity=0.630  Sum_probs=24.0

Q ss_pred             ccccccCCCCCCCceEEEeCCcccccccc
Q psy284          103 GYCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       103 ~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      .+|..|++.+.-.|. +...|+.||..||
T Consensus         8 ~kcg~c~ktvy~aee-vqc~g~sfhk~cf   35 (35)
T d1b8ta1           8 KKCGVCQKAVYFAEE-VQCEGSSFHKSCF   35 (35)
T ss_dssp             EECTTTCCEECSSCC-EEETTEEECTTTC
T ss_pred             ceeccccceEeeeee-eeecCcccccccC
Confidence            389999999987654 5789999999998

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.87  E-value=0.00026  Score=32.52  Aligned_cols=27  Identities=22%  Similarity=0.635  Sum_probs=25.3

Q ss_pred             cccccCCCCCCCceEEEeCCccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLEC  130 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~C  130 (139)
                      .|.+|+....+.|.++...|..||+.|
T Consensus         9 ~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           9 TCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             BCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHccCCCchHHhhcCCCccccccC
Confidence            799999999999999999999999987

>d2cupa3 g.39.1.3 (A:8-34) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.76  E-value=0.00036  Score=29.83  Aligned_cols=26  Identities=27%  Similarity=0.765  Sum_probs=21.0

Q ss_pred             ccccccccccc-eeeeecCccccccCc
Q psy284           41 CAGCGKHITDR-FLLKALDMYWHEDCL   66 (139)
Q Consensus        41 C~~C~~~i~~~-~~~~~~~~~~H~~Cf   66 (139)
                      |..|.++|..+ .-+...++.||..||
T Consensus         1 c~ecrkpigad~ke~h~knr~wh~~cf   27 (27)
T d2cupa3           1 CVECRKPIGADSKEVHYKNRFWHDTCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEEEETTEEEETTTC
T ss_pred             CccccCCcCcchHHhhccccccccccC
Confidence            67799999774 337788999999997

>d1x63a2 g.39.1.3 (A:45-76) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.63  E-value=0.0015  Score=28.65  Aligned_cols=32  Identities=19%  Similarity=0.453  Sum_probs=26.4

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHHHhC
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLRLFG  100 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~~~~  100 (139)
                      .|+.|...++  ...|+.+....||..|.+.+|+
T Consensus         1 tcs~ckq~ig--sgsffpkg~d~ycvtche~kfa   32 (32)
T d1x63a2           1 TCSNCKQVIG--TGSFFPKGEDFYCVTCHETKFA   32 (32)
T ss_dssp             CCSSSCCCCT--TSCEEEETTEEEEHHHHHHHTS
T ss_pred             Ccchhhhhcc--cccccCCCCcEEEEEeeccccC
Confidence            4778888885  4569999999999999988764

>d1wiga1 g.39.1.3 (A:1-32) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.43  E-value=0.00097  Score=29.57  Aligned_cols=29  Identities=38%  Similarity=0.769  Sum_probs=24.5

Q ss_pred             CCCCcccccccccccceeeeecCccccccC
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDC   65 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~C   65 (139)
                      ++..-|..|.+.|... ++++.++.||+.|
T Consensus         3 sgssgC~~C~~~ItGk-VLEAG~khYHP~C   31 (32)
T d1wiga1           3 SGSSGCDSCEKYITGR-VLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCCSCSSSCCCCSSC-CBCCSSCCBCTTT
T ss_pred             Cccchhhhhhhhhhhh-hhhccccccCCCC
Confidence            3455799999999987 7899999999987

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.08  E-value=0.0013  Score=31.16  Aligned_cols=27  Identities=19%  Similarity=0.528  Sum_probs=21.6

Q ss_pred             ccccCCCCCCCceEEEeCCcccccccc
Q psy284          105 CAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       105 C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      |.+|++.....|....-.+..|||.|-
T Consensus         2 C~rC~~mF~EGEEMYLQGs~IWHP~C~   28 (41)
T d1wiga2           2 CVRCGQMFAEGEEMYLQGSSIWHPACR   28 (41)
T ss_dssp             CSSSCCCCCSSCCCEEETTEEECTTHH
T ss_pred             cchhhccccccceeeecCCceeCCccc
Confidence            888998887666666678899999874

