Psyllid ID: psy7479

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170
Protein Sequence
ASSVTQGALAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRRQVTLQVLWIRE
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccEEEEEccccccccccccccccccccccccEEEEEccccccHHHHHHHHccccccccccccccccccEEEEcccEEEcccccccccccccccccEEEEEccEEEEHHcHHHHHHHcccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccccccHEEEEHccHHHHHHHHHHcHccccccccccEEEEccccEEEHHHHHHHHccccccccccccccHHHHHHHHHcccEEEHHEHHHHHHcccccccEEEEEccEEEEcccHHHHHHHHHccccccccccccccccHHHHHHcc
Coil and Loop (DISEMBL)
assvtqgalaggasgglkecascgKRITERFLLKALDlfwhedclkcgccdcrlgevgstLYQKANLILCKRDYLRlfgttgycaacTKVIPAFEMVMRAKNnvyhlecfacqqcnhrfcvgdrfylcdnkilceydyEERQVFAniaynpsslaHLRRQVTLQVLWIRE
Flexible Loop (DISEMBL)
assvtqgalaggasgglkeCASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAynpsslahlrrQVTLQVLWIRE
Low Complexity Region (SEG)
ASSVTQgalaggasgglKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRRQVTLQVLWIRE
Disordered region (IsUnstruct)
***************GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRRQVTLQVLWI**
Disordered Region (DISOPRED)
**********************CGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY********************************
Disordered Region (DISEMBL)
*****************KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRRQVTLQVLWIRE
Disordered Region (DISPRO)
****************LKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANI***********************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
ASSVTQGALAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRRQVTLQVLWIRE
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	170	2.2.26 [Sep-21-2011]
Q3B8H4	156	Rhombotin-1 OS=Xenopus la	N/A	N/A	0.794	0.865	0.725	2e-54
P25800	156	Rhombotin-1 OS=Homo sapie	yes	N/A	0.794	0.865	0.725	2e-54
Q8JFQ2	155	Rhombotin-1 OS=Danio reri	yes	N/A	0.794	0.870	0.725	2e-54
Q0P5B3	156	Rhombotin-1 OS=Bos taurus	yes	N/A	0.794	0.865	0.725	2e-54
Q924W9	156	Rhombotin-1 OS=Mus muscul	yes	N/A	0.776	0.846	0.734	8e-54
Q99MB5	145	LIM domain only protein 3	no	N/A	0.764	0.896	0.734	1e-53
Q9YH16	156	LIM domain only protein 3	N/A	N/A	0.711	0.775	0.772	7e-53
Q5RBW7	145	LIM domain only protein 3	no	N/A	0.711	0.834	0.772	7e-53
Q8BZL8	145	LIM domain only protein 3	no	N/A	0.711	0.834	0.772	7e-53
Q8TAP4	145	LIM domain only protein 3	no	N/A	0.711	0.834	0.772	7e-53

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

 Score =  211 bits (537), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 98/135 (72%), Positives = 115/135 (85%)

Query: 9   LAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLI 68
           L+    G  K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLI
Sbjct: 13  LSVQPKGKQKGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLI 72

Query: 69  LCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC 128
           LC+RDYLRLFGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L 
Sbjct: 73  LCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLK 132

Query: 129 DNKILCEYDYEERQV 143
           +N ILC+ DYEE Q+
Sbjct: 133 NNMILCQMDYEEGQL 147

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

 Score =  211 bits (536), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 98/135 (72%), Positives = 115/135 (85%)

Query: 9   LAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLI 68
           L+    G  K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLI
Sbjct: 13  LSVQPKGKQKGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLI 72

Query: 69  LCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC 128
           LC+RDYLRLFGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L 
Sbjct: 73  LCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLK 132

Query: 129 DNKILCEYDYEERQV 143
           +N ILC+ DYEE Q+
Sbjct: 133 NNMILCQMDYEEGQL 147

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

 Score =  211 bits (536), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 98/135 (72%), Positives = 115/135 (85%)

Query: 9   LAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLI 68
           L+    G  K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLI
Sbjct: 12  LSVQPKGKQKGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLI 71

Query: 69  LCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC 128
           LC+RDYLRLFGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L 
Sbjct: 72  LCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLK 131

Query: 129 DNKILCEYDYEERQV 143
           +N ILC+ DYEE Q+
Sbjct: 132 NNMILCQMDYEEGQL 146

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

 Score =  211 bits (536), Expect = 2e-54,   Method: Compositional matrix adjust.
 Identities = 98/135 (72%), Positives = 115/135 (85%)

Query: 9   LAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLI 68
           L+    G  K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLI
Sbjct: 13  LSVQPKGKQKGCAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLI 72

Query: 69  LCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC 128
           LC+RDYLRLFGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L 
Sbjct: 73  LCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLK 132

Query: 129 DNKILCEYDYEERQV 143
           +N ILC+ DYEE Q+
Sbjct: 133 NNMILCQMDYEEGQL 147

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

 Score =  209 bits (531), Expect = 8e-54,   Method: Compositional matrix adjust.
 Identities = 97/132 (73%), Positives = 113/132 (85%)

Query: 9   LAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLI 68
           L+    G  K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLI
Sbjct: 13  LSVQPKGKQKGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLI 72

Query: 69  LCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC 128
           LC+RDYLRLFGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L 
Sbjct: 73  LCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLK 132

Query: 129 DNKILCEYDYEE 140
           +N ILC+ DYEE
Sbjct: 133 NNMILCQVDYEE 144

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|Q99MB5|LMO3_RAT LIM domain only protein 3 OS=Rattus norvegicus GN=Lmo3 PE=2 SV=2

 Score =  208 bits (529), Expect = 1e-53,   Method: Compositional matrix adjust.
 Identities = 97/132 (73%), Positives = 113/132 (85%)

Query: 9   LAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLI 68
           L+    G  K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLI
Sbjct: 2   LSVQPKGKQKGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLI 61

Query: 69  LCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC 128
           LC+RDYLRLFGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L 
Sbjct: 62  LCRRDYLRLFGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLK 121

Query: 129 DNKILCEYDYEE 140
           +N ILC+ DYEE
Sbjct: 122 NNMILCQTDYEE 133

Rattus norvegicus (taxid: 10116)

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

 Score =  206 bits (523), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 95/123 (77%), Positives = 108/123 (87%)

Query: 18  KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
           K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct: 22  KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 81

Query: 78  FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
           FG TG CAAC+K+IPAFEMVMRAK NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct: 82  FGVTGNCAACSKLIPAFEMVMRAKENVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQTD 141

Query: 138 YEE 140
           YEE
Sbjct: 142 YEE 144

Xenopus laevis (taxid: 8355)

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

 Score =  206 bits (523), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 95/123 (77%), Positives = 109/123 (88%)

Query: 18  KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
           K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct: 11  KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 70

Query: 78  FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
           FG TG CAAC+K+IPAFEMVMRAK+NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct: 71  FGVTGNCAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQTD 130

Query: 138 YEE 140
           YEE
Sbjct: 131 YEE 133

Pongo abelii (taxid: 9601)

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

 Score =  206 bits (523), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 95/123 (77%), Positives = 109/123 (88%)

Query: 18  KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
           K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct: 11  KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 70

Query: 78  FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
           FG TG CAAC+K+IPAFEMVMRAK+NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct: 71  FGVTGNCAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQTD 130

Query: 138 YEE 140
           YEE
Sbjct: 131 YEE 133

Mus musculus (taxid: 10090)

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

 Score =  206 bits (523), Expect = 7e-53,   Method: Compositional matrix adjust.
 Identities = 95/123 (77%), Positives = 109/123 (88%)

Query: 18  KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
           K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct: 11  KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 70

Query: 78  FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
           FG TG CAAC+K+IPAFEMVMRAK+NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct: 71  FGVTGNCAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQTD 130

Query: 138 YEE 140
           YEE
Sbjct: 131 YEE 133

Homo sapiens (taxid: 9606)

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	170
157116702	218	rhombotin [Aedes aegypti] gi|108876328|g	0.964	0.752	0.866	1e-78
270005132	254	hypothetical protein TcasGA2_TC007141 [T	0.929	0.622	0.867	2e-78
242005244	284	LIM-only protein, putative [Pediculus hu	0.876	0.524	0.919	2e-78
158289946	204	AGAP010391-PA [Anopheles gambiae str. PE	0.964	0.803	0.866	2e-78
189236731	231	PREDICTED: similar to AGAP010391-PA [Tri	0.870	0.640	0.912	6e-77
170031972	255	rhombotin [Culex quinquefasciatus] gi|16	0.976	0.650	0.846	2e-76
328712778	388	PREDICTED: hypothetical protein LOC10016	0.947	0.414	0.839	2e-75
91080717	241	PREDICTED: similar to beadex/dLMO protei	0.970	0.684	0.795	8e-75
357622819	359	beadex/dLMO protein [Danaus plexippus]	0.841	0.398	0.860	2e-72
114052529	267	beadex/dLMO protein [Bombyx mori] gi|872	0.841	0.535	0.860	4e-71

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

 Score =  297 bits (760), Expect = 1e-78,   Method: Compositional matrix adjust.
 Identities = 143/165 (86%), Positives = 151/165 (91%), Gaps = 1/165 (0%)

Query: 2   SSVTQGALAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTL 61
           SSV+      G++G  K+CA CGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTL
Sbjct: 49  SSVSSTPNLIGSNGMAKDCAGCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTL 108

Query: 62  YQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV 121
           Y KANLILCKRDYLRLFGTTGYCAAC KVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV
Sbjct: 109 YTKANLILCKRDYLRLFGTTGYCAACNKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV 168

Query: 122 GDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRRQVT-LQV 165
           GDRFYLCDNKILCEYDYEER VFA++A NPSSLAH+RRQV+ LQV
Sbjct: 169 GDRFYLCDNKILCEYDYEERLVFASMACNPSSLAHIRRQVSNLQV 213

Source: Aedes aegypti

Species: Aedes aegypti

Genus: Aedes

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  296 bits (758), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 137/158 (86%), Positives = 145/158 (91%)

Query: 3   SVTQGALAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLY 62
           SV+  A +     G++ECA CGKRITERFLLKALDL+WHEDCLKCGCCDCRLGEVGSTLY
Sbjct: 31  SVSTAANSTATGAGVRECAGCGKRITERFLLKALDLYWHEDCLKCGCCDCRLGEVGSTLY 90

Query: 63  QKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVG 122
            KANLILCKRDYLRLFGTTGYCAAC KVIPAFEMVMRAK+NVYHLECFACQQCNHRFCVG
Sbjct: 91  TKANLILCKRDYLRLFGTTGYCAACNKVIPAFEMVMRAKSNVYHLECFACQQCNHRFCVG 150

Query: 123 DRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRRQ 160
           DRFYLCDNKILCEYDYEER VFAN+ YNPSSLAH+RRQ
Sbjct: 151 DRFYLCDNKILCEYDYEERLVFANMTYNPSSLAHIRRQ 188

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 =  296 bits (758), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 137/149 (91%), Positives = 142/149 (95%)

Query: 13  ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 72
            S G +ECA CGKRITERFLLKA+DLFWHEDCLKCGCCDCRLGEVGSTLY KANLILCKR
Sbjct: 42  PSSGPRECAGCGKRITERFLLKAIDLFWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKR 101

Query: 73  DYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKI 132
           DYLRLFGTTGYCAAC KVIPAFEMVMRAK+NVYHLECFACQQCNHRFCVGDRFYLCDNKI
Sbjct: 102 DYLRLFGTTGYCAACNKVIPAFEMVMRAKSNVYHLECFACQQCNHRFCVGDRFYLCDNKI 161

Query: 133 LCEYDYEERQVFANIAYNPSSLAHLRRQV 161
           LCEYDYEER VFAN+AYNPSSLAH+RRQV
Sbjct: 162 LCEYDYEERLVFANMAYNPSSLAHIRRQV 190

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

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 =  296 bits (757), Expect = 2e-78,   Method: Compositional matrix adjust.
 Identities = 143/165 (86%), Positives = 151/165 (91%), Gaps = 1/165 (0%)

Query: 2   SSVTQGALAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTL 61
           SSV+  A    A+G  K+CA CGKRITERFLLKALD+FWHEDCLKCGCCDCRLGEVGSTL
Sbjct: 35  SSVSATANQVAATGLAKDCAGCGKRITERFLLKALDIFWHEDCLKCGCCDCRLGEVGSTL 94

Query: 62  YQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV 121
           Y KANLILCKRDYLRLFGTTGYCAAC KVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV
Sbjct: 95  YTKANLILCKRDYLRLFGTTGYCAACNKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV 154

Query: 122 GDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRRQVT-LQV 165
           GDRFYLCDNKILCEYDYEER VFA++A NPSSLAH+RRQV+ LQV
Sbjct: 155 GDRFYLCDNKILCEYDYEERLVFASMACNPSSLAHIRRQVSNLQV 199

Source: Anopheles gambiae str. PEST

Species: Anopheles gambiae

Genus: Anopheles

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189236731|ref|XP_974987.2| PREDICTED: similar to AGAP010391-PA [Tribolium castaneum]

 Score =  291 bits (745), Expect = 6e-77,   Method: Compositional matrix adjust.
 Identities = 135/148 (91%), Positives = 142/148 (95%)

Query: 15  GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
           G ++ECA CGKRITERFLLKALDL+WHEDCLKCGCCDCRLGEVGSTLY KANLILCKRDY
Sbjct: 15  GRVRECAGCGKRITERFLLKALDLYWHEDCLKCGCCDCRLGEVGSTLYTKANLILCKRDY 74

Query: 75  LRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILC 134
           LRLFGTTGYCAAC KVIPAFEMVMRAK+NVYHLECFACQQCNHRFCVGDRFYLCDNKILC
Sbjct: 75  LRLFGTTGYCAACNKVIPAFEMVMRAKSNVYHLECFACQQCNHRFCVGDRFYLCDNKILC 134

Query: 135 EYDYEERQVFANIAYNPSSLAHLRRQVT 162
           EYDYEER VFAN+ YNPSSLAH+RRQV+
Sbjct: 135 EYDYEERLVFANMTYNPSSLAHIRRQVS 162

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|170031972|ref|XP_001843857.1| rhombotin [Culex quinquefasciatus] gi|167871437|gb|EDS34820.1| rhombotin [Culex quinquefasciatus]

 Score =  290 bits (741), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 143/169 (84%), Positives = 148/169 (87%), Gaps = 3/169 (1%)

Query: 2   SSVTQGALAGGASGGL--KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGS 59
           SS+      G  S GL  K+CA CGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGS
Sbjct: 62  SSIQSAPNLGLGSTGLANKDCAGCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGS 121

Query: 60  TLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF 119
           TLY KANLILCKRDYLRLFGTTGYCAAC KVIPAFEMVMRAKNNVYHLECFACQQCNHRF
Sbjct: 122 TLYTKANLILCKRDYLRLFGTTGYCAACNKVIPAFEMVMRAKNNVYHLECFACQQCNHRF 181

Query: 120 CVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRRQVTLQV-LW 167
           CVGDRFYLCDNKILCEYDYEER VFA++A NPSSLAH+RRQ    V LW
Sbjct: 182 CVGDRFYLCDNKILCEYDYEERLVFASMACNPSSLAHIRRQRKYIVELW 230

Source: Culex quinquefasciatus

Species: Culex quinquefasciatus

Genus: Culex

Family: Culicidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328712778|ref|XP_001945042.2| PREDICTED: hypothetical protein LOC100161710 [Acyrthosiphon pisum]

 Score =  286 bits (732), Expect = 2e-75,   Method: Compositional matrix adjust.
 Identities = 136/162 (83%), Positives = 145/162 (89%), Gaps = 1/162 (0%)

Query: 2   SSVTQGALAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTL 61
           ++ T   L G  +   +ECA+CGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTL
Sbjct: 41  TATTLTGLNGSTAMIARECANCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTL 100

Query: 62  YQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV 121
           Y KANLILCKRDYLRLFG TG CAAC KVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV
Sbjct: 101 YTKANLILCKRDYLRLFGATGNCAACNKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV 160

Query: 122 GDRFYLCDNKILCEYDYEERQVFANIA-YNPSSLAHLRRQVT 162
           GDRFYLC+NKILCEYDYEER VFAN+A YN SSLAH+RRQV+
Sbjct: 161 GDRFYLCENKILCEYDYEERLVFANMATYNSSSLAHIRRQVS 202

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>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 =  284 bits (727), Expect = 8e-75,   Method: Compositional matrix adjust.
 Identities = 132/166 (79%), Positives = 147/166 (88%), Gaps = 1/166 (0%)

Query: 4   VTQGALAGGASG-GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLY 62
           V++G  A  +SG G +ECA C K ITER+LLKALDL+WHEDCLKCGCCDCRLGEVGSTLY
Sbjct: 19  VSKGEAAKPSSGQGPQECAGCCKTITERYLLKALDLYWHEDCLKCGCCDCRLGEVGSTLY 78

Query: 63  QKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVG 122
            KANLILCKRDYLRLFG TGYCAAC+KVIPAFEMVMRA++NVYHLECFACQQCNHRFCVG
Sbjct: 79  TKANLILCKRDYLRLFGNTGYCAACSKVIPAFEMVMRARSNVYHLECFACQQCNHRFCVG 138

Query: 123 DRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRRQVTLQVLWI 168
           DRFYLC+NKILCEYDYEER VFAN+AYNP  L+HL+RQ ++    I
Sbjct: 139 DRFYLCENKILCEYDYEERLVFANMAYNPPPLSHLKRQTSIPPPNI 184

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

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

 Score =  276 bits (707), Expect = 2e-72,   Method: Compositional matrix adjust.
 Identities = 123/143 (86%), Positives = 130/143 (90%)

Query: 20  CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
           CA C K ITER+LLKALD  WHEDCLKCGCCDCRLGEVG TLY +ANLILCKRDYLRLFG
Sbjct: 167 CAGCSKVITERYLLKALDQLWHEDCLKCGCCDCRLGEVGHTLYTRANLILCKRDYLRLFG 226

Query: 80  TTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYE 139
            TGYCAAC KVIPAFEMVMRA++NVYHLECFACQQCNHRFCVGDRFYLC+NKILCEYDYE
Sbjct: 227 NTGYCAACNKVIPAFEMVMRARSNVYHLECFACQQCNHRFCVGDRFYLCENKILCEYDYE 286

Query: 140 ERQVFANIAYNPSSLAHLRRQVT 162
           ER VFAN+AYNP  LAHL+RQ T
Sbjct: 287 ERLVFANMAYNPPPLAHLKRQTT 309

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|114052529|ref|NP_001040254.1| beadex/dLMO protein [Bombyx mori] gi|87248525|gb|ABD36315.1| beadex/dLMO protein [Bombyx mori]

 Score =  272 bits (695), Expect = 4e-71,   Method: Compositional matrix adjust.
 Identities = 123/143 (86%), Positives = 130/143 (90%)

Query: 20  CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
           CA C K ITER+LLKALD  WHEDCLKCGCCDCRLGEVG TLY +ANLILCKRDYLRLFG
Sbjct: 56  CAGCSKVITERYLLKALDQLWHEDCLKCGCCDCRLGEVGHTLYTRANLILCKRDYLRLFG 115

Query: 80  TTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYE 139
            TGYCAAC KVIPAFEMVMRA++NVYHLECFACQQCNHRFCVGDRFYLC+NKILCEYDYE
Sbjct: 116 NTGYCAACNKVIPAFEMVMRARSNVYHLECFACQQCNHRFCVGDRFYLCENKILCEYDYE 175

Query: 140 ERQVFANIAYNPSSLAHLRRQVT 162
           ER VFAN+AYNP  LAHL+RQ T
Sbjct: 176 ERLVFANMAYNPPPLAHLKRQTT 198

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

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	170
UNIPROTKB|P91608	266	Bx "Dttg protein" [Drosophila	0.811	0.518	0.811	1.4e-64
UNIPROTKB|A9ED79	156	LMO1 "Uncharacterized protein"	0.788	0.858	0.720	6.1e-55
UNIPROTKB|F1NBH5	156	LOC100858792 "Uncharacterized	0.741	0.807	0.761	9.9e-55
UNIPROTKB|Q0P5B3	156	LMO1 "Rhombotin-1" [Bos taurus	0.741	0.807	0.761	9.9e-55
UNIPROTKB|E2RLZ2	156	LMO1 "Uncharacterized protein"	0.741	0.807	0.761	9.9e-55
UNIPROTKB|E9PK83	145	LMO1 "Rhombotin-1" [Homo sapie	0.741	0.868	0.761	9.9e-55
UNIPROTKB|E9PSF5	155	LMO1 "Rhombotin-1" [Homo sapie	0.741	0.812	0.761	9.9e-55
UNIPROTKB|P25800	156	LMO1 "Rhombotin-1" [Homo sapie	0.741	0.807	0.761	9.9e-55
UNIPROTKB|Q3B8H4	156	lmo1 "Rhombotin-1" [Xenopus la	0.741	0.807	0.761	9.9e-55
ZFIN|ZDB-GENE-021115-6	155	lmo1 "LIM domain only 1" [Dani	0.741	0.812	0.761	9.9e-55

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

 Score = 658 (236.7 bits), Expect = 1.4e-64, P = 1.4e-64
 Identities = 112/138 (81%), Positives = 124/138 (89%)

Query:    20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
             CA CGK I +R+LL+ALD+ WHEDCLKCGCCDCRLGEVGSTLY K NL+LCKRDYLRLFG
Sbjct:    45 CAGCGKHIQDRYLLRALDMLWHEDCLKCGCCDCRLGEVGSTLYTKGNLMLCKRDYLRLFG 104

Query:    80 TTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYE 139
              TGYCAAC+KVIPAFEMVMRA+ NVYHLECFACQQCNHRFCVGDRFYLC+NKILCEYDYE
Sbjct:   105 NTGYCAACSKVIPAFEMVMRARTNVYHLECFACQQCNHRFCVGDRFYLCENKILCEYDYE 164

Query:   140 ERQVFANIAYNPSSLAHL 157
             ER VFA++A +P    H+
Sbjct:   165 ERLVFASMANHPMLKRHV 182

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

 Score = 567 (204.7 bits), Expect = 6.1e-55, P = 6.1e-55
 Identities = 98/136 (72%), Positives = 116/136 (85%)

Query:    18 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
             K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct:    22 KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 81

Query:    78 FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
             FGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct:    82 FGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQLD 141

Query:   138 YEERQVFANIAYNPSS 153
             YEE Q+    A+ P +
Sbjct:   142 YEEGQLTG--AFEPQA 155

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|F1NBH5 LOC100858792 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 565 (203.9 bits), Expect = 9.9e-55, P = 9.9e-55
 Identities = 96/126 (76%), Positives = 112/126 (88%)

Query:    18 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
             K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct:    22 KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 81

Query:    78 FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
             FGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct:    82 FGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMD 141

Query:   138 YEERQV 143
             YEE Q+
Sbjct:   142 YEEGQL 147

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 565 (203.9 bits), Expect = 9.9e-55, P = 9.9e-55
 Identities = 96/126 (76%), Positives = 112/126 (88%)

Query:    18 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
             K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct:    22 KGCAGCNRKIKDRYLLKALDQYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 81

Query:    78 FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
             FGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct:    82 FGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMD 141

Query:   138 YEERQV 143
             YEE Q+
Sbjct:   142 YEEGQL 147

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 = 565 (203.9 bits), Expect = 9.9e-55, P = 9.9e-55
 Identities = 96/126 (76%), Positives = 112/126 (88%)

Query:    18 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
             K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct:    22 KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 81

Query:    78 FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
             FGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct:    82 FGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMD 141

Query:   138 YEERQV 143
             YEE Q+
Sbjct:   142 YEEGQL 147

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|E9PK83 LMO1 "Rhombotin-1" [Homo sapiens (taxid:9606)]

 Score = 565 (203.9 bits), Expect = 9.9e-55, P = 9.9e-55
 Identities = 96/126 (76%), Positives = 112/126 (88%)

Query:    18 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
             K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct:    11 KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 70

Query:    78 FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
             FGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct:    71 FGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMD 130

Query:   138 YEERQV 143
             YEE Q+
Sbjct:   131 YEEGQL 136

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

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

 Score = 565 (203.9 bits), Expect = 9.9e-55, P = 9.9e-55
 Identities = 96/126 (76%), Positives = 112/126 (88%)

Query:    18 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
             K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct:    21 KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 80

Query:    78 FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
             FGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct:    81 FGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMD 140

Query:   138 YEERQV 143
             YEE Q+
Sbjct:   141 YEEGQL 146

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 565 (203.9 bits), Expect = 9.9e-55, P = 9.9e-55
 Identities = 96/126 (76%), Positives = 112/126 (88%)

Query:    18 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
             K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct:    22 KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 81

Query:    78 FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
             FGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct:    82 FGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMD 141

Query:   138 YEERQV 143
             YEE Q+
Sbjct:   142 YEEGQL 147

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

 Score = 565 (203.9 bits), Expect = 9.9e-55, P = 9.9e-55
 Identities = 96/126 (76%), Positives = 112/126 (88%)

Query:    18 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
             K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct:    22 KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 81

Query:    78 FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
             FGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct:    82 FGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMD 141

Query:   138 YEERQV 143
             YEE Q+
Sbjct:   142 YEEGQL 147

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 = 565 (203.9 bits), Expect = 9.9e-55, P = 9.9e-55
 Identities = 96/126 (76%), Positives = 112/126 (88%)

Query:    18 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
             K CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+RDYLRL
Sbjct:    21 KGCAGCNRKIKDRYLLKALDKYWHEDCLKCACCDCRLGEVGSTLYTKANLILCRRDYLRL 80

Query:    78 FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
             FGTTG CAAC+K+IPAFEMVMRA++NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ D
Sbjct:    81 FGTTGNCAACSKLIPAFEMVMRARDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMD 140

Query:   138 YEERQV 143
             YEE Q+
Sbjct:   141 YEEGQL 146

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISS

GO:0046872 "metal ion binding" evidence=IEA

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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)
Q8BZL8	LMO3_MOUSE	No assigned EC number	0.7723	0.7117	0.8344	no	N/A
Q9YH16	LMO3_XENLA	No assigned EC number	0.7723	0.7117	0.7756	N/A	N/A
Q503U0	LMO3_DANRE	No assigned EC number	0.7723	0.7117	0.8344	no	N/A
Q5RBW7	LMO3_PONAB	No assigned EC number	0.7723	0.7117	0.8344	no	N/A
Q6DJ06	LMO42_XENTR	No assigned EC number	0.4817	0.8058	0.8303	yes	N/A
Q3B8H4	RBTN1_XENLA	No assigned EC number	0.7259	0.7941	0.8653	N/A	N/A
Q924W9	RBTN1_MOUSE	No assigned EC number	0.7348	0.7764	0.8461	yes	N/A
Q8TAP4	LMO3_HUMAN	No assigned EC number	0.7723	0.7117	0.8344	no	N/A
Q8JFQ2	RBTN1_DANRE	No assigned EC number	0.7259	0.7941	0.8709	yes	N/A
Q99MB5	LMO3_RAT	No assigned EC number	0.7348	0.7647	0.8965	no	N/A
P25800	RBTN1_HUMAN	No assigned EC number	0.7259	0.7941	0.8653	yes	N/A
Q0P5B3	RBTN1_BOVIN	No assigned EC number	0.7259	0.7941	0.8653	yes	N/A
Q2KIA3	LMO3_BOVIN	No assigned EC number	0.7723	0.7117	0.8344	no	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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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	170
cd09390	55	cd09390, LIM2_dLMO, The second LIM domain of dLMO	2e-30
cd09388	55	cd09388, LIM1_LMO1_LMO3, The first LIM domain of L	1e-26
cd09389	55	cd09389, LIM2_LMO1_LMO3, The second LIM domain of	3e-23
cd09386	55	cd09386, LIM1_LMO4, The first LIM domain of LMO4 (	1e-18
cd09387	55	cd09387, LIM2_LMO4, The second LIM domain of LMO4	5e-17
cd09384	56	cd09384, LIM1_LMO2, The first LIM domain of LMO2 (	1e-15
cd09385	56	cd09385, LIM2_LMO2, The second LIM domain of LMO2	8e-15
cd09376	56	cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of	7e-14
cd09377	59	cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of	4e-12
cd09378	55	cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain o	9e-12
cd09379	55	cd09379, LIM2_AWH, The second LIM domain of Arrowh	3e-11
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	3e-11
pfam00412	58	pfam00412, LIM, LIM domain	1e-10
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	1e-10
cd09473	56	cd09473, LIM2_Lhx4, The second LIM domain of Lhx4	1e-10
cd09472	57	cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3	5e-10
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	6e-10
cd09475	59	cd09475, LIM2_Lhx9, The second LIM domain of Lhx9	6e-10
cd09375	56	cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of	1e-09
cd09374	55	cd09374, LIM2_Isl, The second LIM domain of Isl, a	2e-09
pfam00412	58	pfam00412, LIM, LIM domain	4e-09
cd09471	55	cd09471, LIM2_Isl2, The second LIM domain of Isl2	4e-09
cd09383	55	cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of	9e-09
cd09474	59	cd09474, LIM2_Lhx2, The second LIM domain of Lhx2	1e-08
cd09382	55	cd09382, LIM2_Lhx6, The second LIM domain of Lhx6	4e-08
cd09466	56	cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a	6e-08
cd09467	55	cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b	2e-07
cd09369	54	cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of L	6e-07
cd09373	54	cd09373, LIM1_AWH, The first LIM domain of Arrowhe	7e-07
cd09380	54	cd09380, LIM1_Lhx6, The first LIM domain of Lhx6	9e-07
cd09381	56	cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of L	1e-06
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	1e-06
cd09469	64	cd09469, LIM1_Lhx2, The first LIM domain of Lhx2	1e-06
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	2e-06
cd09371	53	cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b	2e-06
cd09468	52	cd09468, LIM1_Lhx4, The first LIM domain of Lhx4	6e-06
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	7e-06
cd09366	55	cd09366, LIM1_Isl, The first LIM domain of Isl, a	7e-06
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	9e-06
cd09370	52	cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a	1e-05
cd09470	54	cd09470, LIM1_Lhx9, The first LIM domain of Lhx9	1e-05
cd09392	53	cd09392, LIM2_Lrg1p_like, The second LIM domain of	2e-05
cd09368	52	cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of L	6e-05
cd09349	87	cd09349, LIM1_Zyxin, The first LIM domain of Zyxin	2e-04
cd09353	60	cd09353, LIM2_Zyxin, The second LIM domain of Zyxi	2e-04
cd09391	57	cd09391, LIM1_Lrg1p_like, The first LIM domain of	6e-04
cd09389	55	cd09389, LIM2_LMO1_LMO3, The second LIM domain of	0.001
cd09351	54	cd09351, LIM1_LPP, The first LIM domain of lipoma	0.001
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	0.002
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	0.002
cd09344	54	cd09344, LIM1_FHL1, The first LIM domain of Four a	0.003

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

 Score =  104 bits (261), Expect = 2e-30
 Identities = 49/55 (89%), Positives = 53/55 (96%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           CAAC+K IPAFEMVMRA+ NVYHLECFACQ+CNHRFCVGDRFYLC+NKILCEYDY
Sbjct: 1   CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFCVGDRFYLCENKILCEYDY 55

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

 Score = 95.3 bits (237), Expect = 1e-26
 Identities = 43/55 (78%), Positives = 49/55 (89%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          CA C ++I +R+LLKALD +WHEDCLKC CCDCRLGEVGSTLY KANLILC+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|188775 cd09389, LIM2_LMO1_LMO3, The second LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

 Score = 86.6 bits (214), Expect = 3e-23
 Identities = 42/55 (76%), Positives = 50/55 (90%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           CAAC+K+IPAFEMVMRAK+NVYHL+CFACQ CN RFCVGD+F+L +N ILC+ DY
Sbjct: 1   CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMDY 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|188772 cd09386, LIM1_LMO4, The first LIM domain of LMO4 (LIM domain only protein 4)

 Score = 74.8 bits (184), Expect = 1e-18
 Identities = 33/55 (60%), Positives = 40/55 (72%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          CA CG +I +RFLL ALD +WH  CLKC CC  +LGE+GS+ Y K  +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|188773 cd09387, LIM2_LMO4, The second LIM domain of LMO4 (LIM domain only protein 4)

 Score = 70.6 bits (173), Expect = 5e-17
 Identities = 27/54 (50%), Positives = 39/54 (72%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
           C+AC + IPA E+VMRA+ NVYHL+CF C  C+++   GDRF+  +  + CE+D
Sbjct: 1   CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHD 54

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

 Score = 66.8 bits (163), Expect = 1e-15
 Identities = 32/56 (57%), Positives = 38/56 (67%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYL 75
          C  C + I +R+ LKA+D +WHEDCL 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|188771 cd09385, LIM2_LMO2, The second LIM domain of LMO2 (LIM domain only protein 2)

 Score = 64.7 bits (157), Expect = 8e-15
 Identities = 31/54 (57%), Positives = 38/54 (70%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
           CA+C K I A+EM MR K+ VYHLECF C  C   FCVGDR+ L ++ I+CE D
Sbjct: 1   CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQD 54

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

 Score = 62.4 bits (152), Expect = 7e-14
 Identities = 28/56 (50%), Positives = 39/56 (69%), Gaps = 1/56 (1%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDY 138
           CA C + IP  ++V RA++NVYHLECFAC  C  +   GD FYL  D++++C+ DY
Sbjct: 1   CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56

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

 Score = 57.7 bits (140), Expect = 4e-12
 Identities = 24/55 (43%), Positives = 30/55 (54%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           CA C   I A E+VMRA++ V+HL CF C  CN     GD F + D  + C   Y
Sbjct: 5   CARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59

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

 Score = 56.7 bits (137), Expect = 9e-12
 Identities = 25/55 (45%), Positives = 33/55 (60%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           C+ C + I   E+VMRA  NVYHL CF C  C  +   GD F L + ++LC+ DY
Sbjct: 1   CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55

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

 Score = 55.5 bits (134), Expect = 3e-11
 Identities = 23/55 (41%), Positives = 36/55 (65%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           CA C++ I A + V RA+++VYHL CFAC  C  +   G+ F L ++++LC+  Y
Sbjct: 1   CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDRVLCKAHY 55

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

 Score = 55.4 bits (134), Expect = 3e-11
 Identities = 24/55 (43%), Positives = 30/55 (54%), Gaps = 2/55 (3%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          CA CGK 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|215907 pfam00412, LIM, LIM domain

 Score = 53.9 bits (130), Expect = 1e-10
 Identities = 24/58 (41%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141
           CA C K I   E+V RA   V+H ECF C  C      GD F+  D K+ C++DY + 
Sbjct: 1   CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGD-FFEKDGKLYCKHDYFKL 57

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

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

 Score = 53.5 bits (129), Expect = 1e-10
 Identities = 22/54 (40%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
           CA C K I   E V+RA   V+H ECF C  C      GD F+  D K+ C+  
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|188857 cd09473, LIM2_Lhx4, The second LIM domain of Lhx4

 Score = 53.9 bits (129), Expect = 1e-10
 Identities = 25/56 (44%), Positives = 37/56 (66%), Gaps = 1/56 (1%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDY 138
           C AC + IP  ++V +A++ VYHL CFAC  C+ +   GD FYL  D +++C+ DY
Sbjct: 1   CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 56

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|188856 cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3b

 Score = 52.4 bits (125), Expect = 5e-10
 Identities = 27/56 (48%), Positives = 38/56 (67%), Gaps = 1/56 (1%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDY 138
           CAAC + IP  ++V RA++ VYHL CFAC  C  +   GD FYL  D++++C+ DY
Sbjct: 2   CAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCKADY 57

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

 Score = 51.9 bits (125), Expect = 6e-10
 Identities = 22/55 (40%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           CA C K I     ++RA    +H ECF C  C      GD FY  D K  CE  Y
Sbjct: 1   CAGCGKPIEG-RELLRALGKKWHPECFKCSVCGKPLG-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|188859 cd09475, LIM2_Lhx9, The second LIM domain of Lhx9

 Score = 52.4 bits (125), Expect = 6e-10
 Identities = 26/55 (47%), Positives = 31/55 (56%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           CA C   I A EMVMRA+ +VYHL CF C  CN     GD F + DN + C   +
Sbjct: 5   CARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCRAHF 59

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

 Score = 51.2 bits (123), Expect = 1e-09
 Identities = 22/56 (39%), Positives = 33/56 (58%), Gaps = 1/56 (1%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCD-NKILCEYDY 138
           CA C + I   ++V RA++ V+HL CF C  C  +   G+  Y+ D NK +C+ DY
Sbjct: 1   CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56

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

 Score = 50.5 bits (121), Expect = 2e-09
 Identities = 21/55 (38%), Positives = 32/55 (58%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           CA C +     + VMRA+  +YH+ECF C  C+ +   GD F L D+ + C+ D+
Sbjct: 1   CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKADH 55

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|215907 pfam00412, LIM, LIM domain

 Score = 50.0 bits (120), Expect = 4e-09
 Identities = 24/60 (40%), Positives = 33/60 (55%), Gaps = 3/60 (5%)

Query: 20 CASCGKRITERFLLK-ALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 78
          CA CGK I +R 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|188855 cd09471, LIM2_Isl2, The second LIM domain of Isl2

 Score = 49.9 bits (119), Expect = 4e-09
 Identities = 22/55 (40%), Positives = 36/55 (65%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           CA C     + ++VMRA+++VYH+ECF C  C+ +   GD F L ++++LC  D+
Sbjct: 1   CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFCLREHELLCRADH 55

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

 Score = 48.9 bits (116), Expect = 9e-09
 Identities = 24/55 (43%), Positives = 32/55 (58%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           C+ C + I + + V RAK NVYHL CFAC  C  +   G+ F L + K+LC   Y
Sbjct: 1   CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55

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|188858 cd09474, LIM2_Lhx2, The second LIM domain of Lhx2

 Score = 48.9 bits (116), Expect = 1e-08
 Identities = 26/55 (47%), Positives = 31/55 (56%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           CA C   I A EMVMRA++ VYHL CF C  CN     GD F + DN + C   +
Sbjct: 5   CARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCRLHF 59

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|188768 cd09382, LIM2_Lhx6, The second LIM domain of Lhx6

 Score = 47.4 bits (112), Expect = 4e-08
 Identities = 24/55 (43%), Positives = 31/55 (56%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           CA C + I A + V RA+ N YHL CFAC  C  +   G+ F L + K+LC   Y
Sbjct: 1   CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCRIHY 55

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|188850 cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a

 Score = 46.7 bits (111), Expect = 6e-08
 Identities = 20/55 (36%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          CA C   I +RF+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|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b

 Score = 45.7 bits (108), Expect = 2e-07
 Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 3/55 (5%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          CA C + I +RF+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|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9 family

 Score = 43.9 bits (104), Expect = 6e-07
 Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          CA CG++I +RF 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|188759 cd09373, LIM1_AWH, The first LIM domain of Arrowhead (AWH)

 Score = 43.9 bits (104), Expect = 7e-07
 Identities = 23/55 (41%), Positives = 28/55 (50%), Gaps = 1/55 (1%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          C  CG+ IT+RFLLK     WH  CL+C  C   L    S  + +   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|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6

 Score = 43.5 bits (102), Expect = 9e-07
 Identities = 24/55 (43%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          C+SCG  I +R+LLK  +L 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|188767 cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of Lhx7 and Lhx8

