Psyllid ID: psy4437

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-
Protein Sequence
MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF
Secondary Structure (PSIPRED)
cccccccccccccccccEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEEccccccccccccccccccccccEEccccEEccccccc
Secondary Structure Prediction (SSPRO)
ccccccccccccccHEEEEEccccHcHHHHcHHHHHccccccEEEccccEEEHHHHHHHHcccccccccccccccccEEccccccccHHEEEEEccccccHHHcEHHHHHccccccEEEccccEEEccccc
Coil and Loop (DISEMBL)
mliscagcekpiLDKFLLNVLErtwhadcvrcydchhtlsdkcfsregklfcrndffrspvrfpsgcgvglsssmliscagcekpiLDKFLLNVLErtwhadcvrcydchhtlsdkcfsregklfcrndff
Flexible Loop (DISEMBL)
mliscagcekpILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTlsdkcfsregklfcrndff
Low Complexity Region (SEG)
MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF
Disordered region (IsUnstruct)
**ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCR****
Disordered Region (DISOPRED)
MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF
Disordered Region (DISEMBL)
MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF
Disordered Region (DISPRO)
*LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRND*F
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF
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	131	2.2.26 [Sep-21-2011]
P29674	403	LIM/homeobox protein Lhx1	N/A	N/A	0.885	0.287	0.413	1e-24
P53411	406	LIM/homeobox protein Lhx1	yes	N/A	0.885	0.285	0.406	4e-24
Q9H2C1	402	LIM/homeobox protein Lhx5	yes	N/A	0.870	0.283	0.430	1e-22
P61376	402	LIM/homeobox protein Lhx5	yes	N/A	0.870	0.283	0.430	1e-22
P61375	402	LIM/homeobox protein Lhx5	yes	N/A	0.870	0.283	0.430	1e-22
P37137	402	LIM/homeobox protein Lhx5	N/A	N/A	0.870	0.283	0.416	7e-21
Q90476	405	LIM/homeobox protein Lhx1	no	N/A	0.877	0.283	0.417	1e-20
P52889	399	LIM/homeobox protein Lhx5	no	N/A	0.870	0.285	0.416	3e-20
P48742	406	LIM/homeobox protein Lhx1	no	N/A	0.885	0.285	0.406	7e-20
Q5IS89	406	LIM/homeobox protein Lhx1	N/A	N/A	0.885	0.285	0.406	8e-20

>sp|P29674|LHX1_XENLA LIM/homeobox protein Lhx1 OS=Xenopus laevis GN=lhx1 PE=1 SV=1

 Score =  111 bits (278), Expect = 1e-24,   Method: Composition-based stats.
 Identities = 55/133 (41%), Positives = 76/133 (57%), Gaps = 17/133 (12%)

Query: 2   LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPV 61
           ++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   L++KCFSREGKL+C+NDFFR   
Sbjct: 1   MVHCAGCERPILDRFLLNVLDRAWHVKCVQCCECKCNLTEKCFSREGKLYCKNDFFRRFG 60

Query: 62  RFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS---DKCF 118
              +GC  G+S S L+  A                + +H +C  C  C+  LS   +   
Sbjct: 61  TKCAGCAQGISPSDLVRRA--------------RSKVFHLNCFTCMMCNKQLSTGEELYI 106

Query: 119 SREGKLFCRNDFF 131
             E K  C+ D+ 
Sbjct: 107 IDENKFVCKEDYL 119

Involved in the establishment of the body plan via the Spemann organizer during gastrulation. Transcriptional activator required to induce organizer gene expression downstream of siamois. Promotes head formation by binding to 5'-TAAT'-3' elements in the promoters of head organizer genes cer1 and gsc to stimulate expression. Binds as a complex with siamois and mix-A/mix.1 to the cer1 promoter, and with ldb1 and otx2 to the gsc promoter. Also involved in neural induction via the organizer, including a role in notochord formation. Acts synergistically with ldb1 and ssbp in subsequent axis formation. Involved in kidney development, acting synergistically with pax8 to establish the pronephric primordium in late gastrulae/early neurulae and with pax2 during pronephric morphogenesis in tailbud stages. Has a later role in mediating the activity of inhibitors of ventralization.
Xenopus laevis (taxid: 8355)

>sp|P53411|LHX1_CHICK LIM/homeobox protein Lhx1 OS=Gallus gallus GN=LHX1 PE=2 SV=1

 Score =  109 bits (273), Expect = 4e-24,   Method: Composition-based stats.
 Identities = 54/133 (40%), Positives = 76/133 (57%), Gaps = 17/133 (12%)

Query: 2   LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPV 61
           ++ CAGC++PILD+FLLNVL+R WH  CV+C +C   L++KCFSREGKL+C+NDFFR   
Sbjct: 1   MVHCAGCKRPILDRFLLNVLDRAWHVKCVQCCECKCNLTEKCFSREGKLYCKNDFFRCFG 60

Query: 62  RFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS---DKCF 118
              +GC  G+S S L+  A                + +H +C  C  C+  LS   +   
Sbjct: 61  TKCAGCAQGISPSDLVRRA--------------RSKVFHLNCFTCMMCNKQLSTGEELYI 106

Query: 119 SREGKLFCRNDFF 131
             E K  C+ D+ 
Sbjct: 107 IDENKFVCKEDYL 119

Transcriptional factor that defines subclasses of motoneurons that segregate into columns in the spinal cord and select distinct axon pathways. Acts in conjunction with ISL-2.

Gallus gallus (taxid: 9031)

>sp|Q9H2C1|LHX5_HUMAN LIM/homeobox protein Lhx5 OS=Homo sapiens GN=LHX5 PE=2 SV=1

 Score =  105 bits (261), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 59/137 (43%), Positives = 80/137 (58%), Gaps = 23/137 (16%)

Query: 1   MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
           M++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   LS+KCFSREGKL+C+NDFFR  
Sbjct: 1   MMVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECKTNLSEKCFSREGKLYCKNDFFR-- 58

Query: 61  VRFPS---GCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--- 114
            RF +   GC  G+S S L+  A                + +H +C  C  C+  LS   
Sbjct: 59  -RFGTKCAGCAQGISPSDLVRKA--------------RSKVFHLNCFTCMVCNKQLSTGE 103

Query: 115 DKCFSREGKLFCRNDFF 131
           +     E K  C++D+ 
Sbjct: 104 ELYVIDENKFVCKDDYL 120

Plays an essential role in the regulation of neuronal differentiation and migration during development of the central nervous system.

Homo sapiens (taxid: 9606)

>sp|P61376|LHX5_RAT LIM/homeobox protein Lhx5 OS=Rattus norvegicus GN=Lhx5 PE=2 SV=1

 Score =  104 bits (260), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 59/137 (43%), Positives = 80/137 (58%), Gaps = 23/137 (16%)

Query: 1   MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
           M++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   LS+KCFSREGKL+C+NDFFR  
Sbjct: 1   MMVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECKTNLSEKCFSREGKLYCKNDFFR-- 58

Query: 61  VRFPS---GCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--- 114
            RF +   GC  G+S S L+  A                + +H +C  C  C+  LS   
Sbjct: 59  -RFGTKCAGCAQGISPSDLVRKA--------------RSKVFHLNCFTCMVCNKQLSTGE 103

Query: 115 DKCFSREGKLFCRNDFF 131
           +     E K  C++D+ 
Sbjct: 104 ELYVIDENKFVCKDDYL 120

Plays an essential role in the regulation of neuronal differentiation and migration during development of the central nervous system.

Rattus norvegicus (taxid: 10116)

>sp|P61375|LHX5_MOUSE LIM/homeobox protein Lhx5 OS=Mus musculus GN=Lhx5 PE=2 SV=1

 Score =  104 bits (260), Expect = 1e-22,   Method: Compositional matrix adjust.
 Identities = 59/137 (43%), Positives = 80/137 (58%), Gaps = 23/137 (16%)

Query: 1   MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
           M++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   LS+KCFSREGKL+C+NDFFR  
Sbjct: 1   MMVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECKTNLSEKCFSREGKLYCKNDFFR-- 58

Query: 61  VRFPS---GCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--- 114
            RF +   GC  G+S S L+  A                + +H +C  C  C+  LS   
Sbjct: 59  -RFGTKCAGCAQGISPSDLVRKA--------------RSKVFHLNCFTCMVCNKQLSTGE 103

Query: 115 DKCFSREGKLFCRNDFF 131
           +     E K  C++D+ 
Sbjct: 104 ELYVIDENKFVCKDDYL 120

Plays an essential role in the regulation of neuronal differentiation and migration during development of the central nervous system.

Mus musculus (taxid: 10090)

>sp|P37137|LHX5_XENLA LIM/homeobox protein Lhx5 OS=Xenopus laevis GN=lhx5 PE=1 SV=2

 Score = 99.4 bits (246), Expect = 7e-21,   Method: Compositional matrix adjust.
 Identities = 57/137 (41%), Positives = 78/137 (56%), Gaps = 23/137 (16%)

Query: 1   MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
           M+  CAGCE+PILD+FLLNVL+R WH  CV+C +C   L++KCFSREGKL+C+ DFFR  
Sbjct: 1   MMAHCAGCERPILDRFLLNVLDRAWHVKCVQCCECKCNLTEKCFSREGKLYCKTDFFR-- 58

Query: 61  VRFPS---GCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--- 114
            RF +   GC +G+S S L+  A                + +H +C  C  C+  LS   
Sbjct: 59  -RFGTKCAGCSLGISPSDLVRKA--------------RNKVFHLNCFTCMVCNKQLSTGE 103

Query: 115 DKCFSREGKLFCRNDFF 131
           +     E K  C+ D+ 
Sbjct: 104 ELYIIDENKFVCKEDYI 120

Probably involved in the patterning of the nervous system, in particular in the early specification of the diencephalon.

Xenopus laevis (taxid: 8355)

>sp|Q90476|LHX1_DANRE LIM/homeobox protein Lhx1 OS=Danio rerio GN=lhx1a PE=2 SV=1

 Score = 98.2 bits (243), Expect = 1e-20,   Method: Compositional matrix adjust.
 Identities = 56/134 (41%), Positives = 77/134 (57%), Gaps = 19/134 (14%)

Query: 2   LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPV 61
           ++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   L++KCFSREGKL+C+NDFFR   
Sbjct: 1   MVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECKCNLTEKCFSREGKLYCKNDFFR--- 57

Query: 62  RFPSGCGVGLSSSMLISCAGCEKPILDKFLL-NVLERTWHADCVRCYDCHHTLS---DKC 117
           RF               CAGC + I    L+     + +H +C  C  C+  LS   +  
Sbjct: 58  RF------------GTKCAGCAQGISPNDLVRRARSKVFHLNCFTCMMCNKQLSTGEELY 105

Query: 118 FSREGKLFCRNDFF 131
              E K  C++D+ 
Sbjct: 106 IIDENKFVCKDDYL 119

Seems to play a role in dorsal axis formation.

Danio rerio (taxid: 7955)

>sp|P52889|LHX5_DANRE LIM/homeobox protein Lhx5 OS=Danio rerio GN=lhx5 PE=2 SV=1

 Score = 96.7 bits (239), Expect = 3e-20,   Method: Compositional matrix adjust.
 Identities = 57/137 (41%), Positives = 80/137 (58%), Gaps = 23/137 (16%)

Query: 1   MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
           M++ CAGCE+PILD+FLLNVL+R WHA CV+C +C+  L++KCFSR+GKL+C+ DFFR  
Sbjct: 1   MMVHCAGCERPILDRFLLNVLDRAWHAKCVQCCECNCNLTEKCFSRDGKLYCKIDFFR-- 58

Query: 61  VRFPS---GCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--- 114
            RF +   GC  G+S S L+  A                + +H +C  C  C+  LS   
Sbjct: 59  -RFGTKCAGCLQGISPSDLVRRA--------------RSKVFHLNCFTCMVCNKQLSTGE 103

Query: 115 DKCFSREGKLFCRNDFF 131
           +     E K  C+ D+ 
Sbjct: 104 ELYVIDENKFVCKEDYL 120

Probably involved in the patterning of the nervous system, in particular in the early specification of the diencephalon.

Danio rerio (taxid: 7955)

>sp|P48742|LHX1_HUMAN LIM/homeobox protein Lhx1 OS=Homo sapiens GN=LHX1 PE=1 SV=2

 Score = 95.5 bits (236), Expect = 7e-20,   Method: Compositional matrix adjust.
 Identities = 54/133 (40%), Positives = 76/133 (57%), Gaps = 17/133 (12%)

Query: 2   LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPV 61
           ++ CAGC++PILD+FLLNVL+R WH  CV+C +C   L++KCFSREGKL+C+NDFFR   
Sbjct: 1   MVHCAGCKRPILDRFLLNVLDRAWHVKCVQCCECKCNLTEKCFSREGKLYCKNDFFRCFG 60

Query: 62  RFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS---DKCF 118
              +GC  G+S S L+  A                + +H +C  C  C+  LS   +   
Sbjct: 61  TKCAGCAQGISPSDLVRRA--------------RSKVFHLNCFTCMMCNKQLSTGEELYI 106

Query: 119 SREGKLFCRNDFF 131
             E K  C+ D+ 
Sbjct: 107 IDENKFVCKEDYL 119

Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis.

Homo sapiens (taxid: 9606)

>sp|Q5IS89|LHX1_SAIBB LIM/homeobox protein Lhx1 OS=Saimiri boliviensis boliviensis GN=LHX1 PE=2 SV=1

 Score = 95.5 bits (236), Expect = 8e-20,   Method: Compositional matrix adjust.
 Identities = 54/133 (40%), Positives = 76/133 (57%), Gaps = 17/133 (12%)

Query: 2   LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPV 61
           ++ CAGC++PILD+FLLNVL+R WH  CV+C +C   L++KCFSREGKL+C+NDFFR   
Sbjct: 1   MVHCAGCKRPILDRFLLNVLDRAWHVKCVQCCECKCNLTEKCFSREGKLYCKNDFFRCFG 60

Query: 62  RFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS---DKCF 118
              +GC  G+S S L+  A                + +H +C  C  C+  LS   +   
Sbjct: 61  TKCAGCAQGISPSDLVRRA--------------RSKVFHLNCFTCMMCNKQLSTGEELYI 106

Query: 119 SREGKLFCRNDFF 131
             E K  C+ D+ 
Sbjct: 107 IDENKFVCKEDYL 119

Potential transcription factor. May play a role in early mesoderm formation and later in lateral mesoderm differentiation and neurogenesis.

Saimiri boliviensis boliviensis (taxid: 39432)

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	131
270009219	511	lim1 [Tribolium castaneum]	0.893	0.228	0.507	1e-30
189238568	497	PREDICTED: similar to LIM homeobox 1b [T	0.893	0.235	0.507	2e-30
328705917	555	PREDICTED: LIM/homeobox protein Lhx5-lik	0.885	0.209	0.421	5e-26
195456664	506	GK16904 [Drosophila willistoni] gi|19417	0.862	0.223	0.469	5e-25
198469300	528	GA10943 [Drosophila pseudoobscura pseudo	0.862	0.214	0.469	6e-25
195480019	500	GE17432 [Drosophila yakuba] gi|194188630	0.862	0.226	0.469	6e-25
194890894	504	GG19023 [Drosophila erecta] gi|190649051	0.862	0.224	0.469	6e-25
18858205	505	Lim1, isoform A [Drosophila melanogaster	0.862	0.223	0.469	6e-25
194769270	500	GF19125 [Drosophila ananassae] gi|190618	0.862	0.226	0.469	6e-25
195400977	498	GJ15180 [Drosophila virilis] gi|19414174	0.862	0.226	0.469	6e-25

>gi|270009219|gb|EFA05667.1| lim1 [Tribolium castaneum]

 Score =  137 bits (345), Expect = 1e-30,   Method: Composition-based stats.
 Identities = 68/134 (50%), Positives = 82/134 (61%), Gaps = 17/134 (12%)

Query: 1   MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
           MLISCA C+KPILDKFLLNVLERTWHADCVRC+DCH  L+DKCFSRE KLFCRNDFFR  
Sbjct: 74  MLISCAACDKPILDKFLLNVLERTWHADCVRCFDCHAPLTDKCFSRENKLFCRNDFFRRY 133

Query: 61  VRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS---DKC 117
                GCG G+S S L+  A               ++ +H +C  C  C   LS   +  
Sbjct: 134 GTKCGGCGQGISPSDLVRKA--------------RDKVFHLNCFTCLVCRKQLSTGEELY 179

Query: 118 FSREGKLFCRNDFF 131
              + K  C++D+ 
Sbjct: 180 VLDDNKFICKDDYL 193

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|189238568|ref|XP_969484.2| PREDICTED: similar to LIM homeobox 1b [Tribolium castaneum]

 Score =  137 bits (344), Expect = 2e-30,   Method: Composition-based stats.
 Identities = 68/134 (50%), Positives = 82/134 (61%), Gaps = 17/134 (12%)

Query: 1   MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
           MLISCA C+KPILDKFLLNVLERTWHADCVRC+DCH  L+DKCFSRE KLFCRNDFFR  
Sbjct: 150 MLISCAACDKPILDKFLLNVLERTWHADCVRCFDCHAPLTDKCFSRENKLFCRNDFFRRY 209

Query: 61  VRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS---DKC 117
                GCG G+S S L+  A               ++ +H +C  C  C   LS   +  
Sbjct: 210 GTKCGGCGQGISPSDLVRKA--------------RDKVFHLNCFTCLVCRKQLSTGEELY 255

Query: 118 FSREGKLFCRNDFF 131
              + K  C++D+ 
Sbjct: 256 VLDDNKFICKDDYL 269

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328705917|ref|XP_001945631.2| PREDICTED: LIM/homeobox protein Lhx5-like [Acyrthosiphon pisum]

 Score =  122 bits (306), Expect = 5e-26,   Method: Composition-based stats.
 Identities = 56/133 (42%), Positives = 84/133 (63%), Gaps = 17/133 (12%)

Query: 1   MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
           +++SCAGC+KPI+DKFLLNVL+R WHA+CV+C DCH TLSDKC+SR+GK+ C+ DF+R  
Sbjct: 113 LMMSCAGCDKPIMDKFLLNVLDRAWHAECVKCADCHGTLSDKCYSRDGKILCKPDFYRRY 172

Query: 61  VRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCF 118
            +  +GC  G+S + L+  A               ++ +H +C  C  C   LS  ++ +
Sbjct: 173 GKKCNGCAQGISPTDLVRKA--------------RDKVFHLNCFTCMICRKQLSTGEELY 218

Query: 119 SRE-GKLFCRNDF 130
             E  K  C++D+
Sbjct: 219 VLEDNKFICKDDY 231

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195456664|ref|XP_002075233.1| GK16904 [Drosophila willistoni] gi|194171318|gb|EDW86219.1| GK16904 [Drosophila willistoni]

 Score =  119 bits (297), Expect = 5e-25,   Method: Composition-based stats.
 Identities = 61/130 (46%), Positives = 78/130 (60%), Gaps = 17/130 (13%)

Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
           CAGC KPILDKFLLNVLER WHA CVRC +C   L+DKCFSRE KL+CRNDFFR      
Sbjct: 27  CAGCNKPILDKFLLNVLERAWHASCVRCCECLQPLTDKCFSRESKLYCRNDFFRRYGTKC 86

Query: 65  SGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFS-RE 121
           SGCG G++ S L+      KP          ++ +H +C  C  C   LS  ++ +   +
Sbjct: 87  SGCGQGIAPSDLV-----RKP---------RDKVFHLNCFTCCICRKQLSTGEQLYVLDD 132

Query: 122 GKLFCRNDFF 131
            K  C++D+ 
Sbjct: 133 NKFICKDDYL 142

Source: Drosophila willistoni

Species: Drosophila willistoni

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|198469300|ref|XP_001354984.2| GA10943 [Drosophila pseudoobscura pseudoobscura] gi|198146805|gb|EAL32040.2| GA10943 [Drosophila pseudoobscura pseudoobscura]

 Score =  119 bits (297), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 61/130 (46%), Positives = 78/130 (60%), Gaps = 17/130 (13%)

Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
           CAGC KPILDKFLLNVLER WHA CVRC +C   L+DKCFSRE KL+CRNDFFR      
Sbjct: 27  CAGCNKPILDKFLLNVLERAWHASCVRCCECLQPLTDKCFSRESKLYCRNDFFRRYGTKC 86

Query: 65  SGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFS-RE 121
           SGCG G++ S L+      KP          ++ +H +C  C  C   LS  ++ +   +
Sbjct: 87  SGCGQGIAPSDLV-----RKP---------RDKVFHLNCFTCCICRKQLSTGEQLYVLDD 132

Query: 122 GKLFCRNDFF 131
            K  C++D+ 
Sbjct: 133 NKFICKDDYL 142

Source: Drosophila pseudoobscura pseudoobscura

Species: Drosophila pseudoobscura

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195480019|ref|XP_002101106.1| GE17432 [Drosophila yakuba] gi|194188630|gb|EDX02214.1| GE17432 [Drosophila yakuba]

 Score =  119 bits (297), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 61/130 (46%), Positives = 78/130 (60%), Gaps = 17/130 (13%)

Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
           CAGC KPILDKFLLNVLER WHA CVRC +C   L+DKCFSRE KL+CRNDFFR      
Sbjct: 27  CAGCNKPILDKFLLNVLERAWHASCVRCCECLQPLTDKCFSRESKLYCRNDFFRRYGTKC 86

Query: 65  SGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFS-RE 121
           SGCG G++ S L+      KP          ++ +H +C  C  C   LS  ++ +   +
Sbjct: 87  SGCGQGIAPSDLV-----RKP---------RDKVFHLNCFTCCICRKQLSTGEQLYVLDD 132

Query: 122 GKLFCRNDFF 131
            K  C++D+ 
Sbjct: 133 NKFICKDDYL 142

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194890894|ref|XP_001977402.1| GG19023 [Drosophila erecta] gi|190649051|gb|EDV46329.1| GG19023 [Drosophila erecta]

 Score =  119 bits (297), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 61/130 (46%), Positives = 78/130 (60%), Gaps = 17/130 (13%)

Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
           CAGC KPILDKFLLNVLER WHA CVRC +C   L+DKCFSRE KL+CRNDFFR      
Sbjct: 27  CAGCNKPILDKFLLNVLERAWHASCVRCCECLQPLTDKCFSRESKLYCRNDFFRRYGTKC 86

Query: 65  SGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFS-RE 121
           SGCG G++ S L+      KP          ++ +H +C  C  C   LS  ++ +   +
Sbjct: 87  SGCGQGIAPSDLV-----RKP---------RDKVFHLNCFTCCICRKQLSTGEQLYVLDD 132

Query: 122 GKLFCRNDFF 131
            K  C++D+ 
Sbjct: 133 NKFICKDDYL 142

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|18858205|ref|NP_572505.1| Lim1, isoform A [Drosophila melanogaster] gi|39841014|gb|AAD55417.2|AF181631_1 GH04929p [Drosophila melanogaster] gi|6252420|dbj|BAA86224.1| dLim1 [Drosophila melanogaster] gi|22833027|gb|AAF46413.2| Lim1, isoform A [Drosophila melanogaster] gi|220943666|gb|ACL84376.1| Lim1-PA [synthetic construct] gi|220953602|gb|ACL89344.1| Lim1-PA [synthetic construct]