>d1x61a1 g.39.1.3 (A:8-34) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.99  E-value=0.0018  Score=27.14  Aligned_cols=26  Identities=35%  Similarity=0.814  Sum_probs=20.4

Q ss_pred             cccccccccc-ceeeeecCccccccCc
Q psy284           41 CAGCGKHITD-RFLLKALDMYWHEDCL   66 (139)
Q Consensus        41 C~~C~~~i~~-~~~~~~~~~~~H~~Cf   66 (139)
                      |.+|++.+.. ..-+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            6789987655 3447789999999987

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.81  E-value=0.0042  Score=27.63  Aligned_cols=27  Identities=26%  Similarity=0.593  Sum_probs=22.8

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhh
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRD   94 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c   94 (139)
                      .|..|..+|. ++.+|...+|.+||+.+
T Consensus         1 tC~tC~n~LV-PGDRFHyvNG~lfCE~D   27 (33)
T d1rutx4           1 TCSTCRNRLV-PGDRFHYINGSLFCEHD   27 (33)
T ss_dssp             BCTTTCCBCC-TTCEEEEETTEEEEGGG
T ss_pred             Cccccccccc-CCceeEEecCEEEEecC
Confidence            3778888886 77889999999999876

>d1x6aa2 g.39.1.3 (A:42-75) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.73  E-value=0.0064  Score=27.53  Aligned_cols=32  Identities=9%  Similarity=0.297  Sum_probs=24.1

Q ss_pred             cccccCCCCcccCCCeeE-eeCCccccHhhHHHH
Q psy284           66 LKCGCCDCRLGEVGSTLY-TKANLILCKRDYLRL   98 (139)
Q Consensus        66 f~C~~C~~~l~~~~~~~~-~~~~~~~C~~cy~~~   98 (139)
                      |.|..|+..+++. ..|. ....++||..||.+.
T Consensus         1 F~C~~C~~fIgdg-dsyaLVerskLYCG~Cy~~~   33 (34)
T d1x6aa2           1 FACMSCKVIIEDG-DAYALVQHATLYCGKCHNEV   33 (34)
T ss_dssp             CBCTTTCCBCCTT-SCEEECSSSCEEEHHHHHHH
T ss_pred             CcccccccEEecC-ceEEEEeeceeeeecchhcc
Confidence            6788899888744 4455 467789999999763

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.64  E-value=0.0034  Score=28.67  Aligned_cols=28  Identities=18%  Similarity=0.515  Sum_probs=22.8

Q ss_pred             CCcccccccccccc-eeeeecCccccccC
Q psy284           38 PQECAGCGKHITDR-FLLKALDMYWHEDC   65 (139)
Q Consensus        38 ~~~C~~C~~~i~~~-~~~~~~~~~~H~~C   65 (139)
                      ...|.+|+..+.+. .++..+|..||..|
T Consensus         7 ~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           7 SATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHHccCCCchHHhhcCCCccccccC
Confidence            45799999998885 45778999999876

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.26  E-value=0.012  Score=25.94  Aligned_cols=29  Identities=14%  Similarity=0.377  Sum_probs=22.5

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHH
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLR   97 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~   97 (139)
                      .|..|+..|..  ..++..++++||+.+...
T Consensus         1 vC~dCg~NLKq--rG~Ffv~~~lyCE~HAr~   29 (31)
T d1x64a2           1 VCADCNLNLKQ--KGYFFVEGELYCETHARA   29 (31)
T ss_dssp             CCSSSCCCTTT--SCCEEETTEEECHHHHHH
T ss_pred             CccccccChhh--cceEEeccEEeehhhhhc
Confidence            37889988854  457788899999988654

>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.05  E-value=0.0036  Score=28.62  Aligned_cols=26  Identities=27%  Similarity=0.636  Sum_probs=22.7