 Score = 43.4 bits (102), Expect = 1e-06
 Identities = 25/56 (44%), Positives = 31/56 (55%), Gaps = 1/56 (1%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYL 75
          C+SCG  I +++LLK  DL 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|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain Kinase 1)

 Score = 44.1 bits (104), Expect = 1e-06
 Identities = 23/61 (37%), Positives = 31/61 (50%), Gaps = 3/61 (4%)

Query: 14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRD 73
             L  CASCG+ I +   L+AL+  WH DC +C  C   L       Y+K   + CK+D
Sbjct: 16 GNVLPVCASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSH---WYYEKDGRLFCKKD 72

Query: 74 Y 74
          Y
Sbjct: 73 Y 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|188853 cd09469, LIM1_Lhx2, The first LIM domain of Lhx2

 Score = 43.5 bits (102), Expect = 1e-06
 Identities = 26/56 (46%), Positives = 34/56 (60%), Gaps = 3/56 (5%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG-EVGSTLYQKANLILCKRDY 74
          CA CG +I++R+ 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 = 42.8 bits (101), Expect = 2e-06
 Identities = 21/55 (38%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 20 CASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRD 73
          CA CGK 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|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b

 Score = 42.4 bits (100), Expect = 2e-06
 Identities = 20/55 (36%), Positives = 32/55 (58%), Gaps = 3/55 (5%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          CA C + I++R+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|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4

 Score = 41.5 bits (97), Expect = 6e-06
 Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 3/55 (5%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          CA C + I ++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|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known as Lim1) and Lhx5

 Score = 41.3 bits (97), Expect = 7e-06
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          CA C + I ++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|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX protein family

 Score = 41.2 bits (97), Expect = 7e-06
 Identities = 23/56 (41%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 20 CASCGKRITERFLLK-ALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          C  CG +I ++++L+ A DL 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|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase )

 Score = 40.9 bits (96), Expect = 9e-06
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          CA C  +I +   ++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|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a

 Score = 40.5 bits (95), Expect = 1e-05
 Identities = 21/55 (38%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          C  C + I +RFLL+  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|188854 cd09470, LIM1_Lhx9, The first LIM domain of Lhx9

 Score = 40.4 bits (94), Expect = 1e-05
 Identities = 26/56 (46%), Positives = 34/56 (60%), Gaps = 3/56 (5%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLG-EVGSTLYQKANLILCKRDY 74
          CA CG +I++R+ 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|188778 cd09392, LIM2_Lrg1p_like, The second LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 40.0 bits (94), Expect = 2e-05
 Identities = 15/39 (38%), Positives = 18/39 (46%)

Query: 100 AKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           A    YH+E F C  C   F   D +Y  + KI C Y Y
Sbjct: 15  ALGRKYHVEHFTCSVCPTVFGPNDSYYEHEGKIYCHYHY 53

The second 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 = 53

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

 Score = 38.6 bits (90), Expect = 6e-05
 Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          C  C + I +RF+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|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin

 Score = 38.3 bits (89), Expect = 2e-04
 Identities = 18/59 (30%), Positives = 29/59 (49%), Gaps = 1/59 (1%)

Query: 80  TTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           T   C  C + +   +  +RA  +++H+ CF C QC  +   G +FY  + K  CE  Y
Sbjct: 30  TNELCGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQL-QGQQFYSLEGKPYCEECY 87

The first 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 cell substratum 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 or scaffolds to support the assembly of multimeric protein. Length = 87

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

 Score = 37.2 bits (86), Expect = 2e-04
 Identities = 23/59 (38%), Positives = 31/59 (52%), Gaps = 2/59 (3%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 78
          CA C ++IT+R +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|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 36.1 bits (84), Expect = 6e-04
 Identities = 22/60 (36%), Positives = 27/60 (45%), Gaps = 8/60 (13%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNK-----ILCEYDY 138
           CA C K I      +RA  +VYHL+CF C  C  +      F + D        LCE DY
Sbjct: 1   CAKCGKPITG--QFVRALGDVYHLDCFTCHDC-GKPVASKFFPVDDPDTSEQVPLCETDY 57

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 = 35.4 bits (81), Expect = 0.001
 Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 2/56 (3%)

Query: 20 CASCGKRITE-RFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          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|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred partner (LPP)

 Score = 35.1 bits (81), Expect = 0.001
 Identities = 20/55 (36%), Positives = 24/55 (43%), Gaps = 1/55 (1%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           C  C + +        A + VYH+ CF C QC      G  FY  D K  CE DY
Sbjct: 1   CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINL-QGKPFYALDGKPYCEEDY 54

The first LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. 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|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM (abLIM) proteins

 Score = 34.6 bits (80), Expect = 0.002
 Identities = 23/56 (41%), Positives = 25/56 (44%), Gaps = 5/56 (8%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRL-GEVGSTLYQKANLILCKRDY 74
          CA CG+ 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|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin like protein family

 Score = 34.2 bits (79), Expect = 0.002
 Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 3/55 (5%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
          C  C K I E ++  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|188730 cd09344, LIM1_FHL1, The first LIM domain of Four and a half LIM domains protein 1

 Score = 34.0 bits (78), Expect = 0.003
 Identities = 20/52 (38%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCE 135
           CA C K I A    +  KN  +H  CF C +C       + F   DNKILC 
Sbjct: 1   CAECRKPIGADSKELHHKNRYWHETCFRCAKCYKPL-ANEPFVAKDNKILCG 51

The first LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. 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 = 54

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	170
KOG4577|consensus	383		99.94
KOG1701|consensus	468		99.92
KOG1701|consensus	468		99.91
KOG2272|consensus	332		99.86
KOG1044|consensus	670		99.84
KOG2272|consensus	332		99.8
KOG1703|consensus	479		99.78
KOG1703|consensus	479		99.76
KOG1044|consensus	670		99.66
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.63
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.54
KOG1700|consensus	200		99.49
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.84
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.82
KOG4577|consensus	383		98.74
KOG0490|consensus	235		98.42
KOG1702|consensus	264		98.39
KOG1700|consensus	200		97.61
KOG1702|consensus	264		97.46
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	94.25
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	89.6
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	89.37
PF14471	51	DUF4428: Domain of unknown function (DUF4428)	89.1
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	88.76
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	88.74
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	87.5
KOG0490|consensus	235		85.26
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	85.01
PF13920	50	zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger);	84.05
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	83.89
PF12773	50	DZR: Double zinc ribbon	82.06
PF06677	41	Auto_anti-p27: Sjogren's syndrome/scleroderma auto	81.57
PF07191	70	zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807	81.5
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	80.92
KOG0320|consensus	187		80.27

>KOG4577|consensus

Probab=99.94  E-value=8e-29  Score=184.90  Aligned_cols=144  Identities=38%  Similarity=0.858  Sum_probs=127.9

Q ss_pred             CcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCCc
Q psy7479          16 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFE   95 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~   95 (170)
                      ..++|++|.+.|.++++++++++.||..|++|+.|...|.   ..+|.++|.+||+++|.++|+.  +|..|...|.+..
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~---drCFsR~~s~yCkedFfKrfGT--KCsaC~~GIpPtq  106 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLA---DRCFSREGSVYCKEDFFKRFGT--KCSACQEGIPPTQ  106 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHH---HHHhhcCCceeehHHHHHHhCC--cchhhcCCCChHH
Confidence            6799999999999999999999999999999999999997   5689999999999999999999  9999999999865


Q ss_pred             eEEecCCcccccCccccccCCcccccCCeEEEe-CCeeccHHhHHHHhh-------------------------hcc--c
Q psy7479          96 MVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDYEERQV-------------------------FAN--I  147 (170)
Q Consensus        96 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~-~~~~~C~~c~~~~~~-------------------------~~~--~  147 (170)
                      .+..|.+.+||..||.|..|+++|..|++||+. |+++.|+..|++...                         ..+  .
T Consensus       107 VVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AY  186 (383)
T KOG4577|consen  107 VVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAY  186 (383)
T ss_pred             HHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHh
Confidence            566799999999999999999999889999975 689999999975432                         111  2


Q ss_pred             cCCCCchHHhhhhccee
Q psy7479         148 AYNPSSLAHLRRQVTLQ  164 (170)
Q Consensus       148 ~~~~~~~~~~~~~~~~~  164 (170)
                      ..+|++++|+||+|++.
T Consensus       187 n~SpKPARHVREQLsse  203 (383)
T KOG4577|consen  187 NTSPKPARHVREQLSSE  203 (383)
T ss_pred             cCCCchhHHHHHHhhhc
Confidence            33489999999999875

>KOG1701|consensus

Probab=99.92  E-value=1.9e-27  Score=185.84  Aligned_cols=131  Identities=26%  Similarity=0.586  Sum_probs=115.8

Q ss_pred             CCCCcccccccccccccc-eeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccc
Q psy7479          13 ASGGLKECASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVI   91 (170)
Q Consensus        13 ~~~~~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i   91 (170)
                      ......+|.+|+|.|.+. ..+.||++.||..||+|..|++.|.  ++.||..|+++||+.||.....   +|..|+++|
T Consensus       270 ~~~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~--Gq~FY~v~~k~~CE~cyq~tle---kC~~Cg~~I  344 (468)
T KOG1701|consen  270 VEDYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLA--GQSFYQVDGKPYCEGCYQDTLE---KCNKCGEPI  344 (468)
T ss_pred             hhhhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhc--cccccccCCcccchHHHHHHHH---HHhhhhhHH
Confidence            344566999999999987 3488999999999999999999997  6889999999999999998876   999999999


Q ss_pred             cCCceEEecCCcccccCccccccCCcccccCCeEEEe-CCeeccHHhHHHHhhhccccCCCCc
Q psy7479          92 PAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDYEERQVFANIAYNPSS  153 (170)
Q Consensus        92 ~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~-~~~~~C~~c~~~~~~~~~~~~~~~~  153 (170)
                      +  |++++|.|+.||+.||+|..|++.| .|..|.+. ++++||..+|.++  |++++.-++.
T Consensus       345 ~--d~iLrA~GkayHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~k--fAPrCs~C~~  402 (468)
T KOG1701|consen  345 M--DRILRALGKAYHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKK--FAPRCSVCGN  402 (468)
T ss_pred             H--HHHHHhcccccCCCceEEEEecccc-CCccccccCCCceeeehhhhhh--cCcchhhccC
Confidence            5  5899999999999999999999999 88899874 7999999999998  6666655443

>KOG1701|consensus

Probab=99.91  E-value=5.6e-26  Score=177.71  Aligned_cols=123  Identities=27%  Similarity=0.636  Sum_probs=108.9

Q ss_pred             CCcccccccccccccceeEEeCCccccccCccccccccccccCCCee-EEeCCccccccceecccccccccccccccccC
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTL-YQKANLILCKRDYLRLFGTTGYCAACTKVIPA   93 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~-~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~   93 (170)
                      ..+.+|..|++.|.++ +|.|+|+.||+.||+|..|.+.|+  +-.| ...++++||..||+++|++  +|+.|+++|++
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            3567899999999999 799999999999999999999997  3445 5778999999999999999  99999999976


Q ss_pred             C---ce--EEecCCcccccCccccccCCcccc---cCCeEEEeCCeeccHHhHHHHh
Q psy7479          94 F---EM--VMRAKNNVYHLECFACQQCNHRFC---VGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        94 ~---~~--~~~~~~~~~H~~Cf~C~~C~~~l~---~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      .   |.  .|.++++.||.+|++|+.|+.+|+   .+...|..||.++|+.|..+++
T Consensus       407 ~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~Rl  463 (468)
T KOG1701|consen  407 RDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKRL  463 (468)
T ss_pred             CCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeechhhhhhh
Confidence            3   21  467999999999999999999996   3567899999999999998874

>KOG2272|consensus

Probab=99.86  E-value=1.7e-23  Score=153.95  Aligned_cols=120  Identities=32%  Similarity=0.754  Sum_probs=111.3

Q ss_pred             CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479          14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA   93 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~   93 (170)
                      .-+.++|..|.++|.+. ++.++|+.||.+.|+|+.|.+++-  +...|++.|..||+.+|.++|+.  .|..|+..|.+
T Consensus       192 ~mgipiCgaC~rpIeer-vi~amgKhWHveHFvCa~CekPFl--GHrHYEkkGlaYCe~h~~qLfG~--~CF~C~~~i~G  266 (332)
T KOG2272|consen  192 KMGIPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEKPFL--GHRHYEKKGLAYCETHYHQLFGN--LCFICNRVIGG  266 (332)
T ss_pred             ccCCcccccccCchHHH-HHHHhccccchhheeehhcCCccc--chhhhhhcCchhHHHHHHHHhhh--hheecCCccCc
Confidence            35789999999999987 789999999999999999999985  56789999999999999999998  99999999966


Q ss_pred             CceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHH
Q psy7479          94 FEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEE  140 (170)
Q Consensus        94 ~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~  140 (170)
                        .++.+.++.|.++||.|+.|++.|.....|++.|-.|.|+.||++
T Consensus       267 --~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r  311 (332)
T KOG2272|consen  267 --DVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR  311 (332)
T ss_pred             --cHHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence              788999999999999999999999778899999999999999985

>KOG1044|consensus

Probab=99.84  E-value=7.6e-22  Score=159.48  Aligned_cols=120  Identities=32%  Similarity=0.682  Sum_probs=111.1

Q ss_pred             CCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccccccccccccccc
Q psy7479          13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIP   92 (170)
Q Consensus        13 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~   92 (170)
                      ...+...|++|++.|..+.++.|+++.||..||+|..|+..|.   ..|+.++|.+||+.||.+.|+.  +|..|.+.|.
T Consensus       129 ~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~---gey~skdg~pyce~dy~~~fgv--kc~~c~~fis  203 (670)
T KOG1044|consen  129 ESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN---GEYMSKDGVPYCEKDYQAKFGV--KCEECEKFIS  203 (670)
T ss_pred             cccCCccccchhhhhhccceeeeeccceeeeeeehhhhccccc---ceeeccCCCcchhhhhhhhcCe--ehHHhhhhhh
Confidence            3347788999999999998899999999999999999999996   5699999999999999999998  9999999997


Q ss_pred             CCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHH
Q psy7479          93 AFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYE  139 (170)
Q Consensus        93 ~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~  139 (170)
                      +  .++.|.|+.||+.|-+|+.|+.+|..|+++|+....+|-..|-.
T Consensus       204 g--kvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~q  248 (670)
T KOG1044|consen  204 G--KVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQ  248 (670)
T ss_pred             h--hhhhccCcccCcchhhhhhhccccccchheeeccccccCCcccc
Confidence            7  89999999999999999999999999999999999988877754

>KOG2272|consensus

Probab=99.80  E-value=5.2e-21  Score=140.91  Aligned_cols=121  Identities=27%  Similarity=0.457  Sum_probs=108.2

Q ss_pred             CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479          14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA   93 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~   93 (170)
                      ..+.-+|.+|+..|.+. .+...+..||+..|+|..|++.|.   +.-....|.+||..|+.+.--|  .|..|.++|  
T Consensus       134 ~~g~YvC~KCh~~iD~~-~l~fr~d~yH~yHFkCt~C~keL~---sdaRevk~eLyClrChD~mgip--iCgaC~rpI--  205 (332)
T KOG2272|consen  134 GRGRYVCQKCHAHIDEQ-PLTFRGDPYHPYHFKCTTCGKELT---SDAREVKGELYCLRCHDKMGIP--ICGACRRPI--  205 (332)
T ss_pred             ccceeehhhhhhhcccc-cccccCCCCCccceeccccccccc---chhhhhccceeccccccccCCc--ccccccCch--
Confidence            44567899999999885 688999999999999999999997   3456778899999999987766  999999999  


Q ss_pred             CceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479          94 FEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus        94 ~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                      +|+++.++|+.||.+.|+|+.|.+|+ .|-+.|++.|..||+.+|.++|.
T Consensus       206 eervi~amgKhWHveHFvCa~CekPF-lGHrHYEkkGlaYCe~h~~qLfG  254 (332)
T KOG2272|consen  206 EERVIFAMGKHWHVEHFVCAKCEKPF-LGHRHYEKKGLAYCETHYHQLFG  254 (332)
T ss_pred             HHHHHHHhccccchhheeehhcCCcc-cchhhhhhcCchhHHHHHHHHhh
Confidence            46899999999999999999999999 78899999999999999999853

>KOG1703|consensus

Probab=99.78  E-value=1.8e-20  Score=154.47  Aligned_cols=118  Identities=26%  Similarity=0.587  Sum_probs=107.9

Q ss_pred             CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCC
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAF   94 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~   94 (170)
                      ...+.|.+|.++|.+. .|.|.+..||++||.|..|++.|.  +..|+..+|.+||+.||.+++.+  +|..|.++|...
T Consensus       361 ~~~p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~~--~~~~~~~~~~pyce~~~~~~~~~--~~~~~~~p~~~~  435 (479)
T KOG1703|consen  361 PFRPNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPLK--NSSFFESDGEPYCEDHYKKLFTT--KCDYCKKPVEFG  435 (479)
T ss_pred             hhCccccccCCchHHh-HhhhccCeechhceeeecccCCCC--CCcccccCCccchhhhHhhhccc--cchhccchhHhh
Confidence            4678899999999999 577889999999999999999997  46699999999999999999998  999999998755


Q ss_pred             ceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhH
Q psy7479          95 EMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY  138 (170)
Q Consensus        95 ~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~  138 (170)
                      +..+.+.+..||..||+|..|.+.| .+..|+...++++|..|+
T Consensus       436 ~~~ie~~~~~~h~~~F~c~~c~~~l-~~~~~~~~~~~p~c~~~~  478 (479)
T KOG1703|consen  436 SRQIEADGSPFHGDCFRCANCMKKL-TKKTFFETLDKPLCQKHF  478 (479)
T ss_pred             hhHhhccCccccccceehhhhhccc-cCCceeecCCccccccCC
Confidence            6788999999999999999999999 788899999999999885

>KOG1703|consensus

Probab=99.76  E-value=1.5e-19  Score=149.03  Aligned_cols=121  Identities=24%  Similarity=0.507  Sum_probs=110.3

Q ss_pred             CcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCCc
Q psy7479          16 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFE   95 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~   95 (170)
                      ..+.|..|...|.+..++.++++.||+.+|.|..|+..+..  ..+...+|++||..|+...+.+  .|.+|+++|.+  
T Consensus       302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~--~~~~~~~g~~~c~~~~~~~~~p--~C~~C~~~i~~--  375 (479)
T KOG1703|consen  302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILD--GGPRELDGKILCHECFHAPFRP--NCKRCLLPILE--  375 (479)
T ss_pred             ccccccccccCcccceeEeeccccccccceeeccccccccC--CCccccCCCccHHHHHHHhhCc--cccccCCchHH--
Confidence            45899999999999447899999999999999999999974  3468899999999999999998  99999999965  


Q ss_pred             eEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479          96 MVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus        96 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                      .+|.+.+..||++||.|..|+++| .+..|+..++.+||..||.+++.
T Consensus       376 ~~v~a~~~~wH~~cf~C~~C~~~~-~~~~~~~~~~~pyce~~~~~~~~  422 (479)
T KOG1703|consen  376 EGVCALGRLWHPECFVCADCGKPL-KNSSFFESDGEPYCEDHYKKLFT  422 (479)
T ss_pred             hHhhhccCeechhceeeecccCCC-CCCcccccCCccchhhhHhhhcc
Confidence            788999999999999999999999 78889999999999999999854

>KOG1044|consensus

Probab=99.66  E-value=1.1e-16  Score=129.98  Aligned_cols=125  Identities=23%  Similarity=0.558  Sum_probs=99.1

Q ss_pred             CCCCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCC-ccccccceec-------------
Q psy7479          11 GGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKAN-LILCKRDYLR-------------   76 (170)
Q Consensus        11 ~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~-~~yC~~c~~~-------------   76 (170)
                      ++.......|.+|.+.-.+. ++.+.++.||..||+|..|+..|.+.+  ||.+++ ++|+......             
T Consensus        10 ~~~~~~~i~c~~c~~kc~ge-vlrv~d~~fhi~cf~c~~cg~~la~~g--ff~k~~~~~ygt~~c~~~~~gevvsa~gkt   86 (670)
T KOG1044|consen   10 PQTGKQGIKCDKCRKKCSGE-VLRVNDNHFHINCFQCKKCGRNLAEGG--FFTKPENRLYGTDDCRAFVEGEVVSTLGKT   86 (670)
T ss_pred             ccccccceehhhhCCccccc-eeEeeccccceeeeeccccCCCccccc--ceecccceeecccchhhhccceeEecccce
Confidence            34455567899999999998 899999999999999999999998643  555443 5666533221             


Q ss_pred             -------------------------------------------ccccccccccccccccCCceEEecCCcccccCccccc
Q psy7479          77 -------------------------------------------LFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQ  113 (170)
Q Consensus        77 -------------------------------------------~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~  113 (170)
                                                                 ..++ ..|++|+..|.. +..+.|.++.||..||+|.
T Consensus        87 yh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~p-s~cagc~~~lk~-gq~llald~qwhv~cfkc~  164 (670)
T KOG1044|consen   87 YHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGP-STCAGCGEELKN-GQALLALDKQWHVSCFKCK  164 (670)
T ss_pred             eccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCC-ccccchhhhhhc-cceeeeeccceeeeeeehh
Confidence                                                       0011 149999998865 4788999999999999999


Q ss_pred             cCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479         114 QCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus       114 ~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      .|+..|  ..+|+..+|.+||..+|.+.|
T Consensus       165 ~c~~vL--~gey~skdg~pyce~dy~~~f  191 (670)
T KOG1044|consen  165 SCSAVL--NGEYMSKDGVPYCEKDYQAKF  191 (670)
T ss_pred             hhcccc--cceeeccCCCcchhhhhhhhc
Confidence            999999  457999999999999998876

>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=99.63  E-value=6.4e-16  Score=92.02  Aligned_cols=58  Identities=36%  Similarity=0.745  Sum_probs=52.1

Q ss_pred             cccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        84 C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      |.+|+++|.+.+.++.+.|+.||++||+|..|+++| .+..|+..+|++||..||.++|
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPL-NDGDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBT-TTSSEEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCcc-CCCeeEeECCEEECHHHHhhhC
Confidence            789999999877677899999999999999999999 4555999999999999999874

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 ....

>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=99.54  E-value=2.9e-15  Score=89.19  Aligned_cols=57  Identities=39%  Similarity=0.864  Sum_probs=50.7

Q ss_pred             ccccccccccceeE-EeCCccccccCccccccccccccCCCeeEEeCCccccccceeccc
Q psy7479          20 CASCGKRITERFLL-KALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF   78 (170)
Q Consensus        20 C~~C~~~I~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~   78 (170)
                      |.+|+++|.+..++ .++|+.||++||+|..|+++|..  ..++..+|++||+.||.++|
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLND--GDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTT--SSEEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCC--CeeEeECCEEECHHHHhhhC
Confidence            78999999987554 69999999999999999999974  34999999999999998765

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 ....

>KOG1700|consensus

Probab=99.49  E-value=4.4e-15  Score=109.28  Aligned_cols=125  Identities=22%  Similarity=0.548  Sum_probs=103.5

Q ss_pred             CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccccc-----------
Q psy7479          14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTG-----------   82 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~-----------   82 (170)
                      +.....|..|++.++-.+.+...|..||+.||+|..|.+.|..  ..+..+++.+||+.+|...+++.+           
T Consensus         4 ~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~--~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~   81 (200)
T KOG1700|consen    4 TGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTL--SGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAG   81 (200)
T ss_pred             ccccchhhhccCcchHHHHHhccCcchhhhHHhcccccccccc--ccccccccccccccchHhhhCcccccccccccccC
Confidence            3455689999999998766778899999999999999999973  457789999999997655433310           


Q ss_pred             ----------------------------ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeecc
Q psy7479          83 ----------------------------YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILC  134 (170)
Q Consensus        83 ----------------------------~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C  134 (170)
                                                  .|..|++.+.+.+ .+...+..||..||+|+.|+..| ....+...++.+||
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~E-k~~~~~~~~hk~cfrc~~~~~~l-s~~~~~~~~g~l~~  159 (200)
T KOG1700|consen   82 GLGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLE-KVTGNGLEFHKSCFRCTHCGKKL-SPKNYAALEGVLYC  159 (200)
T ss_pred             CCCcccccccccccccchhHHhhhccccccccccceeeehH-HHhhhhhhhhhhheeeccccccc-CCcchhhcCCcccc
Confidence                                        3999999998754 44677999999999999999999 67788888999999


Q ss_pred             HHhHHHHh
Q psy7479         135 EYDYEERQ  142 (170)
Q Consensus       135 ~~c~~~~~  142 (170)
                      ..++..++
T Consensus       160 ~~~~~~~~  167 (200)
T KOG1700|consen  160 KHHFAQLF  167 (200)
T ss_pred             chhhheee
Confidence            99887764

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

Probab=98.84  E-value=2.1e-09  Score=58.23  Aligned_cols=37  Identities=43%  Similarity=0.909  Sum_probs=33.6

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCccc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF  119 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l  119 (170)
                      +|.+|+++|.+.+..+.+.++.||++||+|..|+++|
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L   37 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPL   37 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcC
Confidence            5889999998765788899999999999999999998

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.

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

Probab=98.82  E-value=3.2e-09  Score=57.49  Aligned_cols=37  Identities=46%  Similarity=1.076  Sum_probs=33.4

Q ss_pred             cccccccccccc-eeEEeCCccccccCccccccccccc
Q psy7479          19 ECASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLG   55 (170)
Q Consensus        19 ~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~   55 (170)
                      .|.+|+++|.+. ..+.++++.||+.||+|..|+.+|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            489999999986 6788899999999999999999984

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=98.74  E-value=4.5e-10  Score=84.91  Aligned_cols=66  Identities=21%  Similarity=0.569  Sum_probs=57.9

Q ss_pred             cccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhhhccccCC
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYN  150 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~  150 (170)
                      ++|++|.+.|.. ..++.+.++.||..|++|+.|+.+|  ++..+.+++.+||+.+|.++|..+..+..
T Consensus        34 p~CagC~q~IlD-rFilKvl~R~wHs~CLkCs~C~~qL--~drCFsR~~s~yCkedFfKrfGTKCsaC~   99 (383)
T KOG4577|consen   34 PICAGCDQHILD-RFILKVLDRHWHSSCLKCSDCHDQL--ADRCFSREGSVYCKEDFFKRFGTKCSACQ   99 (383)
T ss_pred             ccccchHHHHHH-HHHHHHHhhhhhhhhcchhhhhhHH--HHHHhhcCCceeehHHHHHHhCCcchhhc
Confidence            399999999964 4577899999999999999999999  56777899999999999999887777666

>KOG0490|consensus

Probab=98.42  E-value=2.4e-08  Score=75.22  Aligned_cols=116  Identities=41%  Similarity=0.823  Sum_probs=97.3

Q ss_pred             ccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceec--ccccccccccccccccCCceEEe
Q psy7479          22 SCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLR--LFGTTGYCAACTKVIPAFEMVMR   99 (170)
Q Consensus        22 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~--~~~~~~~C~~C~~~i~~~~~~~~   99 (170)
                      .|+..|.+.+.+.+.+..||..|.+|..|...|.. ....+..+|..||..+|..  .+..  +|.+|...+...+.+..
T Consensus         1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~g~~~~~~d~~~~~~~~~--rr~rt~~~~~ql~~ler   77 (235)
T KOG0490|consen    1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGV-GDTCFSKDGSIYCKRDYQREFKFSK--RCARCKFTISQLDELER   77 (235)
T ss_pred             CCCccccchHHhhcccHHHHHHHHhhhhhcchhcc-CCCcccCCCcccccccchhhhhccc--cccCCCCCcCHHHHHHH
Confidence            37778888877777899999999999999999962 2445555999999999998  5655  99999999977677888


Q ss_pred             cCCcccccCccccccCCcccccCCeEEEeCC-eeccHHhHHHH
Q psy7479         100 AKNNVYHLECFACQQCNHRFCVGDRFYLCDN-KILCEYDYEER  141 (170)
Q Consensus       100 ~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~-~~~C~~c~~~~  141 (170)
                      +..+. |.-||.|..|...+..+..+.+.+. +..|...+.+.
T Consensus        78 ~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~  119 (235)
T KOG0490|consen   78 AFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE  119 (235)
T ss_pred             hhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence            88888 9999999999998878888888765 89998887654

>KOG1702|consensus

Probab=98.39  E-value=1.2e-08  Score=73.84  Aligned_cols=85  Identities=21%  Similarity=0.381  Sum_probs=70.4

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhhhccccCCCCchHH-hhhhc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAH-LRRQV  161 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~~~-~~~~~  161 (170)
                      .|..|++.+.+.| -+.-+++.||..||+|..|+.+| .-.+|-..+.++||..+|.+. +++.++.+|+..+. ...++
T Consensus         6 n~~~cgk~vYPvE-~v~cldk~whk~cfkce~c~mtl-nmKnyKgy~kkpycn~hYpkq-~at~~adTPEm~Rik~n~en   82 (264)
T KOG1702|consen    6 NREDCGKTVYPVE-EVKCLDKVWHKQCFKCEVCGMTL-NMKNYKGYDKKPYCNPHYPKQ-VATVMADTPEMRRIKENTEN   82 (264)
T ss_pred             hhhhhccccccHH-HHhhHHHHHHHHhheeeeccCCh-hhhhccccccCCCcCcccccc-eeeeecCCHHHHHHHhhhcc
Confidence            6788999888754 34778999999999999999999 677888899999999999876 48888888988855 44457


Q ss_pred             ceeeecccC
Q psy7479         162 TLQVLWIRE  170 (170)
Q Consensus       162 ~~~~~~~~~  170 (170)
                      .++|-|++|
T Consensus        83 qS~vkY~~e   91 (264)
T KOG1702|consen   83 QSNVKYHAE   91 (264)
T ss_pred             chhhhhHHH
Confidence            788888865

>KOG1700|consensus

Probab=97.61  E-value=1e-05  Score=59.74  Aligned_cols=64  Identities=23%  Similarity=0.577  Sum_probs=53.5

Q ss_pred             CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccc
Q psy7479          14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG   79 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~   79 (170)
                      ......|..|++.++..+.+...+..||..||+|..|+..|..  ..+...++.+||...+..++-
T Consensus       105 ~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~--~~~~~~~g~l~~~~~~~~~~~  168 (200)
T KOG1700|consen  105 AGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSP--KNYAALEGVLYCKHHFAQLFK  168 (200)
T ss_pred             hccccccccccceeeehHHHhhhhhhhhhhheeecccccccCC--cchhhcCCccccchhhheeec
Confidence            3455779999999998877788899999999999999999973  557888999999877766553

>KOG1702|consensus

Probab=97.46  E-value=1.2e-05  Score=58.57  Aligned_cols=61  Identities=25%  Similarity=0.506  Sum_probs=51.0

Q ss_pred             cccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccc
Q psy7479          17 LKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG   79 (170)
Q Consensus        17 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~   79 (170)
                      ...|..|++.++..+.+.-+++.||..||+|..|+.+|..  ..+-..+.++||..+|.+..+
T Consensus         4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnm--KnyKgy~kkpycn~hYpkq~a   64 (264)
T KOG1702|consen    4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNM--KNYKGYDKKPYCNPHYPKQVA   64 (264)
T ss_pred             cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhh--hhccccccCCCcCccccccee
Confidence            4567889999998777888999999999999999999973  445668899999999987543

>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=94.25  E-value=0.017  Score=30.59  Aligned_cols=33  Identities=33%  Similarity=0.748  Sum_probs=22.4

Q ss_pred             cccccccccCCceEEecCCcccccCccccccCCccc
Q psy7479          84 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF  119 (170)
Q Consensus        84 C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l  119 (170)
                      |..|+++|.+...++...++.||   |-|..|.+.|
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f   33 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF   33 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence            66788888775556777788887   4455555544

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

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=89.60  E-value=0.23  Score=28.66  Aligned_cols=37  Identities=24%  Similarity=0.652  Sum_probs=24.8

Q ss_pred             ccccccccccCCceEEe--cCCcccccCcc----cccc--CCccc
Q psy7479          83 YCAACTKVIPAFEMVMR--AKNNVYHLECF----ACQQ--CNHRF  119 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~--~~~~~~H~~Cf----~C~~--C~~~l  119 (170)
                      +|..|+++|...+.++.  .=+..||.+|+    .|..  |+..+
T Consensus         7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~~   51 (54)
T PF14446_consen    7 KCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTGF   51 (54)
T ss_pred             cChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCCc
Confidence            89999999965444443  33667888887    3655  55543

>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=89.37  E-value=0.28  Score=32.03  Aligned_cols=32  Identities=25%  Similarity=0.571  Sum_probs=20.4

Q ss_pred             CCcccccccccccccc-eeEEeCCccccccCcc
Q psy7479          15 GGLKECASCGKRITER-FLLKALDLFWHEDCLK   46 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~   46 (170)
                      .....|..|+++|... .++...|..+|..|++
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            3456688888888765 3344456667777753

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 [].

>PF14471 DUF4428: Domain of unknown function (DUF4428)

Probab=89.10  E-value=0.44  Score=27.15  Aligned_cols=30  Identities=20%  Similarity=0.490  Sum_probs=23.4

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHH
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEER  141 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~  141 (170)
                      .|..|+..++.-..+-+.|| .+|..|+.+.
T Consensus         1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl   30 (51)
T PF14471_consen    1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL   30 (51)
T ss_pred             CCCccccccccccceeccCc-cchHHHHHHh
Confidence            48889999855455667788 6999999875

>smart00504 Ubox Modified RING finger domain

Probab=88.76  E-value=0.21  Score=29.32  Aligned_cols=46  Identities=7%  Similarity=0.030  Sum_probs=33.6

Q ss_pred             ccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479          45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA   93 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~   93 (170)
                      |.|..|+..+.   .......|..||..+..+.+...+.|..|++++..
T Consensus         2 ~~Cpi~~~~~~---~Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~   47 (63)
T smart00504        2 FLCPISLEVMK---DPVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH   47 (63)
T ss_pred             cCCcCCCCcCC---CCEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence            57888888886   34667788999999887654333478888887744

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

>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=88.74  E-value=0.26  Score=26.08  Aligned_cols=32  Identities=25%  Similarity=0.596  Sum_probs=21.9

Q ss_pred             ccccccccccc-eeEEeCCccccccCcccccccccc
Q psy7479          20 CASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRL   54 (170)
Q Consensus        20 C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l   54 (170)
                      |..|+.+|.+. .++...++.||   |-|..|...+
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f   33 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF   33 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence            67899999887 44667888887   4445554443

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=87.50  E-value=0.44  Score=31.09  Aligned_cols=28  Identities=25%  Similarity=0.502  Sum_probs=18.8

Q ss_pred             ccccccccccCCceEEecCCcccccCcc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      .|..|+++|.....++...|..+|..|+
T Consensus        80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~  107 (109)
T PF10367_consen   80 KCSVCGKPLGNSVFVVFPCGHVVHYSCI  107 (109)
T ss_pred             CccCcCCcCCCceEEEeCCCeEEecccc
Confidence            6888888886533345555667777775

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 [].

>KOG0490|consensus

Probab=85.26  E-value=0.18  Score=37.73  Aligned_cols=52  Identities=27%  Similarity=0.706  Sum_probs=39.3

Q ss_pred             ccccccCCceEEecCCcccccCccccccCCccccc-CCeEEEeCCeeccHHhHHH
Q psy7479          87 CTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV-GDRFYLCDNKILCEYDYEE  140 (170)
Q Consensus        87 C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~c~~~  140 (170)
                      |+..|.+ ...+.+.+..||..|..|..|...+.. ...|.. +|..||...+..
T Consensus         2 ~~~~~~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~   54 (235)
T KOG0490|consen    2 CGRQILD-RYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQR   54 (235)
T ss_pred             CCccccc-hHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchh
Confidence            5556644 234556689999999999999999942 334554 999999999987

>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B

Probab=85.01  E-value=0.97  Score=27.03  Aligned_cols=46  Identities=20%  Similarity=0.379  Sum_probs=24.1

Q ss_pred             ccccccccccccCCCee-EEeCCccccccceecccccccccccccccccCCc
Q psy7479          45 LKCGCCDCRLGEVGSTL-YQKANLILCKRDYLRLFGTTGYCAACTKVIPAFE   95 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~-~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~   95 (170)
                      ++|+.|...|.   ..+ ...=..+||..|....++.  .|+.|+.|....|
T Consensus         8 LrCs~C~~~l~---~pv~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD   54 (65)
T PF14835_consen    8 LRCSICFDILK---EPVCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQD   54 (65)
T ss_dssp             TS-SSS-S--S---S-B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS
T ss_pred             cCCcHHHHHhc---CCceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHH
Confidence            58888988886   233 3555688999999988887  8999998886544

>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=84.05  E-value=0.65  Score=26.03  Aligned_cols=44  Identities=18%  Similarity=0.392  Sum_probs=29.9

Q ss_pred             cccccccccccCCCeeEEeCCcc-ccccceeccccccccccccccccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLI-LCKRDYLRLFGTTGYCAACTKVIP   92 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~-yC~~c~~~~~~~~~~C~~C~~~i~   92 (170)
                      .|..|.....   ...+..=|.. +|..|..+......+|..|..+|.
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            4666666653   3456677777 999999877533348999999884

...

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

Probab=83.89  E-value=1.6  Score=28.61  Aligned_cols=34  Identities=15%  Similarity=0.328  Sum_probs=23.7

Q ss_pred             cccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479         110 FACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus       110 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                      ++|..|+.++-.|+.|.+..+.+.--.||.....
T Consensus         3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~~   36 (101)
T PF09943_consen    3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKAS   36 (101)
T ss_pred             eEEEecCCeeeecceEEEecCCcEeHHHHHHHHh
Confidence            3577777777677777777667777777766543

>PF12773 DZR: Double zinc ribbon

Probab=82.06  E-value=1.2  Score=24.94  Aligned_cols=9  Identities=22%  Similarity=0.597  Sum_probs=4.2

Q ss_pred             ccccccccc
Q psy7479          83 YCAACTKVI   91 (170)
Q Consensus        83 ~C~~C~~~i   91 (170)
                      .|..|+..+
T Consensus        31 ~C~~Cg~~~   39 (50)
T PF12773_consen   31 ICPNCGAEN   39 (50)
T ss_pred             CCcCCcCCC
Confidence            355555443

>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27)

Probab=81.57  E-value=1.1  Score=24.34  Aligned_cols=22  Identities=27%  Similarity=0.531  Sum_probs=15.3

Q ss_pred             cccccccccccCCCeeEEeCCccccccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRD   73 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c   73 (170)
                      .|..|+.+|      +..++|+.||..|
T Consensus        19 ~Cp~C~~PL------~~~k~g~~~Cv~C   40 (41)
T PF06677_consen   19 HCPDCGTPL------MRDKDGKIYCVSC   40 (41)
T ss_pred             ccCCCCCee------EEecCCCEECCCC
Confidence            466777776      3357888888765

It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].