 Score =  119 bits (297), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 61/130 (46%), Positives = 78/130 (60%), Gaps = 17/130 (13%)

Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
           CAGC KPILDKFLLNVLER WHA CVRC +C   L+DKCFSRE KL+CRNDFFR      
Sbjct: 27  CAGCNKPILDKFLLNVLERAWHASCVRCCECLQPLTDKCFSRESKLYCRNDFFRRYGTKC 86

Query: 65  SGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFS-RE 121
           SGCG G++ S L+      KP          ++ +H +C  C  C   LS  ++ +   +
Sbjct: 87  SGCGQGIAPSDLV-----RKP---------RDKVFHLNCFTCCICRKQLSTGEQLYVLDD 132

Query: 122 GKLFCRNDFF 131
            K  C++D+ 
Sbjct: 133 NKFICKDDYL 142

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194769270|ref|XP_001966729.1| GF19125 [Drosophila ananassae] gi|190618250|gb|EDV33774.1| GF19125 [Drosophila ananassae]

 Score =  118 bits (296), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 61/130 (46%), Positives = 78/130 (60%), Gaps = 17/130 (13%)

Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
           CAGC KPILDKFLLNVLER WHA CVRC +C   L+DKCFSRE KL+CRNDFFR      
Sbjct: 27  CAGCNKPILDKFLLNVLERAWHASCVRCCECLQPLTDKCFSRESKLYCRNDFFRRYGTKC 86

Query: 65  SGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFS-RE 121
           SGCG G++ S L+      KP          ++ +H +C  C  C   LS  ++ +   +
Sbjct: 87  SGCGQGIAPSDLV-----RKP---------RDKVFHLNCFTCCICRKQLSTGEQLYVLDD 132

Query: 122 GKLFCRNDFF 131
            K  C++D+ 
Sbjct: 133 NKFICKDDYL 142

Source: Drosophila ananassae

Species: Drosophila ananassae

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195400977|ref|XP_002059092.1| GJ15180 [Drosophila virilis] gi|194141744|gb|EDW58161.1| GJ15180 [Drosophila virilis]

 Score =  118 bits (296), Expect = 6e-25,   Method: Composition-based stats.
 Identities = 61/130 (46%), Positives = 78/130 (60%), Gaps = 17/130 (13%)

Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
           CAGC KPILDKFLLNVLER WHA CVRC +C   L+DKCFSRE KL+CRNDFFR      
Sbjct: 27  CAGCNKPILDKFLLNVLERAWHASCVRCCECLQPLTDKCFSRESKLYCRNDFFRRYGTKC 86

Query: 65  SGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFS-RE 121
           SGCG G++ S L+      KP          ++ +H +C  C  C   LS  ++ +   +
Sbjct: 87  SGCGQGIAPSDLV-----RKP---------RDKVFHLNCFTCCICRKQLSTGEQLYVLDD 132

Query: 122 GKLFCRNDFF 131
            K  C++D+ 
Sbjct: 133 NKFICKDDYL 142

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	131
FB|FBgn0026411	505	Lim1 [Drosophila melanogaster	0.854	0.221	0.472	2.1e-25
UNIPROTKB|A6QQY6	402	LHX5 "Uncharacterized protein"	0.877	0.286	0.432	5.9e-25
UNIPROTKB|E2RRP3	402	LHX5 "Uncharacterized protein"	0.877	0.286	0.432	5.9e-25
UNIPROTKB|Q9H2C1	402	LHX5 "LIM/homeobox protein Lhx	0.877	0.286	0.432	5.9e-25
MGI|MGI:107792	402	Lhx5 "LIM homeobox protein 5"	0.877	0.286	0.432	5.9e-25
RGD|71079	402	Lhx5 "LIM homeobox 5" [Rattus	0.877	0.286	0.432	5.9e-25
UNIPROTKB|F1RKD0	401	LHX5 "Uncharacterized protein"	0.870	0.284	0.432	3.3e-24
UNIPROTKB|B7ZP59	403	lhx1 "Homeobox protein" [Xenop	0.870	0.282	0.421	5.3e-24
UNIPROTKB|P29674	403	lhx1 "LIM/homeobox protein Lhx	0.870	0.282	0.421	5.3e-24
ZFIN|ZDB-GENE-980526-347	405	lhx1a "LIM homeobox 1a" [Danio	0.870	0.281	0.421	5.3e-24

FB|FBgn0026411 Lim1 [Drosophila melanogaster (taxid:7227)]

 Score = 293 (108.2 bits), Expect = 2.1e-25, P = 2.1e-25
 Identities = 61/129 (47%), Positives = 78/129 (60%)

Query:     5 CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
             CAGC KPILDKFLLNVLER WHA CVRC +C   L+DKCFSRE KL+CRNDFFR      
Sbjct:    27 CAGCNKPILDKFLLNVLERAWHASCVRCCECLQPLTDKCFSRESKLYCRNDFFRRYGTKC 86

Query:    65 SGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFSRE- 121
             SGCG G++ S L+      KP          ++ +H +C  C  C   LS  ++ +  + 
Sbjct:    87 SGCGQGIAPSDLV-----RKP---------RDKVFHLNCFTCCICRKQLSTGEQLYVLDD 132

Query:   122 GKLFCRNDF 130
              K  C++D+
Sbjct:   133 NKFICKDDY 141

GO:0006355 "regulation of transcription, DNA-dependent" evidence=ISS

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0007480 "imaginal disc-derived leg morphogenesis" evidence=IMP

GO:0007479 "leg disc proximal/distal pattern formation" evidence=IMP

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=IGI

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IMP

UNIPROTKB|A6QQY6 LHX5 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 284 (105.0 bits), Expect = 5.9e-25, P = 5.9e-25
 Identities = 58/134 (43%), Positives = 81/134 (60%)

Query:     1 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
             M++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   LS+KCFSREGKL+C+NDFFR  
Sbjct:     1 MMVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECKTNLSEKCFSREGKLYCKNDFFR-- 58

Query:    61 VRFPSGCGVGLSSSMLISCAGCEKPILDKFLLN-VLERTWHADCVRCYDCHHTLS--DKC 117
              RF +             CAGC + I    L+     + +H +C  C  C+  LS  ++ 
Sbjct:    59 -RFGT------------KCAGCAQGISPSDLVRKARSKVFHLNCFTCMVCNKQLSTGEEL 105

Query:   118 FS-REGKLFCRNDF 130
             +   E K  C++D+
Sbjct:   106 YVIDENKFVCKDDY 119

GO:0005634 "nucleus" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IEA

GO:0021937 "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation" evidence=IEA

GO:0021879 "forebrain neuron differentiation" evidence=IEA

GO:0021846 "cell proliferation in forebrain" evidence=IEA

GO:0021766 "hippocampus development" evidence=IEA

GO:0021702 "cerebellar Purkinje cell differentiation" evidence=IEA

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

UNIPROTKB|E2RRP3 LHX5 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 284 (105.0 bits), Expect = 5.9e-25, P = 5.9e-25
 Identities = 58/134 (43%), Positives = 81/134 (60%)

Query:     1 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
             M++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   LS+KCFSREGKL+C+NDFFR  
Sbjct:     1 MMVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECKTNLSEKCFSREGKLYCKNDFFR-- 58

Query:    61 VRFPSGCGVGLSSSMLISCAGCEKPILDKFLLN-VLERTWHADCVRCYDCHHTLS--DKC 117
              RF +             CAGC + I    L+     + +H +C  C  C+  LS  ++ 
Sbjct:    59 -RFGT------------KCAGCAQGISPSDLVRKARSKVFHLNCFTCMVCNKQLSTGEEL 105

Query:   118 FS-REGKLFCRNDF 130
             +   E K  C++D+
Sbjct:   106 YVIDENKFVCKDDY 119

GO:0005634 "nucleus" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IEA

GO:0021937 "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation" evidence=IEA

GO:0021879 "forebrain neuron differentiation" evidence=IEA

GO:0021846 "cell proliferation in forebrain" evidence=IEA

GO:0021766 "hippocampus development" evidence=IEA

GO:0021702 "cerebellar Purkinje cell differentiation" evidence=IEA

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

UNIPROTKB|Q9H2C1 LHX5 "LIM/homeobox protein Lhx5" [Homo sapiens (taxid:9606)]

 Score = 284 (105.0 bits), Expect = 5.9e-25, P = 5.9e-25
 Identities = 58/134 (43%), Positives = 81/134 (60%)

Query:     1 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
             M++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   LS+KCFSREGKL+C+NDFFR  
Sbjct:     1 MMVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECKTNLSEKCFSREGKLYCKNDFFR-- 58

Query:    61 VRFPSGCGVGLSSSMLISCAGCEKPILDKFLLN-VLERTWHADCVRCYDCHHTLS--DKC 117
              RF +             CAGC + I    L+     + +H +C  C  C+  LS  ++ 
Sbjct:    59 -RFGT------------KCAGCAQGISPSDLVRKARSKVFHLNCFTCMVCNKQLSTGEEL 105

Query:   118 FS-REGKLFCRNDF 130
             +   E K  C++D+
Sbjct:   106 YVIDENKFVCKDDY 119

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA

GO:0021702 "cerebellar Purkinje cell differentiation" evidence=IEA

GO:0021766 "hippocampus development" evidence=IEA

GO:0021846 "cell proliferation in forebrain" evidence=IEA

GO:0021879 "forebrain neuron differentiation" evidence=IEA

GO:0021937 "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

MGI|MGI:107792 Lhx5 "LIM homeobox protein 5" [Mus musculus (taxid:10090)]

 Score = 284 (105.0 bits), Expect = 5.9e-25, P = 5.9e-25
 Identities = 58/134 (43%), Positives = 81/134 (60%)

Query:     1 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
             M++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   LS+KCFSREGKL+C+NDFFR  
Sbjct:     1 MMVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECKTNLSEKCFSREGKLYCKNDFFR-- 58

Query:    61 VRFPSGCGVGLSSSMLISCAGCEKPILDKFLLN-VLERTWHADCVRCYDCHHTLS--DKC 117
              RF +             CAGC + I    L+     + +H +C  C  C+  LS  ++ 
Sbjct:    59 -RFGT------------KCAGCAQGISPSDLVRKARSKVFHLNCFTCMVCNKQLSTGEEL 105

Query:   118 FS-REGKLFCRNDF 130
             +   E K  C++D+
Sbjct:   106 YVIDENKFVCKDDY 119

GO:0003677 "DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0007267 "cell-cell signaling" evidence=IGI

GO:0008270 "zinc ion binding" evidence=IEA

GO:0021527 "spinal cord association neuron differentiation" evidence=IGI

GO:0021549 "cerebellum development" evidence=IGI

GO:0021702 "cerebellar Purkinje cell differentiation" evidence=IGI

GO:0021766 "hippocampus development" evidence=IMP

GO:0021846 "cell proliferation in forebrain" evidence=IMP

GO:0021879 "forebrain neuron differentiation" evidence=IMP

GO:0021937 "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation" evidence=IGI

GO:0042127 "regulation of cell proliferation" evidence=IMP

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IGI

GO:0046872 "metal ion binding" evidence=IEA

RGD|71079 Lhx5 "LIM homeobox 5" [Rattus norvegicus (taxid:10116)]

 Score = 284 (105.0 bits), Expect = 5.9e-25, P = 5.9e-25
 Identities = 58/134 (43%), Positives = 81/134 (60%)

Query:     1 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
             M++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   LS+KCFSREGKL+C+NDFFR  
Sbjct:     1 MMVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECKTNLSEKCFSREGKLYCKNDFFR-- 58

Query:    61 VRFPSGCGVGLSSSMLISCAGCEKPILDKFLLN-VLERTWHADCVRCYDCHHTLS--DKC 117
              RF +             CAGC + I    L+     + +H +C  C  C+  LS  ++ 
Sbjct:    59 -RFGT------------KCAGCAQGISPSDLVRKARSKVFHLNCFTCMVCNKQLSTGEEL 105

Query:   118 FS-REGKLFCRNDF 130
             +   E K  C++D+
Sbjct:   106 YVIDENKFVCKDDY 119

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0006351 "transcription, DNA-dependent" evidence=IEA

GO:0007267 "cell-cell signaling" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA;ISO

GO:0021549 "cerebellum development" evidence=ISO

GO:0021702 "cerebellar Purkinje cell differentiation" evidence=IEA;ISO

GO:0021766 "hippocampus development" evidence=IEA;ISO

GO:0021846 "cell proliferation in forebrain" evidence=IEA;ISO

GO:0021879 "forebrain neuron differentiation" evidence=IEA;ISO

GO:0021937 "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation" evidence=IEA;ISO

GO:0042127 "regulation of cell proliferation" evidence=ISO

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IEA;ISO

UNIPROTKB|F1RKD0 LHX5 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 277 (102.6 bits), Expect = 3.3e-24, P = 3.3e-24
 Identities = 58/134 (43%), Positives = 82/134 (61%)

Query:     1 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
             M++ CAGCE+PILD+FLLNVL+R WH  CV+C +C + LS+KCFSREGKL+C+NDFFR  
Sbjct:     1 MMVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECTN-LSEKCFSREGKLYCKNDFFR-- 57

Query:    61 VRFPSGCGVGLSSSMLISCAGCEKPILDKFLLN-VLERTWHADCVRCYDCHHTLS--DKC 117
              RF +             CAGC + I    L+     + +H +C  C  C+  LS  ++ 
Sbjct:    58 -RFGT------------KCAGCAQGISPSDLVRKARSKVFHLNCFTCMVCNKQLSTGEEL 104

Query:   118 FS-REGKLFCRNDF 130
             +   E K  C++D+
Sbjct:   105 YVIDENKFVCKDDY 118

GO:0005634 "nucleus" evidence=IEA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IEA

GO:0021937 "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation" evidence=IEA

GO:0021879 "forebrain neuron differentiation" evidence=IEA

GO:0021846 "cell proliferation in forebrain" evidence=IEA

GO:0021766 "hippocampus development" evidence=IEA

GO:0021702 "cerebellar Purkinje cell differentiation" evidence=IEA

GO:0021527 "spinal cord association neuron differentiation" evidence=IEA

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

UNIPROTKB|B7ZP59 lhx1 "Homeobox protein" [Xenopus laevis (taxid:8355)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 56/133 (42%), Positives = 79/133 (59%)

Query:     2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPV 61
             ++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   L++KCFSREGKL+C+NDFFR   
Sbjct:     1 MVHCAGCERPILDRFLLNVLDRAWHVKCVQCCECKCNLTEKCFSREGKLYCKNDFFR--- 57

Query:    62 RFPSGCGVGLSSSMLISCAGCEKPILDKFLLN-VLERTWHADCVRCYDCHHTLS--DKCF 118
             RF +             CAGC + I    L+     + +H +C  C  C+  LS  ++ +
Sbjct:    58 RFGT------------KCAGCAQGISPSDLVRRARSKVFHLNCFTCMMCNKQLSTGEELY 105

Query:   119 S-REGKLFCRNDF 130
                E K  C+ D+
Sbjct:   106 IIDENKFVCKEDY 118

GO:0001071 "nucleic acid binding transcription factor activity" evidence=ISS

GO:0001655 "urogenital system development" evidence=ISS

GO:0001657 "ureteric bud development" evidence=ISS

GO:0001702 "gastrulation with mouth forming second" evidence=ISS

GO:0001705 "ectoderm formation" evidence=ISS

GO:0001706 "endoderm formation" evidence=ISS

GO:0001764 "neuron migration" evidence=ISS

GO:0001822 "kidney development" evidence=ISS

GO:0003714 "transcription corepressor activity" evidence=ISS

GO:0005634 "nucleus" evidence=ISS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS

GO:0007267 "cell-cell signaling" evidence=ISS

GO:0007389 "pattern specification process" evidence=ISS

GO:0008045 "motor neuron axon guidance" evidence=ISS

GO:0009653 "anatomical structure morphogenesis" evidence=ISS

GO:0009791 "post-embryonic development" evidence=ISS

GO:0009880 "embryonic pattern specification" evidence=ISS

GO:0009948 "anterior/posterior axis specification" evidence=ISS

GO:0009952 "anterior/posterior pattern specification" evidence=ISS

GO:0009953 "dorsal/ventral pattern formation" evidence=ISS

GO:0010468 "regulation of gene expression" evidence=ISS

GO:0010842 "retina layer formation" evidence=ISS

GO:0021527 "spinal cord association neuron differentiation" evidence=ISS

GO:0021549 "cerebellum development" evidence=ISS

GO:0021702 "cerebellar Purkinje cell differentiation" evidence=ISS

GO:0021871 "forebrain regionalization" evidence=ISS

GO:0021937 "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation" evidence=ISS

GO:0040019 "positive regulation of embryonic development" evidence=ISS

GO:0043234 "protein complex" evidence=ISS

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISS

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISS

GO:0048646 "anatomical structure formation involved in morphogenesis" evidence=ISS

GO:0048703 "embryonic viscerocranium morphogenesis" evidence=ISS

GO:0060059 "embryonic retina morphogenesis in camera-type eye" evidence=ISS

GO:0060322 "head development" evidence=ISS

GO:0060429 "epithelium development" evidence=ISS

GO:0061205 "paramesonephric duct development" evidence=ISS

GO:0072049 "comma-shaped body morphogenesis" evidence=ISS

GO:0072050 "S-shaped body morphogenesis" evidence=ISS

GO:0072077 "renal vesicle morphogenesis" evidence=ISS

GO:0072178 "nephric duct morphogenesis" evidence=ISS

GO:0090009 "primitive streak formation" evidence=ISS

GO:0090190 "positive regulation of branching involved in ureteric bud morphogenesis" evidence=ISS

GO:2000543 "positive regulation of gastrulation" evidence=ISS

GO:2000744 "positive regulation of anterior head development" evidence=ISS

GO:2000768 "positive regulation of nephron tubule epithelial cell differentiation" evidence=ISS

UNIPROTKB|P29674 lhx1 "LIM/homeobox protein Lhx1" [Xenopus laevis (taxid:8355)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 56/133 (42%), Positives = 79/133 (59%)

Query:     2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPV 61
             ++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   L++KCFSREGKL+C+NDFFR   
Sbjct:     1 MVHCAGCERPILDRFLLNVLDRAWHVKCVQCCECKCNLTEKCFSREGKLYCKNDFFR--- 57

Query:    62 RFPSGCGVGLSSSMLISCAGCEKPILDKFLLN-VLERTWHADCVRCYDCHHTLS--DKCF 118
             RF +             CAGC + I    L+     + +H +C  C  C+  LS  ++ +
Sbjct:    58 RFGT------------KCAGCAQGISPSDLVRRARSKVFHLNCFTCMMCNKQLSTGEELY 105

Query:   119 S-REGKLFCRNDF 130
                E K  C+ D+
Sbjct:   106 IIDENKFVCKEDY 118

GO:0003002 "regionalization" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=IDA

GO:0005667 "transcription factor complex" evidence=IDA

GO:0007517 "muscle organ development" evidence=IMP

GO:0009798 "axis specification" evidence=IMP

GO:0009952 "anterior/posterior pattern specification" evidence=IMP

GO:0022008 "neurogenesis" evidence=IMP

GO:0030903 "notochord development" evidence=IMP

GO:0035565 "regulation of pronephros size" evidence=IGI

GO:0039003 "pronephric field specification" evidence=IGI

GO:0039020 "pronephric nephron tubule development" evidence=IGI

GO:0042074 "cell migration involved in gastrulation" evidence=IMP

GO:0043009 "chordate embryonic development" evidence=IMP

GO:0043565 "sequence-specific DNA binding" evidence=IDA

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=IDA

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

GO:0048793 "pronephros development" evidence=IGI;IMP

GO:0072080 "nephron tubule development" evidence=IGI

ZFIN|ZDB-GENE-980526-347 lhx1a "LIM homeobox 1a" [Danio rerio (taxid:7955)]

 Score = 275 (101.9 bits), Expect = 5.3e-24, P = 5.3e-24
 Identities = 56/133 (42%), Positives = 80/133 (60%)

Query:     2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPV 61
             ++ CAGCE+PILD+FLLNVL+R WH  CV+C +C   L++KCFSREGKL+C+NDFFR   
Sbjct:     1 MVHCAGCERPILDRFLLNVLDRAWHIKCVQCCECKCNLTEKCFSREGKLYCKNDFFR--- 57

Query:    62 RFPSGCGVGLSSSMLISCAGCEKPILDKFLLN-VLERTWHADCVRCYDCHHTLS--DKCF 118
             RF +             CAGC + I    L+     + +H +C  C  C+  LS  ++ +
Sbjct:    58 RFGT------------KCAGCAQGISPNDLVRRARSKVFHLNCFTCMMCNKQLSTGEELY 105

Query:   119 S-REGKLFCRNDF 130
                E K  C++D+
Sbjct:   106 IIDENKFVCKDDY 118

GO:0043565 "sequence-specific DNA binding" evidence=IEA

GO:0003700 "sequence-specific DNA binding transcription factor activity" evidence=IEA

GO:0006355 "regulation of transcription, DNA-dependent" evidence=IEA

GO:0005634 "nucleus" evidence=IEA;ISS

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0001071 "nucleic acid binding transcription factor activity" evidence=ISS

GO:0001706 "endoderm formation" evidence=ISS

GO:0001764 "neuron migration" evidence=ISS

GO:0001822 "kidney development" evidence=ISS

GO:0006366 "transcription from RNA polymerase II promoter" evidence=ISS

GO:0009791 "post-embryonic development" evidence=ISS

GO:0009880 "embryonic pattern specification" evidence=ISS

GO:0010842 "retina layer formation" evidence=ISS

GO:0008045 "motor neuron axon guidance" evidence=ISS

GO:0043234 "protein complex" evidence=ISS

GO:0045892 "negative regulation of transcription, DNA-dependent" evidence=ISS

GO:0060059 "embryonic retina morphogenesis in camera-type eye" evidence=ISS

GO:0072049 "comma-shaped body morphogenesis" evidence=ISS

GO:0072178 "nephric duct morphogenesis" evidence=ISS

GO:0090009 "primitive streak formation" evidence=ISS

GO:2000543 "positive regulation of gastrulation" evidence=ISS

GO:2000768 "positive regulation of nephron tubule epithelial cell differentiation" evidence=ISS

GO:0021702 "cerebellar Purkinje cell differentiation" evidence=ISS

GO:0001657 "ureteric bud development" evidence=ISS

GO:0003714 "transcription corepressor activity" evidence=ISS

GO:0009953 "dorsal/ventral pattern formation" evidence=ISS

GO:0045893 "positive regulation of transcription, DNA-dependent" evidence=ISS

GO:0060322 "head development" evidence=ISS

GO:0060429 "epithelium development" evidence=ISS

GO:0072077 "renal vesicle morphogenesis" evidence=ISS

GO:0090190 "positive regulation of branching involved in ureteric bud morphogenesis" evidence=ISS