Q ss_pred             cccccCCCCCCCceEEEeCCcccccccc
Q psy284          104 YCAACSKVIPAFEMVMRARNNVYHLECF  131 (139)
Q Consensus       104 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf  131 (139)
                      .|..|...|..  ..+.+.+-.|||.+|
T Consensus        10 vC~KCh~iIdd--~pL~Fr~d~YHp~HF   35 (35)
T d2cora2          10 ICQKCHAIIDE--QPLIFKNDPYHPDHF   35 (35)
T ss_dssp             BCTTTCCBCCS--CCCCCSSSCCCTTTS
T ss_pred             HHHHHHhhhhc--CcceecCCCCCCCCC
Confidence            79999998854  788999999999887

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.95  E-value=0.0087  Score=27.13  Aligned_cols=28  Identities=25%  Similarity=0.566  Sum_probs=22.5

Q ss_pred             CCCcccccccccccceeeeecCccccccC
Q psy284           37 GPQECAGCGKHITDRFLLKALDMYWHEDC   65 (139)
Q Consensus        37 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~C   65 (139)
                      -...|..|...|.+. ++.+.+..||++|
T Consensus         7 fge~C~~C~~~itGp-vMvAG~~K~HPEC   34 (34)
T d1x6aa1           7 FGEFCHGCSLLMTGP-FMVAGEFKYHPEC   34 (34)
T ss_dssp             SSCBCTTTCCBCCSC-CBCCTTCCBCTTS
T ss_pred             HHHHhhhhHhhcccc-eeeecccccCCCC
Confidence            356899999977754 6777888999987

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.92  E-value=0.0047  Score=29.23  Aligned_cols=28  Identities=21%  Similarity=0.598  Sum_probs=20.8

Q ss_pred             cccccccccccc-eeeeecCccccccCcc
Q psy284           40 ECAGCGKHITDR-FLLKALDMYWHEDCLK   67 (139)
Q Consensus        40 ~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~   67 (139)
                      .|.+|+..+.+. +.....+..||+.|-.
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~IWHP~C~~   29 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSSIWHPACRQ   29 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTEEECTTHHH
T ss_pred             CcchhhccccccceeeecCCceeCCcccc
Confidence            488999988875 4445567889998855

>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.81  E-value=0.022  Score=25.87  Aligned_cols=30  Identities=23%  Similarity=0.359  Sum_probs=24.6

Q ss_pred             CCCCcccccccccccceeeeecCccccccCc
Q psy284           36 QGPQECAGCGKHITDRFLLKALDMYWHEDCL   66 (139)
Q Consensus        36 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   66 (139)
                      .+..+|..|...|.+. -+...+..||+..|
T Consensus         6 lGk~vC~KCh~iIdd~-pL~Fr~d~YHp~HF   35 (35)
T d2cora2           6 LGKYICQKCHAIIDEQ-PLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCBCTTTCCBCCSC-CCCCSSSCCCTTTS
T ss_pred             hhhHHHHHHHhhhhcC-cceecCCCCCCCCC
Confidence            4567899999999886 36788999999876

>d1x62a1 g.39.1.3 (A:43-73) PDZ and LIM domain protein 1 Elfin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 1 Elfin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.22  E-value=0.011  Score=26.05  Aligned_cols=29  Identities=17%  Similarity=0.417  Sum_probs=22.1

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHH
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLR   97 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~   97 (139)
                      .|..|+..|..  ..++..++++||+.+...
T Consensus         1 vC~dCg~NLKq--rG~Ffve~~lyCE~HAr~   29 (31)
T d1x62a1           1 VCTDCGTNLKQ--KGHFFVEDQIYCEKHARE   29 (31)
T ss_dssp             SCSSSCCCHHH--HCCEESSSCEECHHHHHH
T ss_pred             CccccccChhh--cceEEeccEEehhhhhhh
Confidence            37788888854  346778889999998654

>d2cupa2 g.39.1.3 (A:35-65) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=91.91  E-value=0.072  Score=23.20  Aligned_cols=27  Identities=33%  Similarity=0.598  Sum_probs=21.1

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhH
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDY   95 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy   95 (139)
                      +|..|-.+|  ....|..++++++|..|.
T Consensus         1 RCaKC~hpL--A~E~F~aKd~kI~C~Kc~   27 (31)
T d2cupa2           1 RCAKCLHPL--ANETFVAKDNKILCNKCT   27 (31)
T ss_dssp             CCSSSCCCT--TSSCCEEETTEEECHHHH
T ss_pred             Cchhhcccc--ccCcccccCCeEeecccc
Confidence            466777888  456788999999998875