>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length

Probab=81.50  E-value=3.2  Score=25.25  Aligned_cols=59  Identities=19%  Similarity=0.450  Sum_probs=28.4

Q ss_pred             cccccccccccCCCeeEEeCCccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC  120 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~  120 (170)
                      .|..|+.+|.       ..++..+|..|...... .+.|+.|+.++    .++.|-|..    =|.|..|+..++
T Consensus         3 ~CP~C~~~L~-------~~~~~~~C~~C~~~~~~-~a~CPdC~~~L----e~LkACGAv----dYFC~~c~gLiS   61 (70)
T PF07191_consen    3 TCPKCQQELE-------WQGGHYHCEACQKDYKK-EAFCPDCGQPL----EVLKACGAV----DYFCNHCHGLIS   61 (70)
T ss_dssp             B-SSS-SBEE-------EETTEEEETTT--EEEE-EEE-TTT-SB-----EEEEETTEE----EEE-TTTT-EE-
T ss_pred             cCCCCCCccE-------EeCCEEECcccccccee-cccCCCcccHH----HHHHHhccc----ceeeccCCceee
Confidence            4667777764       22356667777543221 23899999888    455555521    135778887774

Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.

>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional

Probab=80.92  E-value=1.3  Score=26.01  Aligned_cols=14  Identities=43%  Similarity=0.899  Sum_probs=8.1

Q ss_pred             cccccccccccccc
Q psy7479          17 LKECASCGKRITER   30 (170)
Q Consensus        17 ~~~C~~C~~~I~~~   30 (170)
                      .+.|..|+..|.+.
T Consensus         7 ~~~CtSCg~~i~~~   20 (59)
T PRK14890          7 PPKCTSCGIEIAPR   20 (59)
T ss_pred             CccccCCCCcccCC
Confidence            34566666666544

>KOG0320|consensus

Probab=80.27  E-value=0.53  Score=33.99  Aligned_cols=53  Identities=23%  Similarity=0.414  Sum_probs=38.4

Q ss_pred             ccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479          40 WHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA   93 (170)
Q Consensus        40 ~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~   93 (170)
                      --..+++|..|=....+ ...+..+=|.+||..|.........+|..|++.|..
T Consensus       127 ~~~~~~~CPiCl~~~se-k~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~  179 (187)
T KOG0320|consen  127 RKEGTYKCPICLDSVSE-KVPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH  179 (187)
T ss_pred             ccccccCCCceecchhh-ccccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence            34567888888776652 123457889999999998765444489999998853

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	170
2dfy_X	195	Crystal Structure Of A Cyclized Protein Fusion Of L		7e-37
1rut_X	188	Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 L		8e-37
2xjy_A	131	Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21		1e-35
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		3e-23
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		5e-23
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		7e-23
2l4z_A	123	Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-L		1e-16
2lxd_A	125	Backbone 1h, 13c, And 15n Chemical Shift Assignment		1e-16
2l6y_B	96	Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid Length =		2e-16
1m3v_A	122	Flin4: Fusion Of The Lim Binding Domain Of Ldb1 And		8e-16
1j2o_A	114	Structure Of Flin2, A Complex Containing The N-Term		2e-14
1x3h_A	80	Solution Structure Of The Lim Domain Of Human Leupa		3e-05

>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 =  149 bits (376), Expect = 7e-37,   Method: Compositional matrix adjust.
 Identities = 62/120 (51%), Positives = 86/120 (71%)
Query: 18  KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
           K CA CG +I +RFLL A+D +WH  CLKC  C  +LG++G++ Y K+ +ILC+ DY+RL
Sbjct: 4   KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 63
Query: 78  FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
           FG +G C+AC + IPA E+VMRA+ NVYHL+CF C  C +R   GDRF+  +  + CE+D
Sbjct: 64  FGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHD 123

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

Iteration: 1
 Score =  149 bits (376), Expect = 8e-37,   Method: Compositional matrix adjust.
 Identities = 62/120 (51%), Positives = 86/120 (71%)
Query: 18  KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
           K CA CG +I +RFLL A+D +WH  CLKC  C  +LG++G++ Y K+ +ILC+ DY+RL
Sbjct: 6   KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 65
Query: 78  FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
           FG +G C+AC + IPA E+VMRA+ NVYHL+CF C  C +R   GDRF+  +  + CE+D
Sbjct: 66  FGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHD 125

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

Iteration: 1
 Score =  145 bits (365), Expect = 1e-35,   Method: Compositional matrix adjust.
 Identities = 69/121 (57%), Positives = 82/121 (67%)
Query: 20  CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
           C  C + I +R+ LKA+D +WHEDCL C  C CRLGEVG  LY K    LC+RDYLRLFG
Sbjct: 5   CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFG 64
Query: 80  TTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYE 139
             G CA+C K I A+EM MR K+ VYHLECF C  C   FCVGDR+ L ++ I+CE D  
Sbjct: 65  QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIY 124
Query: 140 E 140
           E
Sbjct: 125 E 125

>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 =  104 bits (259), Expect = 3e-23,   Method: Compositional matrix adjust.
 Identities = 51/123 (41%), Positives = 76/123 (61%), Gaps = 6/123 (4%)
Query: 18  KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
            +CA C + I ++F+LK LD  WH  CLKC   DC++ ++    + +A  + CK D+ + 
Sbjct: 7   PQCAGCNQHILDKFILKVLDRHWHSSCLKCA--DCQM-QLADRCFSRAGSVYCKEDFFKR 63
Query: 78  FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEY 136
           FGT   C AC + IP  ++V +A++ VYHL CFAC  CN +   GD FYL  D +++C+ 
Sbjct: 64  FGTK--CTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEFYLMEDGRLVCKE 121
Query: 137 DYE 139
           DYE
Sbjct: 122 DYE 124

>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 =  103 bits (257), Expect = 5e-23,   Method: Compositional matrix adjust.
 Identities = 54/121 (44%), Positives = 72/121 (59%), Gaps = 6/121 (4%)
Query: 20  CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
           CA C + I +RF+LKALD  WH  CLKC  C   L E     + +   + CK D+ + FG
Sbjct: 9   CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE---RCFSRGESVYCKDDFFKRFG 65
Query: 80  TTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDY 138
           T   CAAC   IP  ++V RA++ VYHL CFAC  C  +   GD FYL  D++++C+ DY
Sbjct: 66  TK--CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY 123
Query: 139 E 139
           E
Sbjct: 124 E 124

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

Iteration: 1
 Score =  102 bits (255), Expect = 7e-23,   Method: Compositional matrix adjust.
 Identities = 54/121 (44%), Positives = 72/121 (59%), Gaps = 6/121 (4%)
Query: 20  CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
           CA C + I +RF+LKALD  WH  CLKC  C   L E     + +   + CK D+ + FG
Sbjct: 63  CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE---RCFSRGESVYCKDDFFKRFG 119
Query: 80  TTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDY 138
           T   CAAC   IP  ++V RA++ VYHL CFAC  C  +   GD FYL  D++++C+ DY
Sbjct: 120 TK--CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY 177
Query: 139 E 139
           E
Sbjct: 178 E 178

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

Iteration: 1
 Score = 82.8 bits (203), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 33/62 (53%), Positives = 46/62 (74%)
Query: 18  KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
           K CA CG +I +RFLL A+D +WH  CLKC  C  +LG++G++ Y K+ +ILC+ DY+RL
Sbjct: 62  KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 121
Query: 78  FG 79
           FG
Sbjct: 122 FG 123

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

Iteration: 1
 Score = 82.4 bits (202), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 38/67 (56%), Positives = 45/67 (67%)
Query: 74  YLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKIL 133
           YLRLFG  G CA+C K I A+EM MR K+ VYHLECF C  C   F VGDR+ L ++ I+
Sbjct: 3   YLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIV 62
Query: 134 CEYDYEE 140
           CE D  E
Sbjct: 63  CEQDIYE 69

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

Iteration: 1
 Score = 82.0 bits (201), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 38/67 (56%), Positives = 45/67 (67%)
Query: 74  YLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKIL 133
           YLRLFG  G CA+C K I A+EM MR K+ VYHLECF C  C   F VGDR+ L ++ I+
Sbjct: 1   YLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIV 60
Query: 134 CEYDYEE 140
           CE D  E
Sbjct: 61  CEQDIYE 67

>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 = 79.7 bits (195), Expect = 8e-16,   Method: Compositional matrix adjust.
 Identities = 32/61 (52%), Positives = 45/61 (73%)
Query: 18 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
          K CA CG +I +RFLL A+D +WH  CLKC  C  +LG++G++ Y K+ +ILC+ DY+RL
Sbjct: 6  KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 65
Query: 78 F 78
          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 = 74.7 bits (182), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 34/58 (58%), Positives = 40/58 (68%)
Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
          C  C + I +R+ LKA+D +WHEDCL C  C CRLGEVG  LY K    LC+RDYLRL
Sbjct: 6  CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL 63

>pdb|1X3H|A Chain A, Solution Structure Of The Lim Domain Of Human Leupaxin Length = 80

Iteration: 1
 Score = 44.3 bits (103), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/71 (33%), Positives = 33/71 (46%), Gaps = 5/71 (7%)
Query: 72  RDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNK 131
           +D+L +F     C  C +  P  E  + A + V+H ECF C  C   F  G  F L D +
Sbjct: 8   KDFLAMFSPK--CGGCNR--PVLENYLSAMDTVWHPECFVCGDCFTSFSTGSFFEL-DGR 62
Query: 132 ILCEYDYEERQ 142
             CE  Y  R+
Sbjct: 63  PFCELHYHHRR 73

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	170
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	1e-51
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	1e-06
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	2e-06
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	6e-49
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	1e-45
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	7e-44
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	3e-12
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-29
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	3e-29
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	8e-08
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	6e-29
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	3e-06
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	5e-28
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	9e-11
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	2e-27
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	1e-08
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	7e-24
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	1e-08
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	1e-17
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	7e-07
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	9e-17
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	1e-06
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	1e-14
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	6e-06
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	2e-14
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	2e-09
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	7e-13
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	2e-07
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	8e-13
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	2e-07
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	2e-12
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	7e-07
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	5e-12
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	1e-06
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	7e-12
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	4e-09
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	1e-11
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	7e-09
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	3e-11
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	3e-08
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	3e-11
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	1e-05
2cuq_A	80	Four and A half LIM domains 3; structural genomics	4e-11
2cuq_A	80	Four and A half LIM domains 3; structural genomics	2e-08
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	5e-11
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	9e-05
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	1e-10
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	1e-08
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	1e-10
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	7e-09
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	2e-10
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	4e-08
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	4e-10
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	1e-08
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	5e-10
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	2e-09
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	9e-10
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	1e-09
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	1e-09
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	6e-09
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	2e-09
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	3e-06
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	3e-09
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	3e-08
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	2e-06
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	6e-09
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	1e-08
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	1e-08
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	2e-05
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	5e-08
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	9e-08
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	8e-08
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	7e-04
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	5e-07
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	5e-06
2co8_A	82	NEDD9 interacting protein with calponin homology a	2e-06
2co8_A	82	NEDD9 interacting protein with calponin homology a	3e-04
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	4e-06
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	5e-04
2cor_A	79	Pinch protein; LIM domain, particularly interestin	4e-05
2cor_A	79	Pinch protein; LIM domain, particularly interestin	6e-05

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

 Score =  160 bits (407), Expect = 1e-51
 Identities = 70/124 (56%), Positives = 83/124 (66%)

Query: 17  LKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLR 76
           L  C  C + I +R+ LKA+D +WHEDCL C  C CRLGEVG  LY K    LC+RDYLR
Sbjct: 2   LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 61

Query: 77  LFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEY 136
           LFG  G CA+C K I A+EM MR K+ VYHLECF C  C   FCVGDR+ L ++ I+CE 
Sbjct: 62  LFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQ 121

Query: 137 DYEE 140
           D  E
Sbjct: 122 DIYE 125

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

 Score = 44.7 bits (106), Expect = 1e-06
 Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC-VGDRFYLCDNKILCEYDYEER 141
           C  C + I      ++A +  +H +C +C  C  R   VG R Y    + LC  DY   
Sbjct: 5   CGGCQQNIGD-RYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL 62

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

 Score = 44.4 bits (105), Expect = 2e-06
 Identities = 19/69 (27%), Positives = 28/69 (40%), Gaps = 2/69 (2%)

Query: 15  GGLKECASCGKRITERFL-LKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRD 73
           G    CASC KRI    + ++  D  +H +C KC  C       G       + I+C++D
Sbjct: 64  GQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCV-GDRYLLINSDIVCEQD 122

Query: 74  YLRLFGTTG 82
                   G
Sbjct: 123 IYEWTKING 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 =  155 bits (393), Expect = 6e-49
 Identities = 64/141 (45%), Positives = 91/141 (64%)

Query: 13  ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 72
            S   K CA CG +I +RFLL A+D +WH  CLKC  C  +LG++G++ Y K+ +ILC+ 
Sbjct: 1   GSLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRN 60

Query: 73  DYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKI 132
           DY+RLFG +G C+AC + IPA E+VMRA+ NVYHL+CF C  C +R   GDRF+  +  +
Sbjct: 61  DYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSL 120

Query: 133 LCEYDYEERQVFANIAYNPSS 153
            CE+D     +  ++    S 
Sbjct: 121 FCEHDRPTALINGHLNSGGSG 141

>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 =  146 bits (371), Expect = 1e-45
 Identities = 55/131 (41%), Positives = 75/131 (57%), Gaps = 6/131 (4%)

Query: 12  GASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCK 71
           G +  +  CA C + I +RF+LKALD  WH  CLKC  C   L E     + +   + CK
Sbjct: 55  GGTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE---RCFSRGESVYCK 111

Query: 72  RDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DN 130
            D+ + FGT   CAAC   IP  ++V RA++ VYHL CFAC  C  +   GD FYL  D+
Sbjct: 112 DDFFKRFGTK--CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDS 169

Query: 131 KILCEYDYEER 141
           +++C+ DYE  
Sbjct: 170 RLVCKADYETA 180

>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 =  141 bits (358), Expect = 7e-44
 Identities = 55/131 (41%), Positives = 76/131 (58%), Gaps = 6/131 (4%)

Query: 12  GASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCK 71
           G++  +  CA C + I +RF+LKALD  WH  CLKC  C   L E     + +   + CK
Sbjct: 1   GSTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE---RCFSRGESVYCK 57

Query: 72  RDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DN 130
            D+ + FGT   CAAC   IP  ++V RA++ VYHL CFAC  C  +   GD FYL  D+
Sbjct: 58  DDFFKRFGTK--CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDS 115

Query: 131 KILCEYDYEER 141
           +++C+ DYE  
Sbjct: 116 RLVCKADYETA 126

>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 = 60.6 bits (147), Expect = 3e-12
 Identities = 18/100 (18%), Positives = 30/100 (30%), Gaps = 5/100 (5%)

Query: 20  CASCGKRIT-ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 78
           CA+C   I   + + +A D  +H  C  C  C  +L         + + ++CK DY    
Sbjct: 68  CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK 127

Query: 79  GTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHR 118
                              M A +   H           +
Sbjct: 128 QGG--SGGSGGSGG--GTPMVAASPERHDGGLQANPVEVQ 163

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

 Score =  104 bits (261), Expect = 1e-29
 Identities = 29/124 (23%), Positives = 46/124 (37%), Gaps = 7/124 (5%)

Query: 20  CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
           CA C + I      +A +  WH     C  CD  L   G       +  +CK  Y++   
Sbjct: 6   CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILA--GEIYVMVNDKPVCKPCYVKNHA 63

Query: 80  TTGYCAACTKVIPAFEMVMRAKNNVYHL--ECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
               C  C   I      +   N  +H   ECF C  C+    +G +F   +  + C  +
Sbjct: 64  V--VCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVEGMVFCSVE 120

Query: 138 YEER 141
            ++R
Sbjct: 121 CKKR 124

>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 =  103 bits (258), Expect = 3e-29
 Identities = 38/128 (29%), Positives = 64/128 (50%), Gaps = 16/128 (12%)

Query: 13  ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 72
            S   K CA CG +I +RFLL A+D +WH  CLKC  C  +LG++G++ Y K+ +ILC+ 
Sbjct: 1   GSLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRN 60

Query: 73  DYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKI 132
           DY+RLFG +G   +   +    ++++                      +G  F   D ++
Sbjct: 61  DYIRLFGNSGAGGSGGHMGSGGDVMV----------------VGEPTLMGGEFGDEDERL 104

Query: 133 LCEYDYEE 140
           +   +  +
Sbjct: 105 ITRLENTQ 112

>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 = 47.7 bits (113), Expect = 8e-08
 Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 2/59 (3%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC-VGDRFYLCDNKILCEYDYEER 141
           CA C   I     ++ A ++ +H  C  C  C  +   +G   Y     ILC  DY   
Sbjct: 8   CAGCGGKIAD-RFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 65

>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 = 6e-29
 Identities = 43/105 (40%), Positives = 56/105 (53%)

Query: 15  GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 74
           G L  C  C + I +R+ LKA+D +WHEDCL C  C CRLGEVG  LY K    LC+RDY
Sbjct: 1   GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 60

Query: 75  LRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF 119
           LRL G+ G+  +   V+   E  +         E    +  N +F
Sbjct: 61  LRLGGSGGHMGSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQF 105

>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 = 43.1 bits (101), Expect = 3e-06
 Identities = 18/65 (27%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 79  GTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC-VGDRFYLCDNKILCEYD 137
           G+   C  C + I      ++A +  +H +C +C  C  R   VG R Y    + LC  D
Sbjct: 1   GSLLTCGGCQQNIGD-RYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRD 59

Query: 138 YEERQ 142
           Y    
Sbjct: 60  YLRLG 64

>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 = 97.9 bits (244), Expect = 2e-27
 Identities = 30/104 (28%), Positives = 41/104 (39%), Gaps = 5/104 (4%)

Query: 13  ASGGLKECASCGKRIT-ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCK 71
            S G   C  C K I  +   +   + FWH+ C +C  C   L     T   K N ILC 
Sbjct: 1   GSSGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLA--NETFVAKDNKILCN 58

Query: 72  RDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQC 115
           +   R       C  C K I A +  +  K  V+H +CF+    
Sbjct: 59  KCTTREDSPK--CKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100

>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 = 49.3 bits (118), Expect = 1e-08
 Identities = 20/58 (34%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141
           C  C K I A    +  KN  +H  CF C +C H     + F   DNKILC       
Sbjct: 8   CVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPL-ANETFVAKDNKILCNKCTTRE 64

>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 = 89.8 bits (222), Expect = 7e-24
 Identities = 35/79 (44%), Positives = 48/79 (60%)

Query: 1   ASSVTQGALAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGST 60
                 G   G      K CA CG +I +RFLL A+D +WH  CLKC  C  +LG++G++
Sbjct: 45  LGGGGSGGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTS 104

Query: 61  LYQKANLILCKRDYLRLFG 79
            Y K+ +ILC+ DY+RLFG
Sbjct: 105 SYTKSGMILCRNDYIRLFG 123

>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 = 49.7 bits (118), Expect = 1e-08
 Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 2/59 (3%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC-VGDRFYLCDNKILCEYDYEER 141
           CA C   I     ++ A ++ +H  C  C  C  +   +G   Y     ILC  DY   
Sbjct: 64  CAGCGGKIAD-RFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 121

>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 = 72.1 bits (177), Expect = 1e-17
 Identities = 22/73 (30%), Positives = 28/73 (38%), Gaps = 5/73 (6%)

Query: 14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRD 73
            G   CA C + I     L ALD  WH  C KC  C   L         K  +  C+ D
Sbjct: 12 IRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG---EYISKDGVPYCESD 68

Query: 74 YLRLFGTTGYCAA 86
          Y   FG+    ++
Sbjct: 69 YHAQFGSG--PSS 79

>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 = 44.0 bits (104), Expect = 7e-07
 Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 3/58 (5%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141
           CA C + I      + A +  +H+ CF CQ C+        +   D    CE DY  +
Sbjct: 18  CAGCKEEI-KHGQSLLALDKQWHVSCFKCQTCSVIL--TGEYISKDGVPYCESDYHAQ 72

>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 = 70.2 bits (172), Expect = 9e-17
 Identities = 21/77 (27%), Positives = 30/77 (38%), Gaps = 5/77 (6%)

Query: 66  NLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRF 125
           +     +DY   FG    C  C+ ++      M A    YH ECFAC  C      GD +
Sbjct: 2   SSGSSGKDYWGKFGEF--CHGCSLLMT--GPFMVAGEFKYHPECFACMSCKVIIEDGDAY 57

Query: 126 YLCDN-KILCEYDYEER 141
            L  +  + C   + E 
Sbjct: 58  ALVQHATLYCGKCHNEV 74

>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 = 43.6 bits (103), Expect = 1e-06
 Identities = 10/61 (16%), Positives = 23/61 (37%), Gaps = 1/61 (1%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
          C  C   +T  F+  A +  +H +C  C  C   + +  +    +   + C + +  +  
Sbjct: 18 CHGCSLLMTGPFM-VAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVS 76

Query: 80 T 80
           
Sbjct: 77 G 77

>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 = 64.8 bits (158), Expect = 1e-14
 Identities = 22/68 (32%), Positives = 30/68 (44%), Gaps = 4/68 (5%)

Query: 73  DYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKI 132
           DY RL+GT   C +C + I     V+ A    YH +CF C  C   F  GDR      + 
Sbjct: 9   DYQRLYGTR--CFSCDQFIE--GEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKEC 64

Query: 133 LCEYDYEE 140
           +C+     
Sbjct: 65  MCQKCSLP 72

>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 = 41.7 bits (98), Expect = 6e-06
 Identities = 14/60 (23%), Positives = 22/60 (36%), Gaps = 2/60 (3%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
          C SC + I    +  AL   +H DC  C  C       G  +       +C++  L +  
Sbjct: 18 CFSCDQFIEGEVV-SALGKTYHPDCFVCAVCRLPFPP-GDRVTFNGKECMCQKCSLPVSV 75

>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 = 63.6 bits (155), Expect = 2e-14
 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 80  TTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYE 139
            +  C  C + +      + A + V+H+ CF C  C  +   G  FY  + +  CE  Y 
Sbjct: 4   GSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLR-GQHFYAVERRAYCEGCYV 62

Query: 140 ER 141
             
Sbjct: 63  AT 64

>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 = 50.5 bits (121), Expect = 2e-09
 Identities = 17/74 (22%), Positives = 26/74 (35%), Gaps = 3/74 (4%)

Query: 13 ASGGLKECASCGKRIT-ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCK 71
           S G   C  CG+ +  +   + ALD  +H  C  C  C  +L   G   Y       C+
Sbjct: 1  GSSGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLR--GQHFYAVERRAYCE 58

Query: 72 RDYLRLFGTTGYCA 85
            Y+    +     
Sbjct: 59 GCYVATLESGPSSG 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 = 59.7 bits (145), Expect = 7e-13
 Identities = 16/60 (26%), Positives = 28/60 (46%), Gaps = 1/60 (1%)

Query: 81  TGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEE 140
           +  C  C       E ++ +   +YH +CF C QC  +F     FY  + +  CE+D++ 
Sbjct: 11  SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP-EGLFYEFEGRKYCEHDFQM 69

>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 = 45.1 bits (107), Expect = 2e-07
 Identities = 12/61 (19%), Positives = 20/61 (32%), Gaps = 3/61 (4%)

Query: 20 CASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 78
          C  C         ++ +    +HE C  C  C  +        Y+      C+ D+  LF
Sbjct: 14 CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP--EGLFYEFEGRKYCEHDFQMLF 71

Query: 79 G 79
           
Sbjct: 72 A 72

>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 = 59.7 bits (145), Expect = 8e-13
 Identities = 16/72 (22%), Positives = 24/72 (33%), Gaps = 3/72 (4%)

Query: 70  CKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCD 129
             +   R       C  C K I A +  +  K  V+H +CF C  C         F+   
Sbjct: 6   SGKCTTREDSPK--CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVI-GTGSFFPKG 62

Query: 130 NKILCEYDYEER 141
               C   +E +
Sbjct: 63  EDFYCVTCHETK 74

>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 = 45.8 bits (109), Expect = 2e-07
 Identities = 14/69 (20%), Positives = 26/69 (37%), Gaps = 7/69 (10%)

Query: 20 CASCGKRIT--ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
          C  C K I   ++ + +     WH+DC  C  C   +G    + + K     C   +   
Sbjct: 18 CKGCFKAIVAGDQNV-EYKGTVWHKDCFTCSNCKQVIG--TGSFFPKGEDFYCVTCHETK 74

Query: 78 FGTTGYCAA 86
          F +    ++
Sbjct: 75 FASG--PSS 81

>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 = 58.6 bits (142), Expect = 2e-12
 Identities = 17/72 (23%), Positives = 31/72 (43%), Gaps = 3/72 (4%)

Query: 69  LCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC 128
           + +     L   +  C  C       E ++ +   +YH +CF C QC  +F     FY  
Sbjct: 1   ISEFMANALA--SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQF-PEGLFYEF 57

Query: 129 DNKILCEYDYEE 140
           + +  CE+D++ 
Sbjct: 58  EGRKYCEHDFQM 69

>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 = 43.9 bits (104), Expect = 7e-07
 Identities = 12/61 (19%), Positives = 20/61 (32%), Gaps = 3/61 (4%)

Query: 20 CASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 78
          C  C         ++ +    +HE C  C  C  +        Y+      C+ D+  LF
Sbjct: 14 CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP--EGLFYEFEGRKYCEHDFQMLF 71

Query: 79 G 79
           
Sbjct: 72 A 72

>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 = 57.8 bits (140), Expect = 5e-12
 Identities = 19/70 (27%), Positives = 33/70 (47%), Gaps = 4/70 (5%)

Query: 17 LKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLR 76
          L++CA+C + I +R L +A+   +H  C  C  C   L  +  T     + I C  D+ R
Sbjct: 15 LEKCATCSQPILDRIL-RAMGKAYHPGCFTCVVCHRGLDGIPFT-VDATSQIHCIEDFHR 72

Query: 77 LFGTTGYCAA 86
           F +    ++
Sbjct: 73 KFAS--GPSS 80

>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 = 43.1 bits (102), Expect = 1e-06
 Identities = 17/59 (28%), Positives = 28/59 (47%), Gaps = 4/59 (6%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDYEER 141
           CA C++ I   + ++RA    YH  CF C  C+     G  F +   ++I C  D+  +
Sbjct: 18  CATCSQPI--LDRILRAMGKAYHPGCFTCVVCHRGL-DGIPFTVDATSQIHCIEDFHRK 73

>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 = 57.5 bits (139), Expect = 7e-12
 Identities = 17/86 (19%), Positives = 31/86 (36%), Gaps = 5/86 (5%)

Query: 1  ASSVTQGALAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGST 60
           + VT+     G++  +  C  CG  I    + KA D + H +C  C  C+  L + G  
Sbjct: 9  RAPVTKVHGGAGSAQRMPLCDKCGSGIVGAVV-KARDKYRHPECFVCADCNLNLKQKGY- 66

Query: 61 LYQKANLILCKRDYLRLFGTTGYCAA 86
           +     + C+             + 
Sbjct: 67 -FFVEGELYCETHARARTSGP--SSG 89

>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 = 50.2 bits (120), Expect = 4e-09
 Identities = 15/58 (25%), Positives = 24/58 (41%), Gaps = 3/58 (5%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141
           C  C   I     V++A++   H ECF C  CN        ++  + ++ CE     R
Sbjct: 28  CDKCGSGI--VGAVVKARDKYRHPECFVCADCNLNL-KQKGYFFVEGELYCETHARAR 82

>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 = 56.6 bits (137), Expect = 1e-11
 Identities = 21/72 (29%), Positives = 31/72 (43%), Gaps = 5/72 (6%)

Query: 70  CKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCD 129
             +D+L +F     C  C + +   E  + A + V+H ECF C  C   F     F+  D
Sbjct: 6   SGKDFLAMFSPK--CGGCNRPV--LENYLSAMDTVWHPECFVCGDCFTSF-STGSFFELD 60

Query: 130 NKILCEYDYEER 141
            +  CE  Y  R
Sbjct: 61  GRPFCELHYHHR 72

>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 = 49.3 bits (118), Expect = 7e-09
 Identities = 15/67 (22%), Positives = 27/67 (40%), Gaps = 5/67 (7%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
          C  C + + E +L  A+D  WH +C  CG C         + ++      C+  Y    G
Sbjct: 18 CGGCNRPVLENYL-SAMDTVWHPECFVCGDCFTSFS--TGSFFELDGRPFCELHYHHRRG 74

Query: 80 TTGYCAA 86
          +    ++
Sbjct: 75 SG--PSS 79

>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 = 55.5 bits (134), Expect = 3e-11
 Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141
           C  C K I      M  K + +H  CF C +C         F   DN+  C   YE++
Sbjct: 8   CQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPI-GTKSFIPKDNQNFCVPCYEKQ 64

>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 = 47.4 bits (113), Expect = 3e-08
 Identities = 17/75 (22%), Positives = 25/75 (33%), Gaps = 5/75 (6%)

Query: 13 ASGGLKECASCGKRIT-ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCK 71
           S G   C  C K I      ++     WHE C  C  C   +G    +   K N   C 
Sbjct: 1  GSSGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIG--TKSFIPKDNQNFCV 58

Query: 72 RDYLRLFGTTGYCAA 86
            Y +   +    ++
Sbjct: 59 PCYEKQHASG--PSS 71

>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 = 3e-11
 Identities = 17/70 (24%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRD 73
           GG  +C +CG+ +     ++     +H  C  C  C   L    +T+      + CK  
Sbjct: 4  WGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLD--STTVAIHDAEVYCKSC 61

Query: 74 YLRLFGTTGY 83
          Y + +G  GY
Sbjct: 62 YGKKYGPKGY 71

>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 = 40.9 bits (96), Expect = 1e-05
 Identities = 14/64 (21%), Positives = 24/64 (37%), Gaps = 2/64 (3%)

Query: 78  FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
           +G    C AC + +   E V       +H  CF C  C           + D ++ C+  
Sbjct: 4   WGGGNKCGACGRTVYHAEEVQ-CDGRSFHRCCFLCMVCRKNL-DSTTVAIHDAEVYCKSC 61

Query: 138 YEER 141
           Y ++
Sbjct: 62  YGKK 65

>2cuq_A Four and A half LIM domains 3; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 55.4 bits (134), Expect = 4e-11
 Identities = 16/72 (22%), Positives = 25/72 (34%), Gaps = 5/72 (6%)

Query: 70  CKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCD 129
               Y   F     CA C+K +   +  +  ++  +H EC  C  C      G +F   D
Sbjct: 6   SGPCYENKFAPR--CARCSKTL--TQGGVTYRDQPWHRECLVCTGCQTPL-AGQQFTSRD 60

Query: 130 NKILCEYDYEER 141
               C   + E 
Sbjct: 61  EDPYCVACFGEL 72

>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 = 48.1 bits (115), Expect = 2e-08
 Identities = 17/67 (25%), Positives = 26/67 (38%), Gaps = 5/67 (7%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
          CA C K +T+  +    D  WH +CL C  C   L   G     +     C   +  LF 
Sbjct: 18 CARCSKTLTQGGV-TYRDQPWHRECLVCTGCQTPLA--GQQFTSRDEDPYCVACFGELFA 74

Query: 80 TTGYCAA 86
          +    ++
Sbjct: 75 S--GPSS 79

>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 = 55.2 bits (133), Expect = 5e-11
 Identities = 15/76 (19%), Positives = 25/76 (32%), Gaps = 6/76 (7%)

Query: 68  ILCKRDYLRLFGTTGYCAACTKVIPAF---EMVMRAKNNVYHLECFACQQCNHRFCVGDR 124
                 Y         CA C   I  F     V+  +   +H  CF C++C+       R
Sbjct: 4   GSSGDCYKNFVAKK--CAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNL-ANKR 60

Query: 125 FYLCDNKILCEYDYEE 140
           F     ++ C    ++
Sbjct: 61  FVFHQEQVYCPDCAKK 76

>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 = 38.2 bits (89), Expect = 9e-05
 Identities = 13/62 (20%), Positives = 18/62 (29%), Gaps = 6/62 (9%)

Query: 20 CASCGKRIT----ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYL 75
          CA C   IT       ++      WH+ C  C  C   L             + C     
Sbjct: 18 CAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLA--NKRFVFHQEQVYCPDCAK 75

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

>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 = 54.0 bits (130), Expect = 1e-10
 Identities = 17/72 (23%), Positives = 28/72 (38%), Gaps = 3/72 (4%)

Query: 70  CKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCD 129
               Y   F  T  CA C ++I      +  ++  +H  CF C +C       + F   D
Sbjct: 6   SGPCYDNTFANT--CAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSL-ADEPFTCQD 62

Query: 130 NKILCEYDYEER 141
           +++LC   Y   
Sbjct: 63  SELLCNDCYCSA 74

>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 = 48.6 bits (116), Expect = 1e-08
 Identities = 16/68 (23%), Positives = 26/68 (38%), Gaps = 5/68 (7%)

Query: 20 CASCGKRIT-ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 78
          CA C + I  +   L   D  +HE C +C  C   L         + + +LC   Y   F
Sbjct: 18 CAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSL--ADEPFTCQDSELLCNDCYCSAF 75

Query: 79 GTTGYCAA 86
           +    ++
Sbjct: 76 SS--GPSS 81

>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 = 53.5 bits (129), Expect = 1e-10
 Identities = 12/58 (20%), Positives = 18/58 (31%), Gaps = 1/58 (1%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141
           C+AC + +      +      +H  CF C  C         F        C   YE +
Sbjct: 8   CSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPL-GSRSFVPDKGAHYCVPCYENK 64

>1wyh_A SLIM 2, skeletal muscle LIM-protein 2; structural genomics, riken structural genomics/proteomics initiative, RSGI, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 49.3 bits (118), Expect = 7e-09
 Identities = 17/75 (22%), Positives = 27/75 (36%), Gaps = 5/75 (6%)

Query: 13 ASGGLKECASCGKRITE-RFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCK 71
           S G   C++CG+ +      L+     WHE C  C  C+  LG    +         C 
Sbjct: 1  GSSGSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLG--SRSFVPDKGAHYCV 58

Query: 72 RDYLRLFGTTGYCAA 86
            Y   F +    ++
Sbjct: 59 PCYENKFASG--PSS 71

>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 = 53.2 bits (128), Expect = 2e-10
 Identities = 17/71 (23%), Positives = 26/71 (36%), Gaps = 3/71 (4%)

Query: 10 AGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLIL 69
          + G +  L  C  CG  I   F+ K  D   H +C  C  C   L + G   +   + I 
Sbjct: 8  SIGNAQKLPMCDKCGTGIVGVFV-KLRDRHRHPECYVCTDCGTNLKQKGH--FFVEDQIY 64

Query: 70 CKRDYLRLFGT 80
          C++        
Sbjct: 65 CEKHARERVSG 75

>1x62_A C-terminal LIM domain protein 1; PDZ and LIM domain protein 1, LIM domain protein CLP-36, contractIle protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 79

 Score = 47.4 bits (113), Expect = 4e-08
 Identities = 13/58 (22%), Positives = 23/58 (39%), Gaps = 3/58 (5%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141
           C  C   I    + ++ ++   H EC+ C  C          +  +++I CE    ER
Sbjct: 18  CDKCGTGI--VGVFVKLRDRHRHPECYVCTDCGTNL-KQKGHFFVEDQIYCEKHARER 72

>2d8z_A Four and A half LIM domains 2; skeletal muscle LIM-protein 3, LIM-domain protein DRAL, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 70

 Score = 52.3 bits (126), Expect = 4e-10
 Identities = 16/74 (21%), Positives = 28/74 (37%), Gaps = 5/74 (6%)

Query: 13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 72
           S G   C  C K IT   +    +  WH++C  C  C  +L   G     + +   C  
Sbjct: 1  GSSGSSGCVQCKKPITTGGV-TYREQPWHKECFVCTACRKQLS--GQRFTARDDFAYCLN 57

Query: 73 DYLRLFGTTGYCAA 86
           +  L+ +    ++
Sbjct: 58 CFCDLYAS--GPSS 69

>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 = 48.5 bits (116), Expect = 1e-08
 Identities = 15/61 (24%), Positives = 23/61 (37%), Gaps = 3/61 (4%)

Query: 81  TGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEE 140
           +  C  C K I      +  +   +H ECF C  C  +   G RF   D+   C   + +
Sbjct: 5   SSGCVQCKKPI--TTGGVTYREQPWHKECFVCTACRKQL-SGQRFTARDDFAYCLNCFCD 61

Query: 141 R 141
            
Sbjct: 62  L 62

>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 = 52.0 bits (125), Expect = 5e-10
 Identities = 20/72 (27%), Positives = 32/72 (44%), Gaps = 3/72 (4%)

Query: 13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 72
           S G   C  CG+ I  R + KA++  WH +C +C  C   L ++G    + A   LC+ 
Sbjct: 1  GSSGSSGCHQCGEFIIGRVI-KAMNNSWHPECFRCDLCQEVLADIG--FVKNAGRHLCRP 57

Query: 73 DYLRLFGTTGYC 84
           + R   +    
Sbjct: 58 CHNREKASGPSS 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 = 50.5 bits (121), Expect = 2e-09
 Identities = 16/58 (27%), Positives = 22/58 (37%), Gaps = 3/58 (5%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141
           C  C + I     V++A NN +H ECF C  C         F     + LC   +   
Sbjct: 8   CHQCGEFI--IGRVIKAMNNSWHPECFRCDLCQEVL-ADIGFVKNAGRHLCRPCHNRE 62

>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 = 52.1 bits (125), Expect = 9e-10
 Identities = 16/67 (23%), Positives = 28/67 (41%), Gaps = 5/67 (7%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
          CA C + I   FL  AL   WH +   C  C   +  +G    ++   + C+  Y + F 
Sbjct: 28 CAHCNQVIRGPFL-VALGKSWHPEEFNCAHCKNTMAYIGF--VEEKGALYCELCYEKFFA 84

Query: 80 TTGYCAA 86
          +    ++
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 = 52.1 bits (125), Expect = 1e-09
 Identities = 18/83 (21%), Positives = 27/83 (32%), Gaps = 4/83 (4%)

Query: 59  STLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHR 118
            +   +  L+            T  CA C +VI      + A    +H E F C  C + 
Sbjct: 4   GSSGDQDTLVQRAEHIPA-GKRTPMCAHCNQVI--RGPFLVALGKSWHPEEFNCAHCKNT 60

Query: 119 FCVGDRFYLCDNKILCEYDYEER 141
                 F      + CE  YE+ 
Sbjct: 61  M-AYIGFVEEKGALYCELCYEKF 82

>1nyp_A Pinch protein; LIM domain, protein recognition, cell adhesion; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 PDB: 1u5s_B Length = 66

 Score = 51.1 bits (123), Expect = 1e-09
 Identities = 17/61 (27%), Positives = 27/61 (44%), Gaps = 3/61 (4%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
          C +C + I  R +  A+   WH +   C  C+      G   Y++  L  C+  Y +LFG
Sbjct: 8  CGACRRPIEGRVV-NAMGKQWHVEHFVCAKCEKPFL--GHRHYERKGLAYCETHYNQLFG 64

Query: 80 T 80
           
Sbjct: 65 D 65

>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 = 49.2 bits (118), Expect = 6e-09
 Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 5/64 (7%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV 143
           C AC + I     V+ A    +H+E F C +C   F  G R Y       CE  Y +   
Sbjct: 8   CGACRRPI--EGRVVNAMGKQWHVEHFVCAKCEKPFL-GHRHYERKGLAYCETHYNQL-- 62

Query: 144 FANI 147
           F ++
Sbjct: 63  FGDV 66

>2d8y_A Eplin protein; LIM domain, epithelial protein LOST in neoplasm, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 91

 Score = 51.0 bits (122), Expect = 2e-09
 Identities = 17/69 (24%), Positives = 27/69 (39%), Gaps = 2/69 (2%)