GO:0021527 "spinal cord association neuron differentiation" evidence=ISS

GO:0001705 "ectoderm formation" evidence=ISS

GO:0007267 "cell-cell signaling" evidence=ISS

GO:0040019 "positive regulation of embryonic development" evidence=ISS

GO:0061205 "paramesonephric duct development" evidence=ISS

GO:0072050 "S-shaped body morphogenesis" evidence=ISS

GO:2000744 "positive regulation of anterior head development" evidence=ISS

GO:0021871 "forebrain regionalization" evidence=ISS

GO:0021937 "cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation" evidence=ISS

GO:0046872 "metal ion binding" evidence=IEA

GO:0007275 "multicellular organismal development" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

No confident hit for EC number transfering in SWISSPROT detected by BLAST

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	131
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	1e-25
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	1e-25
cd09466	56	cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a	4e-17
cd09466	56	cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a	4e-17
cd09368	52	cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of L	4e-17
cd09368	52	cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of L	4e-17
cd09371	53	cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b	3e-15
cd09371	53	cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b	3e-15
cd09468	52	cd09468, LIM1_Lhx4, The first LIM domain of Lhx4	2e-14
cd09468	52	cd09468, LIM1_Lhx4, The first LIM domain of Lhx4	2e-14
cd09467	55	cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b	6e-14
cd09467	55	cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b	6e-14
cd09370	52	cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a	3e-11
cd09370	52	cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a	3e-11
cd09369	54	cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of L	3e-11
cd09369	54	cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of L	3e-11
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	3e-11
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	3e-11
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	5e-11
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	5e-11
cd09373	54	cd09373, LIM1_AWH, The first LIM domain of Arrowhe	1e-10
cd09373	54	cd09373, LIM1_AWH, The first LIM domain of Arrowhe	1e-10
pfam00412	58	pfam00412, LIM, LIM domain	2e-10
pfam00412	58	pfam00412, LIM, LIM domain	5e-10
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	4e-09
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	4e-09
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	1e-08
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	1e-08
cd09386	55	cd09386, LIM1_LMO4, The first LIM domain of LMO4 (	1e-08
cd09386	55	cd09386, LIM1_LMO4, The first LIM domain of LMO4 (	1e-08
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	6e-08
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	6e-08
cd09366	55	cd09366, LIM1_Isl, The first LIM domain of Isl, a	2e-07
cd09366	55	cd09366, LIM1_Isl, The first LIM domain of Isl, a	2e-07
cd09469	64	cd09469, LIM1_Lhx2, The first LIM domain of Lhx2	1e-06
cd09469	64	cd09469, LIM1_Lhx2, The first LIM domain of Lhx2	1e-06
cd09470	54	cd09470, LIM1_Lhx9, The first LIM domain of Lhx9	4e-06
cd09470	54	cd09470, LIM1_Lhx9, The first LIM domain of Lhx9	4e-06
cd09336	53	cd09336, LIM1_Paxillin_like, The first LIM domain	7e-06
cd09336	53	cd09336, LIM1_Paxillin_like, The first LIM domain	7e-06
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	9e-06
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	9e-06
cd09381	56	cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of L	1e-05
cd09381	56	cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of L	1e-05
cd09337	52	cd09337, LIM2_Paxillin_like, The second LIM domain	2e-05
cd09337	52	cd09337, LIM2_Paxillin_like, The second LIM domain	2e-05
cd09388	55	cd09388, LIM1_LMO1_LMO3, The first LIM domain of L	3e-05
cd09388	55	cd09388, LIM1_LMO1_LMO3, The first LIM domain of L	3e-05
cd09396	53	cd09396, LIM_DA1, The Lim domain of DA1	6e-05
cd09396	53	cd09396, LIM_DA1, The Lim domain of DA1	6e-05
cd09410	53	cd09410, LIM3_Leupaxin, The third LIM domain of Le	9e-05
cd09410	53	cd09410, LIM3_Leupaxin, The third LIM domain of Le	9e-05
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	3e-04
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	3e-04
cd09457	52	cd09457, LIM2_ENH, The second LIM domain of the En	4e-04
cd09457	52	cd09457, LIM2_ENH, The second LIM domain of the En	4e-04
cd09406	55	cd09406, LIM1_Leupaxin, The first LIM domain of Le	4e-04
cd09406	55	cd09406, LIM1_Leupaxin, The first LIM domain of Le	4e-04
cd09408	52	cd09408, LIM2_Leupaxin, The second LIM domain of L	5e-04
cd09408	52	cd09408, LIM2_Leupaxin, The second LIM domain of L	5e-04
cd09380	54	cd09380, LIM1_Lhx6, The first LIM domain of Lhx6	6e-04
cd09380	54	cd09380, LIM1_Lhx6, The first LIM domain of Lhx6	6e-04
cd09407	52	cd09407, LIM2_Paxillin, The second LIM domain of p	7e-04
cd09407	52	cd09407, LIM2_Paxillin, The second LIM domain of p	7e-04
cd09384	56	cd09384, LIM1_LMO2, The first LIM domain of LMO2 (	0.002
cd09384	56	cd09384, LIM1_LMO2, The first LIM domain of LMO2 (	0.002
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	0.003
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	0.003
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	0.003
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	0.003
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	0.004
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	0.004
cd09422	62	cd09422, LIM1_FHL2, The first LIM domain of Four a	0.004
cd09422	62	cd09422, LIM1_FHL2, The first LIM domain of Four a	0.004

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

 Score = 91.3 bits (227), Expect = 1e-25
 Identities = 39/52 (75%), Positives = 46/52 (88%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 56
          CAGC++PILDKFLLNVL+R WHA CV+C DC   L++KCFSREGKL+CRNDF
Sbjct: 1  CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTEKCFSREGKLYCRNDF 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|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known as Lim1) and Lhx5

 Score = 91.3 bits (227), Expect = 1e-25
 Identities = 39/52 (75%), Positives = 46/52 (88%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 130
           CAGC++PILDKFLLNVL+R WHA CV+C DC   L++KCFSREGKL+CRNDF
Sbjct: 1   CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTEKCFSREGKLYCRNDF 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|188850 cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a

 Score = 69.4 bits (170), Expect = 4e-17
 Identities = 28/53 (52%), Positives = 41/53 (77%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 57
          CAGC+ PI D+F+L V ++ WH+ C++C DC   L+DKCFSR G+++C+ DFF
Sbjct: 4  CAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTDKCFSRGGQVYCKEDFF 56

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

 Score = 69.4 bits (170), Expect = 4e-17
 Identities = 28/53 (52%), Positives = 41/53 (77%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 131
           CAGC+ PI D+F+L V ++ WH+ C++C DC   L+DKCFSR G+++C+ DFF
Sbjct: 4   CAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTDKCFSRGGQVYCKEDFF 56

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

 Score = 69.4 bits (170), Expect = 4e-17
 Identities = 29/52 (55%), Positives = 42/52 (80%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 56
          C GC++ ILD+F+L VL+RTWHA C++C DC   L+DKCF+R G ++C++DF
Sbjct: 1  CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTDKCFARNGHVYCKDDF 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|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4 family

 Score = 69.4 bits (170), Expect = 4e-17
 Identities = 29/52 (55%), Positives = 42/52 (80%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 130
           C GC++ ILD+F+L VL+RTWHA C++C DC   L+DKCF+R G ++C++DF
Sbjct: 1   CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTDKCFARNGHVYCKDDF 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|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b

 Score = 64.7 bits (158), Expect = 3e-15
 Identities = 24/52 (46%), Positives = 38/52 (73%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 56
          CAGC++PI D++LL V ER+WH +C++C  C   L+  C+ R+ KL+C+ D+
Sbjct: 1  CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPLTTSCYFRDRKLYCKQDY 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|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b

 Score = 64.7 bits (158), Expect = 3e-15
 Identities = 24/52 (46%), Positives = 38/52 (73%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 130
           CAGC++PI D++LL V ER+WH +C++C  C   L+  C+ R+ KL+C+ D+
Sbjct: 1   CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPLTTSCYFRDRKLYCKQDY 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 = 62.7 bits (152), Expect = 2e-14
 Identities = 28/52 (53%), Positives = 40/52 (76%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 56
          CAGC + ILDKF+L VL+R WH+ C++C DC   L+++CFSR G ++C+ DF
Sbjct: 1  CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAERCFSRAGNVYCKEDF 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|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4

 Score = 62.7 bits (152), Expect = 2e-14
 Identities = 28/52 (53%), Positives = 40/52 (76%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 130
           CAGC + ILDKF+L VL+R WH+ C++C DC   L+++CFSR G ++C+ DF
Sbjct: 1   CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAERCFSRAGNVYCKEDF 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|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b

 Score = 61.5 bits (149), Expect = 6e-14
 Identities = 26/52 (50%), Positives = 40/52 (76%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 56
          CAGC + I+D+F+L VL+R WH+ C++C DC   L++KCFSR   ++C++DF
Sbjct: 4  CAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAEKCFSRGDSVYCKDDF 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|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b

 Score = 61.5 bits (149), Expect = 6e-14
 Identities = 26/52 (50%), Positives = 40/52 (76%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 130
           CAGC + I+D+F+L VL+R WH+ C++C DC   L++KCFSR   ++C++DF
Sbjct: 4   CAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAEKCFSRGDSVYCKDDF 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|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a

 Score = 54.4 bits (131), Expect = 3e-11
 Identities = 22/52 (42%), Positives = 31/52 (59%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 56
          C GC + I D+FLL V +  WH  C++C  C   L   CF R+ KL+C+ D+
Sbjct: 1  CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPLETTCFYRDKKLYCKEDY 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|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a

 Score = 54.4 bits (131), Expect = 3e-11
 Identities = 22/52 (42%), Positives = 31/52 (59%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 130
           C GC + I D+FLL V +  WH  C++C  C   L   CF R+ KL+C+ D+
Sbjct: 1   CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPLETTCFYRDKKLYCKEDY 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|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9 family

 Score = 54.3 bits (131), Expect = 3e-11
 Identities = 23/54 (42%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD--KCFSREGKLFCRNDF 56
          CAGC + I D+F L  ++R WHA C++C +C   L     CFSR+G ++C+ D+
Sbjct: 1  CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 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|188755 cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of Lhx2 and Lhx9 family

 Score = 54.3 bits (131), Expect = 3e-11
 Identities = 23/54 (42%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD--KCFSREGKLFCRNDF 130
           CAGC + I D+F L  ++R WHA C++C +C   L     CFSR+G ++C+ D+
Sbjct: 1   CAGCGEKIQDRFYLLAVDRQWHASCLKCCECRLPLDSELSCFSRDGNIYCKEDY 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|188711 cd08368, LIM, LIM is a small protein-protein interaction domain, containing two zinc fingers

 Score = 54.2 bits (131), Expect = 3e-11
 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS-DKCFSREGKLFCRNDF 56
          CAGC KPI  + LL  L + WH +C +C  C   L  D  + ++GK +C   +
Sbjct: 1  CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 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|188711 cd08368, LIM, LIM is a small protein-protein interaction domain, containing two zinc fingers

 Score = 54.2 bits (131), Expect = 3e-11
 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS-DKCFSREGKLFCRNDF 130
           CAGC KPI  + LL  L + WH +C +C  C   L  D  + ++GK +C   +
Sbjct: 1   CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 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|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase )

 Score = 54.0 bits (130), Expect = 5e-11
 Identities = 24/53 (45%), Positives = 33/53 (62%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 57
          CAGC   ILD   +  L + WH DC RC  C  +LS+  F ++GKL+CR D++
Sbjct: 1  CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLSNWYFEKDGKLYCRKDYW 53

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

 Score = 54.0 bits (130), Expect = 5e-11
 Identities = 24/53 (45%), Positives = 33/53 (62%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 131
           CAGC   ILD   +  L + WH DC RC  C  +LS+  F ++GKL+CR D++
Sbjct: 1   CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLSNWYFEKDGKLYCRKDYW 53

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

 Score = 52.8 bits (127), Expect = 1e-10
 Identities = 23/54 (42%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CFSREGKLFCRNDF 56
          C GC +PI D+FLL V  R+WH  C+RC  C   L  +  CF+R+ +++C+ D+
Sbjct: 1  CTGCGEPITDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 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|188759 cd09373, LIM1_AWH, The first LIM domain of Arrowhead (AWH)

 Score = 52.8 bits (127), Expect = 1e-10
 Identities = 23/54 (42%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CFSREGKLFCRNDF 130
           C GC +PI D+FLL V  R+WH  C+RC  C   L  +  CF+R+ +++C+ D+
Sbjct: 1   CTGCGEPITDRFLLKVSGRSWHVSCLRCCVCQTPLERQPSCFTRDRQIYCKADY 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|215907 pfam00412, LIM, LIM domain

 Score = 52.0 bits (125), Expect = 2e-10
 Identities = 24/56 (42%), Positives = 35/56 (62%), Gaps = 2/56 (3%)

Query: 5  CAGCEKPILDKFLL-NVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDFFR 58
          CAGC KPI D+ L+   L + WH +C RC  C   L     F ++GKL+C++D+F+
Sbjct: 1  CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFK 56

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

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

 Score = 51.2 bits (123), Expect = 5e-10
 Identities = 24/55 (43%), Positives = 34/55 (61%), Gaps = 2/55 (3%)

Query: 79  CAGCEKPILDKFLL-NVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDFF 131
           CAGC KPI D+ L+   L + WH +C RC  C   L     F ++GKL+C++D+F
Sbjct: 1   CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYF 55

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

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

 Score = 49.5 bits (118), Expect = 4e-09
 Identities = 22/53 (41%), Positives = 32/53 (60%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 57
          CA C + I D   L  L   WHADC RC +C  +LS   + ++G+LFC+ D++
Sbjct: 22 CASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHWYYEKDGRLFCKKDYW 74

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

 Score = 49.5 bits (118), Expect = 4e-09
 Identities = 22/53 (41%), Positives = 32/53 (60%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 131
           CA C + I D   L  L   WHADC RC +C  +LS   + ++G+LFC+ D++
Sbjct: 22  CASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHWYYEKDGRLFCKKDYW 74

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

 Score = 47.9 bits (114), Expect = 1e-08
 Identities = 17/52 (32%), Positives = 27/52 (51%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 56
          C GC   I D F   V++  WH  C +C  C   L++  + ++GKL+C   +
Sbjct: 1  CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLTNWYYEKDGKLYCHKHY 52

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

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

 Score = 47.9 bits (114), Expect = 1e-08
 Identities = 17/52 (32%), Positives = 27/52 (51%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 130
           C GC   I D F   V++  WH  C +C  C   L++  + ++GKL+C   +
Sbjct: 1   CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLTNWYYEKDGKLYCHKHY 52

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

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

 Score = 47.8 bits (114), Expect = 1e-08
 Identities = 22/55 (40%), Positives = 35/55 (63%), Gaps = 3/55 (5%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDF 56
          CAGC   I+D+FLL+ L+R WH  C++C  C   L +    C+++ G + C+ND+
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|188772 cd09386, LIM1_LMO4, The first LIM domain of LMO4 (LIM domain only protein 4)

 Score = 47.8 bits (114), Expect = 1e-08
 Identities = 22/55 (40%), Positives = 35/55 (63%), Gaps = 3/55 (5%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDF 130
           CAGC   I+D+FLL+ L+R WH  C++C  C   L +    C+++ G + C+ND+
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|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 45.8 bits (109), Expect = 6e-08
 Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 4  SCAGCEKPILD-KFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRND 55
           CAGC KPI   + +L  L + WH +C +C  C   LS    F ++GKL+C++ 
Sbjct: 1  KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 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|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 45.8 bits (109), Expect = 6e-08
 Identities = 21/54 (38%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 78  SCAGCEKPILD-KFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRND 129
            CAGC KPI   + +L  L + WH +C +C  C   LS    F ++GKL+C++ 
Sbjct: 1   KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 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|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX protein family

 Score = 44.6 bits (106), Expect = 2e-07
 Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 3/55 (5%)

Query: 5  CAGCEKPILDKFLLNVL-ERTWHADCVRCYDCHHTLSDK--CFSREGKLFCRNDF 56
          C GC   I D+++L V  +  WHA C++C +C   L +   CF R+GK +C+ D+
Sbjct: 1  CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 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|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX protein family

 Score = 44.6 bits (106), Expect = 2e-07
 Identities = 21/55 (38%), Positives = 33/55 (60%), Gaps = 3/55 (5%)

Query: 79  CAGCEKPILDKFLLNVL-ERTWHADCVRCYDCHHTLSDK--CFSREGKLFCRNDF 130
           C GC   I D+++L V  +  WHA C++C +C   L +   CF R+GK +C+ D+
Sbjct: 1   CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 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|188853 cd09469, LIM1_Lhx2, The first LIM domain of Lhx2

 Score = 42.7 bits (100), Expect = 1e-06
 Identities = 21/62 (33%), Positives = 37/62 (59%), Gaps = 2/62 (3%)

Query: 71  LSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CFSREGKLFCRN 128
           +SS     CAGC   I D++ L  +++ WH  C++C +C   L  +  CFS++G ++C+ 
Sbjct: 3   ISSDRAALCAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKE 62

Query: 129 DF 130
           D+
Sbjct: 63  DY 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|188853 cd09469, LIM1_Lhx2, The first LIM domain of Lhx2

 Score = 42.7 bits (100), Expect = 1e-06
 Identities = 19/54 (35%), Positives = 34/54 (62%), Gaps = 2/54 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CFSREGKLFCRNDF 56
          CAGC   I D++ L  +++ WH  C++C +C   L  +  CFS++G ++C+ D+
Sbjct: 11 CAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDY 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|188854 cd09470, LIM1_Lhx9, The first LIM domain of Lhx9

 Score = 41.2 bits (96), Expect = 4e-06
 Identities = 18/54 (33%), Positives = 34/54 (62%), Gaps = 2/54 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CFSREGKLFCRNDF 56
          CAGC   I D++ L  +++ WH  C++C +C   L  +  CF+++G ++C+ D+
Sbjct: 1  CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 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|188854 cd09470, LIM1_Lhx9, The first LIM domain of Lhx9

 Score = 41.2 bits (96), Expect = 4e-06
 Identities = 18/54 (33%), Positives = 34/54 (62%), Gaps = 2/54 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CFSREGKLFCRNDF 130
           CAGC   I D++ L  +++ WH  C++C +C   L  +  CF+++G ++C+ D+
Sbjct: 1   CAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 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|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin like protein family

 Score = 40.4 bits (95), Expect = 7e-06
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFF 57
          CA C+KPI+ + ++  L +TWH +   C +C   L  K F  R+G+ +C  D+ 
Sbjct: 1  CAACKKPIVGQ-VVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDYH 53

The first 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|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin like protein family

 Score = 40.4 bits (95), Expect = 7e-06
 Identities = 19/54 (35%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFF 131
           CA C+KPI+ + ++  L +TWH +   C +C   L  K F  R+G+ +C  D+ 
Sbjct: 1   CAACKKPIVGQ-VVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDYH 53

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

 Score = 40.0 bits (94), Expect = 9e-06
 Identities = 17/52 (32%), Positives = 29/52 (55%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 56
          CAGC + I +   L  L++ WH  C +C +C   L+ +   ++GK +C  D+
Sbjct: 1  CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLTGEYMGKDGKPYCERDY 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|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM (abLIM) proteins

 Score = 40.0 bits (94), Expect = 9e-06
 Identities = 17/52 (32%), Positives = 29/52 (55%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 130
           CAGC + I +   L  L++ WH  C +C +C   L+ +   ++GK +C  D+
Sbjct: 1   CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLTGEYMGKDGKPYCERDY 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|188767 cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of Lhx7 and Lhx8

 Score = 40.0 bits (93), Expect = 1e-05
 Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 2/55 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD--KCFSREGKLFCRNDFF 57
          C+ C   I+DK+LL V +  WH  C+ C  C  +L     C+ ++  +FC+ D+F
Sbjct: 2  CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDYF 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|188767 cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of Lhx7 and Lhx8

 Score = 40.0 bits (93), Expect = 1e-05
 Identities = 19/55 (34%), Positives = 31/55 (56%), Gaps = 2/55 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD--KCFSREGKLFCRNDFF 131
           C+ C   I+DK+LL V +  WH  C+ C  C  +L     C+ ++  +FC+ D+F
Sbjct: 2   CSSCGLEIVDKYLLKVNDLCWHVRCLSCSVCRTSLGRHTSCYIKDKDIFCKLDYF 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|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the paxillin like protein family

 Score = 39.3 bits (92), Expect = 2e-05
 Identities = 21/53 (39%), Positives = 30/53 (56%), Gaps = 2/53 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 56
          CA C  PILDK  +  L++TWH +   C  C     D+ F  ++GK +CR D+
Sbjct: 1  CAYCNGPILDK-CVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

The second 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 = 52

>gnl|CDD|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the paxillin like protein family

 Score = 39.3 bits (92), Expect = 2e-05
 Identities = 21/53 (39%), Positives = 30/53 (56%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           CA C  PILDK  +  L++TWH +   C  C     D+ F  ++GK +CR D+
Sbjct: 1   CAYCNGPILDK-CVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

The second 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 = 52

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

 Score = 38.7 bits (90), Expect = 3e-05
 Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 3/55 (5%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDF 56
          CAGC + I D++LL  L++ WH DC++C  C   L +     +++   + CR D+
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|188774 cd09388, LIM1_LMO1_LMO3, The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

 Score = 38.7 bits (90), Expect = 3e-05
 Identities = 19/55 (34%), Positives = 32/55 (58%), Gaps = 3/55 (5%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDF 130
           CAGC + I D++LL  L++ WH DC++C  C   L +     +++   + CR D+
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|188782 cd09396, LIM_DA1, The Lim domain of DA1

 Score = 38.0 bits (89), Expect = 6e-05
 Identities = 15/41 (36%), Positives = 22/41 (53%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFS 45
          CAGC+  I     L+ L   WH +C RC+ C   +++  FS
Sbjct: 1  CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFS 41

The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. 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|188782 cd09396, LIM_DA1, The Lim domain of DA1

 Score = 38.0 bits (89), Expect = 6e-05
 Identities = 15/41 (36%), Positives = 22/41 (53%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFS 119
           CAGC+  I     L+ L   WH +C RC+ C   +++  FS
Sbjct: 1   CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFS 41

The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. 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|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin

 Score = 37.5 bits (87), Expect = 9e-05
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 2/49 (4%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFC 52
          C+GC +P+ + +L +     WH +C  C DC    +D  F   +G+  C
Sbjct: 1  CSGCGRPVKENYL-SAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLC 48

The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. 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|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin

 Score = 37.5 bits (87), Expect = 9e-05
 Identities = 15/49 (30%), Positives = 25/49 (51%), Gaps = 2/49 (4%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFC 126
           C+GC +P+ + +L +     WH +C  C DC    +D  F   +G+  C
Sbjct: 1   CSGCGRPVKENYL-SAANGVWHPECFVCSDCLKPFTDGSFFELDGRPLC 48

The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. 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|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein (TLP)

 Score = 36.2 bits (84), Expect = 3e-04
 Identities = 19/51 (37%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFS-REGKLFCRN 54
          C  C KP+        L R WH  C+RC  C  TL+    S  EGK +C  
Sbjct: 1  CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 51