>d2cora1 g.39.1.3 (A:43-73) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.17  E-value=0.12  Score=22.51  Aligned_cols=27  Identities=15%  Similarity=0.249  Sum_probs=20.3

Q ss_pred             cccCCCCcccCCCeeEeeCCccccHhhHHH
Q psy284           68 CGCCDCRLGEVGSTLYTKANLILCKRDYLR   97 (139)
Q Consensus        68 C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~   97 (139)
                      |..|++.|.   ..-....+.+||..|..+
T Consensus         2 C~~Cgkelt---adArEl~geLyCLpChdK   28 (31)
T d2cora1           2 CANCGKELT---ADARELKGELYCLPCHDK   28 (31)
T ss_dssp             CSSSCCBCC---TTCEEETTEEECHHHHHT
T ss_pred             ccccccccc---hhHHHhcCCEEEEecccc
Confidence            677888884   234678899999998754

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=90.17  E-value=0.078  Score=28.31  Aligned_cols=35  Identities=23%  Similarity=0.598  Sum_probs=28.1

Q ss_pred             CCCCCcccccccccccceeeeecCccccccCcccc
Q psy284           35 AQGPQECAGCGKHITDRFLLKALDMYWHEDCLKCG   69 (139)
Q Consensus        35 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~   69 (139)
                      ++..-.|..|.+.+.+...+.--...-|+-||.|+
T Consensus         5 ~~~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCs   39 (80)
T d2cs3a1           5 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCS   39 (80)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHH
T ss_pred             CCCceeeeeehhhhcCCceEeCCCCcCCceecccc
Confidence            34457899999999997667777777899999876

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=88.22  E-value=0.16  Score=22.31  Aligned_cols=25  Identities=36%  Similarity=0.830  Sum_probs=17.1

Q ss_pred             cccCCCCcccCCCeeEeeCCccccHhh
Q psy284           68 CGCCDCRLGEVGSTLYTKANLILCKRD   94 (139)
Q Consensus        68 C~~C~~~l~~~~~~~~~~~~~~~C~~c   94 (139)
                      |..|+..|  .+..|...+..++|..|
T Consensus         2 cgkcsvsl--vg~gfltq~~~i~c~~c   26 (34)
T d1x68a2           2 CGKCSVSL--VGKGFLTQNKEIFCQKC   26 (34)
T ss_dssp             CTTTCCBC--SSSCEEEETTEEEETTT
T ss_pred             CccceEEE--EeeeeeeccCcEEehhc
Confidence            45566666  56667777777877666

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.28  E-value=0.19  Score=28.33  Aligned_cols=44  Identities=20%  Similarity=0.400  Sum_probs=30.9

Q ss_pred             cccccCCCCcccCCCeeE-eeCCccccHhhHHHHhCCCccccccCCCCCC
Q psy284           66 LKCGCCDCRLGEVGSTLY-TKANLILCKRDYLRLFGSTGYCAACSKVIPA  114 (139)
Q Consensus        66 f~C~~C~~~l~~~~~~~~-~~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~  114 (139)
                      +.|..|...+.  . ... ..-+..||..|..+.+..  .|..|..++..
T Consensus        23 l~C~IC~~~~~--~-pv~~~~CgH~fC~~Ci~~~~~~--~CP~Cr~~~~~   67 (97)
T d1jm7b_          23 LRCSRCTNILR--E-PVCLGGCEHIFCSNCVSDCIGT--GCPVCYTPAWI   67 (97)
T ss_dssp             TSCSSSCSCCS--S-CBCCCSSSCCBCTTTGGGGTTT--BCSSSCCBCSC
T ss_pred             CCCccCCchhh--c-CceeCCCCCchhHHHHHHHHhc--cccccCCcCch
Confidence            67777877763  2 233 356788888887766665  79999988765

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=86.63  E-value=0.19  Score=25.35  Aligned_cols=46  Identities=13%  Similarity=0.074  Sum_probs=31.3