Query: 14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRD 73
          +   + C  C K +     L A    +H  C +C  C+ +L     T       I CK  
Sbjct: 12 APARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLS--LGTYASLHGRIYCKPH 69

Query: 74 YLRLFGTTG 82
          + +LF + G
Sbjct: 70 FNQLFKSKG 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 = 42.5 bits (100), Expect = 3e-06
 Identities = 15/63 (23%), Positives = 28/63 (44%), Gaps = 2/63 (3%)

Query: 78  FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
                 C  C K +   E ++ A   V+H+ CF C  CN++  +G  +     +I C+  
Sbjct: 12  APARETCVECQKTVYPMERLL-ANQQVFHISCFRCSYCNNKLSLGT-YASLHGRIYCKPH 69

Query: 138 YEE 140
           + +
Sbjct: 70  FNQ 72

>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 = 52.7 bits (126), Expect = 3e-09
 Identities = 19/118 (16%), Positives = 36/118 (30%), Gaps = 4/118 (3%)

Query: 14  SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRD 73
            GG K+C  C K +     ++     +H+ C  C  C   L    +T+    + I CK  
Sbjct: 4   WGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNL--DSTTVAVHGDEIYCKSC 61

Query: 74  YLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNK 131
           Y + +G                        + + E  + +  N       +     + 
Sbjct: 62  YGKKYGPK--GKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDG 117

>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 = 50.0 bits (119), Expect = 3e-08
 Identities = 19/64 (29%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 20  CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
           C  CG+ +     +      WH+ C +C  C   L    +TL  K   I CK  Y + FG
Sbjct: 118 CPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLE--STTLADKDGEIYCKGCYAKNFG 175

Query: 80  TTGY 83
             G+
Sbjct: 176 PKGF 179

>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 = 45.0 bits (106), Expect = 2e-06
 Identities = 14/64 (21%), Positives = 26/64 (40%), Gaps = 2/64 (3%)

Query: 78  FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
           +G    C  C K +   E V + + + +H  CF C  C           +  ++I C+  
Sbjct: 4   WGGGKKCGVCQKAVYFAEEV-QCEGSSFHKSCFLCMVCKKNL-DSTTVAVHGDEIYCKSC 61

Query: 138 YEER 141
           Y ++
Sbjct: 62  YGKK 65

>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 = 6e-09
 Identities = 18/68 (26%), Positives = 21/68 (30%), Gaps = 3/68 (4%)

Query: 13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 72
           S G   C  C K IT   +    D  WH DC  C  C  +L   G       +   C  
Sbjct: 1  GSSGSSGCVKCNKAITSGGI-TYQDQPWHADCFVCVTCSKKLA--GQRFTAVEDQYYCVD 57

Query: 73 DYLRLFGT 80
           Y      
Sbjct: 58 CYKNFVSG 65

>2cur_A Skeletal muscle LIM-protein 1; four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 69

 Score = 48.5 bits (116), Expect = 1e-08
 Identities = 14/58 (24%), Positives = 25/58 (43%), Gaps = 3/58 (5%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEER 141
           C  C K I      +  ++  +H +CF C  C+ +   G RF   +++  C   Y+  
Sbjct: 8   CVKCNKAI--TSGGITYQDQPWHADCFVCVTCSKKL-AGQRFTAVEDQYYCVDCYKNF 62

>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 = 48.5 bits (116), Expect = 1e-08
 Identities = 20/75 (26%), Positives = 30/75 (40%), Gaps = 3/75 (4%)

Query: 10 AGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLIL 69
          + G+SG   +C  C K +     + +L   WH+ CLKC  C   L        +      
Sbjct: 2  SSGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLT--PGGHAEHDGKPF 59

Query: 70 CKRD-YLRLFGTTGY 83
          C +  Y  LFG+   
Sbjct: 60 CHKPCYATLFGSGPS 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 = 39.7 bits (93), Expect = 2e-05
 Identities = 14/61 (22%), Positives = 20/61 (32%), Gaps = 2/61 (3%)

Query: 78  FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYD 137
            G    C  C K +   E V  +    +H  C  C++C+     G      D K  C   
Sbjct: 6   SGMASKCPKCDKTVYFAEKVS-SLGKDWHKFCLKCERCSKTLTPG-GHAEHDGKPFCHKP 63

Query: 138 Y 138
            
Sbjct: 64  C 64

>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 = 46.7 bits (111), Expect = 5e-08
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 3/61 (4%)

Query: 83  YCAACTKVIPAF--EMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEE 140
            CA CT  I        +  +   +H +CF C++C+    VG  F    + ILC    ++
Sbjct: 7   GCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL-VGRGFLTERDDILCPDCGKD 65

Query: 141 R 141
            
Sbjct: 66  I 66

>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 = 46.4 bits (110), Expect = 9e-08
 Identities = 19/70 (27%), Positives = 25/70 (35%), Gaps = 5/70 (7%)

Query: 13 ASGGLKECASCGKRITERF---LLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLIL 69
           S G   CA C   I+       +   +  WH DC  C  C   L  VG     + + IL
Sbjct: 1  GSSGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL--VGRGFLTERDDIL 58

Query: 70 CKRDYLRLFG 79
          C      + G
Sbjct: 59 CPDCGKDISG 68

>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 = 46.6 bits (111), Expect = 8e-08
 Identities = 17/65 (26%), Positives = 23/65 (35%), Gaps = 3/65 (4%)

Query: 20 CASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRD-YLRLF 78
          C  C K +     + +L   WH  CLKC  C   L        +      C    Y  +F
Sbjct: 3  CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLT--SGGHAEHEGKPYCNHPCYSAMF 60

Query: 79 GTTGY 83
          G  G+
Sbjct: 61 GPKGF 65

>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 = 35.8 bits (83), Expect = 7e-04
 Identities = 12/55 (21%), Positives = 19/55 (34%), Gaps = 2/55 (3%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDY 138
           C  C K +   E V  +    +H  C  C++C      G      + K  C +  
Sbjct: 3   CPKCDKEVYFAERVT-SLGKDWHRPCLKCEKCGKTLTSG-GHAEHEGKPYCNHPC 55

>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 = 5e-07
 Identities = 16/55 (29%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 83  YCAACTKVIPAFEM--VMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCE 135
            C AC+K I        +  +++ +H ECF C +C+    VG  F   + +I C+
Sbjct: 7   GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSL-VGKGFLTQNKEIFCQ 60

>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 = 41.8 bits (98), Expect = 5e-06
 Identities = 18/68 (26%), Positives = 26/68 (38%), Gaps = 5/68 (7%)

Query: 14 SGGLKECASCGKRITERF---LLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILC 70
          S G   C +C K I+       +   D  WH +C  CG C   L  VG     +   I C
Sbjct: 2  SSGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSL--VGKGFLTQNKEIFC 59

Query: 71 KRDYLRLF 78
          ++    + 
Sbjct: 60 QKCGSGMD 67

>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 = 43.0 bits (101), Expect = 2e-06
 Identities = 14/70 (20%), Positives = 23/70 (32%)

Query: 13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 72
           +G    CA CG+ +     L     F+H  C +C  C+  L   G   +       C +
Sbjct: 11 EAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQ 70

Query: 73 DYLRLFGTTG 82
             +      
Sbjct: 71 HLPQTDSGPS 80

>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 = 36.9 bits (85), Expect = 3e-04
 Identities = 13/64 (20%), Positives = 20/64 (31%), Gaps = 2/64 (3%)

Query: 78  FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGD-RFYLCDNKILCEY 136
            G    CA C + +   E +     + +H  CF C  C      G    +  D    C  
Sbjct: 12  AGAGDLCALCGEHLYVLERLC-VNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQ 70

Query: 137 DYEE 140
              +
Sbjct: 71  HLPQ 74

>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 73

 Score = 42.0 bits (98), Expect = 4e-06
 Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 2/51 (3%)

Query: 84  CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILC 134
           C +C K I     V+ A    YH  C  C +C   F  G+  YL  + I  
Sbjct: 8   CDSCEKYIT--GRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWH 56

>1wig_A KIAA1808 protein; LIM domain, zinc finger, metal-binding protein, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 73

 Score = 36.2 bits (83), Expect = 5e-04
 Identities = 17/55 (30%), Positives = 23/55 (41%), Gaps = 1/55 (1%)

Query: 13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANL 67
           S G   C SC K IT R L +A +  +H  C  C  C     E      Q +++
Sbjct: 1  GSSGSSGCDSCEKYITGRVL-EAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSI 54

>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 = 39.4 bits (92), Expect = 4e-05
 Identities = 12/66 (18%), Positives = 20/66 (30%), Gaps = 4/66 (6%)

Query: 13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR 72
             G   C  C   I E+ L    +  +H D   C  C   L        +    + C  
Sbjct: 11 RGLGKYICQKCHAIIDEQPL-IFKNDPYHPDHFNCANCGKELTADA---RELKGELYCLP 66

Query: 73 DYLRLF 78
           + ++ 
Sbjct: 67 CHDKMG 72

>2cor_A Pinch protein; LIM domain, particularly interesting NEW Cys- His protein, LIM and senescent cell antigen-like domains 1, structural genomics; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 79

 Score = 38.6 bits (90), Expect = 6e-05
 Identities = 12/60 (20%), Positives = 21/60 (35%), Gaps = 4/60 (6%)

Query: 81  TGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEE 140
              C  C  +I   E  +  KN+ YH + F C  C               ++ C   +++
Sbjct: 15  KYICQKCHAIID--EQPLIFKNDPYHPDHFNCANCGKEL--TADARELKGELYCLPCHDK 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	170
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	100.0
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	100.0
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.97
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.97
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.97
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.96
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.94
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.9
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.86
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.83
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.83
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.82
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.82
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.81
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.79
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.78
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.73
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.72
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.72
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.7
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.69
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.69
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.68
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.68
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.68
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	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
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.66
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.66
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.66
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.65
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.65
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.65
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.65
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.65
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.65
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.65
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.64
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.64
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.64
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.63
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.63
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.63
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.62
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.62
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.62
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.61
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.61
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.61
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.61
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.6
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.6
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.6
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.6
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.6
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.59
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.59
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.58
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.57
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.57
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.55
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.55
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.55
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.55
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.55
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.55
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.54
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.52
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.52
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.51
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.51
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.51
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.5
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.5
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.5
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.49
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.48
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.47
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.47
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.46
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.43
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.39
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.34
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.11
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	97.8
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	92.69
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	88.42
2ect_A	78	Ring finger protein 126; metal binding protein, st	84.49
1iym_A	55	EL5; ring-H2 finger, ubiquitin ligase, DNA binding	83.78
2d8t_A	71	Dactylidin, ring finger protein 146; RNF146, ring	83.72
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	83.51
4ayc_A	138	E3 ubiquitin-protein ligase RNF8; DNA damage, K63	83.24
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	81.77
2kre_A	100	Ubiquitin conjugation factor E4 B; U-box domain, E	81.77
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	81.54
2csy_A	81	Zinc finger protein 183-like 1; ring finger protei	81.34
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	81.0
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	80.58

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

Probab=100.00  E-value=3.1e-34  Score=197.84  Aligned_cols=127  Identities=55%  Similarity=1.169  Sum_probs=116.2

Q ss_pred             cccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCCce
Q psy7479          17 LKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEM   96 (170)
Q Consensus        17 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~   96 (170)
                      .++|.+|+++|.+.+++.++++.||++||+|..|+.+|.+.+..|+.++|++||+.||.+++++.++|..|+++|.+.+.
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            57899999999998788999999999999999999999643467999999999999999999865589999999988778


Q ss_pred             EEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479          97 VMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus        97 ~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                      ++.+.++.||++||+|..|+++|..+..|+..++++||..||.+++.
T Consensus        82 ~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~  128 (131)
T 2xjy_A           82 TMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTK  128 (131)
T ss_dssp             EEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHHHH
T ss_pred             eEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHHhh
Confidence            99999999999999999999999668889999999999999998754

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

Probab=100.00  E-value=4.2e-33  Score=190.94  Aligned_cols=122  Identities=24%  Similarity=0.517  Sum_probs=112.8

Q ss_pred             CcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCCc
Q psy7479          16 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFE   95 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~   95 (170)
                      ..++|.+|+++|.+++++.++|+.||++||+|..|+++|.  +..|+.++|++||+.||.+++++  +|.+|+++|.+.+
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~~~~~--~C~~C~~~I~~~~   77 (126)
T 2xqn_T            2 EKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILA--GEIYVMVNDKPVCKPCYVKNHAV--VCQGCHNAIDPEV   77 (126)
T ss_dssp             CCCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCT--TSEEEEETTEEEEHHHHHHHSCC--BCTTTCSBCCTTS
T ss_pred             cCCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCC--cCEEEeECCEEechHHhCcCcCc--cCcccCCcCCcCc
Confidence            3578999999999877899999999999999999999997  45799999999999999999998  9999999998767


Q ss_pred             eEEecCCcccc--cCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          96 MVMRAKNNVYH--LECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        96 ~~~~~~~~~~H--~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      .+|.+.++.||  ++||+|..|+++| .+..|++.+|++||+.++.++|
T Consensus        78 ~~~~a~~~~~H~~~~CF~C~~C~~~l-~~~~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           78 QRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             CEEEETTEEEESSTTTSBCTTTCCBC-TTSEEEEETTEEESSHHHHHSC
T ss_pred             eEEECCCCEeeCCCCCcCcCCCCCcc-CCCeeEeECCEEcchHHhhhhc
Confidence            88999999999  9999999999999 6889999999999998887753

>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=99.97  E-value=7.9e-33  Score=201.70  Aligned_cols=131  Identities=47%  Similarity=1.061  Sum_probs=116.1

Q ss_pred             CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCC
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAF   94 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~   94 (170)
                      ...++|.+|+++|.+.+++.++++.||++||+|..|+++|...+..|+.++|++||+.||.++|+++++|..|+++|.+.
T Consensus         3 l~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~~   82 (188)
T 1rut_X            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPAS   82 (188)
T ss_dssp             -CCCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECTT
T ss_pred             CCCCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCccccC
Confidence            34688999999999988899999999999999999999997324579999999999999999998634699999999887


Q ss_pred             ceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhhhc
Q psy7479          95 EMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFA  145 (170)
Q Consensus        95 ~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~  145 (170)
                      +.++.+.++.||++||+|..|+++|..+..|+..++++||+.||.+++...
T Consensus        83 e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~~~  133 (188)
T 1rut_X           83 ELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALING  133 (188)
T ss_dssp             SEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC--
T ss_pred             cEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhccc
Confidence            788999999999999999999999966788999999999999998875433

>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=99.97  E-value=2.7e-32  Score=195.73  Aligned_cols=125  Identities=43%  Similarity=0.939  Sum_probs=110.7

Q ss_pred             CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCC
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAF   94 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~   94 (170)
                      .+.++|.+|+++|.+.+++.++|+.||++||+|..|+++|..  . .|.++|++||+.||.++|++  +|.+|+++|.+.
T Consensus         4 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~--~-~f~~~g~~yC~~~y~~~f~~--~C~~C~~~I~~~   78 (169)
T 2rgt_A            4 PEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE--R-CFSRGESVYCKDDFFKRFGT--KCAACQLGIPPT   78 (169)
T ss_dssp             ---CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCS--C-CEESSSCEECHHHHHHHHSC--BCTTTCCBCCTT
T ss_pred             CCCCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCC--C-CcccCCeeeecccccccccc--cccccccccCCC
Confidence            456899999999999878899999999999999999999973  3 36899999999999999998  999999999887


Q ss_pred             ceEEecCCcccccCccccccCCcccccCCeEEE-eCCeeccHHhHHHHhhh
Q psy7479          95 EMVMRAKNNVYHLECFACQQCNHRFCVGDRFYL-CDNKILCEYDYEERQVF  144 (170)
Q Consensus        95 ~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~~C~~c~~~~~~~  144 (170)
                      +.++.+.++.||++||+|..|+++|..++.|+. .+|++||+.||.+++..
T Consensus        79 ~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~~~  129 (169)
T 2rgt_A           79 QVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQG  129 (169)
T ss_dssp             SEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHHHC
T ss_pred             cEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHhhc
Confidence            778899999999999999999999965778865 58999999999987643

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

Probab=99.97  E-value=2.4e-31  Score=192.90  Aligned_cols=123  Identities=44%  Similarity=0.972  Sum_probs=110.8

Q ss_pred             CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479          14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA   93 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~   93 (170)
                      ....++|.+|+++|.+.+++.++++.||++||+|..|+++|..  . .|.++|++||+.||.++|++  +|.+|+++|.+
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 TPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE--R-CFSRGESVYCKDDFFKRFGT--KCAACQLGIPP  131 (182)
T ss_dssp             CCSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSS--C-CEEETTEEECHHHHHHTTSC--CCTTTCCCCCS
T ss_pred             CCCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCC--C-ceeECCEeeecCcccccccc--ccccCCCccCC
Confidence            5567899999999999888899999999999999999999973  3 35899999999999999998  99999999988


Q ss_pred             CceEEecCCcccccCccccccCCcccccCCeEEE-eCCeeccHHhHHHH
Q psy7479          94 FEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYL-CDNKILCEYDYEER  141 (170)
Q Consensus        94 ~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~~C~~c~~~~  141 (170)
                      .+.++.+.++.||++||+|..|+++|..+..|+. .++++||+.||.++
T Consensus       132 ~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~~  180 (182)
T 2jtn_A          132 TQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETA  180 (182)
T ss_dssp             SCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHHH
T ss_pred             CceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHHh
Confidence            6667889999999999999999999965778875 58999999999875

>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=99.96  E-value=1.9e-30  Score=189.63  Aligned_cols=133  Identities=23%  Similarity=0.490  Sum_probs=113.5

Q ss_pred             CCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccc-----------
Q psy7479          13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTT-----------   81 (170)
Q Consensus        13 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~-----------   81 (170)
                      +..+.++|.+|+++|...+.+.++++.||++||+|..|+++|..  ..|+.++|++||+.||.++|++.           
T Consensus         3 ~~~~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~--~~~~~~~g~~yC~~cy~~~f~~~c~~c~~~~g~~   80 (192)
T 1b8t_A            3 NWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDS--TTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGTL   80 (192)
T ss_dssp             CCCCCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCS--SSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCCC
T ss_pred             CCCCCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCC--CeeEecCCEeeChhhhHhhcCccccccccccccE
Confidence            35567899999999986667889999999999999999999974  45999999999999999998761           


Q ss_pred             -----------------------------------cccccccccccCCceEEecCCcccccCccccccCCcccccCCeEE
Q psy7479          82 -----------------------------------GYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFY  126 (170)
Q Consensus        82 -----------------------------------~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~  126 (170)
                                                         ++|.+|+++|.+.+ .+.+.++.||++||+|..|+++| .+..|+
T Consensus        81 ~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~C~~C~~~I~~~~-~v~a~~~~~H~~CF~C~~C~~~L-~~~~~~  158 (192)
T 1b8t_A           81 STDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAE-KVIGAGKSWHKSCFRCAKCGKSL-ESTTLA  158 (192)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECTTTSCEECSSS-CEEETTEEECTTTCBCTTTCCBC-CSSSEE
T ss_pred             ecCCCcccccccccccccCCCCcCccccccccCCCCcCCCCCCEecCcE-EEecCCCccchhcCCccccCCCC-CCCccc
Confidence                                               13889999997644 55799999999999999999999 556799


Q ss_pred             EeCCeeccHHhHHHHhhhccccCCC
Q psy7479         127 LCDNKILCEYDYEERQVFANIAYNP  151 (170)
Q Consensus       127 ~~~~~~~C~~c~~~~~~~~~~~~~~  151 (170)
                      ..++++||+.||.++  +.+.+...
T Consensus       159 ~~~g~~yC~~cy~~~--f~~kc~~C  181 (192)
T 1b8t_A          159 DKDGEIYCKGCYAKN--FGPKGFGF  181 (192)
T ss_dssp             EETTEEEEHHHHHHH--TCCCCCCC
T ss_pred             ccCCEEeCHHHHHHh--cCCcCCCC
Confidence            999999999999998  44444443

>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=99.94  E-value=6.5e-28  Score=158.96  Aligned_cols=98  Identities=30%  Similarity=0.574  Sum_probs=89.9

Q ss_pred             CCccccccccccccc-ceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479          15 GGLKECASCGKRITE-RFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA   93 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~   93 (170)
                      ...++|.+|+++|.. +.++.++++.||++||+|..|+++|.  +..|+.++|++||+.||.+++++  +|.+|+++|.+
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~cy~~~~~~--~C~~C~~~I~~   78 (101)
T 2cup_A            3 SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLA--NETFVAKDNKILCNKCTTREDSP--KCKGCFKAIVA   78 (101)
T ss_dssp             SCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTT--SSCCEEETTEEECHHHHTTCCCC--BCSSSCCBCCS
T ss_pred             CCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCC--cCeeECcCCEEEChhHhhhhcCC--ccccCCCcccc
Confidence            456899999999974 66899999999999999999999996  45689999999999999999998  99999999986


Q ss_pred             CceEEecCCcccccCccccccCC
Q psy7479          94 FEMVMRAKNNVYHLECFACQQCN  116 (170)
Q Consensus        94 ~~~~~~~~~~~~H~~Cf~C~~C~  116 (170)
                      ++.+|.++++.||++||+|..|+
T Consensus        79 ~~~~~~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           79 GDQNVEYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             SSCEEESSSCEEETTTCCCTTCC
T ss_pred             CCeEEEeCCcchHHhCCCCCCCC
Confidence            56899999999999999999985

>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=99.90  E-value=1.9e-25  Score=151.99  Aligned_cols=113  Identities=33%  Similarity=0.737  Sum_probs=96.1

Q ss_pred             CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCC
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAF   94 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~   94 (170)
                      ...++|.+|+++|.+.+++.++++.||++||+|..|+++|.+.+..|+.++|++||+.||.++|+++++|.+|+++|.+ 
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~-   81 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSG-   81 (122)
T ss_dssp             SCCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCC-
T ss_pred             CCCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCc-
Confidence            4568999999999998778999999999999999999999632356899999999999999999976689999999976 


Q ss_pred             ceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479          95 EMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus        95 ~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                       ..+.+.++             ..| .++.|+..++++||..|+.+++.
T Consensus        82 -~~~~~~g~-------------~~l-~g~~f~~~~~~~yC~~~~~~~~~  115 (122)
T 1m3v_A           82 -GDVMVVGE-------------PTL-MGGEFGDEDERLITRLENTQFDA  115 (122)
T ss_dssp             -EESSSSSS-------------SSC-CSCTTCCTTCCCCEECTTTTTTC
T ss_pred             -hheEEcCC-------------cCC-CCCccEecCCEeEccCcchhchh
Confidence             34455542             245 78899999999999999987643

>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=99.86  E-value=3.2e-23  Score=139.33  Aligned_cols=105  Identities=39%  Similarity=0.760  Sum_probs=88.5

Q ss_pred             CcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccCCc
Q psy7479          16 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFE   95 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~   95 (170)
                      ..++|.+|+++|.+.+++.++++.||++||+|..|+++|.+.+..|+.++|++||+.||.++|++  +|..|..   +  
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~--~c~~c~~---~--   74 (114)
T 1j2o_A            2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGS--GGHMGSG---G--   74 (114)
T ss_dssp             CCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTS--CCSSCBS---C--
T ss_pred             cCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCc--ccCcCCC---C--
Confidence            46889999999999888999999999999999999999973235689999999999999999998  9888862   1  


Q ss_pred             eEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          96 MVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        96 ~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      .+|.               |++++..++.|++.++++||..|+.++.
T Consensus        75 ~~~~---------------~~~~~~~g~~f~~~~~~~~C~~~~~~~~  106 (114)
T 1j2o_A           75 DVMV---------------VGEPTLMGGEFGDEDERLITRLENTQFD  106 (114)
T ss_dssp             SCCC---------------SSCSSTTSSBCCCSSSCCCEEEECTTCC
T ss_pred             ceeE---------------cCCccCCCCeeEEcCCEeecchhhhccc
Confidence            2332               4456547889999999999999988763

>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=99.83  E-value=1.9e-21  Score=123.16  Aligned_cols=75  Identities=21%  Similarity=0.417  Sum_probs=69.5

Q ss_pred             CCccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          65 ANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        65 ~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      +|++||+.||.+++++  +|.+|+++|.+++.++.+.++.||++||+|+.|+++| .+..|+..++++||+.||.+++
T Consensus         1 ~g~~yC~~~y~~~~~~--~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~~~~~C~~c~~~~~   75 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFAN--TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSL-ADEPFTCQDSELLCNDCYCSAF   75 (82)
T ss_dssp             CCCCCCCCCCCCCCSC--BCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBC-SSCCEEEETTEEEETTTSSCCG
T ss_pred             CCceechhHhCcccCC--cCccCCCccccCcEEEEeCCccccccCCeecCCCCcc-CCCccEeeCCEEECHHHHhhhc
Confidence            5889999999999998  9999999998656889999999999999999999999 6778999999999999998874

>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=99.83  E-value=8.9e-21  Score=120.05  Aligned_cols=76  Identities=21%  Similarity=0.352  Sum_probs=69.4

Q ss_pred             CCccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479          65 ANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus        65 ~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                      ++.+||++||.+++++  +|.+|+++|.+.+.++.+.++.||++||+|..|+++| .+..|+..++++||+.||.+++.
T Consensus         1 ~~~~yC~~cy~~~~~~--~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f~   76 (82)
T 1x63_A            1 GSSGSSGKCTTREDSP--KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVI-GTGSFFPKGEDFYCVTCHETKFA   76 (82)
T ss_dssp             CCSCCCCCCCSCCCSC--BCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCC-TTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CCCcCchhHHccccCC--cCccCCcccccCceEEEECccccccccCchhhCCCcc-CCCccEeeCCEEECHHHHHHHhC
Confidence            3689999999999998  9999999998767889999999999999999999999 55689999999999999998843

>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=99.82  E-value=7.2e-21  Score=119.07  Aligned_cols=73  Identities=19%  Similarity=0.429  Sum_probs=67.2

Q ss_pred             CCccccccceecccccccccccccccccC---CceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHH
Q psy7479          65 ANLILCKRDYLRLFGTTGYCAACTKVIPA---FEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEE  140 (170)
Q Consensus        65 ~~~~yC~~c~~~~~~~~~~C~~C~~~i~~---~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~  140 (170)
                      ++++||++||.+++++  +|.+|+++|.+   .+.++.+.++.||++||+|..|+++| .+..|+..++++||+.||.+
T Consensus         1 g~~~yC~~cy~~~~~~--~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A            1 GSSGSSGDCYKNFVAK--KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNL-ANKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCSSCCTTCCCSCCCC--CCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBC-TTSCCCEETTEECCHHHHHH
T ss_pred             CCCeEchhHhchhhCc--cCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCC-CCCccEeECCEEEChHHhcc
Confidence            4689999999999998  99999999986   45789999999999999999999999 67789999999999999975

>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=99.82  E-value=1.4e-20  Score=118.54  Aligned_cols=74  Identities=22%  Similarity=0.426  Sum_probs=68.0

Q ss_pred             CCccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479          65 ANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus        65 ~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                      +|++||++||.+++++  +|.+|+++|.+  ..|.+.++.||++||+|..|+++| .+..|+..++++||+.||.+++.
T Consensus         1 gg~~yC~~cy~~~~~~--~C~~C~~~I~~--~~v~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f~   74 (80)
T 2cuq_A            1 GSSGSSGPCYENKFAP--RCARCSKTLTQ--GGVTYRDQPWHRECLVCTGCQTPL-AGQQFTSRDEDPYCVACFGELFA   74 (80)
T ss_dssp             CCCCSCCCCCCCCSSC--CCTTTCCCCCS--CCEESSSSEECTTTCBCSSSCCBC-TTCCEEECSSSEEEHHHHHHHTT
T ss_pred             CCcEEcHHHHccccCC--cCCCCCCEecC--cEEEECCchhhhhhCCcccCCCcC-CCCeeEeECCEEECHHHHHHHcC
Confidence            4789999999999998  99999999976  478999999999999999999999 67789999999999999998843

>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=99.81  E-value=3e-20  Score=117.07  Aligned_cols=73  Identities=27%  Similarity=0.675  Sum_probs=66.9

Q ss_pred             CCccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          65 ANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        65 ~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      +|++||++||.+++++  +|.+|+++|.+  .+|.+.++.||++||+|..|+++| .+..|+..++++||+.||.+++
T Consensus         1 gg~~yC~~~y~~~~~~--~C~~C~~~I~~--~~v~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~~y~~~f   73 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFSP--KCGGCNRPVLE--NYLSAMDTVWHPECFVCGDCFTSF-STGSFFELDGRPFCELHYHHRR   73 (80)
T ss_dssp             CCCCCCCCCCCCCCSC--BCTTTCCBCCS--SCEEETTEEECTTTCBCSSSCCBS-CSSCCEESSSCEECHHHHHHHH
T ss_pred             CCCccchhHHhhhcCC--ccccCCCeecc--eeEEECCCeEecCcCChhhCCCCC-CCCcEEeECCEEECHHHHHHHc
Confidence            4789999999999998  99999999976  578999999999999999999999 5557999999999999999884

>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=99.79  E-value=5.5e-20  Score=116.12  Aligned_cols=74  Identities=28%  Similarity=0.521  Sum_probs=67.0

Q ss_pred             CccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEE-eCCeeccHHhHHHHhh
Q psy7479          66 NLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYL-CDNKILCEYDYEERQV  143 (170)
Q Consensus        66 ~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~~C~~c~~~~~~  143 (170)
                      +.+||+.||.+++++  +|.+|+++|.  +.+|.+.++.||++||+|..|+++|..+..|++ .++++||+.||.+++.
T Consensus         2 ~~~yC~~~y~~~~~~--~C~~C~~~I~--~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~   76 (81)
T 1x6a_A            2 SSGSSGKDYWGKFGE--FCHGCSLLMT--GPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVS   76 (81)
T ss_dssp             CCCCCCCCSSCCSSC--BCTTTCCBCC--SCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHC
T ss_pred             CCccchhHHhhhcCC--cCccCCCCcC--ceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhc
Confidence            678999999999998  9999999997  478899999999999999999999965678884 8999999999998854

>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=99.78  E-value=1.6e-19  Score=113.95  Aligned_cols=72  Identities=25%  Similarity=0.486  Sum_probs=64.8

Q ss_pred             CCccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEe-CCeeccHHhHHHHh
Q psy7479          65 ANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLC-DNKILCEYDYEERQ  142 (170)
Q Consensus        65 ~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~-~~~~~C~~c~~~~~  142 (170)
                      +|++||++||. ++++  +|.+|+++|.+  .+|.+.++.||++||+|..|+++| .+..|+.. ++++||+.||.++|
T Consensus         2 ~g~~yC~~~y~-~~~~--~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~~g~~yC~~cy~~~f   74 (81)
T 2dlo_A            2 SSGSSGEGCYV-ATLE--KCATCSQPILD--RILRAMGKAYHPGCFTCVVCHRGL-DGIPFTVDATSQIHCIEDFHRKF   74 (81)
T ss_dssp             CCCCCCCCCCC-SSCC--BCTTTCCBCCS--CCEEETTEEECTTTCBCSSSCCBC-TTSCEECCTTCCCEEHHHHHHHT
T ss_pred             cCCEECHHHhh-cCCC--ccccCCCeecc--eeEEECCccccHHhcCcccCCCcc-CCCeeEECCCCEEECHHHHHHHh
Confidence            68999999999 6776  99999999974  688999999999999999999999 57778876 78999999999874

>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=99.73  E-value=2.5e-18  Score=108.26  Aligned_cols=70  Identities=33%  Similarity=0.610  Sum_probs=62.4

Q ss_pred             CCCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccccccccc
Q psy7479          12 GASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAA   86 (170)
Q Consensus        12 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~   86 (170)
                      ....+.++|.+|+++|...+.+.++++.||++||+|..|+++|.  + .|+.+++++||+.||.++|++  +|..
T Consensus        10 ~~~~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~--~-~~~~~~g~~yC~~~y~~~fg~--~C~~   79 (80)
T 2dj7_A           10 IKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILT--G-EYISKDGVPYCESDYHAQFGS--GPSS   79 (80)
T ss_dssp             CCCSSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCS--S-CCEEETTEEECTTHHHHHTTC--CSTT
T ss_pred             cCCCCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcC--C-CeEEECCEEECHHHHHHHcCC--CCCC
Confidence            44667889999999999776789999999999999999999997  2 489999999999999999998  8853

>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=99.72  E-value=2.4e-18  Score=107.28  Aligned_cols=71  Identities=23%  Similarity=0.412  Sum_probs=63.8

Q ss_pred             ccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccc-cceeccccccccccccccccc
Q psy7479          18 KECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCK-RDYLRLFGTTGYCAACTKVIP   92 (170)
Q Consensus        18 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~-~c~~~~~~~~~~C~~C~~~i~   92 (170)
                      ++|.+|+++|..++.+.++++.||++||+|..|+++|..  ..|+.++|++||+ .||.++|++  +|.+|++.+.
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~--~~~~~~~g~~yC~~~cy~~~f~~--~C~~C~~~~~   72 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTS--GGHAEHEGKPYCNHPCYSAMFGP--KGFGRGGAES   72 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCT--TTEEEETTEEEETTTHHHHHSSC--CCSSCCCSSS
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCC--CceECcCCeEeeCHHHHHHHhCc--cCCCcCCcee
Confidence            579999999996667899999999999999999999973  4689999999999 699999998  9999997663

>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=99.72  E-value=3e-18  Score=108.10  Aligned_cols=72  Identities=31%  Similarity=0.581  Sum_probs=62.5

Q ss_pred             CccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHH
Q psy7479          66 NLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEER  141 (170)
Q Consensus        66 ~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~  141 (170)
                      +.+||+.||.++|++  +|.+|+++|.+  .+|.+.++.||++||+|..|+++|..+..|...++.+||..||.++
T Consensus         2 ~~~yC~~dy~~~~~~--~C~~C~~~I~~--~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~   73 (81)
T 1v6g_A            2 SSGSSGLDYQRLYGT--RCFSCDQFIEG--EVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPV   73 (81)
T ss_dssp             CCCCCCSCGGGSCCC--BCTTTCCBCCS--CCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCC
T ss_pred             CCCcchHHHHhHhCC--cCccccCEecc--ceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhccc
Confidence            468999999999998  99999999975  6889999999999999999999995555565556678999999654

>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=99.70  E-value=2.9e-18  Score=108.14  Aligned_cols=74  Identities=20%  Similarity=0.401  Sum_probs=55.6

Q ss_pred             CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccc
Q psy7479          14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVI   91 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i   91 (170)
                      ....++|.+|+++|...+.+.++++.||++||+|..|+++|..  ..|+.+++++||+.||.++|++  +|.+|+...
T Consensus         4 ~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~--~~~~~~~~~~yC~~cy~~~f~~--~c~gcg~g~   77 (81)
T 1a7i_A            4 WGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDS--TTVAIHDAEVYCKSCYGKKYGP--KGYGYGQGA   77 (81)
T ss_dssp             ----CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECS--SCCEEETTEEECSHHHHHHCC------------
T ss_pred             CCCCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCC--CCeEeeCCEEECHHHHHHHhCC--cccccCCcc
Confidence            3456899999999986667899999999999999999999973  4589999999999999999998  999998643

>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=99.69  E-value=1.8e-17  Score=103.26  Aligned_cols=69  Identities=23%  Similarity=0.542  Sum_probs=62.2

Q ss_pred             Cccccccccccccc---ceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccccccccccc
Q psy7479          16 GLKECASCGKRITE---RFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACT   88 (170)
Q Consensus        16 ~~~~C~~C~~~I~~---~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~   88 (170)
                      ..++|.+|+++|.+   ..++.++++.||++||+|..|+++|.  +..|+.+++++||+.||.++|++  +|..++
T Consensus         4 ~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~~f~~--~C~~~s   75 (76)
T 1x68_A            4 GSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLV--GKGFLTQNKEIFCQKCGSGMDTD--ISGPSS   75 (76)
T ss_dssp             CCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCS--SSCEEEETTEEEETTTTCCCCCC--SSSSSC
T ss_pred             cCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCC--CCceEeECCEEECHHHhhhhhCC--cCCCCC
Confidence            46789999999996   35789999999999999999999997  45699999999999999999998  998765

>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=2.3e-17  Score=105.89  Aligned_cols=68  Identities=19%  Similarity=0.446  Sum_probs=60.2

Q ss_pred             CCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccc
Q psy7479          13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCA   85 (170)
Q Consensus        13 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~   85 (170)
                      ......+|.+|+++|.+. ++.++++.||++||+|..|++.|..  ..|+.+++++||+.||.++|++  ++.
T Consensus        21 ~~~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~--~~~~~~~g~~yC~~~y~~~f~p--~~~   88 (89)
T 1x64_A           21 SAQRMPLCDKCGSGIVGA-VVKARDKYRHPECFVCADCNLNLKQ--KGYFFVEGELYCETHARARTSG--PSS   88 (89)
T ss_dssp             CCCSCCBCTTTCCBCCSC-CEESSSCEECTTTCCCSSSCCCTTT--SCCEEETTEEECHHHHHHHSSS--CCC
T ss_pred             CCCcCCCcccCCCEeccc-EEEECCceECccCCEecCCCCCCCC--CCeEeECCEEECHHHHHHHhCC--CCC
Confidence            445678999999999986 6889999999999999999999973  4589999999999999999998  654

>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=99.68  E-value=2.7e-17  Score=103.96  Aligned_cols=73  Identities=18%  Similarity=0.320  Sum_probs=61.9

Q ss_pred             CCCCCCCCCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeE--EeCCccccccceeccccc
Q psy7479           6 QGALAGGASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLY--QKANLILCKRDYLRLFGT   80 (170)
Q Consensus         6 ~~~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~--~~~~~~yC~~c~~~~~~~   80 (170)
                      .+++++....+..+|.+|+++|...+.+.++++.||++||+|..|++.|..  ..|+  .++|++||+.||.+++.+
T Consensus         4 ~~~~~~~~~~~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~--~~~~~~~~~g~~yC~~~y~~~~~~   78 (82)
T 2co8_A            4 GSSGQHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWP--GGYEQHPGDGHFYCLQHLPQTDSG   78 (82)
T ss_dssp             CCCCCCCCCCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCT--TSEECCTTTCCCEETTTCCCCCCC
T ss_pred             CCCCCCcCCCCCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCC--CceeEeCcCCEEEChHHHHhhhcC
Confidence            455556667788999999999987767889999999999999999999973  4465  479999999999998875

>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=99.68  E-value=2.1e-17  Score=106.23  Aligned_cols=68  Identities=22%  Similarity=0.471  Sum_probs=60.5

Q ss_pred             CCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccc
Q psy7479          13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCA   85 (170)
Q Consensus        13 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~   85 (170)
                      .....++|.+|+++|.+. .+.++++.||++||+|..|+++|..  ..|+.+++++||+.||.++|++  +|.
T Consensus        21 ~~~~~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~--~~f~~~~g~~yC~~cy~~~f~~--~c~   88 (90)
T 2dar_A           21 AGKRTPMCAHCNQVIRGP-FLVALGKSWHPEEFNCAHCKNTMAY--IGFVEEKGALYCELCYEKFFAS--GPS   88 (90)
T ss_dssp             TTTCCCBBSSSCCBCCSC-EEEETTEEECTTTCBCSSSCCBCSS--SCBEESSSCEECHHHHHHHTSC--CCC
T ss_pred             CCCCCCCCccCCCEecce-EEEECCccccccCCccCCCCCCCCC--CEeEeECCEEECHHHHHHHcCC--CCC
Confidence            345678999999999866 6789999999999999999999973  5689999999999999999998  885