The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. 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|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein (TLP)

 Score = 36.2 bits (84), Expect = 3e-04
 Identities = 19/51 (37%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFS-REGKLFCRN 128
           C  C KP+        L R WH  C+RC  C  TL+    S  EGK +C  
Sbjct: 1   CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 51

The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. 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|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog (ENH) family

 Score = 35.8 bits (82), Expect = 4e-04
 Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 2/53 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSRE-GKLFCRNDF 56
          C  C++ IL + ++N L++TWH  C  C  CH+ + +  F  E G+ +C  D+
Sbjct: 1  CGRCQRKILGE-VINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52

The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. 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|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog (ENH) family

 Score = 35.8 bits (82), Expect = 4e-04
 Identities = 18/53 (33%), Positives = 31/53 (58%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSRE-GKLFCRNDF 130
           C  C++ IL + ++N L++TWH  C  C  CH+ + +  F  E G+ +C  D+
Sbjct: 1   CGRCQRKILGE-VINALKQTWHVSCFVCVACHNPIRNNVFHLEDGEPYCETDY 52

The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. 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|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin

 Score = 36.0 bits (83), Expect = 4e-04
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTL-SDKCFSREGKLFCRNDF 56
          CA C+KPI  + ++  L +TWH +   C  C   L S   F R G+ +C  D+
Sbjct: 3  CASCQKPIAGQ-VVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54

The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. 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|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin

 Score = 36.0 bits (83), Expect = 4e-04
 Identities = 19/53 (35%), Positives = 28/53 (52%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTL-SDKCFSREGKLFCRNDF 130
           CA C+KPI  + ++  L +TWH +   C  C   L S   F R G+ +C  D+
Sbjct: 3   CASCQKPIAGQ-VVTALGQTWHPEHFVCCQCGKELGSRPFFERNGQAYCEEDY 54

The first LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. 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|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin

 Score = 35.6 bits (82), Expect = 5e-04
 Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 56
          CA C  PIL   +L  +++TWH +   C  C     D+ F  R+GK +CR DF
Sbjct: 1  CAYCAGPILQN-VLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52

The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. 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|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin

 Score = 35.6 bits (82), Expect = 5e-04
 Identities = 21/53 (39%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           CA C  PIL   +L  +++TWH +   C  C     D+ F  R+GK +CR DF
Sbjct: 1   CAYCAGPILQN-VLTAMDQTWHPEHFFCSHCGELFGDEGFLERDGKPYCRRDF 52

The second LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. 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|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6

 Score = 35.4 bits (81), Expect = 6e-04
 Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 2/54 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFSREGKLFCRNDF 56
          C+ C   ILD++LL V    WH  C+ C  C  +L   + C+ +  ++FC+ D+
Sbjct: 1  CSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 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|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6

 Score = 35.4 bits (81), Expect = 6e-04
 Identities = 18/54 (33%), Positives = 30/54 (55%), Gaps = 2/54 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFSREGKLFCRNDF 130
           C+ C   ILD++LL V    WH  C+ C  C  +L   + C+ +  ++FC+ D+
Sbjct: 1   CSSCGLEILDRYLLKVNNLIWHVRCLECSVCRTSLRQHNSCYIKNKEIFCKMDY 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|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin

 Score = 35.3 bits (81), Expect = 7e-04
 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 56
          C  C  PILDK ++  L+RTWH +   C  C      + F  ++GK +CR D+
Sbjct: 1  CYYCNGPILDK-VVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52

The second LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. 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|188791 cd09407, LIM2_Paxillin, The second LIM domain of paxillin

 Score = 35.3 bits (81), Expect = 7e-04
 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           C  C  PILDK ++  L+RTWH +   C  C      + F  ++GK +CR D+
Sbjct: 1   CYYCNGPILDK-VVTALDRTWHPEHFFCAQCGAFFGPEGFHEKDGKAYCRKDY 52

The second LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. 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|188770 cd09384, LIM1_LMO2, The first LIM domain of LMO2 (LIM domain only protein 2)

 Score = 34.4 bits (79), Expect = 0.002
 Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFF 57
          C GC++ I D++ L  +++ WH DC+ C  C   L +   + + + G+  CR D+ 
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|188770 cd09384, LIM1_LMO2, The first LIM domain of LMO2 (LIM domain only protein 2)

 Score = 34.4 bits (79), Expect = 0.002
 Identities = 17/56 (30%), Positives = 31/56 (55%), Gaps = 3/56 (5%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFF 131
           C GC++ I D++ L  +++ WH DC+ C  C   L +   + + + G+  CR D+ 
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|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like family

 Score = 33.6 bits (77), Expect = 0.003
 Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSRE-GKLFCRNDF 56
          CA C K IL + +++ L++TWH  C  C  C   + +  F  E G+ +C  D+
Sbjct: 1  CARCHKKILGE-VMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52

The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. 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|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like family

 Score = 33.6 bits (77), Expect = 0.003
 Identities = 18/53 (33%), Positives = 29/53 (54%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSRE-GKLFCRNDF 130
           CA C K IL + +++ L++TWH  C  C  C   + +  F  E G+ +C  D+
Sbjct: 1   CARCHKKILGE-VMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPYCEKDY 52

The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. 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|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin like protein family

 Score = 33.5 bits (77), Expect = 0.003
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 2/53 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 56
          C GC KPIL+ ++ + L   WH +C  C +CH    +  F   EG  +C   +
Sbjct: 1  CGGCNKPILENYI-SALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 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|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin like protein family

 Score = 33.5 bits (77), Expect = 0.003
 Identities = 18/53 (33%), Positives = 27/53 (50%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           C GC KPIL+ ++ + L   WH +C  C +CH    +  F   EG  +C   +
Sbjct: 1   CGGCNKPILENYI-SALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHY 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|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like family

 Score = 33.1 bits (76), Expect = 0.004
 Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSRE-GKLFCRN 54
          CA C + I   FL+  L R+WH +   C  CH +L++  F  E G L+C  
Sbjct: 1  CAHCNQVIRGPFLV-ALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCEL 50

The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. 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|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like family

 Score = 33.1 bits (76), Expect = 0.004
 Identities = 19/51 (37%), Positives = 27/51 (52%), Gaps = 2/51 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSRE-GKLFCRN 128
           CA C + I   FL+  L R+WH +   C  CH +L++  F  E G L+C  
Sbjct: 1   CAHCNQVIRGPFLV-ALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCEL 50

The first LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. 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|188806 cd09422, LIM1_FHL2, The first LIM domain of Four and a half LIM domains protein 2 (FHL2)

 Score = 33.3 bits (76), Expect = 0.004
 Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 2/51 (3%)

Query: 4  SCAGCEKPI-LDKFLLNVLERTWHADCVRCYDCHHTLSDKCFS-REGKLFC 52
          +C  C+KPI  D   L+  +R WH  C  C+ C ++L DK F+ +E  L C
Sbjct: 4  TCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLC 54

The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. 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 = 62

>gnl|CDD|188806 cd09422, LIM1_FHL2, The first LIM domain of Four and a half LIM domains protein 2 (FHL2)

 Score = 33.3 bits (76), Expect = 0.004
 Identities = 20/51 (39%), Positives = 29/51 (56%), Gaps = 2/51 (3%)

Query: 78  SCAGCEKPI-LDKFLLNVLERTWHADCVRCYDCHHTLSDKCFS-REGKLFC 126
           +C  C+KPI  D   L+  +R WH  C  C+ C ++L DK F+ +E  L C
Sbjct: 4   TCEECKKPIGCDCKDLSYKDRHWHESCFHCFQCKNSLVDKPFAAKEEHLLC 54

The first LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung at lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. 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 = 62

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	131
KOG1701|consensus	468		99.93
KOG4577|consensus	383		99.93
KOG1701|consensus	468		99.92
KOG2272|consensus	332		99.91
KOG2272|consensus	332		99.86
KOG1044|consensus	670		99.85
KOG1703|consensus	479		99.82
KOG1703|consensus	479		99.81
KOG1044|consensus	670		99.73
KOG1700|consensus	200		99.63
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.63
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.59
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	99.09
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	99.01
KOG4577|consensus	383		98.94
KOG0490|consensus	235		98.2
KOG1702|consensus	264		98.11
KOG1700|consensus	200		98.09
KOG1702|consensus	264		97.65
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	95.51
KOG0490|consensus	235		93.81
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	92.03
PF13248	26	zf-ribbon_3: zinc-ribbon domain	89.51
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	88.8
PF13240	23	zinc_ribbon_2: zinc-ribbon domain	87.06
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	86.75
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	86.23
PF10235	90	Cript: Microtubule-associated protein CRIPT; Inter	85.79
PF12773	50	DZR: Double zinc ribbon	85.07
PF13717	36	zinc_ribbon_4: zinc-ribbon domain	84.7
KOG2462|consensus	279		84.52
TIGR02098	38	MJ0042_CXXC MJ0042 family finger-like domain. This	83.76
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	83.19
KOG1813|consensus	313		83.03
PRK14559	645	putative protein serine/threonine phosphatase; Pro	81.99
PF13719	37	zinc_ribbon_5: zinc-ribbon domain	81.12
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	80.01

>KOG1701|consensus

Probab=99.93  E-value=1.9e-27  Score=173.62  Aligned_cols=118  Identities=27%  Similarity=0.662  Sum_probs=105.4

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc--CcCCeeecccCcCCCCCCCCCCCccccCCCCcccc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF--SREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISC   79 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f--~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C   79 (131)
                      +.+|..|+++|.|. ++.|+|+.||+.||+|..|.+.|.+..|  ..++++||..||+++|+++|+.|+++|.+.+..  
T Consensus       334 lekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~--  410 (468)
T KOG1701|consen  334 LEKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGK--  410 (468)
T ss_pred             HHHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCC--
Confidence            35799999999988 7899999999999999999999999988  377999999999999999999999999987653  


Q ss_pred             ccCCcccccceeeeecCCcccccCccccccccccccc-----eeccCCeeecCCC
Q psy4437          80 AGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-----CFSREGKLFCRND  129 (131)
Q Consensus        80 ~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-----~~~~~g~~~C~~c  129 (131)
                             .+...|.++++.||.+|++|..|+..|+.+     .|..||.++|+.|
T Consensus       411 -------~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~C  458 (468)
T KOG1701|consen  411 -------DETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTC  458 (468)
T ss_pred             -------cceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeechh
Confidence                   134456899999999999999999999832     7999999999987

>KOG4577|consensus

Probab=99.93  E-value=9.4e-29  Score=172.76  Aligned_cols=115  Identities=37%  Similarity=0.986  Sum_probs=108.2

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccCCCCcccccc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAG   81 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~   81 (131)
                      .++|++|++.|.++.++.++++.||..|++|+.|..+|.+..|.++|.+||+++|.++|+.+|++|..+|.+..+++   
T Consensus        33 ip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVR---  109 (383)
T KOG4577|consen   33 IPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVR---  109 (383)
T ss_pred             cccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHH---
Confidence            47899999999999999999999999999999999999999999999999999999999999999999999877665   


Q ss_pred             CCcccccceeeeecCCcccccCccccccccccccc--ee-ccCCeeecCCCC
Q psy4437          82 CEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CF-SREGKLFCRNDF  130 (131)
Q Consensus        82 C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~--~~-~~~g~~~C~~cy  130 (131)
                                 .|.+..||.+||.|..|++.|..+  || +.|+++.|+.+|
T Consensus       110 -----------kAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DY  150 (383)
T KOG4577|consen  110 -----------KAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDY  150 (383)
T ss_pred             -----------HhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhH
Confidence                       899999999999999999999988  65 578999999987

>KOG1701|consensus

Probab=99.92  E-value=1.3e-27  Score=174.50  Aligned_cols=112  Identities=26%  Similarity=0.692  Sum_probs=101.6

Q ss_pred             CccccCCccccCce-eEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccccCCCCccccc
Q psy4437           3 ISCAGCEKPILDKF-LLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCA   80 (131)
Q Consensus         3 ~~C~~C~~~I~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~   80 (131)
                      .+|.+|+|.|+++. .+.||++.||..||+|..|++.|.++.| .+|+++||+.||+..                +.+|.
T Consensus       275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t----------------lekC~  338 (468)
T KOG1701|consen  275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT----------------LEKCN  338 (468)
T ss_pred             hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH----------------HHHHh
Confidence            48999999998754 4889999999999999999999999877 899999999999754                47899


Q ss_pred             cCCcccccceeeeecCCcccccCccccccccccccc-eec-cCCeeecCCCCC
Q psy4437          81 GCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFS-REGKLFCRNDFF  131 (131)
Q Consensus        81 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~-~~g~~~C~~cy~  131 (131)
                      .|+++|+++.+ .|+|+.||+.||+|..|.+.|++. |.. .++++||..||+
T Consensus       339 ~Cg~~I~d~iL-rA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh  390 (468)
T KOG1701|consen  339 KCGEPIMDRIL-RALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFH  390 (468)
T ss_pred             hhhhHHHHHHH-HhcccccCCCceEEEEeccccCCccccccCCCceeeehhhh
Confidence            99999999888 999999999999999999999998 654 689999999985

>KOG2272|consensus

Probab=99.91  E-value=1.6e-26  Score=159.14  Aligned_cols=127  Identities=23%  Similarity=0.680  Sum_probs=108.8

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCC--------------------
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSP--------------------   60 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~--------------------   60 (131)
                      ++-|++|++.|.++ +|.+++.+||+.||+|..|++.|++..| ...|..+|..|..+..                    
T Consensus        73 aPcC~kC~EFiiGr-VikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~  151 (332)
T KOG2272|consen   73 APCCGKCGEFIIGR-VIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQP  151 (332)
T ss_pred             chhhcccccchhhH-HHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhccccc
Confidence            46799999999988 7899999999999999999999999877 5678888888876522                    


Q ss_pred             -----------CCCCCCCccccCCC-----------------CccccccCCcccccceeeeecCCcccccCccccccccc
Q psy4437          61 -----------VRFPSGCGVGLSSS-----------------MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHT  112 (131)
Q Consensus        61 -----------~~~C~~c~~~i~~~-----------------~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~  112 (131)
                                 ..+|..|++.+.+.                 ..++|..|.+||.++.+ .++|++||.++|+|+.|.+|
T Consensus       152 l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi-~amgKhWHveHFvCa~CekP  230 (332)
T KOG2272|consen  152 LTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVI-FAMGKHWHVEHFVCAKCEKP  230 (332)
T ss_pred             ccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchHHHHH-HHhccccchhheeehhcCCc
Confidence                       24677777666542                 34899999999998777 99999999999999999999


Q ss_pred             cccc-eeccCCeeecCCCC
Q psy4437         113 LSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       113 l~~~-~~~~~g~~~C~~cy  130 (131)
                      +-+. .|++.|.+||+.+|
T Consensus       231 FlGHrHYEkkGlaYCe~h~  249 (332)
T KOG2272|consen  231 FLGHRHYEKKGLAYCETHY  249 (332)
T ss_pred             ccchhhhhhcCchhHHHHH
Confidence            9887 89999999999987

>KOG2272|consensus

Probab=99.86  E-value=2.2e-24  Score=148.55  Aligned_cols=112  Identities=18%  Similarity=0.619  Sum_probs=98.2

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCC-CccCcCCeeecccCcCCCCCCCCCCCccccCCCCccccc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD-KCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCA   80 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~   80 (131)
                      .++|+.|.++|.++ +|.++|+.||.+.|+|+.|.+|+-+ +.|++.|.+||+.+|.++++..|..|...|.+       
T Consensus       195 ipiCgaC~rpIeer-vi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G-------  266 (332)
T KOG2272|consen  195 IPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGG-------  266 (332)
T ss_pred             CcccccccCchHHH-HHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCc-------
Confidence            47899999999766 6889999999999999999999887 56799999999999999999766666655543       


Q ss_pred             cCCcccccceeeeecCCcccccCccccccccccccc--eeccCCeeecCCCC
Q psy4437          81 GCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CFSREGKLFCRNDF  130 (131)
Q Consensus        81 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~--~~~~~g~~~C~~cy  130 (131)
                              ..+ ++.++.|-++||+|+.|++.|...  |++.|.+|.|+.||
T Consensus       267 --------~vv-~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy  309 (332)
T KOG2272|consen  267 --------DVV-SALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCY  309 (332)
T ss_pred             --------cHH-HHhhhhhccccccccccccccccccceeeeccchHHHHHH
Confidence                    333 999999999999999999999877  99999999999887

>KOG1044|consensus

Probab=99.85  E-value=1.5e-22  Score=152.54  Aligned_cols=112  Identities=22%  Similarity=0.581  Sum_probs=96.3

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccCCCCcccccc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAG   81 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~   81 (131)
                      +..|++|++.|..+.++.|+++.||..||+|..|+..|.+++..+||.|||+.||++.|+.+|..|.+.|.+        
T Consensus       133 ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~fgvkc~~c~~fisg--------  204 (670)
T KOG1044|consen  133 PSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAKFGVKCEECEKFISG--------  204 (670)
T ss_pred             CccccchhhhhhccceeeeeccceeeeeeehhhhcccccceeeccCCCcchhhhhhhhcCeehHHhhhhhhh--------
Confidence            457999999998888888999999999999999999999999999999999999999999766666665554        


Q ss_pred             CCcccccceeeeecCCcccccCccccccccccccc--eeccCCeeecCCC
Q psy4437          82 CEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CFSREGKLFCRND  129 (131)
Q Consensus        82 C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~--~~~~~g~~~C~~c  129 (131)
                             +.+ .|.|++|||.|-+|++|+.+++.+  +|+....++=..|
T Consensus       205 -------kvL-qag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C  246 (670)
T KOG1044|consen  205 -------KVL-QAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDC  246 (670)
T ss_pred             -------hhh-hccCcccCcchhhhhhhccccccchheeeccccccCCcc
Confidence                   333 899999999999999999999987  7777666654443

>KOG1703|consensus

Probab=99.82  E-value=2.2e-21  Score=148.27  Aligned_cols=114  Identities=26%  Similarity=0.634  Sum_probs=99.3

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccccCCCCccccc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCA   80 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~   80 (131)
                      .+.|.+|+++|.++ .|.++++.||++||.|..|.++|.+..| ..++.+||+.||.+++.++|..|..++...+     
T Consensus       363 ~p~C~~C~~~i~~~-~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~-----  436 (479)
T KOG1703|consen  363 RPNCKRCLLPILEE-GVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGS-----  436 (479)
T ss_pred             CccccccCCchHHh-HhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhh-----
Confidence            57899999999888 5778899999999999999999998766 8999999999999999877666666554322     


Q ss_pred             cCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          81 GCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        81 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                              ..+ .+++..||.+||+|+.|.+.|.++ |+...++|+|.+|+
T Consensus       437 --------~~i-e~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~  478 (479)
T KOG1703|consen  437 --------RQI-EADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF  478 (479)
T ss_pred             --------hHh-hccCccccccceehhhhhccccCCceeecCCccccccCC
Confidence                    222 899999999999999999999988 99999999999987

>KOG1703|consensus

Probab=99.81  E-value=4.5e-21  Score=146.57  Aligned_cols=113  Identities=23%  Similarity=0.558  Sum_probs=100.2

Q ss_pred             CccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccccCCCCcccccc
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAG   81 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~   81 (131)
                      +.|..|++.|.+..++.++++.||+.+|.|..|...+....+ ..+|++||..|+.+.+.++|.+|+++|.+..      
T Consensus       304 p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~------  377 (479)
T KOG1703|consen  304 PLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEG------  377 (479)
T ss_pred             ccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhH------
Confidence            679999999988557889999999999999999999988777 8999999999999999987777666665443      


Q ss_pred             CCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCCC
Q psy4437          82 CEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDFF  131 (131)
Q Consensus        82 C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy~  131 (131)
                               + .+.++.||++||.|+.|+++|..+ |++.+|.+||+.||+
T Consensus       378 ---------v-~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~  418 (479)
T KOG1703|consen  378 ---------V-CALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYK  418 (479)
T ss_pred             ---------h-hhccCeechhceeeecccCCCCCCcccccCCccchhhhHh
Confidence                     3 777999999999999999999988 999999999999884

>KOG1044|consensus

Probab=99.73  E-value=2.1e-18  Score=130.47  Aligned_cols=128  Identities=25%  Similarity=0.630  Sum_probs=101.5

Q ss_pred             CccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcC-CeeecccCc------------CCCCCCCCCC--
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SRE-GKLFCRNDF------------FRSPVRFPSG--   66 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~-~~~~C~~c~------------~~~~~~~C~~--   66 (131)
                      ..|..|.+.-.+. ++.+.++.||..||+|..|+..|....| .++ ..+|+....            -+.+.++|+.  
T Consensus        17 i~c~~c~~kc~ge-vlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs   95 (670)
T KOG1044|consen   17 IKCDKCRKKCSGE-VLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCS   95 (670)
T ss_pred             eehhhhCCccccc-eeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccceec
Confidence            4688999988666 7899999999999999999999998644 554 456765332            1223344443  


Q ss_pred             -CccccCCC---------------------------CccccccCCcccccceeeeecCCcccccCcccccccccccccee
Q psy4437          67 -CGVGLSSS---------------------------MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF  118 (131)
Q Consensus        67 -c~~~i~~~---------------------------~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~  118 (131)
                       |..+..++                           ....|+.|++.|..++.+.|+++.||..||+|..|+..|.++|+
T Consensus        96 ~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~gey~  175 (670)
T KOG1044|consen   96 TCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGEYM  175 (670)
T ss_pred             ccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccceee
Confidence             33444322                           34689999999999888899999999999999999999999999


Q ss_pred             ccCCeeecCCCCC
Q psy4437         119 SREGKLFCRNDFF  131 (131)
Q Consensus       119 ~~~g~~~C~~cy~  131 (131)
                      .+||.|||++||+
T Consensus       176 skdg~pyce~dy~  188 (670)
T KOG1044|consen  176 SKDGVPYCEKDYQ  188 (670)
T ss_pred             ccCCCcchhhhhh
Confidence            9999999999984

>KOG1700|consensus

Probab=99.63  E-value=5e-17  Score=111.45  Aligned_cols=130  Identities=25%  Similarity=0.497  Sum_probs=108.1

Q ss_pred             CCCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccc---cCC---
Q psy4437           1 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVG---LSS---   73 (131)
Q Consensus         1 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~---i~~---   73 (131)
                      |...|.+|++.++-.+.+...|..||+.||+|..|.+.|....+ .+++.+||+.+|...+++.-..-+..   +.+   
T Consensus         6 ~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (200)
T KOG1700|consen    6 TTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGK   85 (200)
T ss_pred             ccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCc
Confidence            34589999999987777778899999999999999999998766 89999999998777766554444432   111   


Q ss_pred             --------------------CCccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          74 --------------------SMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        74 --------------------~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                                          +....|..|++.+++.+.+...+..||..||+|+.|+..|+.. +...+|.+||..++
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~  163 (200)
T KOG1700|consen   86 DGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHF  163 (200)
T ss_pred             ccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhh
Confidence                                1347899999999998888999999999999999999999998 78889999987765