Q ss_pred             ccccCCCCcccCCCeeEe-eCCccccHhhHHHHhCCCccccccCCCCCCC
Q psy284           67 KCGCCDCRLGEVGSTLYT-KANLILCKRDYLRLFGSTGYCAACSKVIPAF  115 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~-~~~~~~C~~cy~~~~~~~~~C~~C~~~I~~~  115 (139)
                      .|..|...+.   ..+.. ..|..||..|-.+.+...+.|..|++++...
T Consensus         2 ~C~Ic~~~~~---~Pv~~~~cGh~fc~~cI~~~l~~~~~CP~c~~~l~~~   48 (56)
T d2baya1           2 LCAISGKVPR---RPVLSPKSRTIFEKSLLEQYVKDTGNDPITNEPLSIE   48 (56)
T ss_dssp             CCTTTCSCCS---SEEEETTTTEEEEHHHHHHHHHHHSBCTTTCCBCCGG
T ss_pred             CCccCCchHH---hcCccCCCCCcccHHHHHHHHhhccCCCccCCcCCHH
Confidence            4677776662   33444 5789999999654443334899999998763

>d1x4la2 g.39.1.3 (A:37-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.58  E-value=0.28  Score=20.82  Aligned_cols=26  Identities=35%  Similarity=0.581  Sum_probs=18.4

Q ss_pred             cccCCCCcccCCCeeEeeCCccccHhhH
Q psy284           68 CGCCDCRLGEVGSTLYTKANLILCKRDY   95 (139)
Q Consensus        68 C~~C~~~l~~~~~~~~~~~~~~~C~~cy   95 (139)
                      |..|+..|  .+..|....+.++|.+|-
T Consensus         2 c~kcsvsl--vgrgflterddilc~dcg   27 (30)
T d1x4la2           2 CKKCSLSL--VGRGFLTERDDILCPDCG   27 (30)
T ss_dssp             CSSSCCBC--TTSCCEECSSSEECHHHH
T ss_pred             cceeeEEE--EeeeccccccceeccccC
Confidence            55677777  556677777788888874

>d2d8xa1 g.39.1.3 (A:33-64) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.16  E-value=0.49  Score=20.63  Aligned_cols=29  Identities=24%  Similarity=0.411  Sum_probs=21.6

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhhHHH
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRDYLR   97 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~cy~~   97 (139)
                      +|..|...|.  +..|.-.-++.+|..|..+
T Consensus         1 rC~~C~~~LA--D~GFvKnagR~LCrpch~r   29 (32)
T d2d8xa1           1 RCDLCQEVLA--DIGFVKNAGRHLCRPCHNR   29 (32)
T ss_dssp             BCSSSCCBCS--SSCCEEETTEEECHHHHHH
T ss_pred             CchHHHhHHH--Hhhhhhcccccccchhhhh
Confidence            4778888884  3457777888899888754

>d2co8a1 g.39.1.3 (A:44-76) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.00  E-value=0.15  Score=22.57  Aligned_cols=28  Identities=18%  Similarity=0.398  Sum_probs=18.4

Q ss_pred             ccccCCCCcccCCCeeEeeCCccccHhh
Q psy284           67 KCGCCDCRLGEVGSTLYTKANLILCKRD   94 (139)
Q Consensus        67 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c   94 (139)
                      +|..|...|...+......++.+||..+
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~h   28 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQH   28 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTT
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeec
Confidence            4667777876444444467788888765

>d1v6ga2 g.39.1.3 (A:42-81) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.86  E-value=0.59  Score=21.48  Aligned_cols=28  Identities=14%  Similarity=0.451  Sum_probs=15.0

Q ss_pred             cccccCCCCcccCCCeeEeeCCccccHhh
Q psy284           66 LKCGCCDCRLGEVGSTLYTKANLILCKRD   94 (139)
Q Consensus        66 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c   94 (139)
                      |.|..|..++. .+.+........+|..|
T Consensus         1 FvC~vCr~pFP-~GDRVTFnGKeC~CQ~C   28 (40)
T d1v6ga2           1 FVCAVCRLPFP-PGDRVTFNGKECMCQKC   28 (40)
T ss_dssp             SSCSSSCCCCC-SSSCEEEETTEEEEHHH
T ss_pred             CcccccCCCCC-CCCeEEEcCceeehhhc
Confidence            56777777775 33444444444444433