>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=2.5e-17  Score=102.56  Aligned_cols=68  Identities=26%  Similarity=0.485  Sum_probs=60.6

Q ss_pred             CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccc-cceeccccccccccc
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCK-RDYLRLFGTTGYCAA   86 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~-~c~~~~~~~~~~C~~   86 (170)
                      ...++|.+|+++|...+.+.++++.||++||+|..|+++|.  +..|+.+++++||+ .||.++|++  +|.+
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            45689999999999666788999999999999999999997  35689999999999 799999998  8853

>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=99.67  E-value=7.9e-17  Score=99.21  Aligned_cols=63  Identities=27%  Similarity=0.495  Sum_probs=56.8

Q ss_pred             ccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          77 LFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        77 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      ++++  +|.+|+++|.+.+.++.+.++.||++||+|..|+++| .+..|+..++++||+.||.+++
T Consensus         3 ~~~~--~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f   65 (72)
T 1x4k_A            3 SGSS--GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPI-GTKSFIPKDNQNFCVPCYEKQH   65 (72)
T ss_dssp             SCCC--CBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCC-CSSSEEEETTEEEEHHHHHHHT
T ss_pred             ccCC--CCccCCCcccCCceEEEECcCeecccCCcccccCCcc-CCCccCccCCeEECHHHHhHHh
Confidence            4666  9999999998766789999999999999999999999 5668999999999999999873

>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=2.2e-17  Score=100.99  Aligned_cols=67  Identities=25%  Similarity=0.538  Sum_probs=60.3

Q ss_pred             CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccccccccc
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAA   86 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~   86 (170)
                      ...++|.+|+++|.+. .+.++++.||++||+|..|+++|.  +..|+.+++++||+.||.++|++  +|.+
T Consensus         3 ~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~~~~yC~~cy~~~f~~--~C~g   69 (69)
T 2cur_A            3 SGSSGCVKCNKAITSG-GITYQDQPWHADCFVCVTCSKKLA--GQRFTAVEDQYYCVDCYKNFVSG--PSSG   69 (69)
T ss_dssp             CCCCCCSSSCCCCCTT-CEEETTEEECTTTTBCTTTCCBCT--TSCEEECSSCEEEHHHHHHHHTC--SCCC
T ss_pred             CCcCCCcccCCEeCcc-eEEECccccccCcCEECCCCCCCC--CCccEeECCEEECHHHhHHHhcC--CCCC
Confidence            4568999999999986 588999999999999999999997  45699999999999999999998  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=1.2e-17  Score=104.89  Aligned_cols=65  Identities=22%  Similarity=0.447  Sum_probs=58.7

Q ss_pred             CCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccc
Q psy7479          13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT   80 (170)
Q Consensus        13 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~   80 (170)
                      .....++|.+|+++|.+. ++.++++.||++||+|..|++.|..  ..|+.+++++||+.||.++|++
T Consensus        11 ~~~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~--~~~~~~~g~~yC~~cy~~~~~p   75 (79)
T 1x62_A           11 NAQKLPMCDKCGTGIVGV-FVKLRDRHRHPECYVCTDCGTNLKQ--KGHFFVEDQIYCEKHARERVSG   75 (79)
T ss_dssp             CCCCCCCCSSSCCCCCSS-CEECSSCEECTTTTSCSSSCCCHHH--HCCEESSSCEECHHHHHHHHSS
T ss_pred             CCCCCCccccCCCCccCc-EEEECcceeCcCcCeeCCCCCCCCC--CCeEeECCEEECHHHHHHHhCC
Confidence            446678999999999987 6899999999999999999999973  4589999999999999999997

>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=99.66  E-value=1.4e-16  Score=98.12  Aligned_cols=64  Identities=19%  Similarity=0.376  Sum_probs=57.0

Q ss_pred             cccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          76 RLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        76 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      +++++  +|.+|+++|.+.+.++.+.++.||++||+|..|+++| .+..|+..++++||+.||.+++
T Consensus         2 ~~~~~--~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f   65 (72)
T 1wyh_A            2 SSGSS--GCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPL-GSRSFVPDKGAHYCVPCYENKF   65 (72)
T ss_dssp             CCCCC--BCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBT-TTSCEEEETTEEEEHHHHHHHT
T ss_pred             CccCC--CCccCCCccccCccEEEECccccCcccCeECCCCCcC-CCCccCCcCCeEECHHHHHHHc
Confidence            34566  9999999998656789999999999999999999999 5667999999999999999874

>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=99.66  E-value=4.3e-17  Score=99.89  Aligned_cols=66  Identities=23%  Similarity=0.570  Sum_probs=59.6

Q ss_pred             CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccc
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCA   85 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~   85 (170)
                      ...++|.+|+++|.+. .+.++++.||++||+|..|+++|.  +..|+.+++++||+.||.++|++  +|.
T Consensus         3 ~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~~~~yC~~cy~~~f~~--~c~   68 (70)
T 2d8z_A            3 SGSSGCVQCKKPITTG-GVTYREQPWHKECFVCTACRKQLS--GQRFTARDDFAYCLNCFCDLYAS--GPS   68 (70)
T ss_dssp             CCCCBCSSSCCBCCSS-EEESSSSEEETTTSBCSSSCCBCT--TSCCEESSSSEECHHHHHHHTCC--CCT
T ss_pred             CCCCCCcccCCeeccc-eEEECccccCCCCCccCCCCCcCC--cCceEeeCCeEECHHHHHHHhcc--ccC
Confidence            4568899999999987 488999999999999999999997  35689999999999999999998  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=99.66  E-value=5.5e-17  Score=99.96  Aligned_cols=64  Identities=27%  Similarity=0.554  Sum_probs=57.7

Q ss_pred             CCccccccccccccc---ceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccc
Q psy7479          15 GGLKECASCGKRITE---RFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT   80 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~---~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~   80 (170)
                      ...++|.+|+++|.+   ..++.++++.||++||+|..|+++|.  +..|+.+++++||+.||.++|+|
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~c~~~~~~p   69 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLV--GRGFLTERDDILCPDCGKDISGP   69 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCT--TSCCEECSSSEECHHHHHTCCCS
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCC--CCccEeECCEEEChhHcCcccCC
Confidence            457899999999996   35789999999999999999999997  45688999999999999999987

>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=4.6e-17  Score=110.44  Aligned_cols=66  Identities=50%  Similarity=1.188  Sum_probs=58.6

Q ss_pred             CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccc
Q psy7479          14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG   79 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~   79 (170)
                      ....++|.+|+++|.+.+++.++++.||+.||+|..|+++|.+.+..|+.++|++||+.||.++|+
T Consensus        58 ~~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           58 GLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             CSSCSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             CccCCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            445789999999999987799999999999999999999996334568999999999999998875

>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=99.65  E-value=6.3e-17  Score=104.20  Aligned_cols=70  Identities=23%  Similarity=0.423  Sum_probs=61.9

Q ss_pred             CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccc
Q psy7479          14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAAC   87 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C   87 (170)
                      ....++|.+|+++|.+.+.+.++++.||++||+|..|+++|..  ..|+.+++++||+.||.++|++  +|..+
T Consensus        12 ~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~--~~~~~~~g~~yC~~~y~~~f~~--kc~~~   81 (91)
T 2d8y_A           12 APARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSL--GTYASLHGRIYCKPHFNQLFKS--KGNYD   81 (91)
T ss_dssp             SSSSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCT--TTCCCSSSCCCCHHHHHHHSCC--CSCCC
T ss_pred             CCCCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCC--CCcEeECCEEECHHHHHHHhCC--CcCcc
Confidence            3457899999999998767899999999999999999999974  3489999999999999999998  88643

>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=99.65  E-value=8.2e-17  Score=99.51  Aligned_cols=64  Identities=25%  Similarity=0.469  Sum_probs=56.6

Q ss_pred             ccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhhh
Q psy7479          77 LFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVF  144 (170)
Q Consensus        77 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~  144 (170)
                      ++++  +|.+|+++|.+  .+|.++++.||++||+|..|+++|..+..|+..++++||..||.+++..
T Consensus         3 ~~~~--~C~~C~~~I~~--~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~   66 (73)
T 1wig_A            3 SGSS--GCDSCEKYITG--RVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTE   66 (73)
T ss_dssp             CSCC--SCSSSCCCCSS--CCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSS
T ss_pred             cCcC--CcccCCCEecC--eeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhcc
Confidence            4566  99999999976  6889999999999999999999995478899999999999999887543

>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=7.8e-17  Score=99.24  Aligned_cols=66  Identities=24%  Similarity=0.488  Sum_probs=59.7

Q ss_pred             Ccccccccccccccc-eeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccc
Q psy7479          16 GLKECASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCA   85 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~   85 (170)
                      ..++|.+|+++|.+. .++.++++.||++||+|..|+++|..  ..|+.+++++||+.||.++|++  +|.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~--~~~~~~~~~~yC~~cy~~~f~~--~C~   70 (72)
T 1x4k_A            4 GSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGT--KSFIPKDNQNFCVPCYEKQHAS--GPS   70 (72)
T ss_dssp             CCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCS--SSEEEETTEEEEHHHHHHHTSS--CCC
T ss_pred             cCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCC--CccCccCCeEECHHHHhHHhCC--CCC
Confidence            457899999999975 57899999999999999999999973  4689999999999999999998  885

>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=7.3e-17  Score=99.37  Aligned_cols=66  Identities=24%  Similarity=0.533  Sum_probs=59.6

Q ss_pred             Ccccccccccccccc-eeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccc
Q psy7479          16 GLKECASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCA   85 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~   85 (170)
                      ..++|.+|+++|... .++.++++.||++||+|..|+++|..  ..|+.+++++||+.||.++|++  +|.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~--~~~~~~~~~~yC~~cy~~~f~~--~C~   70 (72)
T 1wyh_A            4 GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGS--RSFVPDKGAHYCVPCYENKFAS--GPS   70 (72)
T ss_dssp             CCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTT--SCEEEETTEEEEHHHHHHHTSC--CCC
T ss_pred             cCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCC--CccCCcCCeEECHHHHHHHccC--cCC
Confidence            467899999999964 67899999999999999999999973  4689999999999999999998  885

>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=99.65  E-value=1.3e-16  Score=98.09  Aligned_cols=64  Identities=25%  Similarity=0.584  Sum_probs=56.6

Q ss_pred             cccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          76 RLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        76 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      ..+++  +|.+|+++|.+.+.++.+.++.||++||+|..|+++|.. ..|+..+|++||+.||.++|
T Consensus         8 ~~~~~--~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~-~~~~~~~g~~yC~~~y~~lf   71 (72)
T 3f6q_B            8 GSASA--TCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPE-GLFYEFEGRKYCEHDFQMLF   71 (72)
T ss_dssp             CCTTC--BCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGG-GCCEEETTEEECHHHHHHHT
T ss_pred             CcCCc--cchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCC-CCeEeECCeEeCHHHHHHhh
Confidence            35555  999999999987778899999999999999999999944 47889999999999999874

>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=99.65  E-value=1.7e-16  Score=97.78  Aligned_cols=60  Identities=25%  Similarity=0.595  Sum_probs=55.5

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                      +|.+|+++|.+.+.++.+.++.||++||+|..|+++| .+..|+..++++||+.||.+++.
T Consensus         7 ~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~~~   66 (72)
T 1x61_A            7 GCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQL-RGQHFYAVERRAYCEGCYVATLE   66 (72)
T ss_dssp             CCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBC-TTSCEEESSSCEEEHHHHHHHHH
T ss_pred             CCccCCCccCCCceEEEECCCeEcccCCcccccCCcC-CcCcCEeeCCeEECHHHHHHHHc
Confidence            9999999998766789999999999999999999999 77889999999999999998853

>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=5.6e-17  Score=101.19  Aligned_cols=68  Identities=19%  Similarity=0.461  Sum_probs=58.6

Q ss_pred             CCCccccccccccccc-ceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccc
Q psy7479          14 SGGLKECASCGKRITE-RFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCA   85 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~   85 (170)
                      ....++|.+|+++|.. +.++.++|+.||++||+|..|+++|..  ..|+.++|++||+.||.++|++  +|.
T Consensus         8 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~--~~~~~~~g~~yC~~~y~~~f~~--~C~   76 (77)
T 1g47_A            8 ALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPE--GLFYEFEGRKYCEHDFQMLFAP--CWI   76 (77)
T ss_dssp             CCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGG--GCSEEETTEEECHHHHHHHCCC--C--
T ss_pred             CCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCC--CCeEeECCeEeCHHHHHHHhhc--ccC
Confidence            3456899999999984 456889999999999999999999974  3589999999999999999998  875

>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=99.64  E-value=7.5e-17  Score=100.43  Aligned_cols=64  Identities=25%  Similarity=0.510  Sum_probs=57.0

Q ss_pred             cccccccccccccccccC--CceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          76 RLFGTTGYCAACTKVIPA--FEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        76 ~~~~~~~~C~~C~~~i~~--~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      +++++  +|.+|+++|.+  .+.++.+.++.||++||+|..|+++| .+..|+..++++||+.||.+++
T Consensus         2 ~~~~~--~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~cy~~~f   67 (76)
T 1x68_A            2 SSGSS--GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSL-VGKGFLTQNKEIFCQKCGSGMD   67 (76)
T ss_dssp             TTCCC--CCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBC-SSSCEEEETTEEEETTTTCCCC
T ss_pred             CccCC--CCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcC-CCCceEeECCEEECHHHhhhhh
Confidence            35666  99999999985  55789999999999999999999999 6788999999999999998773

>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=99.64  E-value=1.6e-16  Score=96.21  Aligned_cols=61  Identities=30%  Similarity=0.630  Sum_probs=54.8

Q ss_pred             ccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          77 LFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        77 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      ++++  +|.+|+++|.+  .++.+.++.||++||+|..|+++| .+..|+..++++||+.||.++|
T Consensus         3 ~~~~--~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~~y~~~f   63 (66)
T 1nyp_A            3 MGVP--ICGACRRPIEG--RVVNAMGKQWHVEHFVCAKCEKPF-LGHRHYERKGLAYCETHYNQLF   63 (66)
T ss_dssp             CCCC--EETTTTEECCS--CEECCTTSBEETTTCBCTTTCCBC-SSSCCEEETTEEECHHHHHHHC
T ss_pred             cCCC--CCcccCCEecc--eEEEECccccccCcCEECCCCCCC-CCCceEeECCcEECHHHHHHHh
Confidence            3555  99999999984  688999999999999999999999 6778999999999999999874

>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=99.63  E-value=1.9e-16  Score=100.01  Aligned_cols=67  Identities=24%  Similarity=0.443  Sum_probs=59.6

Q ss_pred             Ccccccccccccc-cceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccccccccc
Q psy7479          16 GLKECASCGKRIT-ERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAA   86 (170)
Q Consensus        16 ~~~~C~~C~~~I~-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~   86 (170)
                      ..++|.+|+++|. +..++.++++.||++||+|..|+++|.  +..|+.+++++||+.||.+++++  +|..
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~--~~~f~~~~~~~~C~~c~~~~~~~--~C~~   81 (82)
T 2ehe_A           14 FANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLA--DEPFTCQDSELLCNDCYCSAFSS--GPSS   81 (82)
T ss_dssp             CSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCS--SCCEEEETTEEEETTTSSCCGGG--SSCC
T ss_pred             cCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccC--CCccEeeCCEEECHHHHhhhcCC--CCCC
Confidence            4578999999999 456788999999999999999999997  35689999999999999999998  8853

>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=99.63  E-value=3.8e-16  Score=100.31  Aligned_cols=71  Identities=23%  Similarity=0.344  Sum_probs=60.2

Q ss_pred             ccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          67 LILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        67 ~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      ....+..+...+.+  +|.+|+++|.+  .+|.+.++.||++||+|..|+++| .+..|+..++++||+.||.++|
T Consensus        13 ~~~~~~~~~~~~~~--~C~~C~~~I~~--~~v~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~cy~~~f   83 (90)
T 2dar_A           13 VQRAEHIPAGKRTP--MCAHCNQVIRG--PFLVALGKSWHPEEFNCAHCKNTM-AYIGFVEEKGALYCELCYEKFF   83 (90)
T ss_dssp             CBCCEEECTTTCCC--BBSSSCCBCCS--CEEEETTEEECTTTCBCSSSCCBC-SSSCBEESSSCEECHHHHHHHT
T ss_pred             hhhcccCCCCCCCC--CCccCCCEecc--eEEEECCccccccCCccCCCCCCC-CCCEeEeECCEEECHHHHHHHc
Confidence            33444455666776  99999999964  688999999999999999999999 5678999999999999999874

>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=99.63  E-value=1.1e-16  Score=97.01  Aligned_cols=62  Identities=29%  Similarity=0.737  Sum_probs=56.3

Q ss_pred             CcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccc
Q psy7479          16 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT   80 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~   80 (170)
                      ..++|.+|+++|.+. .+.++++.||++||+|..|+++|.  +..|+.++|++||+.||.++|++
T Consensus         4 ~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~g~~yC~~~y~~~f~~   65 (66)
T 1nyp_A            4 GVPICGACRRPIEGR-VVNAMGKQWHVEHFVCAKCEKPFL--GHRHYERKGLAYCETHYNQLFGD   65 (66)
T ss_dssp             CCCEETTTTEECCSC-EECCTTSBEETTTCBCTTTCCBCS--SSCCEEETTEEECHHHHHHHCSC
T ss_pred             CCCCCcccCCEecce-EEEECccccccCcCEECCCCCCCC--CCceEeECCcEECHHHHHHHhCC
Confidence            468899999999955 689999999999999999999997  35689999999999999999986

>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=99.62  E-value=1.6e-16  Score=97.88  Aligned_cols=68  Identities=24%  Similarity=0.559  Sum_probs=59.2

Q ss_pred             CCcccccccccccccc-eeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccc
Q psy7479          15 GGLKECASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAAC   87 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C   87 (170)
                      ...++|.+|+++|.+. .++.++++.||++||+|..|+++|.  +..|+.+++++||+.||.+++.   +|..+
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~~~~yC~~cy~~~~~---~~~~~   71 (72)
T 1x61_A            3 SGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLR--GQHFYAVERRAYCEGCYVATLE---SGPSS   71 (72)
T ss_dssp             SCCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCT--TSCEEESSSCEEEHHHHHHHHH---TCSSC
T ss_pred             CCCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCC--cCcCEeeCCeEECHHHHHHHHc---cCCCC
Confidence            4568999999999974 5789999999999999999999996  4669999999999999999886   56543

>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=99.62  E-value=2.3e-16  Score=97.13  Aligned_cols=59  Identities=27%  Similarity=0.569  Sum_probs=54.0

Q ss_pred             ccccccccccC--CceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          83 YCAACTKVIPA--FEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        83 ~C~~C~~~i~~--~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      +|.+|+++|.+  ++.++.+.++.||++||+|..|+++| .+..|+..++++||+.||.+++
T Consensus         7 ~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~c~~~~~   67 (72)
T 1x4l_A            7 GCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL-VGRGFLTERDDILCPDCGKDIS   67 (72)
T ss_dssp             SBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBC-TTSCCEECSSSEECHHHHHTCC
T ss_pred             CCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcC-CCCccEeECCEEEChhHcCccc
Confidence            99999999986  55788999999999999999999999 6788999999999999998763

>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=99.62  E-value=2.4e-16  Score=96.58  Aligned_cols=63  Identities=29%  Similarity=0.632  Sum_probs=57.0

Q ss_pred             CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccc
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT   80 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~   80 (170)
                      ++.++|.+|+++|.+. ++.++++.||++||+|..|+++|..  ..|+.+++++||+.||.+++++
T Consensus         3 ~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~--~~f~~~~g~~yC~~c~~~~~~~   65 (70)
T 2d8x_A            3 SGSSGCHQCGEFIIGR-VIKAMNNSWHPECFRCDLCQEVLAD--IGFVKNAGRHLCRPCHNREKAS   65 (70)
T ss_dssp             CCSSBCSSSCCBCCSC-CEEETTEEECTTTSBCSSSCCBCSS--SCCEEETTEEECHHHHHHHHCC
T ss_pred             CCCCcCccCCCEecce-EEEECcccccccCCEeCCCCCcCCC--CccEeECCeEECHHHhhhhcCC
Confidence            5578999999999976 6899999999999999999999974  4588999999999999999886

>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=99.61  E-value=2.6e-16  Score=103.11  Aligned_cols=85  Identities=25%  Similarity=0.388  Sum_probs=67.9

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhhhccccCCCCchHHhhh--h
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRR--Q  160 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~~~~~~--~  160 (170)
                      +|.+|+++|.+++.++.++++.||++||+|..|+++| .+..|+..+|++||+.||.++  +.+.+......+...+  .
T Consensus         7 ~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~cy~~~--~~~~C~~C~~~I~~~~~~~   83 (101)
T 2cup_A            7 GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPL-ANETFVAKDNKILCNKCTTRE--DSPKCKGCFKAIVAGDQNV   83 (101)
T ss_dssp             BCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCT-TSSCCEEETTEEECHHHHTTC--CCCBCSSSCCBCCSSSCEE
T ss_pred             cCcccCCcccCCceEEEECccChhhcCCcccccCCCC-CcCeeECcCCEEEChhHhhhh--cCCccccCCCccccCCeEE
Confidence            9999999997656789999999999999999999999 677899999999999999887  5666666555443221  1


Q ss_pred             cceeeecccC
Q psy7479         161 VTLQVLWIRE  170 (170)
Q Consensus       161 ~~~~~~~~~~  170 (170)
                      ......||++
T Consensus        84 ~a~~~~~H~~   93 (101)
T 2cup_A           84 EYKGTVWHKD   93 (101)
T ss_dssp             ESSSCEEETT
T ss_pred             EeCCcchHHh
Confidence            2345667764

>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=99.61  E-value=7.3e-16  Score=94.35  Aligned_cols=60  Identities=25%  Similarity=0.527  Sum_probs=54.0

Q ss_pred             cccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          78 FGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        78 ~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      +++  +|.+|+++|.+  ..+.+.++.||++||+|..|+++| .+..|+..++++||+.||.+++
T Consensus         4 ~~~--~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f   63 (70)
T 2d8z_A            4 GSS--GCVQCKKPITT--GGVTYREQPWHKECFVCTACRKQL-SGQRFTARDDFAYCLNCFCDLY   63 (70)
T ss_dssp             CCC--BCSSSCCBCCS--SEEESSSSEEETTTSBCSSSCCBC-TTSCCEESSSSEECHHHHHHHT
T ss_pred             CCC--CCcccCCeecc--ceEEECccccCCCCCccCCCCCcC-CcCceEeeCCeEECHHHHHHHh
Confidence            445  99999999975  568999999999999999999999 6778999999999999999874

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

Probab=99.61  E-value=4e-16  Score=94.25  Aligned_cols=58  Identities=22%  Similarity=0.548  Sum_probs=53.1

Q ss_pred             ccccccccccCCceEEecCCcccc--cCccccccCCcccccCCeEEEeCCeecc-HHhHHHH
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYH--LECFACQQCNHRFCVGDRFYLCDNKILC-EYDYEER  141 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H--~~Cf~C~~C~~~l~~~~~~~~~~~~~~C-~~c~~~~  141 (170)
                      +|.+|+++|.+.+..|.+.++.||  ++||+|..|+++| .+..|+..+|++|| ..||.++
T Consensus         4 ~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~~C~~k~   64 (65)
T 2iyb_E            4 VCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             ECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBC-TTSCCEEETTEEESSHHHHHTT
T ss_pred             CCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcC-CCCceEEECCEEecCHHHhhhh
Confidence            899999999865578999999999  9999999999999 67889999999999 9998754

>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=99.60  E-value=7.2e-16  Score=94.14  Aligned_cols=58  Identities=24%  Similarity=0.639  Sum_probs=53.0

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                      +|.+|+++|.+  ..+.+.++.||++||+|..|+++| .+..|++.++++||+.||.+++.
T Consensus         7 ~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~f~   64 (69)
T 2cur_A            7 GCVKCNKAITS--GGITYQDQPWHADCFVCVTCSKKL-AGQRFTAVEDQYYCVDCYKNFVS   64 (69)
T ss_dssp             CCSSSCCCCCT--TCEEETTEEECTTTTBCTTTCCBC-TTSCEEECSSCEEEHHHHHHHHT
T ss_pred             CCcccCCEeCc--ceEEECccccccCcCEECCCCCCC-CCCccEeECCEEECHHHhHHHhc
Confidence            99999999975  468899999999999999999999 67789999999999999998743

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

Probab=99.60  E-value=4.3e-16  Score=97.12  Aligned_cols=59  Identities=27%  Similarity=0.672  Sum_probs=53.8

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      +|.+|+++|.+.+.++.+.++.||++||+|..|+++| .+..|+..+|++||+.||.+++
T Consensus        13 ~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~~y~~~f   71 (77)
T 1g47_A           13 TCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQF-PEGLFYEFEGRKYCEHDFQMLF   71 (77)
T ss_dssp             BCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCC-GGGCSEEETTEEECHHHHHHHC
T ss_pred             CchhcCCccCCCceEEEeCccEeccccCeECCCCCCC-CCCCeEeECCeEeCHHHHHHHh
Confidence            9999999998767888999999999999999999999 4446899999999999999874

>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=3.4e-16  Score=98.33  Aligned_cols=66  Identities=23%  Similarity=0.590  Sum_probs=59.3

Q ss_pred             CcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccccccccc
Q psy7479          16 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAA   86 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~   86 (170)
                      ..++|.+|+++|.+. .+.++++.||++||+|..|+++|..  ..|+.+++++||+.||.++|++  +|.+
T Consensus        14 ~~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~--~~~~~~~~~~yC~~~y~~~f~~--~C~~   79 (80)
T 1x3h_A           14 FSPKCGGCNRPVLEN-YLSAMDTVWHPECFVCGDCFTSFST--GSFFELDGRPFCELHYHHRRGS--GPSS   79 (80)
T ss_dssp             CSCBCTTTCCBCCSS-CEEETTEEECTTTCBCSSSCCBSCS--SCCEESSSCEECHHHHHHHHSS--SCCC
T ss_pred             cCCccccCCCeecce-eEEECCCeEecCcCChhhCCCCCCC--CcEEeECCEEECHHHHHHHcCC--CCCC
Confidence            357899999999986 5899999999999999999999973  4689999999999999999998  8863

>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=99.60  E-value=5.3e-16  Score=97.28  Aligned_cols=64  Identities=19%  Similarity=0.238  Sum_probs=56.5

Q ss_pred             CCCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccc
Q psy7479          13 ASGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT   80 (170)
Q Consensus        13 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~   80 (170)
                      .....++|.+|+++|.+. .+.++++.||++||+|..|+++|..  . +|.++|++||+.||.++|++
T Consensus        11 ~~~~~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~--~-~f~~~g~~yC~~cy~~~f~p   74 (79)
T 2cor_A           11 RGLGKYICQKCHAIIDEQ-PLIFKNDPYHPDHFNCANCGKELTA--D-ARELKGELYCLPCHDKMGVS   74 (79)
T ss_dssp             CCCCCCBCTTTCCBCCSC-CCCCSSSCCCTTTSBCSSSCCBCCT--T-CEEETTEEECHHHHHTTSCC
T ss_pred             hccCCCCCccCCCEecce-EEEECcceeCCCCCEeCCCCCccCC--C-CEeECCEEeCHHHHHHhCCC
Confidence            445678999999999965 5889999999999999999999973  3 46999999999999999987

>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=99.60  E-value=4.1e-16  Score=98.22  Aligned_cols=67  Identities=28%  Similarity=0.642  Sum_probs=58.6

Q ss_pred             CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEe-CCccccccceeccccccccccc
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQK-ANLILCKRDYLRLFGTTGYCAA   86 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~-~~~~yC~~c~~~~~~~~~~C~~   86 (170)
                      ...++|.+|+++|.+. ++.++++.||++||+|..|+++|.  +..|+.. +|++||+.||.++|++  +|.+
T Consensus        13 ~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~--~~~f~~~~~g~~yC~~cy~~~f~~--~C~~   80 (81)
T 2dlo_A           13 ATLEKCATCSQPILDR-ILRAMGKAYHPGCFTCVVCHRGLD--GIPFTVDATSQIHCIEDFHRKFAS--GPSS   80 (81)
T ss_dssp             SSCCBCTTTCCBCCSC-CEEETTEEECTTTCBCSSSCCBCT--TSCEECCTTCCCEEHHHHHHHTTS--SSCC
T ss_pred             cCCCccccCCCeecce-eEEECCccccHHhcCcccCCCccC--CCeeEECCCCEEECHHHHHHHhcC--cCCC
Confidence            3578999999999976 789999999999999999999997  3456655 7899999999999998  8863

>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=99.59  E-value=1.1e-15  Score=93.59  Aligned_cols=58  Identities=28%  Similarity=0.552  Sum_probs=52.7

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                      +|..|+++|.+  .++.+.++.||++||+|..|+++| .+..|+..++++||+.||.+++.
T Consensus         7 ~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~c~~~~~~   64 (70)
T 2d8x_A            7 GCHQCGEFIIG--RVIKAMNNSWHPECFRCDLCQEVL-ADIGFVKNAGRHLCRPCHNREKA   64 (70)
T ss_dssp             BCSSSCCBCCS--CCEEETTEEECTTTSBCSSSCCBC-SSSCCEEETTEEECHHHHHHHHC
T ss_pred             cCccCCCEecc--eEEEECcccccccCCEeCCCCCcC-CCCccEeECCeEECHHHhhhhcC
Confidence            89999999975  678999999999999999999999 55578889999999999998854

>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=5.2e-16  Score=97.45  Aligned_cols=65  Identities=26%  Similarity=0.510  Sum_probs=59.1

Q ss_pred             CcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccc
Q psy7479          16 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCA   85 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~   85 (170)
                      ..++|.+|+++|.+. .+.++++.||++||+|..|+++|.  +..|+.+++++||+.||.++|++  +|.
T Consensus        14 ~~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~--~~~~~~~~~~~yC~~cy~~~f~~--~c~   78 (80)
T 2cuq_A           14 FAPRCARCSKTLTQG-GVTYRDQPWHRECLVCTGCQTPLA--GQQFTSRDEDPYCVACFGELFAS--GPS   78 (80)
T ss_dssp             SSCCCTTTCCCCCSC-CEESSSSEECTTTCBCSSSCCBCT--TCCEEECSSSEEEHHHHHHHTTC--STT
T ss_pred             cCCcCCCCCCEecCc-EEEECCchhhhhhCCcccCCCcCC--CCeeEeECCEEECHHHHHHHcCC--CCC
Confidence            458899999999987 688999999999999999999996  35689999999999999999998  875

>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=99.58  E-value=8.3e-16  Score=111.92  Aligned_cols=73  Identities=27%  Similarity=0.552  Sum_probs=66.0

Q ss_pred             CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccc
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVI   91 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i   91 (170)
                      .+.++|.+|+++|.+.+.+.++++.||++||+|..|+++|..  ..|+.++|++||+.||.++|++  +|.+|++++
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 GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLES--TTLADKDGEIYCKGCYAKNFGP--KGFGFGQGA  185 (192)
T ss_dssp             CCCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCS--SSEEEETTEEEEHHHHHHHTCC--CCCCCCCCC
T ss_pred             CCCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCC--CcccccCCEEeCHHHHHHhcCC--cCCCCCCcc
Confidence            346789999999997667889999999999999999999973  4589999999999999999998  999999886

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

Probab=99.57  E-value=2.3e-15  Score=102.44  Aligned_cols=82  Identities=21%  Similarity=0.451  Sum_probs=65.1

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhhhccccCCCCchHHhhh--h
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRR--Q  160 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~~~~~~--~  160 (170)
                      +|.+|+++|.. +.++.++|+.||++||+|..|+++| .+..|+..+|++||+.||.++  +++.+......+...+  .
T Consensus         5 ~C~~C~~~I~~-~~~~~a~~~~~H~~CF~C~~C~~~L-~~~~f~~~~g~~yC~~cy~~~--~~~~C~~C~~~I~~~~~~~   80 (126)
T 2xqn_T            5 RCAGCDELIFS-NEYTQAENQNWHLKHFCCFDCDSIL-AGEIYVMVNDKPVCKPCYVKN--HAVVCQGCHNAIDPEVQRV   80 (126)
T ss_dssp             BBTTTSSBCCS-SCEEEETTEEECGGGSBCTTTCCBC-TTSEEEEETTEEEEHHHHHHH--SCCBCTTTCSBCCTTSCEE
T ss_pred             CCccCCCEeCC-ceEEeeCCCCccCCCCCcCCCCCCC-CcCEEEeECCEEechHHhCcC--cCccCcccCCcCCcCceEE
Confidence            99999999985 3578999999999999999999999 677999999999999999987  5566666544433211  1


Q ss_pred             cceeeecc
Q psy7479         161 VTLQVLWI  168 (170)
Q Consensus       161 ~~~~~~~~  168 (170)
                      ......||
T Consensus        81 ~a~~~~~H   88 (126)
T 2xqn_T           81 TYNNFSWH   88 (126)
T ss_dssp             EETTEEEE
T ss_pred             ECCCCEee
Confidence            23456677

>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=99.57  E-value=1.1e-15  Score=94.32  Aligned_cols=64  Identities=28%  Similarity=0.459  Sum_probs=56.2

Q ss_pred             CCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceeccccc
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT   80 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~   80 (170)
                      ...++|.+|+++|.+. ++.++++.||++||+|..|+++|.. +..|+.+++++||..||.+++..
T Consensus         3 ~~~~~C~~C~~~I~~~-~v~a~~~~wH~~CF~C~~C~~~L~~-~~~f~~~~~~~yC~~C~~~~~~~   66 (73)
T 1wig_A            3 SGSSGCDSCEKYITGR-VLEAGEKHYHPSCALCVRCGQMFAE-GEEMYLQGSSIWHPACRQAARTE   66 (73)
T ss_dssp             CSCCSCSSSCCCCSSC-CBCCSSCCBCTTTSCCSSSCCCCCS-SCCCEEETTEEECTTHHHHTSSS
T ss_pred             cCcCCcccCCCEecCe-eEEeCCCCCCCCcCEeCCCCCCCCC-CCeeEeeCCEEEChHHChHhhcc
Confidence            3568999999999986 6889999999999999999999963 45689999999999999887764

>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=99.55  E-value=4e-15  Score=92.48  Aligned_cols=58  Identities=19%  Similarity=0.394  Sum_probs=52.3

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccH-HhHHHHh
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCE-YDYEERQ  142 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~-~c~~~~~  142 (170)
                      +|.+|+++|.+. ..+.+.++.||++||+|..|+++| .+..|+..++++||+ .||.+++
T Consensus        11 ~C~~C~~~I~~~-~~v~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~~cy~~~f   69 (76)
T 2cu8_A           11 KCPKCDKTVYFA-EKVSSLGKDWHKFCLKCERCSKTL-TPGGHAEHDGKPFCHKPCYATLF   69 (76)
T ss_dssp             BCTTTCCBCCTT-TEEEETTEEEETTTCBCSSSCCBC-CTTSCEEETTEEECTTTHHHHHS
T ss_pred             CCcCCCCEeECC-eEEEECCeEeeCCCCCCCCCCCcc-CCCceEeECCEEecchHHHHHhc
Confidence            999999999864 467899999999999999999999 577899999999999 7999874

>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=99.55  E-value=2.1e-15  Score=95.09  Aligned_cols=66  Identities=21%  Similarity=0.472  Sum_probs=58.1

Q ss_pred             Ccccccccccccccc-eeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccccccccc
Q psy7479          16 GLKECASCGKRITER-FLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCA   85 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~   85 (170)
                      ..++|.+|+++|... .++.++++.||++||+|..|+++|..  ..|+.+++++||+.||.++|++  ++.
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~--~~~~~~~~~~yC~~cy~~~f~~--~~~   80 (82)
T 1x63_A           14 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGT--GSFFPKGEDFYCVTCHETKFAS--GPS   80 (82)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTT--SCEEEETTEEEEHHHHHHHTSC--CCS
T ss_pred             cCCcCccCCcccccCceEEEECccccccccCchhhCCCccCC--CccEeeCCEEECHHHHHHHhCC--CCC
Confidence            457999999999954 36889999999999999999999973  4689999999999999999998  653

>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=99.55  E-value=1.2e-15  Score=95.67  Aligned_cols=58  Identities=22%  Similarity=0.624  Sum_probs=52.9

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                      +|.+|+++|.+  .+|.+.++.||++||+|..|+++| .+..|+..++++||+.||.+++.
T Consensus        17 ~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~cy~~~~~   74 (79)
T 1x62_A           17 MCDKCGTGIVG--VFVKLRDRHRHPECYVCTDCGTNL-KQKGHFFVEDQIYCEKHARERVS   74 (79)
T ss_dssp             CCSSSCCCCCS--SCEECSSCEECTTTTSCSSSCCCH-HHHCCEESSSCEECHHHHHHHHS
T ss_pred             ccccCCCCccC--cEEEECcceeCcCcCeeCCCCCCC-CCCCeEeECCEEECHHHHHHHhC
Confidence            99999999986  588999999999999999999999 56678999999999999998854

>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=99.55  E-value=4.6e-15  Score=92.93  Aligned_cols=56  Identities=21%  Similarity=0.477  Sum_probs=50.0

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      +|.+|+++|.+  .+|.+.++.||++||+|..|+++| .+..| ..++++||+.||.+++
T Consensus        17 ~C~~C~~~I~~--~~v~a~~~~~H~~CF~C~~C~~~L-~~~~f-~~~g~~yC~~cy~~~f   72 (79)
T 2cor_A           17 ICQKCHAIIDE--QPLIFKNDPYHPDHFNCANCGKEL-TADAR-ELKGELYCLPCHDKMG   72 (79)
T ss_dssp             BCTTTCCBCCS--CCCCCSSSCCCTTTSBCSSSCCBC-CTTCE-EETTEEECHHHHHTTS
T ss_pred             CCccCCCEecc--eEEEECcceeCCCCCEeCCCCCcc-CCCCE-eECCEEeCHHHHHHhC
Confidence            99999999974  678999999999999999999999 45444 8999999999999873

>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=99.55  E-value=5.3e-15  Score=91.94  Aligned_cols=67  Identities=16%  Similarity=0.396  Sum_probs=56.1

Q ss_pred             cccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccH-HhHHHHhhhccccCCCC
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCE-YDYEERQVFANIAYNPS  152 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~-~c~~~~~~~~~~~~~~~  152 (170)
                      |+|.+|+++|... ..+.+.++.||++||+|..|+++| .+..|+..++++||. .||.++  +.+.+....
T Consensus         1 p~C~~C~~~I~~~-~~v~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~~cy~~~--f~~~C~~C~   68 (76)
T 1iml_A            1 PKCPKCDKEVYFA-ERVTSLGKDWHRPCLKCEKCGKTL-TSGGHAEHEGKPYCNHPCYSAM--FGPKGFGRG   68 (76)
T ss_dssp             CBCTTTSSBCCGG-GEEEETTEEEETTTCBCTTTCCBC-CTTTEEEETTEEEETTTHHHHH--SSCCCSSCC
T ss_pred             CcCCCCCCEEECc-eEEEECCccccCCCCCccccCccC-CCCceECcCCeEeeCHHHHHHH--hCccCCCcC
Confidence            3899999999853 567899999999999999999999 555799999999999 699987  555555443