>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=6.6e-17  Score=90.20  Aligned_cols=56  Identities=30%  Similarity=0.869  Sum_probs=49.8

Q ss_pred             cccCCccccCceeE-eecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCC
Q psy4437           5 CAGCEKPILDKFLL-NVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSP   60 (131)
Q Consensus         5 C~~C~~~I~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~   60 (131)
                      |.+|+++|.+++++ .++|+.||++||+|+.|+++|.+..| ..+|++||++||.++|
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence            78999999877665 69999999999999999999998766 8999999999987643

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=99.59  E-value=3.1e-16  Score=87.45  Aligned_cols=52  Identities=31%  Similarity=0.963  Sum_probs=46.6

Q ss_pred             cccCCcccccceee-eecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          79 CAGCEKPILDKFLL-NVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        79 C~~C~~~I~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      |.+|+++|.+...+ .++|+.||++||+|+.|+++|.++ +++.+|+|||+.||
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~   54 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCY   54 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHH
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHH
Confidence            67788888876664 699999999999999999999988 89999999999887

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

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

Probab=99.09  E-value=1e-10  Score=59.58  Aligned_cols=37  Identities=41%  Similarity=1.078  Sum_probs=33.6

Q ss_pred             ccccCCccccCc-eeEeecCCccccCCcccCCCcCcCC
Q psy4437           4 SCAGCEKPILDK-FLLNVLERTWHADCVRCYDCHHTLS   40 (131)
Q Consensus         4 ~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~   40 (131)
                      +|.+|+++|.+. ..+.++++.||++||+|..|+.+|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            589999999886 6788899999999999999999986

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=99.01  E-value=2.7e-10  Score=57.99  Aligned_cols=36  Identities=42%  Similarity=1.107  Sum_probs=30.9

Q ss_pred             cccCCcccccc-eeeeecCCcccccCccccccccccc
Q psy4437          79 CAGCEKPILDK-FLLNVLERTWHADCVRCYDCHHTLS  114 (131)
Q Consensus        79 C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~  114 (131)
                      |..|+++|.+. ..+.+.++.||++||+|..|+++|.
T Consensus         2 C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        2 CAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             ccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            67788888775 5558899999999999999999986

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=98.94  E-value=2.2e-11  Score=86.09  Aligned_cols=57  Identities=54%  Similarity=1.371  Sum_probs=53.8

Q ss_pred             CccccccCCcccccceeeeecCCcccccCccccccccccccceeccCCeeecCCCCC
Q psy4437          75 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF  131 (131)
Q Consensus        75 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~g~~~C~~cy~  131 (131)
                      +.++|+.|.+.|+++.++.+++++||..|++|+.|+.+|....|.++|.+||+++||
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFsR~~s~yCkedFf   88 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFSREGSVYCKEDFF   88 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhhcCCceeehHHHH
Confidence            457899999999999999999999999999999999999999999999999999986

>KOG0490|consensus

Probab=98.20  E-value=1.3e-07  Score=66.23  Aligned_cols=107  Identities=31%  Similarity=0.712  Sum_probs=80.3

Q ss_pred             cCCccccCceeEeecCCccccCCcccCCCcCcCC--CCccCcCCeeecccCcCC--CCCCCCCCCccccCCCCccccccC
Q psy4437           7 GCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFSREGKLFCRNDFFR--SPVRFPSGCGVGLSSSMLISCAGC   82 (131)
Q Consensus         7 ~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~--~~~f~~~~~~~C~~c~~~--~~~~~C~~c~~~i~~~~~~~C~~C   82 (131)
                      .|+..|.+...+.+.+..||..|..|..|...|.  ...|.++|..||..++.+  .+..+|.+|...+...+...    
T Consensus         1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~le----   76 (235)
T KOG0490|consen    1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELE----   76 (235)
T ss_pred             CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHHH----
Confidence            4778888888788889999999999999999998  677766999999999998  66667777776664433221    


Q ss_pred             CcccccceeeeecCCcccccCccccccccccccc--eecc-CCeeecCC
Q psy4437          83 EKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CFSR-EGKLFCRN  128 (131)
Q Consensus        83 ~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~--~~~~-~g~~~C~~  128 (131)
                                .+..+. |..||.|..|...+...  +.+. ..+..+.+
T Consensus        77 ----------r~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak  114 (235)
T KOG0490|consen   77 ----------RAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAK  114 (235)
T ss_pred             ----------HhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHh
Confidence                      556666 99999999988877655  4332 33555543

>KOG1702|consensus

Probab=98.11  E-value=2.4e-07  Score=63.06  Aligned_cols=60  Identities=22%  Similarity=0.535  Sum_probs=52.9

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPV   61 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~   61 (131)
                      ...|..|++.++..+.|.-+++.||..||+|..|+.+|..+.+ .-+.++||..+|.+..+
T Consensus         4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a   64 (264)
T KOG1702|consen    4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA   64 (264)
T ss_pred             cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence            4457889999988777888999999999999999999999888 68999999999987654

>KOG1700|consensus

Probab=98.09  E-value=7.8e-07  Score=61.27  Aligned_cols=59  Identities=29%  Similarity=0.584  Sum_probs=51.8

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSP   60 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~   60 (131)
                      ...|..|.+.+++.+.+...+..||..||+|+.|+..|+...+ ..++.+||...+...+
T Consensus       108 ~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~  167 (200)
T KOG1700|consen  108 KEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF  167 (200)
T ss_pred             ccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence            4679999999998877888999999999999999999999888 7888998887776654

>KOG1702|consensus

Probab=97.65  E-value=5.4e-06  Score=56.56  Aligned_cols=54  Identities=24%  Similarity=0.579  Sum_probs=46.4

Q ss_pred             cccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      ..+..|++.+++.+.+.-+++.||..||+|..|+.+|.-. +-..+.++||..+|
T Consensus         5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hY   59 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHY   59 (264)
T ss_pred             chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccc
Confidence            3467788888876666889999999999999999999877 66789999999887

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=95.51  E-value=0.012  Score=31.83  Aligned_cols=40  Identities=23%  Similarity=0.605  Sum_probs=24.7

Q ss_pred             CCCCCCCccccC-CCCccccccCCcccccceeeeecCCcccccCc----cccc--ccccc
Q psy4437          61 VRFPSGCGVGLS-SSMLISCAGCEKPILDKFLLNVLERTWHADCV----RCYD--CHHTL  113 (131)
Q Consensus        61 ~~~C~~c~~~i~-~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf----~C~~--C~~~l  113 (131)
                      +.+|..|++.+. +.+.++|+.|+.             .||++|.    .|..  |+.++
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~Cga-------------pyHR~C~~~~g~C~~~~c~~~~   51 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGA-------------PYHRDCWEKAGGCINYSCGTGF   51 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCC-------------cccHHHHhhCCceEeccCCCCc
Confidence            456777777765 445566666654             4898887    3554  55443

>KOG0490|consensus

Probab=93.81  E-value=0.013  Score=40.85  Aligned_cols=50  Identities=46%  Similarity=1.270  Sum_probs=40.7

Q ss_pred             CCcccccceeeeecCCcccccCccccccccccc--cceeccCCeeecCCCCC
Q psy4437          82 CEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFSREGKLFCRNDFF  131 (131)
Q Consensus        82 C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~--~~~~~~~g~~~C~~cy~  131 (131)
                      |+..|.+...+.+.+..||..|..|..|...+.  ...+..+|..||..+|.
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~   53 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQ   53 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccch
Confidence            566777777778889999999999999999998  44444499999998773

>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=92.03  E-value=0.098  Score=26.08  Aligned_cols=25  Identities=16%  Similarity=0.429  Sum_probs=18.7

Q ss_pred             cccCCccccCcee-EeecCCccccCC
Q psy4437           5 CAGCEKPILDKFL-LNVLERTWHADC   29 (131)
Q Consensus         5 C~~C~~~I~~~~~-~~~~~~~~H~~C   29 (131)
                      |.-|+.+|.+..+ +...++.|+.-|
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~fCC   26 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYYFCC   26 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEEEEC
Confidence            6789999987654 666788887544

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

>PF13248 zf-ribbon_3: zinc-ribbon domain

Probab=89.51  E-value=0.27  Score=22.38  Aligned_cols=14  Identities=29%  Similarity=0.536  Sum_probs=9.7

Q ss_pred             CCCccccCCccccC
Q psy4437           1 MLISCAGCEKPILD   14 (131)
Q Consensus         1 ~~~~C~~C~~~I~~   14 (131)
                      |...|..|+..|.+
T Consensus         1 m~~~Cp~Cg~~~~~   14 (26)
T PF13248_consen    1 MEMFCPNCGAEIDP   14 (26)
T ss_pred             CcCCCcccCCcCCc
Confidence            66778888876643

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

Probab=88.80  E-value=0.62  Score=26.17  Aligned_cols=45  Identities=16%  Similarity=0.208  Sum_probs=19.6

Q ss_pred             cccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccccCCC
Q psy4437          30 VRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSSS   74 (131)
Q Consensus        30 f~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~   74 (131)
                      ++|+.|...|....- ..=+.+||..|-.+.++..|..|..|....
T Consensus         8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~~~CPvC~~Paw~q   53 (65)
T PF14835_consen    8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIGSECPVCHTPAWIQ   53 (65)
T ss_dssp             TS-SSS-S--SS-B---SSS--B-TTTGGGGTTTB-SSS--B-S-S
T ss_pred             cCCcHHHHHhcCCceeccCccHHHHHHhHHhcCCCCCCcCChHHHH
Confidence            578888777765322 344677888888776666566666555443

>PF13240 zinc_ribbon_2: zinc-ribbon domain

Probab=87.06  E-value=0.52  Score=20.81  Aligned_cols=9  Identities=22%  Similarity=0.671  Sum_probs=3.6

Q ss_pred             CCCCccccC
Q psy4437          64 PSGCGVGLS   72 (131)
Q Consensus        64 C~~c~~~i~   72 (131)
                      |..|+..|.
T Consensus         2 Cp~CG~~~~   10 (23)
T PF13240_consen    2 CPNCGAEIE   10 (23)
T ss_pred             CcccCCCCC
Confidence            333444443

>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=86.75  E-value=0.59  Score=28.42  Aligned_cols=29  Identities=21%  Similarity=0.576  Sum_probs=19.4

Q ss_pred             cccccCCcccccceeeee-cCCcccccCcc
Q psy4437          77 ISCAGCEKPILDKFLLNV-LERTWHADCVR  105 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~-~~~~~H~~Cf~  105 (131)
                      ..|+.|+++|.....+.+ .|..+|..|++
T Consensus        79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            568888888876554344 45667887753

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 [].

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

Probab=86.23  E-value=0.23  Score=30.42  Aligned_cols=29  Identities=31%  Similarity=0.600  Sum_probs=22.8

Q ss_pred             ccccCCcccccceeeeec-CCcccccCccc
Q psy4437          78 SCAGCEKPILDKFLLNVL-ERTWHADCVRC  106 (131)
Q Consensus        78 ~C~~C~~~I~~~~~~~~~-~~~~H~~Cf~C  106 (131)
                      .|..|+++|..++.+++. +..-|.+||+=
T Consensus         4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~   33 (101)
T PF09943_consen    4 KCYICGKPIYEGQLFTFTKKGPVHYECFRE   33 (101)
T ss_pred             EEEecCCeeeecceEEEecCCcEeHHHHHH
Confidence            588899999887777764 46779999874

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

Probab=85.79  E-value=0.55  Score=28.24  Aligned_cols=44  Identities=25%  Similarity=0.588  Sum_probs=26.7

Q ss_pred             ccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccCCCCccccccCCcccccc
Q psy4437          24 TWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDK   89 (131)
Q Consensus        24 ~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~   89 (131)
                      .|-+.=-.|..|...+..     .|.-||..|..+.                 -+|+.|++.|.+.
T Consensus        39 Py~~~~~~C~~CK~~v~q-----~g~~YCq~CAYkk-----------------GiCamCGKki~dt   82 (90)
T PF10235_consen   39 PYAPYSSKCKICKTKVHQ-----PGAKYCQTCAYKK-----------------GICAMCGKKILDT   82 (90)
T ss_pred             cccccCcccccccccccc-----CCCccChhhhccc-----------------CcccccCCeeccc
Confidence            344433456667655532     3667888887664                 3577777777653

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

>PF12773 DZR: Double zinc ribbon

Probab=85.07  E-value=1.4  Score=23.08  Aligned_cols=9  Identities=22%  Similarity=0.671  Sum_probs=4.0

Q ss_pred             cccccCCcc
Q psy4437          77 ISCAGCEKP   85 (131)
Q Consensus        77 ~~C~~C~~~   85 (131)
                      ..|..|+..
T Consensus        30 ~~C~~Cg~~   38 (50)
T PF12773_consen   30 KICPNCGAE   38 (50)
T ss_pred             CCCcCCcCC
Confidence            344444443

>PF13717 zinc_ribbon_4: zinc-ribbon domain

Probab=84.70  E-value=0.3  Score=24.12  Aligned_cols=33  Identities=33%  Similarity=0.753  Sum_probs=19.6

Q ss_pred             CCCccccCCccc-cCceeEeecCCccccCCcccCCCcCc
Q psy4437           1 MLISCAGCEKPI-LDKFLLNVLERTWHADCVRCYDCHHT   38 (131)
Q Consensus         1 ~~~~C~~C~~~I-~~~~~~~~~~~~~H~~Cf~C~~C~~~   38 (131)
                      |...|..|+... .+.+.|...+..     ++|+.|+..
T Consensus         1 M~i~Cp~C~~~y~i~d~~ip~~g~~-----v~C~~C~~~   34 (36)
T PF13717_consen    1 MIITCPNCQAKYEIDDEKIPPKGRK-----VRCSKCGHV   34 (36)
T ss_pred             CEEECCCCCCEEeCCHHHCCCCCcE-----EECCCCCCE
Confidence            667788888764 233334444443     677777654

>KOG2462|consensus

Probab=84.52  E-value=0.68  Score=33.44  Aligned_cols=90  Identities=21%  Similarity=0.404  Sum_probs=50.8

Q ss_pred             cCCcccCCCcCcCCCCc-cCcCCe-------------eecccCcCCCC-----------CCCCCCCccccC---------
Q psy4437          27 ADCVRCYDCHHTLSDKC-FSREGK-------------LFCRNDFFRSP-----------VRFPSGCGVGLS---------   72 (131)
Q Consensus        27 ~~Cf~C~~C~~~l~~~~-f~~~~~-------------~~C~~c~~~~~-----------~~~C~~c~~~i~---------   72 (131)
                      ...++|..|++.++... ..+...             .+|..-|..+-           .-.|..|++.+.         
T Consensus       128 ~~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaFSRPWLLQGHi  207 (279)
T KOG2462|consen  128 HPRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAFSRPWLLQGHI  207 (279)
T ss_pred             CCceeccccccccccccccchhhcccccccccccccCCCCCceeeehHHHhhHhhccCCCcccccccccccchHHhhccc
Confidence            34588899998887632 122222             23333332221           136777777653         


Q ss_pred             ----CCCccccccCCcccccceeeeec-CCcccccCccccccccccccc
Q psy4437          73 ----SSMLISCAGCEKPILDKFLLNVL-ERTWHADCVRCYDCHHTLSDK  116 (131)
Q Consensus        73 ----~~~~~~C~~C~~~I~~~~~~~~~-~~~~H~~Cf~C~~C~~~l~~~  116 (131)
                          |+..+.|+.|+|...|+--++|. .-+=+..=|.|..|++.++..
T Consensus       208 RTHTGEKPF~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsFsl~  256 (279)
T KOG2462|consen  208 RTHTGEKPFSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSFALK  256 (279)
T ss_pred             ccccCCCCccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHHHHH
Confidence                34457888888888776443432 122233457788888877654

>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain

Probab=83.76  E-value=0.34  Score=23.93  Aligned_cols=34  Identities=29%  Similarity=0.512  Sum_probs=19.4

Q ss_pred             CCCccccCCcccc-CceeEeecCCccccCCcccCCCcCcC
Q psy4437           1 MLISCAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTL   39 (131)
Q Consensus         1 ~~~~C~~C~~~I~-~~~~~~~~~~~~H~~Cf~C~~C~~~l   39 (131)
                      |...|..|+..+. +.+.+...+.     -++|..|+..+
T Consensus         1 M~~~CP~C~~~~~v~~~~~~~~~~-----~v~C~~C~~~~   35 (38)
T TIGR02098         1 MRIQCPNCKTSFRVVDSQLGANGG-----KVRCGKCGHVW   35 (38)
T ss_pred             CEEECCCCCCEEEeCHHHcCCCCC-----EEECCCCCCEE
Confidence            6678888888752 2212222221     26778887665

This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.

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

Probab=83.19  E-value=0.39  Score=29.46  Aligned_cols=30  Identities=30%  Similarity=0.548  Sum_probs=22.7

Q ss_pred             ccccCCccccCceeEee-cCCccccCCcccC
Q psy4437           4 SCAGCEKPILDKFLLNV-LERTWHADCVRCY   33 (131)
Q Consensus         4 ~C~~C~~~I~~~~~~~~-~~~~~H~~Cf~C~   33 (131)
                      +|..|+++|..++..++ .+..-|-.||+=.
T Consensus         4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~   34 (101)
T PF09943_consen    4 KCYICGKPIYEGQLFTFTKKGPVHYECFREK   34 (101)
T ss_pred             EEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence            68899999988777555 3567888888654

>KOG1813|consensus

Probab=83.03  E-value=0.89  Score=33.22  Aligned_cols=46  Identities=15%  Similarity=0.327  Sum_probs=36.1

Q ss_pred             cccCCCcCcCCCCccCcCCeeecccCcCCCC--CCCCCCCccccCCCC
Q psy4437          30 VRCYDCHHTLSDKCFSREGKLFCRNDFFRSP--VRFPSGCGVGLSSSM   75 (131)
Q Consensus        30 f~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~--~~~C~~c~~~i~~~~   75 (131)
                      |.|..|++.........-+..+|+.|..+.+  +++|..|++.+.+..
T Consensus       242 f~c~icr~~f~~pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g~~  289 (313)
T KOG1813|consen  242 FKCFICRKYFYRPVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHGSF  289 (313)
T ss_pred             ccccccccccccchhhcCCceeehhhhccccccCCcceeccccccccc
Confidence            7888888887765556678899999998776  468888888887643

>PRK14559 putative protein serine/threonine phosphatase; Provisional

Probab=81.99  E-value=2.2  Score=34.82  Aligned_cols=37  Identities=16%  Similarity=0.306  Sum_probs=21.6

Q ss_pred             ecccCcCCCCCCCCCCCccccCCCCccccccCCccccc
Q psy4437          51 FCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILD   88 (131)
Q Consensus        51 ~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~   88 (131)
                      ||..|-.+.-...|..|+..+.++.. -|..|+.+...
T Consensus        17 FC~~CG~~l~~~~Cp~CG~~~~~~~~-fC~~CG~~~~~   53 (645)
T PRK14559         17 FCQKCGTSLTHKPCPQCGTEVPVDEA-HCPNCGAETGT   53 (645)
T ss_pred             cccccCCCCCCCcCCCCCCCCCcccc-cccccCCcccc
Confidence            44444433333467777777665554 57777776543

>PF13719 zinc_ribbon_5: zinc-ribbon domain

Probab=81.12  E-value=0.55  Score=23.27  Aligned_cols=34  Identities=32%  Similarity=0.658  Sum_probs=19.3

Q ss_pred             CCCccccCCcccc-CceeEeecCCccccCCcccCCCcCcC
Q psy4437           1 MLISCAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTL   39 (131)
Q Consensus         1 ~~~~C~~C~~~I~-~~~~~~~~~~~~H~~Cf~C~~C~~~l   39 (131)
                      |..+|..|+.... +.+.+...+..     .+|+.|+..+
T Consensus         1 M~i~CP~C~~~f~v~~~~l~~~~~~-----vrC~~C~~~f   35 (37)
T PF13719_consen    1 MIITCPNCQTRFRVPDDKLPAGGRK-----VRCPKCGHVF   35 (37)
T ss_pred             CEEECCCCCceEEcCHHHcccCCcE-----EECCCCCcEe
Confidence            6778888887642 22224333332     6677776543

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

Probab=80.01  E-value=1.4  Score=24.24  Aligned_cols=13  Identities=23%  Similarity=0.588  Sum_probs=7.4

Q ss_pred             CccccCCccccCc
Q psy4437           3 ISCAGCEKPILDK   15 (131)
Q Consensus         3 ~~C~~C~~~I~~~   15 (131)
                      +.|..|+..|.+.
T Consensus         8 ~~CtSCg~~i~~~   20 (59)
T PRK14890          8 PKCTSCGIEIAPR   20 (59)
T ss_pred             ccccCCCCcccCC
Confidence            3566666666443

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	131
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		7e-17
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		5e-15
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		5e-14
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		7e-13
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		5e-14
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		2e-13
1rut_X	188	Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 L		3e-10
1rut_X	188	Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 L		2e-07
2dfy_X	195	Crystal Structure Of A Cyclized Protein Fusion Of L		4e-10
2dfy_X	195	Crystal Structure Of A Cyclized Protein Fusion Of L		2e-07
2l4z_A	123	Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-L		3e-08
2l4z_A	123	Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-L		1e-07
1m3v_A	122	Flin4: Fusion Of The Lim Binding Domain Of Ldb1 And		4e-08
1m3v_A	122	Flin4: Fusion Of The Lim Binding Domain Of Ldb1 And		2e-07
2xjy_A	131	Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21		7e-08
1j2o_A	114	Structure Of Flin2, A Complex Containing The N-Term		1e-05
1j2o_A	114	Structure Of Flin2, A Complex Containing The N-Term		5e-05
2dj7_A	80	Solution Structure Of 3rd Lim Domain Of Actin-Bindi		9e-05
2dj7_A	80	Solution Structure Of 3rd Lim Domain Of Actin-Bindi		1e-04
1x3h_A	80	Solution Structure Of The Lim Domain Of Human Leupa		7e-04
1x3h_A	80	Solution Structure Of The Lim Domain Of Human Leupa		7e-04

>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 = 82.0 bits (201), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 46/134 (34%), Positives = 73/134 (54%), Gaps = 19/134 (14%)
Query: 1   MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSP 60
            +  CAGC + ILDKF+L VL+R WH+ C++C DC   L+D+CFSR G ++C+ DFF+  
Sbjct: 5   QIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGSVYCKEDFFK-- 62
Query: 61  VRFPSGCGVGLSSSMLISCAGCEKPI-LDKFLLNVLERTWHADCVRCYDCHHTLS--DKC 117
            RF +             C  C++ I   + +    +  +H  C  C  C+  L+  D+ 
Sbjct: 63  -RFGT------------KCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDEF 109
Query: 118 FSRE-GKLFCRNDF 130
           +  E G+L C+ D+
Sbjct: 110 YLMEDGRLVCKEDY 123

>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 = 76.3 bits (186), Expect = 5e-15,   Method: Compositional matrix adjust.
 Identities = 31/60 (51%), Positives = 43/60 (71%)
Query: 72  SSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 131
           S   +  CAGC + ILDKF+L VL+R WH+ C++C DC   L+D+CFSR G ++C+ DFF
Sbjct: 2   SMQQIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGSVYCKEDFF 61

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

Iteration: 1
 Score = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 40/129 (31%), Positives = 70/129 (54%), Gaps = 17/129 (13%)
Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
           CAGC++ ILD+F+L  L+R WH+ C++C DCH  L+++CFSR   ++C++DFF+      
Sbjct: 63  CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFGTKC 122
Query: 65  SGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFSRE- 121
           + C +G+  + ++  A               +  +H  C  C  C   L+  D+ +  E 
Sbjct: 123 AACQLGIPPTQVVRRAQ--------------DFVYHLHCFACVVCKRQLATGDEFYLMED 168
Query: 122 GKLFCRNDF 130
            +L C+ D+
Sbjct: 169 SRLVCKADY 177

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

Iteration: 1
 Score = 68.9 bits (167), Expect = 7e-13,   Method: Compositional matrix adjust.
 Identities = 27/53 (50%), Positives = 42/53 (79%)
Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 131
           CAGC++ ILD+F+L  L+R WH+ C++C DCH  L+++CFSR   ++C++DFF
Sbjct: 63  CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFF 115

>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 = 72.8 bits (177), Expect = 5e-14,   Method: Compositional matrix adjust.
 Identities = 39/129 (30%), Positives = 69/129 (53%), Gaps = 17/129 (13%)
Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
           CAGC++ ILD+F+L  L+R WH+ C++C DCH  L+++CFSR   ++C++DFF+      
Sbjct: 9   CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFGTKC 68
Query: 65  SGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DKCFSRE- 121
           + C +G+  + ++                  +  +H  C  C  C   L+  D+ +  E 
Sbjct: 69  AACQLGIPPTQVVR--------------RAQDFVYHLHCFACVVCKRQLATGDEFYLMED 114
Query: 122 GKLFCRNDF 130
            +L C+ D+
Sbjct: 115 SRLVCKADY 123

>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 = 70.5 bits (171), Expect = 2e-13,   Method: Compositional matrix adjust.
 Identities = 28/60 (46%), Positives = 45/60 (75%)
Query: 72  SSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 131
           S+  +  CAGC++ ILD+F+L  L+R WH+ C++C DCH  L+++CFSR   ++C++DFF
Sbjct: 2   STPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFF 61

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

Iteration: 1
 Score = 60.1 bits (144), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 38/131 (29%), Positives = 60/131 (45%), Gaps = 19/131 (14%)
Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFRSPV 61
           CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ R  +
Sbjct: 8   CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR--L 65
Query: 62  RFPSGCGVGLSSSMLISCAGCEKPI-LDKFLLNVLERTWHADCVRCYDCHHTL--SDKCF 118
              SG           +C+ C + I   + ++      +H  C  C  C + L   D+  
Sbjct: 66  FGNSG-----------ACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFH 114
Query: 119 SREGKLFCRND 129
              G LFC +D
Sbjct: 115 YINGSLFCEHD 125

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFF 131
           CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ 
Sbjct: 8   CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

>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 = 60.1 bits (144), Expect = 4e-10,   Method: Compositional matrix adjust.
 Identities = 38/131 (29%), Positives = 60/131 (45%), Gaps = 19/131 (14%)
Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFRSPV 61
           CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ R  +
Sbjct: 6   CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR--L 63
Query: 62  RFPSGCGVGLSSSMLISCAGCEKPI-LDKFLLNVLERTWHADCVRCYDCHHTL--SDKCF 118
              SG           +C+ C + I   + ++      +H  C  C  C + L   D+  
Sbjct: 64  FGNSG-----------ACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFH 112
Query: 119 SREGKLFCRND 129
              G LFC +D
Sbjct: 113 YINGSLFCEHD 123

>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 = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFF 131
           CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ 
Sbjct: 6   CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 61

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

Iteration: 1
 Score = 53.5 bits (127), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFR 58
           CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ R
Sbjct: 64  CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 120

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

Iteration: 1
 Score = 51.2 bits (121), Expect = 1e-07,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFF 131
           CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ 
Sbjct: 64  CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 119

>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 = 53.1 bits (126), Expect = 4e-08,   Method: Compositional matrix adjust.
 Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 3/57 (5%)
Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFR 58
          CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ R
Sbjct: 8  CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 64

>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 = 51.2 bits (121), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 32/56 (57%), Gaps = 3/56 (5%)
Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFF 131
           CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ 
Sbjct: 8   CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

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

Iteration: 1
 Score = 52.4 bits (124), Expect = 7e-08,   Method: Compositional matrix adjust.
 Identities = 36/136 (26%), Positives = 64/136 (47%), Gaps = 19/136 (13%)
Query: 2   LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFR 58
           L++C GC++ I D++ L  +++ WH DC+ C  C   L +   + + + G+  CR D+ R
Sbjct: 2   LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 61
Query: 59  SPVRFPSGCGVGLSSSMLISCAGCEKPILD-KFLLNVLERTWHADCVRCYDC--HHTLSD 115
               F      GL       CA C+K I   +  + V ++ +H +C +C  C  H  + D
Sbjct: 62  L---FGQD---GL-------CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGD 108
Query: 116 KCFSREGKLFCRNDFF 131
           +       + C  D +
Sbjct: 109 RYLLINSDIVCEQDIY 124

>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 = 45.1 bits (105), Expect = 1e-05,   Method: Compositional matrix adjust.
 Identities = 19/60 (31%), Positives = 35/60 (58%), Gaps = 3/60 (5%)
Query: 2  LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFR 58
          L++C GC++ I D++ L  +++ WH DC+ C  C   L +   + + + G+  CR D+ R
Sbjct: 3  LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 62

>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 = 42.7 bits (99), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 18/59 (30%), Positives = 34/59 (57%), Gaps = 3/59 (5%)
Query: 76  LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFF 131
           L++C GC++ I D++ L  +++ WH DC+ C  C   L +   + + + G+  CR D+ 
Sbjct: 3   LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 61

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

Iteration: 1
 Score = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 3/66 (4%)
Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
          CAGC++ I     L  L++ WH  C +C  C   L+ +  S++G  +C +D+     +F 
Sbjct: 18 CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEYISKDGVPYCESDYH---AQFG 74
Query: 65 SGCGVG 70
          SG   G
Sbjct: 75 SGPSSG 80

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

Iteration: 1
 Score = 41.6 bits (96), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 17/52 (32%), Positives = 29/52 (55%)
Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 130
           CAGC++ I     L  L++ WH  C +C  C   L+ +  S++G  +C +D+
Sbjct: 18  CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEYISKDGVPYCESDY 69

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKC-FSREGKLFCR 53
          C GC +P+L+ +L + ++  WH +C  C DC  + S    F  +G+ FC 
Sbjct: 18 CGGCNRPVLENYL-SAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCE 66

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

Iteration: 1
 Score = 38.9 bits (89), Expect = 7e-04,   Method: Compositional matrix adjust.
 Identities = 17/50 (34%), Positives = 28/50 (56%), Gaps = 2/50 (4%)
Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKC-FSREGKLFCR 127
           C GC +P+L+ +L + ++  WH +C  C DC  + S    F  +G+ FC 
Sbjct: 18  CGGCNRPVLENYL-SAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCE 66

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	131
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	3e-25
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	3e-17
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	5e-25
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	1e-16
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	5e-06
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	6e-25
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	1e-22
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	4e-13
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	2e-05
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	4e-20
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	2e-04
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	5e-18
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	2e-17
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	2e-17
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	4e-17
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	1e-15
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	4e-11
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	2e-15
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	8e-14
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	7e-15
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	4e-14
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	1e-13
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	2e-12
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	7e-12
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	6e-12
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	1e-11
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	1e-10
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	1e-10
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	2e-10
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	1e-09
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	9e-10
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	1e-08
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	1e-09
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	2e-09
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	2e-09
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	7e-09
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	3e-09
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	1e-08
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	6e-09
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	6e-09
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	4e-08
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	4e-08
2cuq_A	80	Four and A half LIM domains 3; structural genomics	4e-08
2cuq_A	80	Four and A half LIM domains 3; structural genomics	5e-08
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	6e-08
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	6e-08
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	8e-08
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	2e-07
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	9e-08
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	2e-07
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	1e-07
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	4e-07
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	2e-07
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	2e-07
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	2e-07
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	3e-07
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	3e-07
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	3e-07
2cor_A	79	Pinch protein; LIM domain, particularly interestin	3e-07
2cor_A	79	Pinch protein; LIM domain, particularly interestin	3e-07
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	4e-07
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	4e-07
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	6e-07
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	8e-07
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	8e-07
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	2e-06
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	9e-07
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	9e-07
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	7e-06
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	7e-06
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	8e-06
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	9e-06
2co8_A	82	NEDD9 interacting protein with calponin homology a	8e-06
2co8_A	82	NEDD9 interacting protein with calponin homology a	8e-06
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	1e-05
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	1e-05
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	3e-05
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	3e-05
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	7e-05
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	1e-04

>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 = 93.1 bits (231), Expect = 3e-25
 Identities = 41/130 (31%), Positives = 67/130 (51%), Gaps = 19/130 (14%)

Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
           CAGC++ ILD+F+L  L+R WH+ C++C DCH  L+++CFSR   ++C++DFF+   RF 
Sbjct: 63  CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFK---RF- 118

Query: 65  SGCGVGLSSSMLISCAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDK---CFSR 120
                         CA C+  I   + +    +  +H  C  C  C   L+         
Sbjct: 119 -----------GTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLME 167

Query: 121 EGKLFCRNDF 130
           + +L C+ D+
Sbjct: 168 DSRLVCKADY 177

>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 = 72.6 bits (178), Expect = 3e-17
 Identities = 29/101 (28%), Positives = 48/101 (47%), Gaps = 15/101 (14%)

Query: 31  RCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKF 90
           R  +     ++      G            +                 CAGC++ ILD+F
Sbjct: 30  RLENTQFDAANGIDDEGGSGGHMGSGGTPEIP---------------MCAGCDQHILDRF 74

Query: 91  LLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 131
           +L  L+R WH+ C++C DCH  L+++CFSR   ++C++DFF
Sbjct: 75  ILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFF 115

>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 = 92.2 bits (229), Expect = 5e-25
 Identities = 41/130 (31%), Positives = 68/130 (52%), Gaps = 19/130 (14%)

Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
           CAGC++ ILD+F+L  L+R WH+ C++C DCH  L+++CFSR   ++C++DFF+   RF 
Sbjct: 9   CAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFK---RFG 65

Query: 65  SGCGVGLSSSMLISCAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDK---CFSR 120
           +             CA C+  I   + +    +  +H  C  C  C   L+         
Sbjct: 66  T------------KCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLME 113

Query: 121 EGKLFCRNDF 130
           + +L C+ D+
Sbjct: 114 DSRLVCKADY 123

>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 = 71.0 bits (174), Expect = 1e-16
 Identities = 28/60 (46%), Positives = 45/60 (75%)

Query: 72  SSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 131
           S+  +  CAGC++ ILD+F+L  L+R WH+ C++C DCH  L+++CFSR   ++C++DFF
Sbjct: 2   STPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFF 61

>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 = 42.5 bits (100), Expect = 5e-06
 Identities = 14/106 (13%), Positives = 29/106 (27%), Gaps = 20/106 (18%)

Query: 5   CAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDK---CFSREGKLFCRNDFFRSP 60
           CA C+  I   + +    +  +H  C  C  C   L+         + +L C+ D+    
Sbjct: 68  CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY---- 123

Query: 61  VRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRC 106
                       ++      G          +       H   ++ 
Sbjct: 124 -----------ETAKQGGSGGSGGSGGGTP-MVAASPERHDGGLQA 157

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

 Score = 91.0 bits (226), Expect = 6e-25
 Identities = 33/136 (24%), Positives = 60/136 (44%), Gaps = 19/136 (13%)

Query: 2   LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFR 58
           L++C GC++ I D++ L  +++ WH DC+ C  C   L +   + + + G+  CR D+ R
Sbjct: 2   LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 61

Query: 59  SPVRFPSGCGVGLSSSMLISCAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLS--D 115
               F               CA C+K I   +  + V ++ +H +C +C  C       D
Sbjct: 62  ---LF----------GQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGD 108

Query: 116 KCFSREGKLFCRNDFF 131
           +       + C  D +
Sbjct: 109 RYLLINSDIVCEQDIY 124

>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 = 87.0 bits (215), Expect = 1e-22
 Identities = 36/133 (27%), Positives = 57/133 (42%), Gaps = 19/133 (14%)

Query: 4   SCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFRSP 60
            CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ R  
Sbjct: 7   RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 66

Query: 61  VRFPSGCGVGLSSSMLISCAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLS--DKC 117
                            +C+ C + I   + ++      +H  C  C  C + L   D+ 
Sbjct: 67  GNSG-------------ACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRF 113

Query: 118 FSREGKLFCRNDF 130
               G LFC +D 
Sbjct: 114 HYINGSLFCEHDR 126

>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 = 62.0 bits (150), Expect = 4e-13
 Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 3/57 (5%)

Query: 78  SCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFF 131
            CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ 
Sbjct: 7   RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

>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 = 41.2 bits (96), Expect = 2e-05
 Identities = 16/73 (21%), Positives = 27/73 (36%), Gaps = 3/73 (4%)

Query: 5   CAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLS--DKCFSREGKLFCRNDFFRSPV 61
           C+ C + I   + ++      +H  C  C  C + L   D+     G LFC +D   + +
Sbjct: 72  CSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALI 131

Query: 62  RFPSGCGVGLSSS 74
                 G    S 
Sbjct: 132 NGHLNSGGSGGSG 144

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

 Score = 78.6 bits (194), Expect = 4e-20
 Identities = 29/132 (21%), Positives = 48/132 (36%), Gaps = 20/132 (15%)

Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRF 63
           CAGC++ I          + WH     C+DC   L+ + +     K  C+  + +     
Sbjct: 6   CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVK----- 60

Query: 64  PSGCGVGLSSSMLISCAGCEKPILDKFL-LNVLERTWHA--DCVRCYDCHHTLSDKCF-S 119
                     +  + C GC   I  +   +     +WHA  +C  C  C   L  + F  
Sbjct: 61  ----------NHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMP 110

Query: 120 REGKLFCRNDFF 131
            EG +FC  +  
Sbjct: 111 VEGMVFCSVECK 122

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

 Score = 37.4 bits (87), Expect = 2e-04
 Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 4/58 (6%)

Query: 5   CAGCEKPILDKFL-LNVLERTWHA--DCVRCYDCHHTLSDKCF-SREGKLFCRNDFFR 58
           C GC   I  +   +     +WHA  +C  C  C   L  + F   EG +FC  +  +
Sbjct: 66  CQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKK 123

>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 = 5e-18
 Identities = 21/66 (31%), Positives = 34/66 (51%), Gaps = 3/66 (4%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFP 64
          CAGC++ I     L  L++ WH  C +C  C   L+ +  S++G  +C +D+     +F 
Sbjct: 18 CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEYISKDGVPYCESDYHA---QFG 74

Query: 65 SGCGVG 70
          SG   G
Sbjct: 75 SGPSSG 80

>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 = 70.2 bits (172), Expect = 2e-17
 Identities = 17/53 (32%), Positives = 29/53 (54%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFF 131
           CAGC++ I     L  L++ WH  C +C  C   L+ +  S++G  +C +D+ 
Sbjct: 18  CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEYISKDGVPYCESDYH 70

>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 = 71.3 bits (174), Expect = 2e-17
 Identities = 22/57 (38%), Positives = 33/57 (57%), Gaps = 3/57 (5%)

Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFR 58
           CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ R
Sbjct: 64  CAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 120

>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 = 70.9 bits (173), Expect = 4e-17
 Identities = 24/76 (31%), Positives = 36/76 (47%), Gaps = 3/76 (3%)

Query: 59  SPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD--- 115
                 SG  +G        CAGC   I D+FLL  ++  WH+ C++C  C   L D   
Sbjct: 44  KLGGGGSGGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGT 103

Query: 116 KCFSREGKLFCRNDFF 131
             +++ G + CRND+ 
Sbjct: 104 SSYTKSGMILCRNDYI 119

>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 = 66.7 bits (163), Expect = 1e-15
 Identities = 28/108 (25%), Positives = 39/108 (36%), Gaps = 18/108 (16%)

Query: 5   CAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVR 62
           C  C KPI  D   ++   R WH  C RC  C H L+++ F +++ K+ C     R    
Sbjct: 8   CVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTR---- 63

Query: 63  FPSGCGVGLSSSMLISCAGCEKPIL-DKFLLNVLERTWHADCVRCYDC 109
                           C GC K I+     +      WH DC      
Sbjct: 64  -----------EDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 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 = 54.7 bits (132), Expect = 4e-11
 Identities = 18/55 (32%), Positives = 27/55 (49%), Gaps = 2/55 (3%)

Query: 79  CAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFF 131
           C  C KPI  D   ++   R WH  C RC  C H L+++ F +++ K+ C     
Sbjct: 8   CVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTT 62

>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 = 66.2 bits (161), Expect = 2e-15
 Identities = 22/116 (18%), Positives = 46/116 (39%), Gaps = 15/116 (12%)

Query: 1   MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFF 57
            L++C GC++ I D++ L  +++ WH DC+ C  C   L +   + + + G+  CR D+ 
Sbjct: 2   SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 61

Query: 58  RSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTL 113
           R                     +G +  ++ +  L   E     + +     +   
Sbjct: 62  RLGGSGGHM------------GSGGDVMVVGEPTLMGGEFGDEDERLITRLENTQF 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 = 62.0 bits (150), Expect = 8e-14
 Identities = 18/60 (30%), Positives = 34/60 (56%), Gaps = 3/60 (5%)

Query: 75  MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFF 131
            L++C GC++ I D++ L  +++ WH DC+ C  C   L +   + + + G+  CR D+ 
Sbjct: 2   SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 61

>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 = 65.0 bits (158), Expect = 7e-15
 Identities = 23/67 (34%), Positives = 35/67 (52%), Gaps = 6/67 (8%)

Query: 4  SCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFRSP 60
           CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ R  
Sbjct: 7  RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR-- 64

Query: 61 VRFPSGC 67
            F +  
Sbjct: 65 -LFGNSG 70

>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 = 63.1 bits (153), Expect = 4e-14
 Identities = 21/57 (36%), Positives = 32/57 (56%), Gaps = 3/57 (5%)

Query: 78  SCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFF 131
            CAGC   I D+FLL  ++  WH+ C++C  C   L D     +++ G + CRND+ 
Sbjct: 7   RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

>1b8t_A Protein (CRP1); LIM domain, muscle differentiation, contractIle; NMR {Gallus gallus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 1ibi_A 1qli_A 1cxx_A 1ctl_A 2o13_A Length = 192

 Score = 63.5 bits (154), Expect = 1e-13
 Identities = 21/161 (13%), Positives = 47/161 (29%), Gaps = 35/161 (21%)

Query: 5   CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF------- 56
           C  C+K +     +     ++H  C  C  C   L          +++C++ +       
Sbjct: 10  CGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPK 69

Query: 57  --------------------------FRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKF 90
                                            P+   +         C  C + +    
Sbjct: 70  GKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAE 129

Query: 91  LLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF 130
            +    ++WH  C RC  C  +L       ++G+++C+  +
Sbjct: 130 KVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCY 170

>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 = 57.4 bits (139), Expect = 2e-12
 Identities = 23/68 (33%), Positives = 32/68 (47%), Gaps = 6/68 (8%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFS--REGKLFCRNDFFRSPVR 62
          CA C +PILD+ L   + + +H  C  C  CH  L    F+     ++ C  DF R   +
Sbjct: 18 CATCSQPILDRIL-RAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHR---K 73

Query: 63 FPSGCGVG 70
          F SG   G
Sbjct: 74 FASGPSSG 81

>2dlo_A Thyroid receptor-interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 56.2 bits (136), Expect = 7e-12
 Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 3/55 (5%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFS--REGKLFCRNDFF 131
           CA C +PILD+ L   + + +H  C  C  CH  L    F+     ++ C  DF 
Sbjct: 18  CATCSQPILDRIL-RAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFH 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 = 56.3 bits (136), Expect = 6e-12
 Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 2/55 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKC-FSREGKLFCRNDFFR 58
          C  C   I+  F+  + +R  H +C  C DC   L  K  F  E +++C      
Sbjct: 18 CDKCGTGIVGVFV-KLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARE 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 = 55.5 bits (134), Expect = 1e-11
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 72  SSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKC-FSREGKLFCRNDF 130
           ++  L  C  C   I+  F+  + +R  H +C  C DC   L  K  F  E +++C    
Sbjct: 11  NAQKLPMCDKCGTGIVGVFV-KLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHA 69

Query: 131 F 131
            
Sbjct: 70  R 70

>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 = 53.3 bits (128), Expect = 1e-10
 Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 2/55 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFR 58
          C  C   I+   +    ++  H +C  C DC+  L  K +   EG+L+C      
Sbjct: 28 CDKCGSGIVGAVV-KARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARA 81

>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 = 53.3 bits (128), Expect = 1e-10
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 72  SSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           S+  +  C  C   I+   +    ++  H +C  C DC+  L  K +   EG+L+C    
Sbjct: 21  SAQRMPLCDKCGSGIVGAVV-KARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHA 79

Query: 131 F 131
            
Sbjct: 80  R 80

>1x3h_A Leupaxin; paxillin family, protein-protein interaction, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 52.3 bits (126), Expect = 2e-10
 Identities = 21/67 (31%), Positives = 33/67 (49%), Gaps = 5/67 (7%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRF 63
          C GC +P+L+ +L + ++  WH +C  C DC  + S   F   +G+ FC   +     R 
Sbjct: 18 CGGCNRPVLENYL-SAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHH---RR 73

Query: 64 PSGCGVG 70
           SG   G
Sbjct: 74 GSGPSSG 80

>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 = 50.4 bits (121), Expect = 1e-09
 Identities = 17/54 (31%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFF 131
           C GC +P+L+ +L + ++  WH +C  C DC  + S   F   +G+ FC   + 
Sbjct: 18  CGGCNRPVLENYL-SAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYH 70

>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 = 50.5 bits (121), Expect = 1e-09
 Identities = 9/55 (16%), Positives = 22/55 (40%), Gaps = 1/55 (1%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFR 58
          C  C + +     +    R++H  C  C  C   L        + +++C++ + +
Sbjct: 10 CGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGK 64

>1a7i_A QCRP2 (LIM1); LIM domain containing proteins, metal-binding protein, zinc finger; NMR {Coturnix japonica} SCOP: g.39.1.3 g.39.1.3 PDB: 2o10_A Length = 81

 Score = 49.7 bits (119), Expect = 2e-09
 Identities = 9/53 (16%), Positives = 21/53 (39%), Gaps = 1/53 (1%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           C  C + +     +    R++H  C  C  C   L        + +++C++ +
Sbjct: 10  CGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCY 62