>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=99.55  E-value=3.9e-15  Score=95.37  Aligned_cols=58  Identities=26%  Similarity=0.680  Sum_probs=52.7

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                      +|.+|+++|.+  .++.+.++.||++||+|..|+++| .+..|+..++++||+.||.++|.
T Consensus        27 ~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~~y~~~f~   84 (89)
T 1x64_A           27 LCDKCGSGIVG--AVVKARDKYRHPECFVCADCNLNL-KQKGYFFVEGELYCETHARARTS   84 (89)
T ss_dssp             BCTTTCCBCCS--CCEESSSCEECTTTCCCSSSCCCT-TTSCCEEETTEEECHHHHHHHSS
T ss_pred             CcccCCCEecc--cEEEECCceECccCCEecCCCCCC-CCCCeEeECCEEECHHHHHHHhC
Confidence            89999999976  678999999999999999999999 56678899999999999998743

>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=99.54  E-value=4.3e-15  Score=93.32  Aligned_cols=59  Identities=29%  Similarity=0.592  Sum_probs=52.1

Q ss_pred             cccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhh
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV  143 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~  143 (170)
                      ++|.+|+++|... .++.++++.||++||+|..|+++| .+ .|+..++++||+.||.++|.
T Consensus        16 ~~C~~C~~~I~~~-~~v~a~~~~wH~~CF~C~~C~~~L-~~-~~~~~~g~~yC~~~y~~~fg   74 (80)
T 2dj7_A           16 SHCAGCKEEIKHG-QSLLALDKQWHVSCFKCQTCSVIL-TG-EYISKDGVPYCESDYHAQFG   74 (80)
T ss_dssp             SCCTTTCCCCSSS-CCEEETTEEECTTTCBCSSSCCBC-SS-CCEEETTEEECTTHHHHHTT
T ss_pred             CCCcCcCCeeCCC-eEEEECCcccccccCCcCcCCCCc-CC-CeEEECCEEECHHHHHHHcC
Confidence            3899999999753 567899999999999999999999 45 69999999999999998843

>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=99.52  E-value=3.6e-15  Score=91.54  Aligned_cols=63  Identities=21%  Similarity=0.520  Sum_probs=55.0

Q ss_pred             CCcccccccccccccce-eEEeCCccccccCccccccccccccCCCeeEEeCCccccccceecccc
Q psy7479          15 GGLKECASCGKRITERF-LLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG   79 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~   79 (170)
                      ...++|.+|+++|...+ ++.++++.||++||+|..|+++|..  ..|+.++|++||+.||.++|+
T Consensus         9 ~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~--~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B            9 SASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPE--GLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             CTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGG--GCCEEETTEEECHHHHHHHTC
T ss_pred             cCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCC--CCeEeECCeEeCHHHHHHhhC
Confidence            35678999999999653 5789999999999999999999974  368999999999999998874

>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=99.52  E-value=5.9e-15  Score=92.82  Aligned_cols=64  Identities=20%  Similarity=0.573  Sum_probs=52.9

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhhhccccCC
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYN  150 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~  150 (170)
                      +|.+|+++|...+ .+.+.++.||++||+|..|+++| .+..|+..++++||+.||.++  +.+.+..
T Consensus         9 ~C~~C~~~I~~~~-~~~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~~~~yC~~cy~~~--f~~~c~g   72 (81)
T 1a7i_A            9 KCGACGRTVYHAE-EVQCDGRSFHRCCFLCMVCRKNL-DSTTVAIHDAEVYCKSCYGKK--YGPKGYG   72 (81)
T ss_dssp             BCSSSCCBCSSTT-EEEETTEEEESSSEECSSSCCEE-CSSCCEEETTEEECSHHHHHH--CC-----
T ss_pred             cCcCcCccccCce-eEEeCCcccccccCccCCCCCCC-CCCCeEeeCCEEECHHHHHHH--hCCcccc
Confidence            9999999997544 67899999999999999999999 566799999999999999987  4444443

>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=99.51  E-value=6.8e-15  Score=99.71  Aligned_cols=59  Identities=27%  Similarity=0.600  Sum_probs=53.0

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCccccc-CCeEEEeCCeeccHHhHHHHh
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV-GDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      +|.+|+++|.+ ..++.+.++.||++||+|..|+++|.. +..|+.++|++||+.||.++|
T Consensus        63 ~C~~C~~~I~~-~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~F  122 (123)
T 2l4z_A           63 RCAGCGGKIAD-RFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF  122 (123)
T ss_dssp             BBSSSSSBCCS-SSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHC
T ss_pred             cCcCCCCCcCC-cEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhc
Confidence            99999999986 346899999999999999999999952 578999999999999999875

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

Probab=99.51  E-value=1.2e-14  Score=99.43  Aligned_cols=87  Identities=18%  Similarity=0.381  Sum_probs=65.7

Q ss_pred             cccccccccccCCceEEecCCcccccCccccccCCccccc-CCeEEEeCCeeccHHhHHHHhhhccccCCCCchHHhhh-
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV-GDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRR-  159 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~~~~~~-  159 (170)
                      ++|.+|+++|.+ ..++.++++.||++||+|..|+++|.. +..|+..+|++||+.||.+++.....+..........+ 
T Consensus         3 ~~C~~C~~~I~~-~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~~e~   81 (131)
T 2xjy_A            3 LTCGGCQQNIGD-RYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEM   81 (131)
T ss_dssp             CBBTTTCCBCCS-SEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECTTSE
T ss_pred             ccCcCCCCEeCC-cEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCccce
Confidence            489999999986 347899999999999999999999953 56899999999999999998554336666544433211 


Q ss_pred             hc-ceeeeccc
Q psy7479         160 QV-TLQVLWIR  169 (170)
Q Consensus       160 ~~-~~~~~~~~  169 (170)
                      .+ .....||.
T Consensus        82 ~~~a~~~~~H~   92 (131)
T 2xjy_A           82 TMRVKDKVYHL   92 (131)
T ss_dssp             EEEETTEEEEG
T ss_pred             eEeeCCceECc
Confidence            11 24556765

>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=99.50  E-value=5.3e-15  Score=93.02  Aligned_cols=66  Identities=15%  Similarity=0.356  Sum_probs=56.5

Q ss_pred             CcccccccccccccceeEEeCCccccccCccccccccccccCCCeeE-EeCCccccccceecccccccccc
Q psy7479          16 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLY-QKANLILCKRDYLRLFGTTGYCA   85 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~-~~~~~~yC~~c~~~~~~~~~~C~   85 (170)
                      ..++|.+|+++|.+. ++.++++.||++||+|..|+++|.. +..|+ .+++++||+.||.++|++  .|.
T Consensus        14 ~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~-g~~f~~~~~~~~~C~~c~~~~~~~--~~s   80 (81)
T 1x6a_A           14 FGEFCHGCSLLMTGP-FMVAGEFKYHPECFACMSCKVIIED-GDAYALVQHATLYCGKCHNEVVSG--PSS   80 (81)
T ss_dssp             SSCBCTTTCCBCCSC-CBCCTTCCBCTTSCBCTTTCCBCCT-TSCEEECSSSCEEEHHHHHHHHCT--TSC
T ss_pred             cCCcCccCCCCcCce-EEEECCceeccccCCccCCCCccCC-CCcEEEeeCCEEECHHHHHHHhcC--CCC
Confidence            457899999999965 6889999999999999999999963 34566 489999999999999987  553

>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=99.50  E-value=9.9e-15  Score=97.68  Aligned_cols=64  Identities=25%  Similarity=0.556  Sum_probs=55.6

Q ss_pred             cccccccccccCCceEEecCCcccccCccccccCCccccc-CCeEEEeCCeeccHHhHHHHhhhcc
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV-GDRFYLCDNKILCEYDYEERQVFAN  146 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~c~~~~~~~~~  146 (170)
                      ++|.+|+++|.+ ..++.+.++.||++||+|..|+++|.. +..|+..++++||+.||.++|....
T Consensus         4 ~~C~~C~~~I~~-~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c   68 (114)
T 1j2o_A            4 LTCGGCQQNIGD-RYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGG   68 (114)
T ss_dssp             BCBSSSCSCBCS-SEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCC
T ss_pred             CCCcCCCCeeCC-cEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCccc
Confidence            489999999986 348899999999999999999999953 4689999999999999999865543

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

Probab=99.50  E-value=7.2e-15  Score=88.64  Aligned_cols=59  Identities=22%  Similarity=0.587  Sum_probs=51.9

Q ss_pred             cccccccccccccc-eeEEeCCcccc--ccCccccccccccccCCCeeEEeCCcccc-ccceecc
Q psy7479          17 LKECASCGKRITER-FLLKALDLFWH--EDCLKCGCCDCRLGEVGSTLYQKANLILC-KRDYLRL   77 (170)
Q Consensus        17 ~~~C~~C~~~I~~~-~~~~~~~~~~H--~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC-~~c~~~~   77 (170)
                      .+.|.+|+++|... ..+.++++.||  ++||+|..|+++|.  +..|+.++|++|| .+||.++
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 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI--GQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCT--TSCCEEETTEEESSHHHHHTT
T ss_pred             cCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCC--CCceEEECCEEecCHHHhhhh
Confidence            46899999999963 57899999999  99999999999997  4669999999999 8888653

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

Probab=99.49  E-value=3e-14  Score=102.79  Aligned_cols=99  Identities=14%  Similarity=0.248  Sum_probs=71.3

Q ss_pred             CCcccccccee---cccccccccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHH
Q psy7479          65 ANLILCKRDYL---RLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEER  141 (170)
Q Consensus        65 ~~~~yC~~c~~---~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~  141 (170)
                      ++..||...+.   ....+  +|.+|+++|.+ ..++.+.++.||++||+|..|+++| .+..| .++|++||+.||.++
T Consensus        43 ~~~~~~~~~~~~~~~~~~~--~C~~C~~~I~~-~~~~~a~~~~wH~~CF~C~~C~~~L-~~~~f-~~~g~~yC~~~y~~~  117 (182)
T 2jtn_A           43 DDEGGSGGHMGSGGTPEIP--MCAGCDQHILD-RFILKALDRHWHSKCLKCSDCHVPL-AERCF-SRGESVYCKDDFFKR  117 (182)
T ss_dssp             SSSCSSSSSCCCCCCCSCC--BCBTSSSBCCC-SEEEEETTEEECSSTTSCTTTCCCC-SSCCE-EETTEEECHHHHHHT
T ss_pred             ccccccccccccCCCCCCC--cCccCCCCccC-ceeEEecCCeEccccCccCCCCCcc-CCCce-eECCEeeecCccccc
Confidence            45567777664   22333  99999999986 4577899999999999999999999 45455 689999999999997


Q ss_pred             hhhccccCCCCchHHhhhh--cceeeecccC
Q psy7479         142 QVFANIAYNPSSLAHLRRQ--VTLQVLWIRE  170 (170)
Q Consensus       142 ~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~  170 (170)
                        +.+.+..+...+...+.  ......||++
T Consensus       118 --f~~kC~~C~~~I~~~~~v~~a~~~~~H~~  146 (182)
T 2jtn_A          118 --FGTKCAACQLGIPPTQVVRRAQDFVYHLH  146 (182)
T ss_dssp             --TSCCCTTTCCCCCSSCCCCEETTEECCTT
T ss_pred             --cccccccCCCccCCCceEEecCCCCEEeC
Confidence              55666665443322211  1244577753

>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=99.48  E-value=9.4e-15  Score=90.98  Aligned_cols=59  Identities=22%  Similarity=0.492  Sum_probs=52.5

Q ss_pred             Cccccccccccccc----ceeEEeCCccccccCccccccccccccCCCeeEEeCCccccccceec
Q psy7479          16 GLKECASCGKRITE----RFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLR   76 (170)
Q Consensus        16 ~~~~C~~C~~~I~~----~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~   76 (170)
                      ..++|.+|+++|.+    ..++.++++.||++||+|..|+++|.  +..|+.++|++||+.||.+
T Consensus        14 ~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~--~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A           14 VAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLA--NKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCT--TSCCCEETTEECCHHHHHH
T ss_pred             hCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCC--CCccEeECCEEEChHHhcc
Confidence            45789999999995    46789999999999999999999997  3568899999999999865

>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=99.47  E-value=1.9e-14  Score=92.45  Aligned_cols=60  Identities=23%  Similarity=0.608  Sum_probs=52.8

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhhh
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVF  144 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~  144 (170)
                      +|.+|+++|.+.+ .+.+.++.||++||+|..|+++| .+..|+..++++||+.||.+++..
T Consensus        17 ~C~~C~~~I~~~~-~v~a~~~~~H~~CF~C~~C~~~L-~~~~~~~~~g~~yC~~~y~~~f~~   76 (91)
T 2d8y_A           17 TCVECQKTVYPME-RLLANQQVFHISCFRCSYCNNKL-SLGTYASLHGRIYCKPHFNQLFKS   76 (91)
T ss_dssp             BCTTTCCBCCTTS-EEECSSSEEETTTCBCTTTCCBC-CTTTCCCSSSCCCCHHHHHHHSCC
T ss_pred             cCccCCCccCCce-eEEECCCEECCCCCeeCCCCCCC-CCCCcEeECCEEECHHHHHHHhCC
Confidence            9999999998644 56899999999999999999999 455688999999999999988543

>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=99.47  E-value=1.5e-14  Score=97.94  Aligned_cols=69  Identities=23%  Similarity=0.450  Sum_probs=57.3

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCccccc-CCeEEEeCCeeccHHhHHHHhhhccccCCCC
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV-GDRFYLCDNKILCEYDYEERQVFANIAYNPS  152 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~  152 (170)
                      +|.+|+++|.+. .++.+.++.||++||+|..|+++|.. +..|+..+|++||+.||.++|.....+..+.
T Consensus         7 ~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~   76 (122)
T 1m3v_A            7 RCAGCGGKIADR-FLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGG   76 (122)
T ss_dssp             CBSSSSSCCCSS-CCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSS
T ss_pred             CCcccCCEeCCc-EEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCC
Confidence            999999999863 36789999999999999999999942 4679999999999999999865432555543

>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=99.46  E-value=4.5e-14  Score=102.38  Aligned_cols=87  Identities=18%  Similarity=0.345  Sum_probs=66.1

Q ss_pred             ccccccccccCCceEEecCCcccccCccccccCCccccc-CCeEEEeCCeeccHHhHHHHhhhccccCCCCchHHhhh-h
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCV-GDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRR-Q  160 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~~~~~~-~  160 (170)
                      +|.+|+++|.+ ..++.++++.||++||+|..|+++|.. +..|+..+|++||+.||.+++....++..+.......+ .
T Consensus         7 ~C~~C~~~I~~-~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~~e~~   85 (188)
T 1rut_X            7 RCAGCGGKIAD-RFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELV   85 (188)
T ss_dssp             BBTTTCCBCCC-SEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECTTSEE
T ss_pred             cCccCCCEeCC-ceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCccccCcEE
Confidence            99999999986 347899999999999999999999954 57899999999999999998554325666554433222 1


Q ss_pred             c-ceeeecccC
Q psy7479         161 V-TLQVLWIRE  170 (170)
Q Consensus       161 ~-~~~~~~~~~  170 (170)
                      + .....||.+
T Consensus        86 i~a~~~~~H~~   96 (188)
T 1rut_X           86 MRAQGNVYHLK   96 (188)
T ss_dssp             EEETTEEECGG
T ss_pred             EEcCCCEEeCC
Confidence            1 245567753

>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=99.43  E-value=1.4e-14  Score=91.33  Aligned_cols=59  Identities=19%  Similarity=0.515  Sum_probs=50.2

Q ss_pred             cccccccccccCCceEEecCCcccccCccccccCCcccccCCeEE--EeCCeeccHHhHHHHh
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFY--LCDNKILCEYDYEERQ  142 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~--~~~~~~~C~~c~~~~~  142 (170)
                      ++|.+|+++|...+ .+.+.++.||++||+|..|+++| .+..|+  +.++++||+.||.+++
T Consensus        16 ~~C~~C~~~I~~~e-~v~a~~~~wH~~CF~C~~C~~~L-~~~~~~~~~~~g~~yC~~~y~~~~   76 (82)
T 2co8_A           16 DLCALCGEHLYVLE-RLCVNGHFFHRSCFRCHTCEATL-WPGGYEQHPGDGHFYCLQHLPQTD   76 (82)
T ss_dssp             CBCSSSCCBCCTTT-BCCBTTBCCBTTTCBCSSSCCBC-CTTSEECCTTTCCCEETTTCCCCC
T ss_pred             CCCcccCCCcccce-EEEECCCeeCCCcCEEcCCCCCc-CCCceeEeCcCCEEEChHHHHhhh
Confidence            38999999997644 45699999999999999999999 566677  4689999999998763

>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=99.39  E-value=2.2e-13  Score=97.17  Aligned_cols=83  Identities=17%  Similarity=0.395  Sum_probs=61.8

Q ss_pred             cccccccccccCCceEEecCCcccccCccccccCCcccccCCeEEEeCCeeccHHhHHHHhhhccccCCCCchHHhhhh-
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLRRQ-  160 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~~~~~~~~~~~~-  160 (170)
                      ++|.+|+++|.+ ..++.+.|+.||++||+|..|+++| .+..| ..+|++||+.||.++  +++.+..+...+...+. 
T Consensus         7 ~~C~~C~~~I~~-~~~~~a~~~~wH~~CF~C~~C~~~L-~~~~f-~~~g~~yC~~~y~~~--f~~~C~~C~~~I~~~~~v   81 (169)
T 2rgt_A            7 PMCAGCDQHILD-RFILKALDRHWHSKCLKCSDCHVPL-AERCF-SRGESVYCKDDFFKR--FGTKCAACQLGIPPTQVV   81 (169)
T ss_dssp             CBBSSSSSBCCS-SSCEECSSCEECTTTSBCTTTCCBC-CSCCE-ESSSCEECHHHHHHH--HSCBCTTTCCBCCTTSEE
T ss_pred             CccccCCCccCC-cEEEEECCcEEccccCccCCCCCcC-CCCCc-ccCCeeeeccccccc--ccccccccccccCCCcEE
Confidence            399999999986 3467899999999999999999999 44445 789999999999998  55566655443322211 


Q ss_pred             -cceeeeccc
Q psy7479         161 -VTLQVLWIR  169 (170)
Q Consensus       161 -~~~~~~~~~  169 (170)
                       ......||.
T Consensus        82 ~~a~~~~~H~   91 (169)
T 2rgt_A           82 RRAQDFVYHL   91 (169)
T ss_dssp             EEETTEEEEG
T ss_pred             EEcCCceEee
Confidence             124456665

>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=99.34  E-value=6.8e-13  Score=83.28  Aligned_cols=62  Identities=21%  Similarity=0.395  Sum_probs=50.7

Q ss_pred             CcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCC-ccccccceeccccc
Q psy7479          16 GLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKAN-LILCKRDYLRLFGT   80 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~-~~yC~~c~~~~~~~   80 (170)
                      ..++|.+|+++|.+. ++.++++.||++||+|..|+++|..  ..++..++ .+||..||.+.++.
T Consensus        14 ~~~~C~~C~~~I~~~-~v~a~~~~wH~~CF~C~~C~~~L~~--~~~~~~~~~~~~C~~C~~~~~~~   76 (81)
T 1v6g_A           14 YGTRCFSCDQFIEGE-VVSALGKTYHPDCFVCAVCRLPFPP--GDRVTFNGKECMCQKCSLPVSVS   76 (81)
T ss_dssp             CCCBCTTTCCBCCSC-CEEETTEEECTTTSSCSSSCCCCCS--SSCEEEETTEEEEHHHHSCCSSC
T ss_pred             hCCcCccccCEeccc-eEEECCceeCccCCccccCCCCCCC--CCEEEeCCCCEEChhhhcccCCC
Confidence            456899999999965 7899999999999999999999973  33455555 57999999877653

>1zfo_A LAsp-1; LIM domain, zinc-finger, metal-binding protein; NMR {Sus scrofa} SCOP: g.39.1.4

Probab=98.11  E-value=6.3e-07  Score=45.34  Aligned_cols=29  Identities=38%  Similarity=0.870  Sum_probs=26.4

Q ss_pred             cccccccccccccceeEEeCCccccccCc
Q psy7479          17 LKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        17 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      .+.|..|++.|+..+.+.+.|+.||..||
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            46899999999988788899999999998

>1zfo_A LAsp-1; LIM domain, zinc-finger, metal-binding protein; NMR {Sus scrofa} SCOP: g.39.1.4

Probab=97.80  E-value=5.3e-06  Score=41.86  Aligned_cols=27  Identities=30%  Similarity=0.722  Sum_probs=23.7

Q ss_pred             ccccccccccCCceEEecCCcccccCcc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      +|..|++.+.+.| .+.+.|+.||..||
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            8999999998865 45688999999998

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=92.69  E-value=0.11  Score=34.13  Aligned_cols=102  Identities=14%  Similarity=0.229  Sum_probs=62.2

Q ss_pred             ccccccccccccC----CCeeEEeCCccccccceecccccccccccccccccCCceEEecCCcccccCccccccCCcccc
Q psy7479          45 LKCGCCDCRLGEV----GSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFC  120 (170)
Q Consensus        45 f~C~~C~~~l~~~----~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~  120 (170)
                      +.|..|...+.+.    .......=|..||..|..+.+.....|..|.+.+...+.....    .-.+=+.|..|...+.
T Consensus         8 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~l~~l~----i~~~~~~C~iC~~~~~   83 (133)
T 4ap4_A            8 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRYHPIY----IGSGTVSCPICMDGYS   83 (133)
T ss_dssp             CBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTCEEECB----CSSSSCBCTTTCCBHH
T ss_pred             CCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCccccccccc----cCCCCCCCCCCCCccc
Confidence            5677776666421    1114556678889888876644334899999998653322111    1234466888888773


Q ss_pred             c----CCe-EEEeCCeeccHHhHHHHhhhccccCC
Q psy7479         121 V----GDR-FYLCDNKILCEYDYEERQVFANIAYN  150 (170)
Q Consensus       121 ~----~~~-~~~~~~~~~C~~c~~~~~~~~~~~~~  150 (170)
                      .    +.. ....=|..||..|..+.+.....++.
T Consensus        84 ~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~  118 (133)
T 4ap4_A           84 EIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPT  118 (133)
T ss_dssp             HHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTT
T ss_pred             cccccCcceEeCCCCChhhHHHHHHHHHcCCCCCC
Confidence            2    122 33334899999999877655544444

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=88.42  E-value=0.28  Score=29.11  Aligned_cols=48  Identities=4%  Similarity=0.133  Sum_probs=34.4

Q ss_pred             cCccccccccccccCCCeeEEeCCccccccceeccccc-ccccccccccccC
Q psy7479          43 DCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT-TGYCAACTKVIPA   93 (170)
Q Consensus        43 ~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~-~~~C~~C~~~i~~   93 (170)
                      +-|.|..|...+.   ......-|..||..|..+.+.. ...|..|+.++..
T Consensus         7 ~~~~C~IC~~~~~---~Pv~~~CgH~fc~~Ci~~~~~~~~~~CP~C~~~~~~   55 (78)
T 1t1h_A            7 EYFRCPISLELMK---DPVIVSTGQTYERSSIQKWLDAGHKTCPKSQETLLH   55 (78)
T ss_dssp             SSSSCTTTSCCCS---SEEEETTTEEEEHHHHHHHHTTTCCBCTTTCCBCSS
T ss_pred             ccCCCCCcccccc---CCEEcCCCCeecHHHHHHHHHHCcCCCCCCcCCCCh
Confidence            3478888888775   3466678889999997665432 2378888888754

>2ect_A Ring finger protein 126; metal binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus}

Probab=84.49  E-value=0.67  Score=27.38  Aligned_cols=16  Identities=25%  Similarity=0.466  Sum_probs=9.3

Q ss_pred             CCcccccccccccccc
Q psy7479          15 GGLKECASCGKRITER   30 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~   30 (170)
                      .....|..|...+...
T Consensus        13 ~~~~~C~IC~~~~~~~   28 (78)
T 2ect_A           13 GSGLECPVCKEDYALG   28 (78)
T ss_dssp             SSSCCCTTTTSCCCTT
T ss_pred             CCCCCCeeCCccccCC
Confidence            3445677776666543

>1iym_A EL5; ring-H2 finger, ubiquitin ligase, DNA binding protein; NMR {Oryza sativa} SCOP: g.44.1.1

Probab=83.78  E-value=0.81  Score=24.90  Aligned_cols=26  Identities=12%  Similarity=0.197  Sum_probs=12.6

Q ss_pred             Cccccccceecccccccccccccccc
Q psy7479          66 NLILCKRDYLRLFGTTGYCAACTKVI   91 (170)
Q Consensus        66 ~~~yC~~c~~~~~~~~~~C~~C~~~i   91 (170)
                      |..||..|..+.+.....|..|...|
T Consensus        28 ~H~f~~~Ci~~w~~~~~~CP~Cr~~~   53 (55)
T 1iym_A           28 GHGFHAECVDMWLGSHSTCPLCRLTV   53 (55)
T ss_dssp             CCEECTTHHHHTTTTCCSCSSSCCCS
T ss_pred             CCcccHHHHHHHHHcCCcCcCCCCEe
Confidence            44455555443332223566666554

>2d8t_A Dactylidin, ring finger protein 146; RNF146, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=83.72  E-value=0.62  Score=27.09  Aligned_cols=28  Identities=21%  Similarity=0.313  Sum_probs=15.2

Q ss_pred             CCccccccceeccccccccccccccccc
Q psy7479          65 ANLILCKRDYLRLFGTTGYCAACTKVIP   92 (170)
Q Consensus        65 ~~~~yC~~c~~~~~~~~~~C~~C~~~i~   92 (170)
                      =|..||..|..+.+.....|..|...|.
T Consensus        33 CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (71)
T 2d8t_A           33 CKHVFCYLCVKGASWLGKRCALCRQEIP   60 (71)
T ss_dssp             TTEEEEHHHHHHCTTCSSBCSSSCCBCC
T ss_pred             CCCHHHHHHHHHHHHCCCcCcCcCchhC
Confidence            3445555555443322226888877774

>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=83.51  E-value=0.74  Score=27.91  Aligned_cols=52  Identities=15%  Similarity=0.419  Sum_probs=38.3

Q ss_pred             CCCcccccccccccccceeEEeCCccccccCccccccccccccCCCeeEEeCCcccccc
Q psy7479          14 SGGLKECASCGKRITERFLLKALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKR   72 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~   72 (170)
                      ....-.|.-|.+.+.+...+.--...-|+-||.|+  ...|..     ....+.+||..
T Consensus        12 ~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCs--r~sIk~-----q~~~~EvyCPS   63 (93)
T 2cs3_A           12 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCS--RESIKA-----QGATGEVYCPS   63 (93)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHH--HHHHHH-----HHSSSCCCCTT
T ss_pred             CCCeeEeecchhhhccCceeeCCCccCCeeecccc--HHHHHh-----cCCCCcEECCC
Confidence            45567799999999998667778888999999985  334431     12456788864

>4ayc_A E3 ubiquitin-protein ligase RNF8; DNA damage, K63 chains; HET: CPQ; 1.90A {Homo sapiens} PDB: 4epo_C

Probab=83.24  E-value=0.57  Score=31.25  Aligned_cols=45  Identities=18%  Similarity=0.270  Sum_probs=27.6

Q ss_pred             ccccccccccccCCCeeEEeCCccccccceeccccccccccccccccc
Q psy7479          45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIP   92 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~   92 (170)
                      +.|..|...+.   ......=|..||..|..+.+.....|+.|..+|.
T Consensus        54 ~~C~iC~~~~~---~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~   98 (138)
T 4ayc_A           54 LQCIICSEYFI---EAVTLNCAHSFCSYCINEWMKRKIECPICRKDIK   98 (138)
T ss_dssp             SBCTTTCSBCS---SEEEETTSCEEEHHHHHHHTTTCSBCTTTCCBCC
T ss_pred             CCCcccCcccC---CceECCCCCCccHHHHHHHHHcCCcCCCCCCcCC
Confidence            46777777664   3455566777787776554332236777766663

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=81.77  E-value=0.95  Score=29.43  Aligned_cols=8  Identities=25%  Similarity=1.140  Sum_probs=3.9

Q ss_pred             cccCCccc
Q psy7479         112 CQQCNHRF  119 (170)
Q Consensus       112 C~~C~~~l  119 (170)
                      |-.|...+
T Consensus       116 CP~Cr~~~  123 (133)
T 4ap4_A          116 CPTCRKKI  123 (133)
T ss_dssp             CTTTCCBC
T ss_pred             CCCCCCcC
Confidence            44444444

>2kre_A Ubiquitin conjugation factor E4 B; U-box domain, E3 ubiquitin ligase, E4 polyubiquitin chain EL factor, phosphoprotein, UBL conjugation pathway; NMR {Homo sapiens} PDB: 3l1x_A 3l1z_B

Probab=81.77  E-value=1  Score=28.43  Aligned_cols=49  Identities=10%  Similarity=0.021  Sum_probs=37.1

Q ss_pred             ccCccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479          42 EDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA   93 (170)
Q Consensus        42 ~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~   93 (170)
                      +.-|.|..|...+.   ..+....|..||..|..+.+...+.|..|+.++..
T Consensus        27 p~~~~CpI~~~~m~---dPV~~~cGhtf~r~~I~~~l~~~~~cP~~~~~l~~   75 (100)
T 2kre_A           27 PDEFRDPLMDTLMT---DPVRLPSGTIMDRSIILRHLLNSPTDPFNRQTLTE   75 (100)
T ss_dssp             STTTBCTTTCSBCS---SEEEETTTEEEEHHHHHHHTTSCSBCSSSCCBCCT
T ss_pred             cHhhCCcCccCccc---CCeECCCCCEEchHHHHHHHHcCCCCCCCCCCCCh
Confidence            56789999988885   56777899999999876654333478888887754

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.54  E-value=0.36  Score=27.67  Aligned_cols=46  Identities=22%  Similarity=0.427  Sum_probs=27.4

Q ss_pred             ccccccccccccCCCeeEEeCCccccccceeccc-ccccccccccccccC
Q psy7479          45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF-GTTGYCAACTKVIPA   93 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~-~~~~~C~~C~~~i~~   93 (170)
                      +.|..|...+.+   .....=|..||..|..+.+ .....|..|..+|..
T Consensus        16 ~~C~IC~~~~~~---p~~~~CgH~fC~~Ci~~~~~~~~~~CP~Cr~~~~~   62 (66)
T 2ecy_A           16 YKCEKCHLVLCS---PKQTECGHRFCESCMAALLSSSSPKCTACQESIVK   62 (66)
T ss_dssp             EECTTTCCEESS---CCCCSSSCCCCHHHHHHHHTTSSCCCTTTCCCCCT
T ss_pred             CCCCCCChHhcC---eeECCCCCHHHHHHHHHHHHhCcCCCCCCCcCCCh
Confidence            456666555541   2234556777888876654 212378888888754

>2csy_A Zinc finger protein 183-like 1; ring finger protein 161, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.34  E-value=0.45  Score=28.50  Aligned_cols=45  Identities=20%  Similarity=0.423  Sum_probs=23.0

Q ss_pred             ccccccccccccCCCeeEEeCCccccccceeccccccccccccccccc
Q psy7479          45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIP   92 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~   92 (170)
                      +.|..|...+.   ......=|..||..|..+.+.....|..|..++.
T Consensus        16 ~~C~IC~~~~~---~p~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~   60 (81)
T 2csy_A           16 FRCFICRQAFQ---NPVVTKCRHYFCESCALEHFRATPRCYICDQPTG   60 (81)
T ss_dssp             SBCSSSCSBCC---SEEECTTSCEEEHHHHHHHHHHCSBCSSSCCBCC
T ss_pred             CCCcCCCchhc---CeeEccCCCHhHHHHHHHHHHCCCcCCCcCcccc
Confidence            34555555443   2233444556666666544332226777776663

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.00  E-value=0.5  Score=27.57  Aligned_cols=46  Identities=22%  Similarity=0.409  Sum_probs=25.6

Q ss_pred             ccccccccccccCCCeeEE-eCCccccccceecccccccccccccccccC
Q psy7479          45 LKCGCCDCRLGEVGSTLYQ-KANLILCKRDYLRLFGTTGYCAACTKVIPA   93 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~~-~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~   93 (170)
                      +.|..|...+.   ..... .=|..||..|..+.+.....|..|...|..
T Consensus        16 ~~C~IC~~~~~---~p~~~~~CgH~fC~~Ci~~~~~~~~~CP~Cr~~~~~   62 (72)
T 2djb_A           16 ILCSICKGYLI---DATTITECLHTFCKSCIVRHFYYSNRCPKCNIVVHQ   62 (72)
T ss_dssp             GSCTTTSSCCS---SCEECSSSCCEECHHHHHHHHHHCSSCTTTCCCCCS
T ss_pred             CCCCCCChHHH---CcCEECCCCCHHHHHHHHHHHHcCCcCCCcCcccCc
Confidence            45555555553   12332 455667777765543222378888887754

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=80.58  E-value=0.94  Score=26.25  Aligned_cols=46  Identities=13%  Similarity=0.205  Sum_probs=25.3

Q ss_pred             ccccccccccccCCCeeEEeCCccccccceecccc---cccccccccccccC
Q psy7479          45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG---TTGYCAACTKVIPA   93 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~---~~~~C~~C~~~i~~   93 (170)
                      +.|..|...+.   ......=|..||..|..+.+.   ....|..|..+|..
T Consensus        21 ~~C~IC~~~~~---~~~~~~CgH~fC~~Ci~~~~~~~~~~~~CP~Cr~~~~~   69 (73)
T 2ysl_A           21 VICPICLDILQ---KPVTIDCGHNFCLKCITQIGETSCGFFKCPLCKTSVRK   69 (73)
T ss_dssp             CBCTTTCSBCS---SEEECTTCCEEEHHHHHHHCSSSCSCCCCSSSCCCCCC
T ss_pred             CEeccCCcccC---CeEEcCCCChhhHHHHHHHHHcCCCCCCCCCCCCcCCc
Confidence            34555555543   223334556667777655442   11278888887754

---

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	170
d1rutx2	34	g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus m	3e-13
d1j2oa2	33	g.39.1.3 (A:31-63) Rhombotin-2 (Lmo2) {Mouse (Mus	3e-13
d1rutx3	31	g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus	2e-11
d1j2oa1	30	g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus m	2e-09
d1rutx1	30	g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus m	3e-09
d1x3ha1	35	g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [	8e-04

>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 = 58.6 bits (142), Expect = 3e-13
 Identities = 17/34 (50%), Positives = 26/34 (76%)

Query: 46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 79
          KC  C  +LG++G++ Y K+ +ILC+ DY+RLFG
Sbjct: 1  KCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG 34

>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 = 58.3 bits (141), Expect = 3e-13
 Identities = 21/33 (63%), Positives = 22/33 (66%)

Query: 45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 77
          L C  C CRLGEVG  LY K    LC+RDYLRL
Sbjct: 1  LSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL 33

>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 = 53.6 bits (129), Expect = 2e-11
 Identities = 19/30 (63%), Positives = 25/30 (83%)

Query: 81  TGYCAACTKVIPAFEMVMRAKNNVYHLECF 110
           +G C+AC + IPA E+VMRA+ NVYHL+CF
Sbjct: 2   SGACSACGQSIPASELVMRAQGNVYHLKCF 31

>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 = 48.6 bits (116), Expect = 2e-09
 Identities = 15/30 (50%), Positives = 20/30 (66%)

Query: 15 GGLKECASCGKRITERFLLKALDLFWHEDC 44
          G L  C  C + I +R+ LKA+D +WHEDC
Sbjct: 1  GSLLTCGGCQQNIGDRYFLKAIDQYWHEDC 30

>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 = 47.8 bits (114), Expect = 3e-09
 Identities = 16/28 (57%), Positives = 20/28 (71%)

Query: 18 KECASCGKRITERFLLKALDLFWHEDCL 45
          K CA CG +I +RFLL A+D +WH  CL
Sbjct: 3  KRCAGCGGKIADRFLLYAMDSYWHSRCL 30

>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 = 33.5 bits (77), Expect = 8e-04
 Identities = 12/39 (30%), Positives = 20/39 (51%), Gaps = 4/39 (10%)

Query: 72  RDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECF 110
           +D+L +F     C  C + +   E  + A + V+H ECF
Sbjct: 1   KDFLAMFSPK--CGGCNRPVL--ENYLSAMDTVWHPECF 35

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	170
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.24
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	99.07
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.96
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.83
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.81
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.8
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.71
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.65
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.65
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.64
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.6
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.6
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.58
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.58
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.57
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.51
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.5
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.42
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.41
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.39
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.38
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.32
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.31
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.3
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	98.29
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.28
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	98.26
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.22
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.22
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.2
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.19
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.18
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.17
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.15
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.14
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	98.12
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.11
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	98.09
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.06
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.06
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	98.04
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.03
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.02
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.02
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.01
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.0
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	97.98
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.96
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	97.94
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.93
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.91
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.89
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.89
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	97.88
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.88
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.87
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.85
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.85
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.82
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.81
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.8
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	97.78
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	97.77
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.77
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.75
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.75
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.75
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	97.74
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.74
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.74
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.73
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.71
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.68
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.66
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.64
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.64
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.58
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.56
d2co8a2	36	Nedd9 interacting protein with calponin homology,	97.55
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.54
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.52
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.48
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.48
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.43
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.42
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.39
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.39
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	97.38
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.35
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.34
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.33
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.33
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.33
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.32
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.25
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.18
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.18
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.14
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.02
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.95
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	96.95
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	96.89
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.85
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	96.84
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.69
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	96.58
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.46
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.37
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.33
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.29
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.2
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	96.14
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.87
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	95.7
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.65
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	95.58
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	95.48
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	95.28
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.26
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	95.12
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	95.11
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	95.02
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	94.87
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	94.51
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	94.47
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	94.42
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	94.36
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	91.64
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	91.54
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	90.67
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	90.55
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	89.19
d2co8a1	33	Nedd9 interacting protein with calponin homology,	86.05
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	84.82
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	81.72

>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=99.24  E-value=1.1e-12  Score=67.16  Aligned_cols=35  Identities=31%  Similarity=0.824  Sum_probs=32.6

Q ss_pred             cceecccccccccccccccccCCceEEecCCcccccCcc
Q psy7479          72 RDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        72 ~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      +||.++|++  +|.+|+++|.+  .+|+|+|+.||++||
T Consensus         1 ~DY~~~fap--kC~~C~~~I~g--~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           1 KDFLAMFSP--KCGGCNRPVLE--NYLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCCCCCSC--BCTTTCCBCCS--SCEEETTEEECTTTC
T ss_pred             CcHHHHhCh--hhhhcCCcccc--hheeecCCccCcccC
Confidence            479999998  99999999976  799999999999998

>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=99.07  E-value=3.2e-11  Score=63.78  Aligned_cols=43  Identities=28%  Similarity=0.385  Sum_probs=36.6