>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 = 49.8 bits (119), Expect = 2e-09
 Identities = 21/68 (30%), Positives = 33/68 (48%), Gaps = 5/68 (7%)

Query: 5  CAGCEKPI-LDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVR 62
          CA C++ I  D   L   +R +H  C RC  C  +L+D+ F  ++ +L C + +      
Sbjct: 18 CAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCS---A 74

Query: 63 FPSGCGVG 70
          F SG   G
Sbjct: 75 FSSGPSSG 82

>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 = 7e-09
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 79  CAGCEKPI-LDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFF 131
           CA C++ I  D   L   +R +H  C RC  C  +L+D+ F  ++ +L C + + 
Sbjct: 18  CAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYC 72

>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 = 49.4 bits (118), Expect = 3e-09
 Identities = 20/67 (29%), Positives = 31/67 (46%), Gaps = 5/67 (7%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRF 63
          CA C + I   FL   L ++WH +   C  C +T++   F   +G L+C   + +    F
Sbjct: 28 CAHCNQVIRGPFL-VALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEK---FF 83

Query: 64 PSGCGVG 70
           SG   G
Sbjct: 84 ASGPSSG 90

>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 = 47.8 bits (114), Expect = 1e-08
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           CA C + I   FL   L ++WH +   C  C +T++   F   +G L+C   +
Sbjct: 28  CAHCNQVIRGPFL-VALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCY 79

>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 = 6e-09
 Identities = 18/55 (32%), Positives = 26/55 (47%), Gaps = 2/55 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFR 58
          C  C+KPI    +    E+ WH +C  C  C   LS + F +R+   +C N F  
Sbjct: 8  CVQCKKPITTGGV-TYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCD 61

>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 = 48.1 bits (115), Expect = 6e-09
 Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           C  C+KPI    +    E+ WH +C  C  C   LS + F +R+   +C N F
Sbjct: 8   CVQCKKPITTGGV-TYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCF 59

>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 = 46.1 bits (110), Expect = 4e-08
 Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 2/53 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 56
          C  C +PI  + + N + + WH +   C  C           R+G  +C   +
Sbjct: 8  CGACRRPIEGRVV-NAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHY 59

>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 = 46.1 bits (110), Expect = 4e-08
 Identities = 12/53 (22%), Positives = 21/53 (39%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           C  C +PI  + + N + + WH +   C  C           R+G  +C   +
Sbjct: 8   CGACRRPIEGRVV-NAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHY 59

>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 = 46.6 bits (111), Expect = 4e-08
 Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFR 58
          CA C K +    +    ++ WH +C+ C  C   L+ + F SR+   +C   F  
Sbjct: 18 CARCSKTLTQGGV-TYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGE 71

>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 = 46.2 bits (110), Expect = 5e-08
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           CA C K +    +    ++ WH +C+ C  C   L+ + F SR+   +C   F
Sbjct: 18  CARCSKTLTQGGV-TYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACF 69

>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 = 45.6 bits (108), Expect = 6e-08
 Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 4/56 (7%)

Query: 5  CAGCEKPILDKF---LLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 56
          CAGC  PI        ++  ER WH DC  C  C  +L  + F +    + C +  
Sbjct: 8  CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCG 63

>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 = 45.6 bits (108), Expect = 6e-08
 Identities = 17/56 (30%), Positives = 24/56 (42%), Gaps = 4/56 (7%)

Query: 79  CAGCEKPILDKF---LLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           CAGC  PI        ++  ER WH DC  C  C  +L  + F +    + C +  
Sbjct: 8   CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCG 63

>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 = 45.4 bits (108), Expect = 8e-08
 Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 5/68 (7%)

Query: 5  CAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVR 62
          C+ C + ++     L    +TWH  C  C  C   L  + F   +G  +C   +     +
Sbjct: 8  CSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYEN---K 64

Query: 63 FPSGCGVG 70
          F SG   G
Sbjct: 65 FASGPSSG 72

>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 = 44.7 bits (106), Expect = 2e-07
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 2/54 (3%)

Query: 79  CAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           C+ C + ++     L    +TWH  C  C  C   L  + F   +G  +C   +
Sbjct: 8   CSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCY 61

>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 = 45.5 bits (108), Expect = 9e-08
 Identities = 16/68 (23%), Positives = 28/68 (41%), Gaps = 5/68 (7%)

Query: 5  CAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVR 62
          C  C+K I+     +     +WH  C  C+ C   +  K F  ++ + FC   + +   +
Sbjct: 8  CQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEK---Q 64

Query: 63 FPSGCGVG 70
            SG   G
Sbjct: 65 HASGPSSG 72

>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 = 44.3 bits (105), Expect = 2e-07
 Identities = 13/54 (24%), Positives = 23/54 (42%), Gaps = 2/54 (3%)

Query: 79  CAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           C  C+K I+     +     +WH  C  C+ C   +  K F  ++ + FC   +
Sbjct: 8   CQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCY 61

>1iml_A CRIP, cysteine rich intestinal protein; metal-binding protein, LIM domain protein; NMR {Rattus rattus} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 45.0 bits (107), Expect = 1e-07
 Identities = 22/72 (30%), Positives = 33/72 (45%), Gaps = 4/72 (5%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTL-SDKCFSREGKLFCRNDFFRSPVRF 63
          C  C+K +     +  L + WH  C++C  C  TL S      EGK +C +  + +   F
Sbjct: 3  CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSA--MF 60

Query: 64 -PSGCGVGLSSS 74
           P G G G + S
Sbjct: 61 GPKGFGRGGAES 72

>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 = 43.5 bits (103), Expect = 4e-07
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTL-SDKCFSREGKLFCRNDFF 131
           C  C+K +     +  L + WH  C++C  C  TL S      EGK +C +  +
Sbjct: 3   CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCY 56

>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 = 44.7 bits (106), Expect = 2e-07
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 2/53 (3%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 56
          C  C K I    +    ++ WHADC  C  C   L+ + F + E + +C + +
Sbjct: 8  CVKCNKAITSGGI-TYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCY 59

>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 = 44.7 bits (106), Expect = 2e-07
 Identities = 15/53 (28%), Positives = 25/53 (47%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           C  C K I    +    ++ WHADC  C  C   L+ + F + E + +C + +
Sbjct: 8   CVKCNKAITSGGI-TYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCY 59

>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 = 44.3 bits (105), Expect = 2e-07
 Identities = 19/67 (28%), Positives = 28/67 (41%), Gaps = 5/67 (7%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRF 63
          C  C + I+ + +   +  +WH +C RC  C   L+D  F    G+  CR    R     
Sbjct: 8  CHQCGEFIIGRVI-KAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNR---EK 63

Query: 64 PSGCGVG 70
           SG   G
Sbjct: 64 ASGPSSG 70

>2d8x_A Protein pinch; LIM domain, pinch protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 70

 Score = 44.0 bits (104), Expect = 3e-07
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 2/53 (3%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           C  C + I+ + +   +  +WH +C RC  C   L+D  F    G+  CR   
Sbjct: 8   CHQCGEFIIGRVI-KAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCH 59

>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 = 44.1 bits (104), Expect = 3e-07
 Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 5  CAGCEKPILDKF---LLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRN 54
          C  C KPI        +   +  WH++C  C  C  +L  K F ++  ++FC+ 
Sbjct: 8  CVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQK 61

>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 = 44.1 bits (104), Expect = 3e-07
 Identities = 15/54 (27%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 79  CAGCEKPILDKF---LLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRN 128
           C  C KPI        +   +  WH++C  C  C  +L  K F ++  ++FC+ 
Sbjct: 8   CVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQK 61

>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 = 44.0 bits (104), Expect = 3e-07
 Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 1/52 (1%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 56
          C  C   I ++ L+      +H D   C +C   L+      +G+L+C    
Sbjct: 18 CQKCHAIIDEQPLI-FKNDPYHPDHFNCANCGKELTADARELKGELYCLPCH 68

>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 = 44.0 bits (104), Expect = 3e-07
 Identities = 12/52 (23%), Positives = 21/52 (40%), Gaps = 1/52 (1%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF 130
           C  C   I ++ L+      +H D   C +C   L+      +G+L+C    
Sbjct: 18  CQKCHAIIDEQPLI-FKNDPYHPDHFNCANCGKELTADARELKGELYCLPCH 68

>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 = 44.1 bits (104), Expect = 4e-07
 Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF 56
          C  C+K +     L   ++ +H  C RC  C++ LS     S  G+++C+  F
Sbjct: 18 CVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHF 70

>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 = 44.1 bits (104), Expect = 4e-07
 Identities = 15/53 (28%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF 130
           C  C+K +     L   ++ +H  C RC  C++ LS     S  G+++C+  F
Sbjct: 18  CVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHF 70

>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 = 43.2 bits (102), Expect = 6e-07
 Identities = 14/66 (21%), Positives = 26/66 (39%), Gaps = 3/66 (4%)

Query: 5  CAGCEKPILDK-FLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVR 62
          C GC + ++     +  L+R +H  C  C  C   L  + F + E + +C   +  +   
Sbjct: 8  CGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLES 67

Query: 63 FPSGCG 68
               G
Sbjct: 68 -GPSSG 72

>1x61_A Thyroid receptor interacting protein 6; LIM domain, OPA-interacting protein 1, zyxin related protein 1 (ZRP-1), structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 42.8 bits (101), Expect = 8e-07
 Identities = 15/61 (24%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 73  SSMLISCAGCEKPILDK-FLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           SS    C GC + ++     +  L+R +H  C  C  C   L  + F + E + +C   +
Sbjct: 2   SSGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCY 61

Query: 131 F 131
            
Sbjct: 62  V 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 = 42.8 bits (101), Expect = 8e-07
 Identities = 19/65 (29%), Positives = 28/65 (43%), Gaps = 1/65 (1%)

Query: 68  GVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTL-SDKCFSREGKLFC 126
           G   SS M   C  C+K +     ++ L + WH  C++C  C  TL        +GK FC
Sbjct: 1   GSSGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFC 60

Query: 127 RNDFF 131
               +
Sbjct: 61  HKPCY 65

>2cu8_A Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein, zinc-binding, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 42.0 bits (99), Expect = 2e-06
 Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTL-SDKCFSREGKLFCRNDFF 57
          C  C+K +     ++ L + WH  C++C  C  TL        +GK FC    +
Sbjct: 12 CPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCY 65

>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 = 42.8 bits (101), Expect = 9e-07
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 2/54 (3%)

Query: 5  CAGCEKPI-LDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 56
          C  C+      + ++N     +H  C  C  C     +  F   EG+ +C +DF
Sbjct: 14 CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDF 67

>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 = 42.8 bits (101), Expect = 9e-07
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 2/54 (3%)

Query: 79  CAGCEKPI-LDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           C  C+      + ++N     +H  C  C  C     +  F   EG+ +C +DF
Sbjct: 14  CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDF 67

>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 = 40.5 bits (95), Expect = 7e-06
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 2/54 (3%)

Query: 5  CAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 56
          C  C+      + ++N     +H  C  C  C     +  F   EG+ +C +DF
Sbjct: 14 CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDF 67

>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 = 40.5 bits (95), Expect = 7e-06
 Identities = 13/54 (24%), Positives = 22/54 (40%), Gaps = 2/54 (3%)

Query: 79  CAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDF 130
           C  C+      + ++N     +H  C  C  C     +  F   EG+ +C +DF
Sbjct: 14  CERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDF 67

>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 = 40.4 bits (95), Expect = 8e-06
 Identities = 17/68 (25%), Positives = 24/68 (35%), Gaps = 5/68 (7%)

Query: 5  CAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDFFRSPVR 62
          C GC K I+     +      WH DC  C +C   +     F +    +C         +
Sbjct: 18 CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHET---K 74

Query: 63 FPSGCGVG 70
          F SG   G
Sbjct: 75 FASGPSSG 82

>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 = 40.4 bits (95), Expect = 9e-06
 Identities = 13/54 (24%), Positives = 19/54 (35%), Gaps = 2/54 (3%)

Query: 79  CAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF 130
           C GC K I+     +      WH DC  C +C   +     F +    +C    
Sbjct: 18  CKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCH 71

>2co8_A NEDD9 interacting protein with calponin homology and LIM domains; zinc finger protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 82

 Score = 40.3 bits (94), Expect = 8e-06
 Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 3/55 (5%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDF 56
          CA C + +     L V    +H  C RC+ C  TL     +    +G  +C    
Sbjct: 18 CALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHL 72

>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 = 40.3 bits (94), Expect = 8e-06
 Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 3/55 (5%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDF 130
           CA C + +     L V    +H  C RC+ C  TL     +    +G  +C    
Sbjct: 18  CALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHL 72

>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 = 39.8 bits (93), Expect = 1e-05
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 5/57 (8%)

Query: 5  CAGCEKPIL----DKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF 56
          CAGC+ PI        ++    ++WH  C  C  C   L++K     + +++C +  
Sbjct: 18 CAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCA 74

>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 = 39.8 bits (93), Expect = 1e-05
 Identities = 14/57 (24%), Positives = 26/57 (45%), Gaps = 5/57 (8%)

Query: 79  CAGCEKPIL----DKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF 130
           CAGC+ PI        ++    ++WH  C  C  C   L++K     + +++C +  
Sbjct: 18  CAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCA 74

>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 = 39.0 bits (91), Expect = 3e-05
 Identities = 14/63 (22%), Positives = 23/63 (36%), Gaps = 3/63 (4%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF--SREGKLFCRNDFFRSPVR 62
          C  C++ I  + + + L +T+H DC  C  C               +  C+       V 
Sbjct: 18 CFSCDQFIEGEVV-SALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSVS 76

Query: 63 FPS 65
           PS
Sbjct: 77 GPS 79

>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 = 38.6 bits (90), Expect = 3e-05
 Identities = 11/52 (21%), Positives = 20/52 (38%), Gaps = 3/52 (5%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF--SREGKLFCRN 128
           C  C++ I  + + + L +T+H DC  C  C               +  C+ 
Sbjct: 18  CFSCDQFIEGEVV-SALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQK 68

>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 = 37.8 bits (88), Expect = 7e-05
 Identities = 14/86 (16%), Positives = 24/86 (27%), Gaps = 19/86 (22%)

Query: 48  GKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCY 107
                  D++    +F               C GC   +   F+    E  +H +C  C 
Sbjct: 2   SSGSSGKDYWG---KFG------------EFCHGCSLLMTGPFM-VAGEFKYHPECFACM 45

Query: 108 DCHHTLSDK---CFSREGKLFCRNDF 130
            C   + D       +   L+C    
Sbjct: 46  SCKVIIEDGDAYALVQHATLYCGKCH 71

>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 = 37.5 bits (87), Expect = 1e-04
 Identities = 12/55 (21%), Positives = 19/55 (34%), Gaps = 4/55 (7%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK---CFSREGKLFCRNDF 56
          C GC   +   F+    E  +H +C  C  C   + D       +   L+C    
Sbjct: 18 CHGCSLLMTGPFM-VAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCH 71

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	131
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	100.0
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	100.0
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	100.0
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.97
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.97
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.97
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.95
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.91
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.87
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.85
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.82
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.8
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.8
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.8
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.79
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.79
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.79
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.79
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.77
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.76
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.75
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.75
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.74
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.74
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.74
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.74
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.73
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.72
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.72
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.71
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.71
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.71
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.71
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.71
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.69
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.69
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.69
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.69
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.69
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.68
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.68
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.67
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.66
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.66
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.66
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.64
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.64
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.64
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.63
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.63
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.62
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.62
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.62
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.62
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.61
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.61
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.6
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.6
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.6
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.59
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.59
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.59
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.59
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.58
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.58
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.58
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.58
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.58
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.57
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.56
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.56
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.56
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.56
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.56
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.55
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.53
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.51
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.51
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.51
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.48
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.47
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.45
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.44
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.44
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.68
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.4
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	90.51
2kwj_A	114	Zinc finger protein DPF3; acetyl-lysine, transcrip	89.83
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	87.02
2e6s_A	77	E3 ubiquitin-protein ligase UHRF2; PHD domain, str	85.03
1bor_A	56	Transcription factor PML; proto-oncogene, nuclear	82.55
1jm7_B	117	BARD1, BRCA1-associated ring domain protein 1; rin	80.38

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

Probab=100.00  E-value=1.8e-34  Score=184.35  Aligned_cols=115  Identities=22%  Similarity=0.576  Sum_probs=102.3

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccccCCCCccccc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCA   80 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~   80 (131)
                      .++|++|+++|.+++++.++|+.||++||+|+.|+++|.++.| .++|++||+.||.++++++|.+|+++|.+.+.    
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~----   78 (126)
T 2xqn_T            3 KPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEVQ----   78 (126)
T ss_dssp             CCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCTTTCSBCCTTSC----
T ss_pred             CCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCcccCCcCCcCce----
Confidence            5789999999998878999999999999999999999998766 89999999999999999887777777765433    


Q ss_pred             cCCcccccceeeeecCCccc--ccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          81 GCEKPILDKFLLNVLERTWH--ADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        81 ~C~~~I~~~~~~~~~~~~~H--~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                                +++++++.||  ++||+|..|+++|++. |++.+|++||..+|
T Consensus        79 ----------~~~a~~~~~H~~~~CF~C~~C~~~l~~~~f~~~~~~~yC~~~~  121 (126)
T 2xqn_T           79 ----------RVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVEC  121 (126)
T ss_dssp             ----------EEEETTEEEESSTTTSBCTTTCCBCTTSEEEEETTEEESSHHH
T ss_pred             ----------EEECCCCEeeCCCCCcCcCCCCCccCCCeeEeECCEEcchHHh
Confidence                      2389999999  9999999999999977 88899999998654

>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=3.3e-34  Score=184.19  Aligned_cols=116  Identities=23%  Similarity=0.709  Sum_probs=99.2

Q ss_pred             CCCccccCCccccCceeEeecCCccccCCcccCCCcCcCCC--Ccc-CcCCeeecccCcCCCCCC--CCCCCccccCCCC
Q psy4437           1 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD--KCF-SREGKLFCRNDFFRSPVR--FPSGCGVGLSSSM   75 (131)
Q Consensus         1 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~--~~f-~~~~~~~C~~c~~~~~~~--~C~~c~~~i~~~~   75 (131)
                      ++++|++|+++|.+++++.++|+.||++||+|+.|+.+|.+  ..| .++|++||+.||.+++++  +|.+|+++|.+.+
T Consensus         1 s~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~~e   80 (131)
T 2xjy_A            1 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYE   80 (131)
T ss_dssp             CCCBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECTTS
T ss_pred             CcccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCccc
Confidence            36789999999999888999999999999999999999963  444 899999999999999887  5666665554432


Q ss_pred             ccccccCCcccccceeeeecCCcccccCccccccccccc-cc-eeccCCeeecCCCC
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS-DK-CFSREGKLFCRNDF  130 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~-~~-~~~~~g~~~C~~cy  130 (131)
                                    .+++++++.||++||+|..|+++|+ +. |++.+|++||..||
T Consensus        81 --------------~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~  123 (131)
T 2xjy_A           81 --------------MTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDI  123 (131)
T ss_dssp             --------------EEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGH
T ss_pred             --------------eeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHH
Confidence                          2348999999999999999999995 44 88999999999986

>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=100.00  E-value=5e-34  Score=194.11  Aligned_cols=128  Identities=18%  Similarity=0.514  Sum_probs=113.1

Q ss_pred             CccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccccCC--------
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSS--------   73 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~--------   73 (131)
                      ++|.+|+++|.+++.+.++|+.||++||+|+.|+++|.+..| .++|++||+.||.++++++|.+|+++...        
T Consensus         8 ~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~c~~c~~~~g~~~~~~~~~   87 (192)
T 1b8t_A            8 KKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGTLSTDKGES   87 (192)
T ss_dssp             EECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCCCCCCCCCC
T ss_pred             CcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCccccccccccccEecCCCcc
Confidence            579999999987777889999999999999999999999766 89999999999999999999988754210        


Q ss_pred             -------------------------CCccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecC
Q psy4437          74 -------------------------SMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCR  127 (131)
Q Consensus        74 -------------------------~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~  127 (131)
                                               +...+|..|+++|.+.+.+.++++.||++||+|+.|+++|.++ |++++|++||+
T Consensus        88 ~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~  167 (192)
T 1b8t_A           88 LGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCK  167 (192)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCCCCCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEH
T ss_pred             cccccccccccCCCCcCccccccccCCCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccccCCEEeCH
Confidence                                     1134699999999987777999999999999999999999877 89999999999


Q ss_pred             CCC
Q psy4437         128 NDF  130 (131)
Q Consensus       128 ~cy  130 (131)
                      .||
T Consensus       168 ~cy  170 (192)
T 1b8t_A          168 GCY  170 (192)
T ss_dssp             HHH
T ss_pred             HHH
Confidence            886

>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=4.2e-33  Score=188.15  Aligned_cols=115  Identities=32%  Similarity=0.918  Sum_probs=102.7

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccCCCCcccccc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAG   81 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~   81 (131)
                      .++|.+|+++|.+++++.++|+.||++||+|+.|+++|.+..|.++|++||+.||.++++++|.+|+++|.+.+..+   
T Consensus        60 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~g~~yC~~~y~~~f~~kC~~C~~~I~~~~~v~---  136 (182)
T 2jtn_A           60 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVR---  136 (182)
T ss_dssp             CCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCEEETTEEECHHHHHHTTSCCCTTTCCCCCSSCCCC---
T ss_pred             CCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCceeECCEeeecCccccccccccccCCCccCCCceEE---
Confidence            46899999999998888999999999999999999999998889999999999999999998888888887654432   


Q ss_pred             CCcccccceeeeecCCcccccCccccccccccccc--ee-ccCCeeecCCCC
Q psy4437          82 CEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CF-SREGKLFCRNDF  130 (131)
Q Consensus        82 C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~--~~-~~~g~~~C~~cy  130 (131)
                                 .+.++.||++||+|..|+++|..+  |+ ..+|++||..||
T Consensus       137 -----------~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy  177 (182)
T 2jtn_A          137 -----------RAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY  177 (182)
T ss_dssp             -----------EETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHH
T ss_pred             -----------ecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHH
Confidence                       799999999999999999999854  65 568999998876

>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=3.8e-33  Score=186.37  Aligned_cols=115  Identities=32%  Similarity=0.912  Sum_probs=100.8

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccCCCCcccccc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAG   81 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~   81 (131)
                      .++|.+|+++|.+++++.++|+.||++||+|+.|+++|.+..|+++|++||+.||.++++++|.+|+++|.+.+..    
T Consensus         6 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~g~~yC~~~y~~~f~~~C~~C~~~I~~~~~v----   81 (169)
T 2rgt_A            6 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVV----   81 (169)
T ss_dssp             -CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCCEESSSCEECHHHHHHHHSCBCTTTCCBCCTTSEE----
T ss_pred             CCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCCcccCCeeeecccccccccccccccccccCCCcEE----
Confidence            4689999999999888899999999999999999999999888999999999999999998888877777654432    