Q ss_pred             CCCCCCCCCCCCCCCcccccccccccccceeEEeCCccccccCc
Q psy7479           2 SSVTQGALAGGASGGLKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus         2 ss~~~~~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      +|+++.+...+.....++|..|+++|.+. .+.|+|+.||++||
T Consensus         3 ~~~~q~a~~~p~~~r~P~C~~C~~pI~g~-~vtAlgk~WHPEhF   45 (45)
T d2dara2           3 DTLVQRAEHIPAGKRTPMCAHCNQVIRGP-FLVALGKSWHPEEF   45 (45)
T ss_dssp             CCSCBCCEEECTTTCCCBBSSSCCBCCSC-EEEETTEEECTTTC
T ss_pred             chhhhhccccCCCCCCeeccccCCcccCc-eeeecCCccCcCCC
Confidence            45666666666778889999999999998 68999999999998

>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=98.96  E-value=1.7e-10  Score=58.98  Aligned_cols=37  Identities=30%  Similarity=0.467  Sum_probs=34.7

Q ss_pred             cceecccccccccccccccccCCceEEecCCcccccCcc
Q psy7479          72 RDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        72 ~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      .||.+.+++  +|.+|.++|.++++.|.+.|+.||..||
T Consensus         1 kCy~~~~a~--~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           1 KCTTREDSP--KCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCCSCCCSC--BCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             CccccccCc--ccccCCCccCCCCeEeEeCCccchhccC
Confidence            488899998  9999999999888999999999999998

>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=98.83  E-value=7e-10  Score=54.99  Aligned_cols=35  Identities=26%  Similarity=0.556  Sum_probs=31.7

Q ss_pred             cceecccccccccccccccccCCceEEecCCcccccCcc
Q psy7479          72 RDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        72 ~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      .||++.|++  +|..|+++|..  ..|+..++.||.+||
T Consensus         1 PCyE~kfa~--~C~~Ckk~It~--GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           1 PCYENKFAP--RCARCSKTLTQ--GGVTYRDQPWHRECL   35 (35)
T ss_dssp             CCCCCCSSC--CCTTTCCCCCS--CCEESSSSEECTTTC
T ss_pred             CchHHHHHH--HHhhcCCcccc--CceeecCCcchhhhC
Confidence            489999998  99999999976  467999999999998

>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=98.81  E-value=7.9e-10  Score=55.07  Aligned_cols=35  Identities=31%  Similarity=0.722  Sum_probs=30.0

Q ss_pred             ccceecccccccccccccccccCCceEEecCCcccccCcc
Q psy7479          71 KRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        71 ~~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      +.||.....   +|..|+++|+  |++++|.|+.||+.||
T Consensus         1 E~Cy~~tlE---kC~~C~~~I~--driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           1 EGCYVATLE---KCATCSQPIL--DRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCCCCSSCC---BCTTTCCBCC--SCCEEETTEEECTTTC
T ss_pred             ChhHHHHHH---HHHHhchHHH--HHHHHHhCCCCCCCCC
Confidence            357776655   8999999995  5999999999999998

>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=98.80  E-value=7.9e-10  Score=56.23  Aligned_cols=30  Identities=30%  Similarity=0.781  Sum_probs=27.4

Q ss_pred             CCcccccccccccccceeEEeCCccccccCc
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      ...++|.+|+++|.+. +|.|+|+.||++||
T Consensus         6 ~fapkC~~C~~~I~g~-~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           6 MFSPKCGGCNRPVLEN-YLSAMDTVWHPECF   35 (35)
T ss_dssp             CCSCBCTTTCCBCCSS-CEEETTEEECTTTC
T ss_pred             HhChhhhhcCCcccch-heeecCCccCcccC
Confidence            3568999999999988 78999999999998

>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=98.71  E-value=1.2e-09  Score=55.45  Aligned_cols=34  Identities=24%  Similarity=0.538  Sum_probs=31.1

Q ss_pred             ccccccccccccCCCeeEEeCCccccccceeccccc
Q psy7479          45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT   80 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~   80 (170)
                      |+|..|+++|.+  ..|+.++|++||+.||.++|+|
T Consensus         1 F~C~~C~~~f~~--~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFPE--GLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCGG--GCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCCC--CCeEEECCEecChHhHHhhcCC
Confidence            789999999984  5699999999999999999986

>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=98.65  E-value=5.7e-09  Score=51.89  Aligned_cols=31  Identities=32%  Similarity=0.821  Sum_probs=28.3

Q ss_pred             CCCcccccccccccccceeEEeCCccccccCc
Q psy7479          14 SGGLKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      .....+|..|+++|.+. ++.|+|+.||+.||
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            34678999999999999 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=98.65  E-value=3.9e-09  Score=53.53  Aligned_cols=32  Identities=31%  Similarity=0.698  Sum_probs=29.6

Q ss_pred             cccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479         110 FACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus       110 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      |+|+.|+++| .+..|++++|++||..||.++|
T Consensus         1 F~C~~C~~~f-~~~~F~e~~G~pYCe~~Y~~lF   32 (35)
T d1g47a2           1 FVCAQCFQQF-PEGLFYEFEGRKYCEHDFQMLF   32 (35)
T ss_dssp             CCCTTTCCCC-GGGCSEEETTEEECHHHHHHHC
T ss_pred             CCCCCCcCCC-CCCCeEEECCEecChHhHHhhc
Confidence            7899999999 6778999999999999999984

>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=98.60  E-value=1e-08  Score=49.45  Aligned_cols=29  Identities=55%  Similarity=1.266  Sum_probs=26.8

Q ss_pred             cccccccccccccceeEEeCCccccccCc
Q psy7479          17 LKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        17 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      ...|++|+++|.+++++.++++.||..|+
T Consensus         2 ~~~CaGC~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           2 WKRCAGCGGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CCBBTTTCCBCCCSEEEEETTEEECGGGC
T ss_pred             ccccCCCCCccchhhhhccchhhhhhhhC
Confidence            35799999999999999999999999985

>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=98.60  E-value=7.2e-09  Score=50.29  Aligned_cols=29  Identities=66%  Similarity=1.255  Sum_probs=27.7

Q ss_pred             cccccccccccCCceEEecCCcccccCcc
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      +.|.+|++.|.+.|.++++++..||.+||
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

>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=98.58  E-value=1e-08  Score=53.95  Aligned_cols=26  Identities=35%  Similarity=0.613  Sum_probs=24.7

Q ss_pred             ccccccccccCCceEEecCCcccccCcc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      +|..|+++|.+  .+++|+|+.||++||
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            89999999976  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=98.58  E-value=9.6e-09  Score=53.10  Aligned_cols=34  Identities=41%  Similarity=0.854  Sum_probs=31.5

Q ss_pred             cceecccccccccccccccccCCceEEecCCcccccCc
Q psy7479          72 RDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLEC  109 (170)
Q Consensus        72 ~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~C  109 (170)
                      .||.++|+.  +|..|++.|.+  .+|.|.++.||++|
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            589999999  99999999976  89999999999998

>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=98.57  E-value=1.6e-08  Score=48.54  Aligned_cols=28  Identities=50%  Similarity=1.242  Sum_probs=26.2

Q ss_pred             cccccccccccccceeEEeCCccccccC
Q psy7479          17 LKECASCGKRITERFLLKALDLFWHEDC   44 (170)
Q Consensus        17 ~~~C~~C~~~I~~~~~~~~~~~~~H~~C   44 (170)
                      ...|++|+++|.+++.+.++++.||..|
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            5679999999999999999999999987

>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=98.51  E-value=3.6e-08  Score=52.17  Aligned_cols=34  Identities=24%  Similarity=0.620  Sum_probs=30.3

Q ss_pred             CCCCCcccccccccccccceeEEeCCccccccCc
Q psy7479          12 GASGGLKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        12 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      ....+.+.|..|++.++..+.+.+.|+.||..||
T Consensus        10 ~~~g~~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          10 QKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCCCCCEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             cccCCCCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            4455679999999999999889999999999998

>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=98.50  E-value=2.9e-08  Score=48.29  Aligned_cols=31  Identities=23%  Similarity=0.517  Sum_probs=28.6

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      .|..|.++| .|++|..+|++|||..||..+|
T Consensus         1 ~C~~C~~~L-~GQry~~rd~~PyC~~Cf~~lf   31 (32)
T d2d8za2           1 VCTACRKQL-SGQRFTARDDFAYCLNCFCDLY   31 (32)
T ss_dssp             BCSSSCCBC-TTSCCEESSSSEECHHHHHHHT
T ss_pred             CcccCCccc-cCceeeecCCCeehHHhhHhhc
Confidence            488999999 8999999999999999999875

>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=98.42  E-value=3.5e-08  Score=47.43  Aligned_cols=29  Identities=28%  Similarity=0.684  Sum_probs=25.9

Q ss_pred             CCcccccccccccccceeEEeCCccccccC
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDC   44 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~C   44 (170)
                      .+.++|+.|.+||.+. ++.|+|+.||+++
T Consensus         3 mg~p~C~~C~~PI~~~-~vtAlgk~WHpEH   31 (31)
T d1u5sb1           3 MGVPICGACRRPIEGR-VVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCCEETTTTEECCSC-EECCTTSBEETTT
T ss_pred             cCCcchhhcCCchhhh-HhhhhccccCCCC
Confidence            3578999999999997 8999999999974

>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=98.41  E-value=7.9e-08  Score=47.31  Aligned_cols=33  Identities=36%  Similarity=0.680  Sum_probs=29.7

Q ss_pred             CCCCcccccccccccccceeEEeCCccccccCc
Q psy7479          13 ASGGLKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        13 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      ...+...|++|++.|..+..+.|+++.||..||
T Consensus         4 ~~~g~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           4 KIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CCSSCSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             cccCCccccccchhhhCCceeeeeecceeeeeC
Confidence            355678899999999999889999999999998

>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=98.39  E-value=5e-08  Score=52.66  Aligned_cols=39  Identities=31%  Similarity=0.495  Sum_probs=33.6

Q ss_pred             cccccccccccCCCeeEEeCCccccccceeccccccccccccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACT   88 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~   88 (170)
                      +|..|++.|++  ....++|+++||+.||.++|+|  +..+.+
T Consensus         1 KC~~C~k~Lds--~t~~ehdg~~YCk~CY~k~fGP--KG~g~G   39 (49)
T d1b8ta4           1 RCAKCGKSLES--TTLADKDGEIYCKGCYAKNFGP--KGFGFG   39 (49)
T ss_dssp             BCTTTCCBCCS--SSEEEETTEEEEHHHHHHHTCC--CCCCCC
T ss_pred             ChhhcCCccCC--CcccccCCcccchhhhhhccCC--CccCcc
Confidence            68999999984  4688999999999999999998  666554

>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=98.38  E-value=1.3e-07  Score=45.30  Aligned_cols=31  Identities=23%  Similarity=0.477  Sum_probs=28.7

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      .|+.|+++| .|++|..+|..|||.+||..+|
T Consensus         1 vCt~Ck~~L-aGqrFTSrde~pYC~~Cfg~Lf   31 (32)
T d2cuqa1           1 VCTGCQTPL-AGQQFTSRDEDPYCVACFGELF   31 (32)
T ss_dssp             BCSSSCCBC-TTCCEEECSSSEEEHHHHHHHT
T ss_pred             CccccCccc-cCCccccCCCCccHHHHhHhhc
Confidence            489999999 8999999999999999998874

>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=98.32  E-value=9.7e-08  Score=45.87  Aligned_cols=26  Identities=31%  Similarity=0.600  Sum_probs=23.3

Q ss_pred             cccccccccccCCceEEecCCcccccCc
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLEC  109 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~C  109 (170)
                      |+|..|++||.+  ++++|+|+.||++.
T Consensus         6 p~C~~C~~PI~~--~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           6 PICGACRRPIEG--RVVNAMGKQWHVEH   31 (31)
T ss_dssp             CEETTTTEECCS--CEECCTTSBEETTT
T ss_pred             cchhhcCCchhh--hHhhhhccccCCCC
Confidence            399999999965  89999999999974

>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=98.31  E-value=8.1e-08  Score=45.99  Aligned_cols=31  Identities=32%  Similarity=0.672  Sum_probs=27.5

Q ss_pred             cccccccccccCCCeeEEeCCccccccceecccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG   79 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~   79 (170)
                      +|..|++.|.   ..|..+||.+||+.||...|+
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            5889999996   569999999999999998875

>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=98.29  E-value=1.2e-07  Score=46.18  Aligned_cols=34  Identities=35%  Similarity=0.794  Sum_probs=30.8

Q ss_pred             cceecccccccccccccccccCCceEEecCCcccccCc
Q psy7479          72 RDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLEC  109 (170)
Q Consensus        72 ~c~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~~H~~C  109 (170)
                      .+|..+|+.  .|..|...|++  .+|.|.+..||++|
T Consensus         1 kdYw~kfge--~C~~C~~~itG--pvMvAG~~K~HPEC   34 (34)
T d1x6aa1           1 KDYWGKFGE--FCHGCSLLMTG--PFMVAGEFKYHPEC   34 (34)
T ss_dssp             CCSSCCSSC--BCTTTCCBCCS--CCBCCTTCCBCTTS
T ss_pred             CcHHHHHHH--HhhhhHhhccc--ceeeecccccCCCC
Confidence            378899998  99999999976  89999999999998

>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=98.28  E-value=1.8e-07  Score=47.12  Aligned_cols=33  Identities=27%  Similarity=0.520  Sum_probs=29.8

Q ss_pred             CCCCcccccccccccccceeEEeCCccccccCc
Q psy7479          13 ASGGLKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        13 ~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      ..+...+|..|++.++..+.+.++|+.||..||
T Consensus         4 ~~g~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           4 EAGAGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CCCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             cCCCCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            455678999999999999889999999999998

>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=98.26  E-value=4.6e-07  Score=47.00  Aligned_cols=40  Identities=28%  Similarity=0.572  Sum_probs=33.9

Q ss_pred             CCCCCCCCCCCCcccccccccccccceeEEeCCccccccCc
Q psy7479           5 TQGALAGGASGGLKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus         5 ~~~~~~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      +...+..++....++|.+|+.-|.+. ++.+.++.+|++||
T Consensus         6 tK~~~~~~~~QkLP~CdkCg~GIVG~-~VK~rDK~rHPeCf   45 (45)
T d1x64a1           6 TKVHGGAGSAQRMPLCDKCGSGIVGA-VVKARDKYRHPECF   45 (45)
T ss_dssp             CCCCCCCSCCCSCCBCTTTCCBCCSC-CEESSSCEECTTTC
T ss_pred             cccCCCCCccccCccccccCCCcEEE-EEEeccccCCCCCC
Confidence            33445556778899999999999999 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=98.22  E-value=1.3e-07  Score=44.58  Aligned_cols=29  Identities=38%  Similarity=0.870  Sum_probs=26.6

Q ss_pred             cccccccccccccceeEEeCCccccccCc
Q psy7479          17 LKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        17 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      .+.|++|++.++..+.+.-+++.||+.||
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            36799999999999888999999999998

>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=98.22  E-value=3.5e-07  Score=42.84  Aligned_cols=30  Identities=20%  Similarity=0.546  Sum_probs=27.3

Q ss_pred             cccccCCcccccCCeEEEeCCeeccHHhHHH
Q psy7479         110 FACQQCNHRFCVGDRFYLCDNKILCEYDYEE  140 (170)
Q Consensus       110 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~  140 (170)
                      |+|..|++.| .+.....+||.+||+.||.+
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 77788889999999999965

>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=98.20  E-value=4e-07  Score=44.42  Aligned_cols=30  Identities=30%  Similarity=0.755  Sum_probs=27.3

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHH
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEER  141 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~  141 (170)
                      .|..|.+++ .+..|++.+|+|||..+|.++
T Consensus         1 VC~~C~~PF-~~~~Fy~~~g~PyCe~HyH~~   30 (32)
T d1x3ha2           1 VCGDCFTSF-STGSFFELDGRPFCELHYHHR   30 (32)
T ss_dssp             BCSSSCCBS-CSSCCEESSSCEECHHHHHHH
T ss_pred             CcCccCCcC-CCCCeEeECCccchHHhhhhh
Confidence            489999999 788999999999999999875

>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=98.19  E-value=3.8e-07  Score=45.75  Aligned_cols=31  Identities=23%  Similarity=0.405  Sum_probs=28.5

Q ss_pred             CCcccccccccccccceeEEeCCccccccCc
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      .....|..|++.++..+.+.++|+.||..||
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            4467899999999999899999999999998

>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=98.18  E-value=6.5e-07  Score=43.40  Aligned_cols=32  Identities=31%  Similarity=0.754  Sum_probs=30.1

Q ss_pred             cccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479         110 FACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus       110 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      |.|+.|.+++ .|.+.++++|..||+.+|.++|
T Consensus         1 FvCA~CekPF-~G~rhyE~~g~ayCe~Hy~qLf   32 (35)
T d1u5sb2           1 FVCAKCEKPF-LGHRHYERKGLAYCETHYNQLF   32 (35)
T ss_dssp             CBCTTTCCBC-SSSCCEEETTEEECHHHHHHHC
T ss_pred             CcccccCCcc-CCchhhhhcCchHHHHHHHHHh
Confidence            7899999999 8999999999999999999985

>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=98.17  E-value=3.3e-07  Score=43.77  Aligned_cols=29  Identities=28%  Similarity=0.578  Sum_probs=26.5

Q ss_pred             cccccccccccccceeEEeCCccccccCc
Q psy7479          17 LKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        17 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      .+.|++|+++++..+.+..+|+.||..|+
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            47899999999999889999999999985

>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=98.15  E-value=2.9e-07  Score=47.93  Aligned_cols=36  Identities=14%  Similarity=0.348  Sum_probs=30.7

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHHhhhccc
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANI  147 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~  147 (170)
                      +|+.|++.| ....|...+|.+||+.||.++|..+..
T Consensus         1 rC~~C~~~L-s~~~yas~~G~lYCkpHf~qLF~~kGn   36 (42)
T d2d8ya2           1 RCSYCNNKL-SLGTYASLHGRIYCKPHFNQLFKSKGN   36 (42)
T ss_dssp             BCTTTCCBC-CTTTCCCSSSCCCCHHHHHHHSCCCSC
T ss_pred             CcCcCCCCc-cCCcchhhCCEeccHHHHHHHHHhhcC
Confidence            689999999 566899999999999999999765543

>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=98.14  E-value=1.6e-07  Score=44.01  Aligned_cols=30  Identities=33%  Similarity=0.650  Sum_probs=26.4

Q ss_pred             ccccccccccccCCCeeEEeCCccccccceec
Q psy7479          45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLR   76 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~   76 (170)
                      |+|+.|++.|.  ......+||.+||+.||.+
T Consensus         1 frca~cgk~le--stt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLE--STTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEEC--SSCSEEETTEEECHHHHHH
T ss_pred             CccccccCccc--cceeeccCCcEEEeeeeec
Confidence            78999999997  3668999999999999864

>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=98.12  E-value=6.2e-07  Score=41.00  Aligned_cols=27  Identities=33%  Similarity=0.630  Sum_probs=25.2

Q ss_pred             cccccccccCCceEEecCCcccccCcc
Q psy7479          84 CAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        84 C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      |..|.+.|++..+.+...|..||..||
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            788999999988899999999999998

>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=98.09  E-value=6.8e-07  Score=41.81  Aligned_cols=27  Identities=30%  Similarity=0.752  Sum_probs=23.5

Q ss_pred             cccccccccCC--ceEEecCCcccccCcc
Q psy7479          84 CAACTKVIPAF--EMVMRAKNNVYHLECF  110 (170)
Q Consensus        84 C~~C~~~i~~~--~~~~~~~~~~~H~~Cf  110 (170)
                      |..|.+||++.  ..+|++.++.||.+||
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            78899999763  4589999999999998

>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=98.06  E-value=4.4e-07  Score=44.02  Aligned_cols=32  Identities=19%  Similarity=0.575  Sum_probs=28.2

Q ss_pred             cccccccccccCCCeeEEeCCccccccceecccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG   79 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~   79 (170)
                      .|..|+++|.  ++.|..+|+++||-.||..+|+
T Consensus         1 ~C~~C~~~L~--GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQLS--GQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBCT--TSCCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCcccc--CceeeecCCCeehHHhhHhhcC
Confidence            3778999997  7889999999999999988764

>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=98.06  E-value=1.1e-06  Score=44.56  Aligned_cols=31  Identities=26%  Similarity=0.568  Sum_probs=26.9

Q ss_pred             CCcccccccccccccc-eeEEeCCccccccCc
Q psy7479          15 GGLKECASCGKRITER-FLLKALDLFWHEDCL   45 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf   45 (170)
                      ..+..|.+|+++|..+ ..+.+.|+.||..||
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            4568899999999755 568999999999998

>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=98.04  E-value=1.6e-06  Score=42.10  Aligned_cols=33  Identities=30%  Similarity=0.612  Sum_probs=29.5

Q ss_pred             CCCCCcccccccccccccceeEEeCCccccccCc
Q psy7479          12 GASGGLKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        12 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      ++....++|.+|+.-|.+. ++.+.++.+|++||
T Consensus         3 g~~qklp~CdkCg~GIVG~-~VK~rDk~rHPeCf   35 (35)
T d1x62a2           3 GNAQKLPMCDKCGTGIVGV-FVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCCCCCCSSSCCCCCSS-CEECSSCEECTTTT
T ss_pred             CccccCccccccCCCcEeE-EEEeccccCCCCCC
Confidence            4456789999999999999 68999999999998

>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=98.03  E-value=1.3e-06  Score=43.04  Aligned_cols=31  Identities=32%  Similarity=0.626  Sum_probs=27.0

Q ss_pred             CCCcccccccccccccceeEEeCCccccccCc
Q psy7479          14 SGGLKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      ...++.|..|+++|..+. |...++.||.+||
T Consensus         5 ~kfa~~C~~Ckk~It~GG-vtY~dqpWHkeCF   35 (35)
T d2cuqa2           5 NKFAPRCARCSKTLTQGG-VTYRDQPWHRECL   35 (35)
T ss_dssp             CCSSCCCTTTCCCCCSCC-EESSSSEECTTTC
T ss_pred             HHHHHHHhhcCCccccCc-eeecCCcchhhhC
Confidence            346789999999999884 7789999999998

>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=98.02  E-value=1.2e-06  Score=39.93  Aligned_cols=27  Identities=22%  Similarity=0.573  Sum_probs=25.1

Q ss_pred             cccccccccCCceEEecCCcccccCcc
Q psy7479          84 CAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        84 C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      |..|.+.|++..+.+...|..||..||
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

>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=98.01  E-value=2.7e-06  Score=45.67  Aligned_cols=37  Identities=16%  Similarity=0.314  Sum_probs=30.2

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHHhhhcccc
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANIA  148 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~  148 (170)
                      +|..|++.| +.....++|+++||+.||.++|......
T Consensus         1 KC~~C~k~L-ds~t~~ehdg~~YCk~CY~k~fGPKG~g   37 (49)
T d1b8ta4           1 RCAKCGKSL-ESTTLADKDGEIYCKGCYAKNFGPKGFG   37 (49)
T ss_dssp             BCTTTCCBC-CSSSEEEETTEEEEHHHHHHHTCCCCCC
T ss_pred             ChhhcCCcc-CCCcccccCCcccchhhhhhccCCCccC
Confidence            589999999 5567888999999999999986544433

>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=98.00  E-value=1.8e-06  Score=41.21  Aligned_cols=30  Identities=27%  Similarity=0.540  Sum_probs=26.3

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      +|..|++.|  ..+|..+||.|||+.+|..+|
T Consensus         1 kC~~C~~vL--~gEYm~kdG~PyCe~DY~~~F   30 (31)
T d2dj7a1           1 KCQTCSVIL--TGEYISKDGVPYCESDYHAQF   30 (31)
T ss_dssp             BCSSSCCBC--SSCCEEETTEEECTTHHHHHT
T ss_pred             CccccCccc--cceeecCCCCcccHHHHHHhc
Confidence            589999999  447999999999999999875

>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=97.98  E-value=1.1e-06  Score=46.68  Aligned_cols=33  Identities=24%  Similarity=0.462  Sum_probs=29.5

Q ss_pred             cccccccccccCCCeeEEeCCcccc-ccceeccccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILC-KRDYLRLFGT   80 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC-~~c~~~~~~~   80 (170)
                      +|..|++.|+.  ....++++++|| +.||..+|+|
T Consensus         1 kC~~C~K~L~s--g~~aeHdg~pYC~k~CY~~~FGP   34 (48)
T d1imla2           1 KCEKCGKTLTS--GGHAEHEGKPYCNHPCYSAMFGP   34 (48)
T ss_dssp             BCTTTCCBCCT--TTEEEETTEEEETTTHHHHHSSC
T ss_pred             CchhcCcCcCC--CChhhcCCcccccccchhhccCC
Confidence            68899999984  558999999999 7799999998

>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=97.94  E-value=9.1e-07  Score=43.11  Aligned_cols=31  Identities=16%  Similarity=0.417  Sum_probs=26.9

Q ss_pred             cccccccccccCCCeeEEeCCccccccceeccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF   78 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~   78 (170)
                      .|..|.+++.  +..||..+|++||+.+|.++.
T Consensus         1 VC~~C~~PF~--~~~Fy~~~g~PyCe~HyH~~~   31 (32)
T d1x3ha2           1 VCGDCFTSFS--TGSFFELDGRPFCELHYHHRR   31 (32)
T ss_dssp             BCSSSCCBSC--SSCCEESSSCEECHHHHHHHH
T ss_pred             CcCccCCcCC--CCCeEeECCccchHHhhhhhc
Confidence            4889999997  467999999999999998764

>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=97.93  E-value=1.8e-06  Score=40.26  Aligned_cols=27  Identities=33%  Similarity=0.805  Sum_probs=23.3

Q ss_pred             cccccccccCC--ceEEecCCcccccCcc
Q psy7479          84 CAACTKVIPAF--EMVMRAKNNVYHLECF  110 (170)
Q Consensus        84 C~~C~~~i~~~--~~~~~~~~~~~H~~Cf  110 (170)
                      |..|.+||.+.  ..+|.+.++.||.+||
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            77899999763  4589999999999998

>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=97.91  E-value=1.6e-06  Score=41.45  Aligned_cols=32  Identities=22%  Similarity=0.465  Sum_probs=28.1

Q ss_pred             cccccccccccCCCeeEEeCCccccccceecccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG   79 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~   79 (170)
                      .|..|+++|.  ++.|..+|..+||..||.++|+
T Consensus         1 vCt~Ck~~La--GqrFTSrde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1           1 VCTGCQTPLA--GQQFTSRDEDPYCVACFGELFA   32 (32)
T ss_dssp             BCSSSCCBCT--TCCEEECSSSEEEHHHHHHHTT
T ss_pred             CccccCcccc--CCccccCCCCccHHHHhHhhcC
Confidence            4889999997  6889999999999999987763

>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=97.89  E-value=6.5e-06  Score=39.44  Aligned_cols=30  Identities=20%  Similarity=0.405  Sum_probs=27.2

Q ss_pred             cccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479         112 CQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus       112 C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      |..|.++| ....|...++..||..||+++|
T Consensus         2 C~~C~qPI-GtkSFip~~~~~yCvpCYE~kf   31 (32)
T d1wyha1           2 CSGCEQPL-GSRSFVPDKGAHYCVPCYENKF   31 (32)
T ss_dssp             CTTTCCBT-TTSCEEEETTEEEEHHHHHHHT
T ss_pred             cccccCcc-cccccccCCCcEEEEecccccc
Confidence            78899999 6778999999999999999875

>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=97.88  E-value=1.7e-06  Score=41.91  Aligned_cols=34  Identities=29%  Similarity=0.726  Sum_probs=30.5

Q ss_pred             ccccccccccccCCCeeEEeCCccccccceeccccc
Q psy7479          45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT   80 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~   80 (170)
                      |.|+.|.+++-  +...+.++|..||+.+|.++|+.
T Consensus         1 FvCA~CekPF~--G~rhyE~~g~ayCe~Hy~qLfg~   34 (35)
T d1u5sb2           1 FVCAKCEKPFL--GHRHYERKGLAYCETHYNQLFGD   34 (35)
T ss_dssp             CBCTTTCCBCS--SSCCEEETTEEECHHHHHHHCSC
T ss_pred             CcccccCCccC--CchhhhhcCchHHHHHHHHHhcc
Confidence            78999999985  67789999999999999999873

>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=97.88  E-value=1.7e-06  Score=41.47  Aligned_cols=31  Identities=19%  Similarity=0.658  Sum_probs=26.9

Q ss_pred             cccccccccccCCCeeEEeCCccccccceeccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF   78 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~   78 (170)
                      .|+.|+.+|.+.+  |...+|.+||+.||.+.|
T Consensus         1 nCa~C~~sL~d~g--FVEE~g~lYCe~Cye~ff   31 (32)
T d2dara1           1 NCAHCKNTMAYIG--FVEEKGALYCELCYEKFF   31 (32)
T ss_dssp             BCSSSCCBCSSSC--BEESSSCEECHHHHHHHT
T ss_pred             CcccccccHhhcc--eeeecCcEeHHHHHHHhc
Confidence            3788999998655  999999999999998765

>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=97.87  E-value=6.7e-06  Score=39.44  Aligned_cols=30  Identities=27%  Similarity=0.585  Sum_probs=27.2

Q ss_pred             cccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479         112 CQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus       112 C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      |..|..+| ....|..+++..||..||+++|
T Consensus         2 C~~C~qPI-Gtksfipk~~~~yCvpCyE~kf   31 (32)
T d1x4ka1           2 CHRCQQPI-GTKSFIPKDNQNFCVPCYEKQH   31 (32)
T ss_dssp             CSSSCCCC-CSSSEEEETTEEEEHHHHHHHT
T ss_pred             cccccCcc-cccccccCCCCceEeecchhhc
Confidence            78899999 6778999999999999999875

>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=97.85  E-value=5.2e-06  Score=39.76  Aligned_cols=31  Identities=23%  Similarity=0.436  Sum_probs=27.4

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      .|+.|.++| ....|.+.+|++||..||++-|
T Consensus         1 nCa~C~~sL-~d~gFVEE~g~lYCe~Cye~ff   31 (32)
T d2dara1           1 NCAHCKNTM-AYIGFVEEKGALYCELCYEKFF   31 (32)
T ss_dssp             BCSSSCCBC-SSSCBEESSSCEECHHHHHHHT
T ss_pred             CcccccccH-hhcceeeecCcEeHHHHHHHhc
Confidence            488999999 7788999999999999998753

>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=97.85  E-value=6.2e-06  Score=38.89  Aligned_cols=29  Identities=24%  Similarity=0.726  Sum_probs=26.6

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHH
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEE  140 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~  140 (170)
                      .|..|.++| .|.+|...++++||-+||..
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            488999999 89999999999999999964

>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=97.82  E-value=3.4e-06  Score=39.38  Aligned_cols=26  Identities=31%  Similarity=0.754  Sum_probs=22.3

Q ss_pred             ccccccccccc---eeEEeCCccccccCc
Q psy7479          20 CASCGKRITER---FLLKALDLFWHEDCL   45 (170)
Q Consensus        20 C~~C~~~I~~~---~~~~~~~~~~H~~Cf   45 (170)
                      |..|.+||.+-   ..|...++.||.+||
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            78999999753   458899999999998

>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=97.81  E-value=8.2e-06  Score=38.86  Aligned_cols=26  Identities=23%  Similarity=0.678  Sum_probs=23.0

Q ss_pred             ccccccccccCCceEEecCCcccccCc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLEC  109 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~C  109 (170)
                      .|++|+++|.. ..++.+.++.||.+|
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            79999999975 457899999999987

>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=97.80  E-value=5.5e-06  Score=39.42  Aligned_cols=28  Identities=25%  Similarity=0.478  Sum_probs=23.8

Q ss_pred             cccccccccccCCceEEecCCcccccCcc
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      ++|++|++++...|.+ ...|+.||..|+
T Consensus         3 ~~CprC~K~VYfaEk~-~~lgk~WHk~Cl   30 (30)
T d2cu8a1           3 SKCPKCDKTVYFAEKV-SSLGKDWHKFCL   30 (30)
T ss_dssp             CBCTTTCCBCCTTTEE-EETTEEEETTTC
T ss_pred             CcCCCCCCceeeHHhh-ccCCcccccccC
Confidence            3899999999987655 677999999884

>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=97.78  E-value=3e-06  Score=39.78  Aligned_cols=27  Identities=30%  Similarity=0.722  Sum_probs=23.9

Q ss_pred             ccccccccccCCceEEecCCcccccCcc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      .|++|++.+.+.| .+.-.++.||..||
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            8999999999865 45788999999998

>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=97.77  E-value=7.1e-06  Score=43.51  Aligned_cols=33  Identities=15%  Similarity=0.280  Sum_probs=28.5

Q ss_pred             ccccCCcccccCCeEEEeCCeecc-HHhHHHHhhh
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILC-EYDYEERQVF  144 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C-~~c~~~~~~~  144 (170)
                      +|..|++.| ......+++++||| +.||.++|..
T Consensus         1 kC~~C~K~L-~sg~~aeHdg~pYC~k~CY~~~FGP   34 (48)
T d1imla2           1 KCEKCGKTL-TSGGHAEHEGKPYCNHPCYSAMFGP   34 (48)
T ss_dssp             BCTTTCCBC-CTTTEEEETTEEEETTTHHHHHSSC
T ss_pred             CchhcCcCc-CCCChhhcCCcccccccchhhccCC
Confidence            589999999 66789999999999 8899998543

>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=97.77  E-value=5.2e-06  Score=40.23  Aligned_cols=27  Identities=22%  Similarity=0.605  Sum_probs=24.8

Q ss_pred             cccccccccccCCceEEecCCcccccCcc
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      |.|.+|+..|.+  .++.++++.+|++||
T Consensus         9 p~CdkCg~GIVG--~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           9 PMCDKCGTGIVG--VFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCSSSCCCCCS--SCEECSSCEECTTTT
T ss_pred             ccccccCCCcEe--EEEEeccccCCCCCC
Confidence            489999999987  789999999999998

>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=97.75  E-value=3.3e-06  Score=47.95  Aligned_cols=35  Identities=29%  Similarity=0.573  Sum_probs=30.3

Q ss_pred             cccccccccccCCCeeEEeCCccccccceeccccccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTG   82 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~   82 (170)
                      .|..|++.|+.  ..+..+++.+||+.||.++|+|++
T Consensus         1 ~C~~C~K~LdS--~~~~eh~~e~YCk~CY~k~fGPkG   35 (65)
T d1b8ta2           1 LCMVCKKNLDS--TTVAVHGDEIYCKSCYGKKYGPKG   35 (65)
T ss_dssp             BCTTTCCBCCS--SSEEEETTEEEEHHHHHHHHSCCC
T ss_pred             CchhcCCccCC--CccccCCCcccchhhhccccCCCc
Confidence            37889999984  558999999999999999999843

>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=97.75  E-value=1.7e-06  Score=41.91  Aligned_cols=34  Identities=50%  Similarity=1.262  Sum_probs=31.1

Q ss_pred             cccccccccccCCCeeEEeCCccccccceecccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG   79 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~   79 (170)
                      +|+.|+..|.+.+...|.+.|.++|+.||.++|+
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            5888999999888999999999999999998875

>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=97.75  E-value=8.2e-06  Score=39.00  Aligned_cols=27  Identities=26%  Similarity=0.666  Sum_probs=23.6

Q ss_pred             ccccccccccCCceEEecCCcccccCcc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      .|++|+++|.. ..++.+.++.||..|.
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            89999999975 4578999999999984

>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=97.74  E-value=5.3e-06  Score=40.65  Aligned_cols=27  Identities=30%  Similarity=0.690  Sum_probs=24.6

Q ss_pred             ccccccccccCCceEEecCCcccccCcc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      .|++|++.|.. +..+.|.++.||..||
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            79999999976 5788999999999998

>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=97.74  E-value=2.1e-06  Score=44.61  Aligned_cols=33  Identities=27%  Similarity=0.603  Sum_probs=29.4

Q ss_pred             cccccccccccCCCeeEEeCCccccccceeccccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT   80 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~   80 (170)
                      +|..|++.|..  ..|...+|.+||+.+|.++|.+
T Consensus         1 rC~~C~~~Ls~--~~yas~~G~lYCkpHf~qLF~~   33 (42)
T d2d8ya2           1 RCSYCNNKLSL--GTYASLHGRIYCKPHFNQLFKS   33 (42)
T ss_dssp             BCTTTCCBCCT--TTCCCSSSCCCCHHHHHHHSCC
T ss_pred             CcCcCCCCccC--CcchhhCCEeccHHHHHHHHHh
Confidence            68999999974  4588999999999999999986

>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=97.74  E-value=8.5e-06  Score=40.66  Aligned_cols=28  Identities=32%  Similarity=0.813  Sum_probs=24.8

Q ss_pred             cccccccccccCCceEEecCCcccccCcc
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      .+|..|++.+.+.| .+.+.|+.||..||
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            48999999999865 55899999999998

>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=97.73  E-value=6.5e-06  Score=43.24  Aligned_cols=28  Identities=29%  Similarity=0.591  Sum_probs=24.8

Q ss_pred             cccccccccccCCceEEecCCcccccCcc
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      .+|..|++.+...|++ .+.|+.||..||
T Consensus        16 ~kC~~C~k~VY~~E~~-~~~g~~~Hk~CF   43 (43)
T d1b8ta3          16 DGCPRCGQAVYAAEKV-IGAGKSWHKSCF   43 (43)
T ss_dssp             EECTTTSCEECSSSCE-EETTEEECTTTC
T ss_pred             CcCccCCCEeeHHHHh-hcCCCccccCCC
Confidence            4899999999987755 788999999998

>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=97.71  E-value=1e-05  Score=38.86  Aligned_cols=34  Identities=24%  Similarity=0.424  Sum_probs=29.8

Q ss_pred             CCCCCcccccccccccccceeEEeCCccccccCc
Q psy7479          12 GASGGLKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        12 ~~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      +...+..+|..|++.++-.+-+...|++||+.||
T Consensus         2 pn~ggg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           2 PNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCCCCCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CccCCCceeccccceEeeeeeeeecCcccccccC
Confidence            3456778999999999988778999999999998

>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=97.68  E-value=8.2e-06  Score=37.18  Aligned_cols=26  Identities=31%  Similarity=0.689  Sum_probs=22.6

Q ss_pred             ccccccccccc-eeEEeCCccccccCc
Q psy7479          20 CASCGKRITER-FLLKALDLFWHEDCL   45 (170)
Q Consensus        20 C~~C~~~I~~~-~~~~~~~~~~H~~Cf   45 (170)
                      |..|.+.|.++ ..+...|..||..||
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            77899999876 458889999999998

>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=97.66  E-value=9.5e-06  Score=41.94  Aligned_cols=27  Identities=33%  Similarity=0.705  Sum_probs=24.9

Q ss_pred             cccccccccccCCceEEecCCcccccCcc
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      |.|.+|+..|.+  .++.++++.+|++||
T Consensus        19 P~CdkCg~GIVG--~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          19 PLCDKCGSGIVG--AVVKARDKYRHPECF   45 (45)
T ss_dssp             CBCTTTCCBCCS--CCEESSSCEECTTTC
T ss_pred             ccccccCCCcEE--EEEEeccccCCCCCC
Confidence            389999999987  789999999999998

>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=97.64  E-value=1.5e-05  Score=38.26  Aligned_cols=31  Identities=19%  Similarity=0.403  Sum_probs=25.9

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHH-hHHHHh
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEY-DYEERQ  142 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~-c~~~~~  142 (170)
                      +|..|++.| ......+++|+|||.. ||..+|
T Consensus         1 kCekC~ktL-~~G~HaEH~gkPYC~~PCY~aLF   32 (33)
T d2cu8a2           1 KCERCSKTL-TPGGHAEHDGKPFCHKPCYATLF   32 (33)
T ss_dssp             BCSSSCCBC-CTTSCEEETTEEECTTTHHHHHS
T ss_pred             Cchhccccc-CCCCccccCCCcCcCcchHHhhc
Confidence            589999999 5557889999999955 998764

>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=97.64  E-value=8.7e-06  Score=37.88  Aligned_cols=26  Identities=31%  Similarity=0.779  Sum_probs=22.2

Q ss_pred             ccccccccccc---eeEEeCCccccccCc
Q psy7479          20 CASCGKRITER---FLLKALDLFWHEDCL   45 (170)
Q Consensus        20 C~~C~~~I~~~---~~~~~~~~~~H~~Cf   45 (170)
                      |..|.+||.+-   ..+...++.||.+||
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            78899999753   568899999999998

>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=97.58  E-value=1.1e-05  Score=36.60  Aligned_cols=26  Identities=31%  Similarity=0.783  Sum_probs=22.3

Q ss_pred             ccccccccccc-eeEEeCCccccccCc
Q psy7479          20 CASCGKRITER-FLLKALDLFWHEDCL   45 (170)
Q Consensus        20 C~~C~~~I~~~-~~~~~~~~~~H~~Cf   45 (170)
                      |..|.+.|.++ ..+...|..||..||
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            77899999876 457889999999998

>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=97.56  E-value=2.1e-05  Score=35.64  Aligned_cols=27  Identities=37%  Similarity=0.659  Sum_probs=23.3

Q ss_pred             cccccccccCCceEEecCCcccccCcc
Q psy7479          84 CAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        84 C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      |..|.+||..+..-+...++.||..||
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            678999997766678899999999998

>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=97.55  E-value=1.6e-05  Score=39.79  Aligned_cols=28  Identities=25%  Similarity=0.677  Sum_probs=24.7

Q ss_pred             cccccccccccCCceEEecCCcccccCcc
Q psy7479          82 GYCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        82 ~~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      .+|..|++.+.+.|. +.+.|+.||..||
T Consensus         9 ~~C~~C~K~VY~~Er-l~a~g~~yHk~CF   36 (36)
T d2co8a2           9 DLCALCGEHLYVLER-LCVNGHFFHRSCF   36 (36)
T ss_dssp             CBCSSSCCBCCTTTB-CCBTTBCCBTTTC
T ss_pred             CcccccCCEEeeeeE-EEecCcEeccccC
Confidence            389999999998764 4899999999998

>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=97.54  E-value=3.7e-05  Score=43.52  Aligned_cols=36  Identities=14%  Similarity=0.314  Sum_probs=30.0

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHHhhhccc
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFANI  147 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~  147 (170)
                      .|..|++.| ....+.++++.+||+.||.++|.....
T Consensus         1 ~C~~C~K~L-dS~~~~eh~~e~YCk~CY~k~fGPkG~   36 (65)
T d1b8ta2           1 LCMVCKKNL-DSTTVAVHGDEIYCKSCYGKKYGPKGK   36 (65)
T ss_dssp             BCTTTCCBC-CSSSEEEETTEEEEHHHHHHHHSCCCC
T ss_pred             CchhcCCcc-CCCccccCCCcccchhhhccccCCCcc
Confidence            388999999 677799999999999999999754333

>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=97.52  E-value=1.5e-05  Score=36.72  Aligned_cols=27  Identities=22%  Similarity=0.693  Sum_probs=23.9

Q ss_pred             ccccccccccccceeEEeCCccccccC
Q psy7479          18 KECASCGKRITERFLLKALDLFWHEDC   44 (170)
Q Consensus        18 ~~C~~C~~~I~~~~~~~~~~~~~H~~C   44 (170)
                      ..|.+|++.++..+.+.-.|+.||..|
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            579999999999877777899999987

>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=97.48  E-value=1.9e-05  Score=37.91  Aligned_cols=32  Identities=28%  Similarity=0.559  Sum_probs=26.0

Q ss_pred             cccccccccccCCCeeEEeCCcccccc-ceecccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKR-DYLRLFG   79 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~-c~~~~~~   79 (170)
                      +|..|++.|..  ....+++|++||.. ||..+|+
T Consensus         1 kCekC~ktL~~--G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTP--GGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCT--TSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCC--CCccccCCCcCcCcchHHhhcC
Confidence            58899999984  34789999999974 9887764

>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=97.48  E-value=2.5e-05  Score=37.48  Aligned_cols=29  Identities=24%  Similarity=0.717  Sum_probs=25.1

Q ss_pred             cccccccccccccc-eeEEeCCccccccCc
Q psy7479          17 LKECASCGKRITER-FLLKALDLFWHEDCL   45 (170)
Q Consensus        17 ~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf   45 (170)
                      ...|.+|++.|... .+..|.++.||..||
T Consensus         2 ~g~Ca~C~~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3           2 SGACSACGQSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             CEECTTTCCEECTTSEEEEETTEEECGGGC
T ss_pred             CcccccccCcCChhHhheecccceeeeccC
Confidence            35799999999776 568899999999998

>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=97.43  E-value=2.6e-05  Score=35.87  Aligned_cols=26  Identities=31%  Similarity=0.631  Sum_probs=22.3

Q ss_pred             ccccccccccCCceEEecCCcccccCc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLEC  109 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~C  109 (170)
                      +|.+|++.+...|.+|.+ |+.||..|
T Consensus         3 ~CpRC~~~VyaAEkviGa-G~~WHk~C   28 (28)
T d1ibia1           3 KCSRCGDSVYAAEKVIGA-GKPWHKNC   28 (28)
T ss_dssp             ECTTTSSEESSSSCEESS-SSEECSSC
T ss_pred             cCcccchhHHHHHHHhcC-CCccccCC
Confidence            799999999988777655 88999987

>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=97.42  E-value=1.7e-05  Score=37.56  Aligned_cols=31  Identities=26%  Similarity=0.540  Sum_probs=26.3

Q ss_pred             ccccccccccCCCeeEEeCCccccccceecccc
Q psy7479          47 CGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG   79 (170)
Q Consensus        47 C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~   79 (170)
                      |-.|.+.|+  ..+...+++.+||+.||-++++
T Consensus         2 C~~C~K~Ld--StTva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNLD--STTVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEEC--SSCCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhccC--cceeeeecceEEehhhccccCC
Confidence            667999997  3678999999999999988764

>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=97.39  E-value=5.3e-05  Score=35.69  Aligned_cols=29  Identities=28%  Similarity=0.744  Sum_probs=26.3

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHH
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEE  140 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~  140 (170)
                      .|..|+..| .|+.|+..+.+.||+.||-.
T Consensus         1 vC~tC~~kL-RGqpFYAvekkayCE~CYi~   29 (32)
T d1x61a2           1 VCSTCRAQL-RGQHFYAVERRAYCEGCYVA   29 (32)
T ss_dssp             BCSSSCCBC-TTSCEEESSSCEEEHHHHHH
T ss_pred             CeeEeCcee-cCCcceEeeccccccceeee
Confidence            488899999 89999999999999999964

>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=97.39  E-value=3.1e-05  Score=39.63  Aligned_cols=28  Identities=32%  Similarity=0.579  Sum_probs=24.9

Q ss_pred             CcccccccccccccceeEEeCCccccccC
Q psy7479          16 GLKECASCGKRITERFLLKALDLFWHEDC   44 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~C   44 (170)
                      .-..|..|++.|.+. ++.|.++.||++|
T Consensus        14 fG~~C~~C~~~ItG~-V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          14 YGTRCFSCDQFIEGE-VVSALGKTYHPDC   41 (41)
T ss_dssp             CCCBCTTTCCBCCSC-CEEETTEEECTTT
T ss_pred             hCcccccccCEeeee-eeEecCcccCCCC
Confidence            446799999999877 8999999999998

>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=97.38  E-value=8.6e-05  Score=35.77  Aligned_cols=32  Identities=28%  Similarity=0.520  Sum_probs=28.6

Q ss_pred             cccccCCcccccCCeEEEeC-CeeccHHhHHHH
Q psy7479         110 FACQQCNHRFCVGDRFYLCD-NKILCEYDYEER  141 (170)
Q Consensus       110 f~C~~C~~~l~~~~~~~~~~-~~~~C~~c~~~~  141 (170)
                      |.|..|+.-|+.++.|.+.+ .++||..||.+.
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy~~~   33 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCHNEV   33 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecchhcc
Confidence            78999999999999999876 799999999875

>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=97.35  E-value=5.4e-05  Score=35.76  Aligned_cols=30  Identities=17%  Similarity=0.511  Sum_probs=26.4

Q ss_pred             cccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479         112 CQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus       112 C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      |-.|.+.| .+.....+++.+||+.||.+++
T Consensus         2 C~~C~K~L-dStTva~h~~eiYCKsCygkky   31 (32)
T d1a7ia2           2 CMVCRKNL-DSTTVAIHDAEVYCKSCYGKKY   31 (32)
T ss_dssp             CSSSCCEE-CSSCCEEETTEEECSHHHHHHC
T ss_pred             chhhhhcc-CcceeeeecceEEehhhccccC
Confidence            67899999 7778889999999999998864

>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=97.34  E-value=3.2e-05  Score=36.39  Aligned_cols=25  Identities=36%  Similarity=0.740  Sum_probs=23.2

Q ss_pred             ccccccccccCCceEEecCCcccccCc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLEC  109 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~C  109 (170)
                      -|..|.+.|.+  .++.+.++.||+.|
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            69999999977  89999999999988

>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=97.33  E-value=3.2e-05  Score=36.36  Aligned_cols=29  Identities=21%  Similarity=0.454  Sum_probs=25.3

Q ss_pred             cccccccccccCCCeeEEeCCccccccceec
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLR   76 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~   76 (170)
                      .|..|.+.|.  +..|...++++||-+||..
T Consensus         1 vC~~C~K~La--g~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKLA--GQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBCT--TSCEEECSSCEEEHHHHHH
T ss_pred             Ccccccchhc--CceeEEecceEEEeeeecc
Confidence            4888999997  6789999999999999864

>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=97.33  E-value=4.8e-05  Score=35.75  Aligned_cols=29  Identities=41%  Similarity=0.772  Sum_probs=25.5

Q ss_pred             CCcccccccccccccceeEEeCCccccccC
Q psy7479          15 GGLKECASCGKRITERFLLKALDLFWHEDC   44 (170)
Q Consensus        15 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~C   44 (170)
                      ++..-|..|.+.|.++ ++.|.++.||+.|
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            3456699999999998 8999999999988

>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=97.33  E-value=3.2e-05  Score=37.03  Aligned_cols=31  Identities=23%  Similarity=0.479  Sum_probs=27.0

Q ss_pred             ccccccccccCCCeeEEeCCccccccceecccc
Q psy7479          47 CGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG   79 (170)
Q Consensus        47 C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~   79 (170)
                      |..|..+|+  ...|..+++..||..||++.|+
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            778999997  4668999999999999998774

>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=97.32  E-value=4e-05  Score=34.87  Aligned_cols=27  Identities=19%  Similarity=0.549  Sum_probs=24.8

Q ss_pred             cccccccccccceeEEeCCccccccCc
Q psy7479          19 ECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        19 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      +|+.|.+.++..+-+..+|++||..||
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            689999999988778999999999997

>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=97.25  E-value=4.5e-05  Score=36.43  Aligned_cols=31  Identities=23%  Similarity=0.509  Sum_probs=26.8

Q ss_pred             ccccccccccCCCeeEEeCCccccccceecccc
Q psy7479          47 CGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG   79 (170)
Q Consensus        47 C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~   79 (170)
                      |..|..+|+  ...|..+++..||..||+++|+
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            778999997  4668999999999999998774

>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=97.18  E-value=8.4e-05  Score=33.56  Aligned_cols=26  Identities=31%  Similarity=0.802  Sum_probs=21.2

Q ss_pred             ccccccccccc-eeEEeCCccccccCc
Q psy7479          20 CASCGKRITER-FLLKALDLFWHEDCL   45 (170)
Q Consensus        20 C~~C~~~I~~~-~~~~~~~~~~H~~Cf   45 (170)
                      |..|.+||..+ .-+-..+++||..||
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            67899999655 346778999999998

>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=97.18  E-value=7.3e-05  Score=35.22  Aligned_cols=29  Identities=24%  Similarity=0.634  Sum_probs=25.5

Q ss_pred             cccccccccccCCCeeEEeCCccccccceec
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLR   76 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~   76 (170)
                      .|..|+..|.  ++.||..+.+.||+.||..
T Consensus         1 vC~tC~~kLR--GqpFYAvekkayCE~CYi~   29 (32)
T d1x61a2           1 VCSTCRAQLR--GQHFYAVERRAYCEGCYVA   29 (32)
T ss_dssp             BCSSSCCBCT--TSCEEESSSCEEEHHHHHH
T ss_pred             CeeEeCceec--CCcceEeeccccccceeee
Confidence            3788999997  6889999999999999964

>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=97.14  E-value=0.00015  Score=35.03  Aligned_cols=31  Identities=23%  Similarity=0.510  Sum_probs=27.2

Q ss_pred             ccccCCcccccCCeEEEe-CCeeccHHhHHHHh
Q psy7479         111 ACQQCNHRFCVGDRFYLC-DNKILCEYDYEERQ  142 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~-~~~~~C~~c~~~~~  142 (170)
                      .|..|++.| .|..|... ++++||..+|.++|
T Consensus         1 tCvvC~~~L-DGvPFtvD~~n~i~Cv~DyHrkf   32 (33)
T d2dloa2           1 TCVVCHRGL-DGIPFTVDATSQIHCIEDFHRKF   32 (33)
T ss_dssp             BCSSSCCBC-TTSCEECCTTCCCEEHHHHHHHT
T ss_pred             CeeEcCccc-CCCcEEEcCCCCEeehhhhhhhc
Confidence            488899999 89999975 69999999999875

>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=97.02  E-value=0.00017  Score=31.99  Aligned_cols=27  Identities=26%  Similarity=0.619  Sum_probs=23.7

Q ss_pred             cccccccccCCceEEecCCcccccCcc
Q psy7479          84 CAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        84 C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      |.+|+..+.++...+.+.++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            678999888877778899999999997

>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=96.95  E-value=6.4e-05  Score=36.41  Aligned_cols=32  Identities=28%  Similarity=0.588  Sum_probs=25.6

Q ss_pred             cccccccccccCCCeeE-EeCCccccccceecccc
Q psy7479          46 KCGCCDCRLGEVGSTLY-QKANLILCKRDYLRLFG   79 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~-~~~~~~yC~~c~~~~~~   79 (170)
                      .|..|++.|+  +-.|. ..++++||-+||+++|+
T Consensus         1 tCvvC~~~LD--GvPFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           1 TCVVCHRGLD--GIPFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             BCSSSCCBCT--TSCEECCTTCCCEEHHHHHHHTT
T ss_pred             CeeEcCcccC--CCcEEEcCCCCEeehhhhhhhcC
Confidence            4778999997  45564 67889999999998874

>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=96.95  E-value=0.00025  Score=33.07  Aligned_cols=29  Identities=10%  Similarity=0.275  Sum_probs=23.6

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHH
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEER  141 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~  141 (170)
                      .|+.|++.|  .....+..|.+||.+|++++
T Consensus         1 nC~~Cgkel--tadArEl~geLyCLpChdKm   29 (31)
T d2cora1           1 NCANCGKEL--TADARELKGELYCLPCHDKM   29 (31)
T ss_dssp             BCSSSCCBC--CTTCEEETTEEECHHHHHTT
T ss_pred             Ccccccccc--chhHHHhcCCEEEEeccccc
Confidence            488999999  33456789999999999875

>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=96.89  E-value=0.00062  Score=31.57  Aligned_cols=31  Identities=16%  Similarity=0.393  Sum_probs=26.5

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHHh
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      .|+.|...+ ....|+......||..|++.+|
T Consensus         1 tcs~ckq~i-gsgsffpkg~d~ycvtche~kf   31 (32)
T d1x63a2           1 TCSNCKQVI-GTGSFFPKGEDFYCVTCHETKF   31 (32)
T ss_dssp             CCSSSCCCC-TTSCEEEETTEEEEHHHHHHHT
T ss_pred             Ccchhhhhc-ccccccCCCCcEEEEEeecccc
Confidence            488999999 5557999999999999999874

>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=96.85  E-value=0.00052  Score=32.11  Aligned_cols=30  Identities=20%  Similarity=0.674  Sum_probs=25.0

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHH
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEER  141 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~  141 (170)
                      .|+.|+..| ....++..++++||+.|...+
T Consensus         1 vC~dCg~NL-KqrG~Ffv~~~lyCE~HAr~R   30 (31)
T d1x64a2           1 VCADCNLNL-KQKGYFFVEGELYCETHARAR   30 (31)
T ss_dssp             CCSSSCCCT-TTSCCEEETTEEECHHHHHHH
T ss_pred             CccccccCh-hhcceEEeccEEeehhhhhcc
Confidence            489999999 667788899999999987643

>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=96.84  E-value=0.00021  Score=34.57  Aligned_cols=27  Identities=22%  Similarity=0.641  Sum_probs=25.0

Q ss_pred             ccccccccccCCceEEecCCcccccCc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLEC  109 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~C  109 (170)
                      .|.+|+..+.+.|.++...|..||..|
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            799999999998999999999999987

>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=96.69  E-value=0.00082  Score=31.64  Aligned_cols=27  Identities=37%  Similarity=0.925  Sum_probs=24.3

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHh
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYD  137 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c  137 (170)
                      .|+.|...|-.|++|...+|.+||+..
T Consensus         1 tC~tC~n~LVPGDRFHyvNG~lfCE~D   27 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYINGSLFCEHD   27 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEETTEEEEGGG
T ss_pred             CcccccccccCCceeEEecCEEEEecC
Confidence            488999999889999999999999865

>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=96.58  E-value=0.00023  Score=33.58  Aligned_cols=32  Identities=63%  Similarity=1.228  Sum_probs=28.4

Q ss_pred             ccccccccccccCCCeeEEeCCccccccceec
Q psy7479          45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLR   76 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~   76 (170)
                      ++|..|+..|++.++..|.+.+.++|+.+|.+
T Consensus         1 LkC~cC~cRLGEVG~tlytk~nliLCkrDYlR   32 (33)
T d1j2oa2           1 LSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR   32 (33)
T ss_dssp             CCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHH
T ss_pred             CccccccccccchhhHHHhhcceeeehhhhhc
Confidence            46888999999888899999999999999865

>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=96.46  E-value=0.00063  Score=30.12  Aligned_cols=26  Identities=31%  Similarity=0.732  Sum_probs=21.7

Q ss_pred             ccccccccccc-eeEEeCCccccccCc
Q psy7479          20 CASCGKRITER-FLLKALDLFWHEDCL   45 (170)
Q Consensus        20 C~~C~~~I~~~-~~~~~~~~~~H~~Cf   45 (170)
                      |.+|++.+.+. .-+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            78899998765 447789999999997

>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=96.37  E-value=0.0012  Score=29.86  Aligned_cols=27  Identities=30%  Similarity=0.666  Sum_probs=22.7

Q ss_pred             ccccccccccCCceEEecCCcccccCcc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      +|..|.+.+.-.|.+ .-.|+.||..||
T Consensus         2 kcg~c~ktvy~aeev-qc~grsfhk~cf   28 (28)
T d1a7ia1           2 KCGACGRTVYHAEEV-QCDGRSFHRCCF   28 (28)
T ss_dssp             BCSSSCCBCSSTTEE-EETTEEEESSSE
T ss_pred             ccccccceEeeeeee-eecCceeccccC
Confidence            799999999876544 788999999997

>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=96.33  E-value=0.00055  Score=32.04  Aligned_cols=28  Identities=14%  Similarity=0.393  Sum_probs=22.9

Q ss_pred             cccccccccccCCCeeEEeCCcccccccee
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYL   75 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~   75 (170)
                      .|+.|+..|.+  ..+|..++++||+.+..
T Consensus         1 vC~dCg~NLKq--rG~Ffv~~~lyCE~HAr   28 (31)
T d1x64a2           1 VCADCNLNLKQ--KGYFFVEGELYCETHAR   28 (31)
T ss_dssp             CCSSSCCCTTT--SCCEEETTEEECHHHHH
T ss_pred             CccccccChhh--cceEEeccEEeehhhhh
Confidence            48999999985  34888999999998754

>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=96.29  E-value=0.00098  Score=32.03  Aligned_cols=28  Identities=21%  Similarity=0.430  Sum_probs=23.7

Q ss_pred             CcccccccccccccceeEEeCCccccccC
Q psy7479          16 GLKECASCGKRITERFLLKALDLFWHEDC   44 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~C   44 (170)
                      ....|.+|.+.|.+- ++.|.+..||++|
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            456799999988865 7888999999998

>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=96.20  E-value=0.0005  Score=32.24  Aligned_cols=30  Identities=23%  Similarity=0.672  Sum_probs=24.5

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHH
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEER  141 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~  141 (170)
                      .|+.|+..| ....++..++++||+.|...+
T Consensus         1 vC~dCg~NL-KqrG~Ffve~~lyCE~HAr~r   30 (31)
T d1x62a1           1 VCTDCGTNL-KQKGHFFVEDQIYCEKHARER   30 (31)
T ss_dssp             SCSSSCCCH-HHHCCEESSSCEECHHHHHHH
T ss_pred             CccccccCh-hhcceEEeccEEehhhhhhhc
Confidence            488999999 556677799999999997654

>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=96.14  E-value=0.0011  Score=31.60  Aligned_cols=27  Identities=30%  Similarity=0.696  Sum_probs=23.1

Q ss_pred             ccccccccccCCceEEecCCcccccCcc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      +|..|.+.+.-.|.+ .-.|+.||+.||
T Consensus         9 kcg~c~ktvy~aeev-qc~g~sfhk~cf   35 (35)
T d1b8ta1           9 KCGVCQKAVYFAEEV-QCEGSSFHKSCF   35 (35)
T ss_dssp             ECTTTCCEECSSCCE-EETTEEECTTTC
T ss_pred             eeccccceEeeeeee-eecCcccccccC
Confidence            899999999876554 678999999998

>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=95.87  E-value=0.0051  Score=29.37  Aligned_cols=32  Identities=28%  Similarity=0.607  Sum_probs=27.0

Q ss_pred             ccccCCcccc-cCCeEEEeCCeeccHHhHHHHh
Q psy7479         111 ACQQCNHRFC-VGDRFYLCDNKILCEYDYEERQ  142 (170)
Q Consensus       111 ~C~~C~~~l~-~~~~~~~~~~~~~C~~c~~~~~  142 (170)
                      +|+-|+..|. .|...+.+.|.++|+.+|.++|
T Consensus         1 KCscC~~~LgeiG~s~ytk~~mILCk~DY~rlF   33 (34)
T d1rutx2           1 KCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF   33 (34)
T ss_dssp             BCTTTCCBHHHHCSEEEEETTEEECHHHHHHHH
T ss_pred             CCcchhcChhhccchheecCCEEEEchhHHHhc
Confidence            4778888885 3778899999999999999875

>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=95.70  E-value=0.002  Score=29.74  Aligned_cols=31  Identities=19%  Similarity=0.470  Sum_probs=25.6

Q ss_pred             cccccccccccCCCeeEEeCCccccccceeccc
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF   78 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~   78 (170)
                      .|+.|...++.  ..|+.+...+||..|.+.+|
T Consensus         1 tcs~ckq~igs--gsffpkg~d~ycvtche~kf   31 (32)
T d1x63a2           1 TCSNCKQVIGT--GSFFPKGEDFYCVTCHETKF   31 (32)
T ss_dssp             CCSSSCCCCTT--SCEEEETTEEEEHHHHHHHT
T ss_pred             Ccchhhhhccc--ccccCCCCcEEEEEeecccc
Confidence            48889999974  45899999999999987665

>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=95.65  E-value=0.005  Score=30.37  Aligned_cols=30  Identities=27%  Similarity=0.549  Sum_probs=26.5

Q ss_pred             cccccCCcccccCCeEEEeCCeeccHHhHH
Q psy7479         110 FACQQCNHRFCVGDRFYLCDNKILCEYDYE  139 (170)
Q Consensus       110 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~  139 (170)
                      |.|+.|.+++..|++.......-+|..|-.
T Consensus         1 FvC~vCr~pFP~GDRVTFnGKeC~CQ~Cs~   30 (40)
T d1v6ga2           1 FVCAVCRLPFPPGDRVTFNGKECMCQKCSL   30 (40)
T ss_dssp             SSCSSSCCCCCSSSCEEEETTEEEEHHHHS
T ss_pred             CcccccCCCCCCCCeEEEcCceeehhhcCC
Confidence            789999999988999998888999999853

>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=95.58  E-value=0.00066  Score=31.84  Aligned_cols=28  Identities=21%  Similarity=0.493  Sum_probs=22.8

Q ss_pred             cccccccccccCCCeeEEeCCcccccccee
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYL   75 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~   75 (170)
                      .|+.|+..|.+.+  +|..++++||+.+..
T Consensus         1 vC~dCg~NLKqrG--~Ffve~~lyCE~HAr   28 (31)
T d1x62a1           1 VCTDCGTNLKQKG--HFFVEDQIYCEKHAR   28 (31)
T ss_dssp             SCSSSCCCHHHHC--CEESSSCEECHHHHH
T ss_pred             CccccccChhhcc--eEEeccEEehhhhhh
Confidence            4889999998544  888999999998754

>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=95.48  E-value=0.0049  Score=28.56  Aligned_cols=28  Identities=36%  Similarity=0.685  Sum_probs=24.4

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHH
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYE  139 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~  139 (170)
                      +|..|-.+| ..+.|...|++++|..|-.
T Consensus         1 RCaKC~hpL-A~E~F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPL-ANETFVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCT-TSSCCEEETTEEECHHHHT
T ss_pred             Cchhhcccc-ccCcccccCCeEeeccccc
Confidence            478889999 7889999999999998853

>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=95.28  E-value=0.0055  Score=29.52  Aligned_cols=31  Identities=26%  Similarity=0.288  Sum_probs=26.1

Q ss_pred             CCCcccccccccccccceeEEeCCccccccCc
Q psy7479          14 SGGLKECASCGKRITERFLLKALDLFWHEDCL   45 (170)
Q Consensus        14 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   45 (170)
                      ..+.-+|.+|...|.+.. +...+..||+..|
T Consensus         5 glGk~vC~KCh~iIdd~p-L~Fr~d~YHp~HF   35 (35)
T d2cora2           5 GLGKYICQKCHAIIDEQP-LIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCCBCTTTCCBCCSCC-CCCSSSCCCTTTS
T ss_pred             chhhHHHHHHHhhhhcCc-ceecCCCCCCCCC
Confidence            456788999999998874 7788999999876

>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=95.26  E-value=0.0033  Score=31.41  Aligned_cols=27  Identities=26%  Similarity=0.559  Sum_probs=11.6

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHh
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYD  137 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c  137 (170)
                      -|++|+..|..|+..|+..+.++-..|
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~IWHP~C   27 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSSIWHPAC   27 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTEEECTTH
T ss_pred             CcchhhccccccceeeecCCceeCCcc
Confidence            034444444444444444444444444

>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=95.12  E-value=0.0048  Score=28.60  Aligned_cols=28  Identities=32%  Similarity=0.557  Sum_probs=23.1

Q ss_pred             cccccccccccCCCeeEEeCCcccccccee
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYL   75 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~   75 (170)
                      +|..|-.+|.  ...|..+|++++|..|..
T Consensus         1 RCaKC~hpLA--~E~F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPLA--NETFVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCTT--SSCCEEETTEEECHHHHT
T ss_pred             Cchhhccccc--cCcccccCCeEeeccccc
Confidence            5888999997  467999999999987743

>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=95.11  E-value=0.0077  Score=28.92  Aligned_cols=29  Identities=17%  Similarity=0.502  Sum_probs=22.6

Q ss_pred             Ccccccccccccccc-eeEEeCCccccccC
Q psy7479          16 GLKECASCGKRITER-FLLKALDLFWHEDC   44 (170)
Q Consensus        16 ~~~~C~~C~~~I~~~-~~~~~~~~~~H~~C   44 (170)
                      ....|.+|+.-..+. .++..+|..||..|
T Consensus         6 ~~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           6 ASATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHHHccCCCchHHhhcCCCccccccC
Confidence            456799998888665 46777899999877

>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=95.02  E-value=0.012  Score=27.42  Aligned_cols=30  Identities=17%  Similarity=0.334  Sum_probs=25.9

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhHHHH
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDYEER  141 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~  141 (170)
                      +|..|...| .+..|.-..|+.+|..|..+.
T Consensus         1 rC~~C~~~L-AD~GFvKnagR~LCrpch~re   30 (32)
T d2d8xa1           1 RCDLCQEVL-ADIGFVKNAGRHLCRPCHNRE   30 (32)
T ss_dssp             BCSSSCCBC-SSSCCEEETTEEECHHHHHHH
T ss_pred             CchHHHhHH-HHhhhhhcccccccchhhhhc
Confidence            588999999 778899888999999998753

>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=94.87  E-value=0.0048  Score=29.72  Aligned_cols=26  Identities=35%  Similarity=0.639  Sum_probs=22.3

Q ss_pred             ccccccccccCCceEEecCCcccccCcc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLECF  110 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf  110 (170)
                      .|..|...|  +|.-+.+++..||+..|
T Consensus        10 vC~KCh~iI--dd~pL~Fr~d~YHp~HF   35 (35)
T d2cora2          10 ICQKCHAII--DEQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             BCTTTCCBC--CSCCCCCSSSCCCTTTS
T ss_pred             HHHHHHhhh--hcCcceecCCCCCCCCC
Confidence            799999988  45778899999999876

>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=94.51  E-value=0.012  Score=27.58  Aligned_cols=27  Identities=26%  Similarity=0.627  Sum_probs=23.1

Q ss_pred             ccccCCcccccCCeEEEeCCeeccHHhH
Q psy7479         111 ACQQCNHRFCVGDRFYLCDNKILCEYDY  138 (170)
Q Consensus       111 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~  138 (170)
                      .|..|+..| .|+.|...+..++|.+|-
T Consensus         1 ncgkcsvsl-vg~gfltq~~~i~c~~cg   27 (34)
T d1x68a2           1 NCGKCSVSL-VGKGFLTQNKEIFCQKCG   27 (34)
T ss_dssp             BCTTTCCBC-SSSCEEEETTEEEETTTT
T ss_pred             CCccceEEE-EeeeeeeccCcEEehhcC
Confidence            367788889 899999999999999884

>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=94.47  E-value=0.0066  Score=28.97  Aligned_cols=31  Identities=10%  Similarity=0.271  Sum_probs=23.6

Q ss_pred             ccccccccccccCCCeeE-EeCCccccccceec
Q psy7479          45 LKCGCCDCRLGEVGSTLY-QKANLILCKRDYLR   76 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~-~~~~~~yC~~c~~~   76 (170)
                      |.|..|+.-|++. ..|. ....++||..||.+
T Consensus         1 F~C~~C~~fIgdg-dsyaLVerskLYCG~Cy~~   32 (34)
T d1x6aa2           1 FACMSCKVIIEDG-DAYALVQHATLYCGKCHNE   32 (34)
T ss_dssp             CBCTTTCCBCCTT-SCEEECSSSCEEEHHHHHH
T ss_pred             CcccccccEEecC-ceEEEEeeceeeeecchhc
Confidence            6789999999864 4554 45568999999865

>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=94.42  E-value=0.019  Score=26.82  Aligned_cols=28  Identities=25%  Similarity=0.553  Sum_probs=22.7

Q ss_pred             cccccccccccCCCeeEEeCCccccccce
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDY   74 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~   74 (170)
                      .|+.|...|- .+..|...+|.+||+.+-
T Consensus         1 tC~tC~n~LV-PGDRFHyvNG~lfCE~D~   28 (33)
T d1rutx4           1 TCSTCRNRLV-PGDRFHYINGSLFCEHDR   28 (33)
T ss_dssp             BCTTTCCBCC-TTCEEEEETTEEEEGGGC
T ss_pred             Cccccccccc-CCceeEEecCEEEEecCC
Confidence            4788888886 467788899999999874

>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=94.36  E-value=0.006  Score=28.24  Aligned_cols=28  Identities=14%  Similarity=0.271  Sum_probs=22.4

Q ss_pred             cccccccccccCCCeeEEeCCccccccceec
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLR   76 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~   76 (170)
                      .|+.|++.|.   ..-....|.+||..|..+
T Consensus         1 nC~~Cgkelt---adArEl~geLyCLpChdK   28 (31)
T d2cora1           1 NCANCGKELT---ADARELKGELYCLPCHDK   28 (31)
T ss_dssp             BCSSSCCBCC---TTCEEETTEEECHHHHHT
T ss_pred             Cccccccccc---hhHHHhcCCEEEEecccc
Confidence            3788999996   346788999999998764

>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=91.64  E-value=0.034  Score=25.89  Aligned_cols=29  Identities=28%  Similarity=0.602  Sum_probs=23.5

Q ss_pred             cccccccccccCCCeeEEeCCccccccceec
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYLR   76 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~   76 (170)
                      +|..|+..|.+.+  |...-|+.+|..|..+
T Consensus         1 rC~~C~~~LAD~G--FvKnagR~LCrpch~r   29 (32)
T d2d8xa1           1 RCDLCQEVLADIG--FVKNAGRHLCRPCHNR   29 (32)
T ss_dssp             BCSSSCCBCSSSC--CEEETTEEECHHHHHH
T ss_pred             CchHHHhHHHHhh--hhhcccccccchhhhh
Confidence            5889999998655  8888899999888643

>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=91.54  E-value=0.048  Score=27.02  Aligned_cols=27  Identities=19%  Similarity=0.547  Sum_probs=20.3

Q ss_pred             ccccccccccCCceEEecCCcccccCc
Q psy7479          83 YCAACTKVIPAFEMVMRAKNNVYHLEC  109 (170)
Q Consensus        83 ~C~~C~~~i~~~~~~~~~~~~~~H~~C  109 (170)
                      .|.+|++.+...|....-.+..||+.|
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~IWHP~C   27 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSSIWHPAC   27 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTEEECTTH
T ss_pred             CcchhhccccccceeeecCCceeCCcc
Confidence            388999988655555556678999976

>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=90.67  E-value=0.075  Score=23.92  Aligned_cols=26  Identities=31%  Similarity=0.636  Sum_probs=21.9

Q ss_pred             cccCCcccccCCeEEEeCCeeccHHhH
Q psy7479         112 CQQCNHRFCVGDRFYLCDNKILCEYDY  138 (170)
Q Consensus       112 C~~C~~~l~~~~~~~~~~~~~~C~~c~  138 (170)
                      |..|...| .|..|....+.++|..|-
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            67788888 888898888899999885

>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=90.55  E-value=0.091  Score=31.53  Aligned_cols=44  Identities=23%  Similarity=0.415  Sum_probs=31.7

Q ss_pred             ccccccccccccCCCeeE-EeCCccccccceecccccccccccccccccC
Q psy7479          45 LKCGCCDCRLGEVGSTLY-QKANLILCKRDYLRLFGTTGYCAACTKVIPA   93 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~-~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~   93 (170)
                      +.|..|...+.   .... ..=|..||..|..+.+..  .|..|+.++..
T Consensus        23 l~C~IC~~~~~---~pv~~~~CgH~fC~~Ci~~~~~~--~CP~Cr~~~~~   67 (97)
T d1jm7b_          23 LRCSRCTNILR---EPVCLGGCEHIFCSNCVSDCIGT--GCPVCYTPAWI   67 (97)
T ss_dssp             TSCSSSCSCCS---SCBCCCSSSCCBCTTTGGGGTTT--BCSSSCCBCSC
T ss_pred             CCCccCCchhh---cCceeCCCCCchhHHHHHHHHhc--cccccCCcCch
Confidence            67888888875   2333 345888999998777765  78888877754

>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=89.19  E-value=0.052  Score=29.25  Aligned_cols=46  Identities=13%  Similarity=0.058  Sum_probs=33.4

Q ss_pred             cccccccccccCCCeeEE-eCCccccccceecccccccccccccccccCC
Q psy7479          46 KCGCCDCRLGEVGSTLYQ-KANLILCKRDYLRLFGTTGYCAACTKVIPAF   94 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~-~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~~   94 (170)
                      .|..|...+.   ..+.. ..|..||.+|..+.+...++|..|++++...
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            5778888775   44555 5799999999766544344899999988653

>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=86.05  E-value=0.099  Score=24.40  Aligned_cols=30  Identities=17%  Similarity=0.342  Sum_probs=20.4

Q ss_pred             cccccccccccCCCeeEEeCCcccccccee
Q psy7479          46 KCGCCDCRLGEVGSTLYQKANLILCKRDYL   75 (170)
Q Consensus        46 ~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~   75 (170)
                      +|..|...|..++-.....||.+||..+..
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hlp   30 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHLP   30 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTCC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeeccC
Confidence            577888888744422345688999987653

>d1bora_ g.44.1.1 (A:) Acute promyelocytic leukaemia proto-oncoprotein PML {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: Acute promyelocytic leukaemia proto-oncoprotein PML
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.82  E-value=0.25  Score=26.44  Aligned_cols=43  Identities=19%  Similarity=0.287  Sum_probs=26.0

Q ss_pred             ccccccccccccCCCeeEEeCCccccccceecccccccccccccccccC
Q psy7479          45 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA   93 (170)
Q Consensus        45 f~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~~~~C~~C~~~i~~   93 (170)
                      +.|..|...+.+   .....=|..||..|..+.. .  +|..|+..|..
T Consensus         7 l~C~IC~~~~~~---p~~lpCgH~fC~~Ci~~~~-~--~CP~Cr~~~~~   49 (56)
T d1bora_           7 LRCQQCQAEAKC---PKLLPCLHTLCSGCLEASG-M--QCPICQAPWPL   49 (56)
T ss_dssp             SSCSSSCSSCBC---CSCSTTSCCSBTTTCSSSS-S--SCSSCCSSSSC
T ss_pred             CCCcccCcccCC---CEEecCCCHHhHHHHHcCC-C--cCcCCCCcccC
Confidence            466666666542   2233456677777765432 2  78888887754

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=81.72  E-value=0.32  Score=27.84  Aligned_cols=49  Identities=6%  Similarity=-0.009  Sum_probs=36.2

Q ss_pred             ccCccccccccccccCCCeeEEeCCccccccceeccccc-ccccccccccccC
Q psy7479          42 EDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT-TGYCAACTKVIPA   93 (170)
Q Consensus        42 ~~Cf~C~~C~~~l~~~~~~~~~~~~~~yC~~c~~~~~~~-~~~C~~C~~~i~~   93 (170)
                      ++-|.|..|...+.   .......|..||..|..+.+.. ...|..|+.+|..
T Consensus         5 P~~l~CpIc~~l~~---dPv~~~cGhtfc~~ci~~~l~~~~~~cP~c~~~l~~   54 (80)
T d2c2la2           5 PDYLCGKISFELMR---EPCITPSGITYDRKDIEEHLQRVGHFNPVTRSPLTQ   54 (80)
T ss_dssp             CSTTBCTTTCSBCS---SEEECSSCCEEETTHHHHHHHHTCSSCTTTCCCCCG
T ss_pred             CccccCcCcCchhh---hhcccCCcCeecHHHHHHHHhcCCccCCCccccccc
Confidence            56789999998886   4567788999999997664321 1268888887754