Q ss_pred             CCcccccceeeeecCCcccccCccccccccccccc--ee-ccCCeeecCCCC
Q psy4437          82 CEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CF-SREGKLFCRNDF  130 (131)
Q Consensus        82 C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~--~~-~~~g~~~C~~cy  130 (131)
                                +.++++.||++||+|..|+++|..+  |+ ..||++||..||
T Consensus        82 ----------~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~  123 (169)
T 2rgt_A           82 ----------RRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY  123 (169)
T ss_dssp             ----------EEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHH
T ss_pred             ----------EEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHH
Confidence                      3899999999999999999999744  65 568999998876

>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=1.4e-32  Score=186.41  Aligned_cols=115  Identities=31%  Similarity=0.771  Sum_probs=98.2

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCC---CccCcCCeeecccCcCCCCCC--CCCCCccccCCCCc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFRSPVR--FPSGCGVGLSSSML   76 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~---~~f~~~~~~~C~~c~~~~~~~--~C~~c~~~i~~~~~   76 (131)
                      .++|++|+++|.+++++.++++.||++||+|+.|+++|.+   .+|.++|++||+.||.+++++  +|.+|+++|.+.+ 
T Consensus         5 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~~e-   83 (188)
T 1rut_X            5 WKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPASE-   83 (188)
T ss_dssp             CCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECTTS-
T ss_pred             CCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCccccCc-
Confidence            4689999999999888999999999999999999999985   345899999999999999886  4555555554332 


Q ss_pred             cccccCCcccccceeeeecCCcccccCcccccccccccc-c-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD-K-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~-~~~~~g~~~C~~cy  130 (131)
                                   .++.++++.||++||+|..|+++|.. . |++.++++||..||
T Consensus        84 -------------~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~  126 (188)
T 1rut_X           84 -------------LVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDR  126 (188)
T ss_dssp             -------------EEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGC
T ss_pred             -------------EEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHH
Confidence                         23489999999999999999999964 3 88999999999998

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3

Probab=99.95  E-value=5e-29  Score=153.38  Aligned_cols=95  Identities=26%  Similarity=0.563  Sum_probs=83.5

Q ss_pred             CCccccCCcccc-CceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccccCCCCcccc
Q psy4437           2 LISCAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISC   79 (131)
Q Consensus         2 ~~~C~~C~~~I~-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C   79 (131)
                      .++|.+|+++|. +++++.++|+.||++||+|+.|+++|.+..| .++|++||+.||.++++++|.+|+++|.+++..  
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~--   82 (101)
T 2cup_A            5 SSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQN--   82 (101)
T ss_dssp             CCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCSSSCCBCCSSSCE--
T ss_pred             CCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccccCCCccccCCeE--
Confidence            468999999996 4778999999999999999999999988766 899999999999999998888877777654332  


Q ss_pred             ccCCcccccceeeeecCCcccccCccccccc
Q psy4437          80 AGCEKPILDKFLLNVLERTWHADCVRCYDCH  110 (131)
Q Consensus        80 ~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~  110 (131)
                                  ++++++.||++||+|+.|+
T Consensus        83 ------------~~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           83 ------------VEYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             ------------EESSSCEEETTTCCCTTCC
T ss_pred             ------------EEeCCcchHHhCCCCCCCC
Confidence                        3899999999999999985

>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=99.91  E-value=1.1e-25  Score=142.92  Aligned_cols=100  Identities=29%  Similarity=0.576  Sum_probs=82.6

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCC---CccCcCCeeecccCcCCCCCC--CCCCCccccCCCCc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFRSPVR--FPSGCGVGLSSSML   76 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~---~~f~~~~~~~C~~c~~~~~~~--~C~~c~~~i~~~~~   76 (131)
                      .++|++|+++|.+++++.++++.||++||+|+.|+++|.+   .+|.++|++||+.||.++|++  +|.+|+++|.+..+
T Consensus         5 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~~~   84 (122)
T 1m3v_A            5 WKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGDV   84 (122)
T ss_dssp             CCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCEES
T ss_pred             CCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCchhe
Confidence            5789999999999887899999999999999999999972   345899999999999999988  77777666655332


Q ss_pred             cccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                                      ++.++             .+|.+. |++++++|||..||
T Consensus        85 ----------------~~~g~-------------~~l~g~~f~~~~~~~yC~~~~  110 (122)
T 1m3v_A           85 ----------------MVVGE-------------PTLMGGEFGDEDERLITRLEN  110 (122)
T ss_dssp             ----------------SSSSS-------------SSCCSCTTCCTTCCCCEECTT
T ss_pred             ----------------EEcCC-------------cCCCCCccEecCCEeEccCcc
Confidence                            44442             246555 99999999999987

>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=99.87  E-value=3.3e-23  Score=129.92  Aligned_cols=95  Identities=24%  Similarity=0.558  Sum_probs=78.2

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCC---CccCcCCeeecccCcCCCCCCCCCCCccccCCCCccc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLIS   78 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~---~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~   78 (131)
                      +++|++|+++|.+++++.++++.||++||+|+.|+++|.+   .+|.++|+|||+.||.++|+++|..|...    ..  
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c~~~----~~--   76 (114)
T 1j2o_A            3 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGSGG----DV--   76 (114)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSCBSC----SC--
T ss_pred             CCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcCCCC----ce--
Confidence            5789999999999988999999999999999999999974   44599999999999999999998887521    11  


Q ss_pred             cccCCcccccceeeeecCCcccccCccccccccc-cccc-eeccCCeeecCCCC
Q psy4437          79 CAGCEKPILDKFLLNVLERTWHADCVRCYDCHHT-LSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        79 C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~-l~~~-~~~~~g~~~C~~cy  130 (131)
                             |      .               |+.+ |.+. |++++++|||..||
T Consensus        77 -------~------~---------------~~~~~~~g~~f~~~~~~~~C~~~~  102 (114)
T 1j2o_A           77 -------M------V---------------VGEPTLMGGEFGDEDERLITRLEN  102 (114)
T ss_dssp             -------C------C---------------SSCSSTTSSBCCCSSSCCCEEEEC
T ss_pred             -------e------E---------------cCCccCCCCeeEEcCCEeecchhh
Confidence                   0      1               2233 4444 88999999999887

>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=99.85  E-value=2.3e-21  Score=114.78  Aligned_cols=71  Identities=17%  Similarity=0.348  Sum_probs=61.2

Q ss_pred             CCeeecccCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeee
Q psy4437          47 EGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLF  125 (131)
Q Consensus        47 ~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~  125 (131)
                      +|+|||++||.++++++|.+|+++|.+.+.              ++.++++.||++||+|+.|+++|++. |++++|+||
T Consensus         1 ~g~~yC~~~y~~~~~~~C~~C~~~I~~~~~--------------~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~   66 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFANTCAECQQLIGHDSR--------------ELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELL   66 (82)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSSCC--------------BCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEE
T ss_pred             CCceechhHhCcccCCcCccCCCccccCcE--------------EEEeCCccccccCCeecCCCCccCCCccEeeCCEEE
Confidence            589999999999999877777777764332              33889999999999999999999987 889999999


Q ss_pred             cCCCCC
Q psy4437         126 CRNDFF  131 (131)
Q Consensus       126 C~~cy~  131 (131)
                      |+.||.
T Consensus        67 C~~c~~   72 (82)
T 2ehe_A           67 CNDCYC   72 (82)
T ss_dssp             ETTTSS
T ss_pred             CHHHHh
Confidence            999984

>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=2.9e-21  Score=113.01  Aligned_cols=73  Identities=14%  Similarity=0.309  Sum_probs=60.6

Q ss_pred             CCeeecccCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeee
Q psy4437          47 EGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLF  125 (131)
Q Consensus        47 ~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~  125 (131)
                      +++|||++||.++++++|.+|+++|.+.+.           +..++.++++.||++||+|+.|+++|++. |++.+|+||
T Consensus         1 g~~~yC~~cy~~~~~~~C~~C~~~I~~~g~-----------~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~y   69 (77)
T 2egq_A            1 GSSGSSGDCYKNFVAKKCAGCKNPITGFGK-----------GSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVY   69 (77)
T ss_dssp             CCSSCCTTCCCSCCCCCCSSSCCCCCCCSS-----------CCCEEEETTEEEETTTCBCSSSCCBCTTSCCCEETTEEC
T ss_pred             CCCeEchhHhchhhCccCcccCCcccCCCC-----------CceeEEECcceeCcccCEehhcCCCCCCCccEeECCEEE
Confidence            478999999999999877777777764110           22345999999999999999999999987 889999999


Q ss_pred             cCCCC
Q psy4437         126 CRNDF  130 (131)
Q Consensus       126 C~~cy  130 (131)
                      |+.||
T Consensus        70 C~~cy   74 (77)
T 2egq_A           70 CPDCA   74 (77)
T ss_dssp             CHHHH
T ss_pred             ChHHh
Confidence            98876

>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=99.80  E-value=1.5e-20  Score=109.68  Aligned_cols=70  Identities=26%  Similarity=0.484  Sum_probs=63.4

Q ss_pred             CccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecc-cCcCCCCCCCCCCCccccC
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCR-NDFFRSPVRFPSGCGVGLS   72 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~-~c~~~~~~~~C~~c~~~i~   72 (131)
                      ++|.+|+++|.+++.|.++|+.||++||+|+.|+++|.+..| .++|++||+ .||.++++++|.+|++++.
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 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGGAES   72 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSCCCSSS
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCCCcCCcee
Confidence            579999999986667899999999999999999999998666 899999999 6999999999999987654

>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=99.80  E-value=1.4e-20  Score=110.84  Aligned_cols=68  Identities=18%  Similarity=0.371  Sum_probs=58.0

Q ss_pred             CCeeecccCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeee
Q psy4437          47 EGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLF  125 (131)
Q Consensus        47 ~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~  125 (131)
                      +|+|||++||.++++++|.+|+++|.+               . .+.++++.||++||+|+.|+++|.+. |++++++||
T Consensus         1 gg~~yC~~cy~~~~~~~C~~C~~~I~~---------------~-~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~y   64 (80)
T 2cuq_A            1 GSSGSSGPCYENKFAPRCARCSKTLTQ---------------G-GVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPY   64 (80)
T ss_dssp             CCCCSCCCCCCCCSSCCCTTTCCCCCS---------------C-CEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEE
T ss_pred             CCcEEcHHHHccccCCcCCCCCCEecC---------------c-EEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEE
Confidence            588999999999998776666666543               2 23899999999999999999999876 899999999


Q ss_pred             cCCCC
Q psy4437         126 CRNDF  130 (131)
Q Consensus       126 C~~cy  130 (131)
                      |+.||
T Consensus        65 C~~cy   69 (80)
T 2cuq_A           65 CVACF   69 (80)
T ss_dssp             EHHHH
T ss_pred             CHHHH
Confidence            98876

>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=99.80  E-value=1.6e-20  Score=111.04  Aligned_cols=70  Identities=16%  Similarity=0.343  Sum_probs=58.9

Q ss_pred             CCeeecccCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeee
Q psy4437          47 EGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLF  125 (131)
Q Consensus        47 ~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~  125 (131)
                      ++.+||++||.++++++|.+|+++|.+.+.              ++.++++.||++||+|..|+++|.++ |+++++++|
T Consensus         1 ~~~~yC~~cy~~~~~~~C~~C~~~I~~~~~--------------~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~y   66 (82)
T 1x63_A            1 GSSGSSGKCTTREDSPKCKGCFKAIVAGDQ--------------NVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFY   66 (82)
T ss_dssp             CCSCCCCCCCSCCCSCBCSSSCCBCCSSSC--------------EEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEE
T ss_pred             CCCcCchhHHccccCCcCccCCcccccCce--------------EEEECccccccccCchhhCCCccCCCccEeeCCEEE
Confidence            468999999999998776666666654332              23899999999999999999999988 899999999


Q ss_pred             cCCCC
Q psy4437         126 CRNDF  130 (131)
Q Consensus       126 C~~cy  130 (131)
                      |+.||
T Consensus        67 C~~cy   71 (82)
T 1x63_A           67 CVTCH   71 (82)
T ss_dssp             EHHHH
T ss_pred             CHHHH
Confidence            98876

>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=99.79  E-value=2.1e-20  Score=110.07  Aligned_cols=68  Identities=24%  Similarity=0.598  Sum_probs=57.7

Q ss_pred             CCeeecccCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeee
Q psy4437          47 EGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLF  125 (131)
Q Consensus        47 ~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~  125 (131)
                      +|++||++||.++++++|.+|+++|.               +.. +.++++.||++||+|+.|+++|.++ |++++|+||
T Consensus         1 gg~~yC~~~y~~~~~~~C~~C~~~I~---------------~~~-v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~y   64 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFSPKCGGCNRPVL---------------ENY-LSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPF   64 (80)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCC---------------SSC-EEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEE
T ss_pred             CCCccchhHHhhhcCCccccCCCeec---------------cee-EEECCCeEecCcCChhhCCCCCCCCcEEeECCEEE
Confidence            57899999999999876666665554               322 3899999999999999999999887 999999999


Q ss_pred             cCCCC
Q psy4437         126 CRNDF  130 (131)
Q Consensus       126 C~~cy  130 (131)
                      |+.||
T Consensus        65 C~~~y   69 (80)
T 1x3h_A           65 CELHY   69 (80)
T ss_dssp             CHHHH
T ss_pred             CHHHH
Confidence            98876

>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=99.79  E-value=1.3e-19  Score=105.81  Aligned_cols=67  Identities=22%  Similarity=0.563  Sum_probs=61.0

Q ss_pred             CCccccCCccccC---ceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCc
Q psy4437           2 LISCAGCEKPILD---KFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCG   68 (131)
Q Consensus         2 ~~~C~~C~~~I~~---~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~   68 (131)
                      .++|++|+++|.+   .+++.++++.||++||+|+.|+++|.+..| .+++++||+.||.++++++|..++
T Consensus         5 ~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C~~~s   75 (76)
T 1x68_A            5 SSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISGPSS   75 (76)
T ss_dssp             CCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSSSSSC
T ss_pred             CCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcCCCCC
Confidence            4789999999985   467899999999999999999999998766 899999999999999999998765

>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=99.79  E-value=4e-20  Score=108.98  Aligned_cols=65  Identities=29%  Similarity=0.680  Sum_probs=59.5

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSG   66 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~   66 (131)
                      .++|.+|+++|.+++.|.++++.||++||+|..|+++|.+++|.+++++||+.||.++|+++|++
T Consensus        15 ~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~g~~yC~~~y~~~fg~~C~~   79 (80)
T 2dj7_A           15 PSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEYISKDGVPYCESDYHAQFGSGPSS   79 (80)
T ss_dssp             CSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSSCCEEETTEEECTTHHHHHTTCCSTT
T ss_pred             CCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCCCeEEECCEEECHHHHHHHcCCCCCC
Confidence            46799999999877789999999999999999999999987669999999999999999998864

>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=99.79  E-value=1.7e-20  Score=110.79  Aligned_cols=70  Identities=17%  Similarity=0.420  Sum_probs=55.1

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCcccc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGL   71 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i   71 (131)
                      ..+|.+|+++|.+.+.+.++++.||++||+|+.|+++|.+..| .+++++||+.||.++++++|.+|+++.
T Consensus         7 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~gcg~g~   77 (81)
T 1a7i_A            7 GNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGYGYGQGA   77 (81)
T ss_dssp             -CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC----------
T ss_pred             CCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCcccccCCcc
Confidence            3679999999987778899999999999999999999998766 899999999999999999999998764

>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=99.77  E-value=1.4e-19  Score=105.59  Aligned_cols=66  Identities=27%  Similarity=0.553  Sum_probs=59.6

Q ss_pred             CCCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecc-cCcCCCCCCCCCC
Q psy4437           1 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCR-NDFFRSPVRFPSG   66 (131)
Q Consensus         1 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~-~c~~~~~~~~C~~   66 (131)
                      +.++|.+|+++|.+.+.|.++++.||++||+|+.|+++|.+..| .+++++||+ .||.++|+++|.+
T Consensus         8 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~kc~g   75 (76)
T 2cu8_A            8 MASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGPSS   75 (76)
T ss_dssp             CCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSSCSC
T ss_pred             CCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccccCC
Confidence            35789999999997767889999999999999999999998766 899999999 7999999998864

>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=99.76  E-value=2.2e-19  Score=105.91  Aligned_cols=68  Identities=19%  Similarity=0.458  Sum_probs=55.5

Q ss_pred             CCeeecccCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCccccccccccccc--ee-ccCCe
Q psy4437          47 EGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK--CF-SREGK  123 (131)
Q Consensus        47 ~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~--~~-~~~g~  123 (131)
                      ++.+||++||.++++++|.+|+++|.               +.. +.++++.||++||+|+.|+++|..+  |+ +.+++
T Consensus         1 g~~~yC~~~y~~~~~~~C~~C~~~I~---------------~~~-~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~   64 (81)
T 1x6a_A            1 GSSGSSGKDYWGKFGEFCHGCSLLMT---------------GPF-MVAGEFKYHPECFACMSCKVIIEDGDAYALVQHAT   64 (81)
T ss_dssp             CCCCCCCCCSSCCSSCBCTTTCCBCC---------------SCC-BCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSC
T ss_pred             CCCccchhHHhhhcCCcCccCCCCcC---------------ceE-EEECCceeccccCCccCCCCccCCCCcEEEeeCCE
Confidence            36799999999999976666666655               222 3899999999999999999999753  66 58999


Q ss_pred             eecCCCC
Q psy4437         124 LFCRNDF  130 (131)
Q Consensus       124 ~~C~~cy  130 (131)
                      |||+.||
T Consensus        65 ~~C~~c~   71 (81)
T 1x6a_A           65 LYCGKCH   71 (81)
T ss_dssp             EEEHHHH
T ss_pred             EECHHHH
Confidence            9998876

>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=99.75  E-value=9.9e-19  Score=103.34  Aligned_cols=65  Identities=29%  Similarity=0.615  Sum_probs=59.0

Q ss_pred             CCccccCCcccc-CceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCC
Q psy4437           2 LISCAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSG   66 (131)
Q Consensus         2 ~~~C~~C~~~I~-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~   66 (131)
                      .++|++|+++|. ++.++.++++.||++||+|+.|+++|.+..| .+++++||+.||.++++++|.+
T Consensus        15 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C~~   81 (82)
T 2ehe_A           15 ANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGPSS   81 (82)
T ss_dssp             SCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGGGSSCC
T ss_pred             CCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCccEeeCCEEECHHHHhhhcCCCCCC
Confidence            468999999998 5667889999999999999999999998777 8999999999999999998864

>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=99.75  E-value=3.2e-19  Score=105.26  Aligned_cols=67  Identities=25%  Similarity=0.636  Sum_probs=54.1

Q ss_pred             CCeeecccCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCccccccccccccc-eecc-CCee
Q psy4437          47 EGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSR-EGKL  124 (131)
Q Consensus        47 ~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~-~g~~  124 (131)
                      +|+|||++||. +++++               |.+|+++|.+. ++.++++.||++||+|+.|+++|++. |+.. +|+|
T Consensus         2 ~g~~yC~~~y~-~~~~~---------------C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~   64 (81)
T 2dlo_A            2 SSGSSGEGCYV-ATLEK---------------CATCSQPILDR-ILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQI   64 (81)
T ss_dssp             CCCCCCCCCCC-SSCCB---------------CTTTCCBCCSC-CEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCC
T ss_pred             cCCEECHHHhh-cCCCc---------------cccCCCeecce-eEEECCccccHHhcCcccCCCccCCCeeEECCCCEE
Confidence            68999999998 66655               55555555543 34999999999999999999999977 6665 7999


Q ss_pred             ecCCCC
Q psy4437         125 FCRNDF  130 (131)
Q Consensus       125 ~C~~cy  130 (131)
                      ||+.||
T Consensus        65 yC~~cy   70 (81)
T 2dlo_A           65 HCIEDF   70 (81)
T ss_dssp             EEHHHH
T ss_pred             ECHHHH
Confidence            998876

>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=99.74  E-value=5.8e-19  Score=101.34  Aligned_cols=64  Identities=31%  Similarity=0.643  Sum_probs=58.1

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSG   66 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~   66 (131)
                      .++|.+|+++|.+. .+.++++.||++||+|+.|+++|.+..| .+++++||+.||.++++++|.+
T Consensus         5 ~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~~   69 (70)
T 2d8z_A            5 SSGCVQCKKPITTG-GVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPSS   69 (70)
T ss_dssp             CCBCSSSCCBCCSS-EEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCTT
T ss_pred             CCCCcccCCeeccc-eEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccCC
Confidence            46899999999876 4889999999999999999999998766 8999999999999999998864

>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=99.74  E-value=1e-18  Score=100.90  Aligned_cols=63  Identities=27%  Similarity=0.601  Sum_probs=57.0

Q ss_pred             CCccccCCccccC---ceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCC
Q psy4437           2 LISCAGCEKPILD---KFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFP   64 (131)
Q Consensus         2 ~~~C~~C~~~I~~---~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C   64 (131)
                      .++|.+|+++|.+   .+++.++++.||++||+|+.|+++|.+..| .+++++||+.||.++++|++
T Consensus         5 ~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p~~   71 (72)
T 1x4l_A            5 SSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPSS   71 (72)
T ss_dssp             SCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCSSC
T ss_pred             CCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCCCC
Confidence            4689999999985   467889999999999999999999998877 79999999999999998764

>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=99.74  E-value=5.3e-19  Score=102.00  Aligned_cols=65  Identities=23%  Similarity=0.562  Sum_probs=58.9

Q ss_pred             CCccccCCccccCc-eeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDK-FLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSG   66 (131)
Q Consensus         2 ~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~   66 (131)
                      .++|.+|+++|.+. +++.++++.||++||+|+.|+++|.+..| .+++++||+.||.++++++|+.
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1wyh_A            5 SSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGPSS   71 (72)
T ss_dssp             CCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCCCC
T ss_pred             CCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcCCC
Confidence            47899999999863 67889999999999999999999998766 8999999999999999998864

>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=99.74  E-value=6.6e-19  Score=101.60  Aligned_cols=65  Identities=23%  Similarity=0.588  Sum_probs=59.0

Q ss_pred             CCccccCCccccCc-eeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDK-FLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSG   66 (131)
Q Consensus         2 ~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~   66 (131)
                      .++|.+|+++|.+. .++.++++.||++||+|..|+++|.+..| .+++++||+.||.++++++|+.
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1x4k_A            5 SSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGPSS   71 (72)
T ss_dssp             CCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCCCC
T ss_pred             CCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCCCC
Confidence            46899999999875 57899999999999999999999998766 8999999999999999998863

>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=99.73  E-value=4.8e-19  Score=101.43  Aligned_cols=64  Identities=27%  Similarity=0.600  Sum_probs=58.2

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSG   66 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~   66 (131)
                      .++|.+|+++|.+. .|.++++.||++||+|+.|+++|.+..| .+++++||+.||.++++++|.+
T Consensus         5 ~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~g   69 (69)
T 2cur_A            5 SSGCVKCNKAITSG-GITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSSG   69 (69)
T ss_dssp             CCCCSSSCCCCCTT-CEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSCCC
T ss_pred             cCCCcccCCEeCcc-eEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCCCC
Confidence            46899999999876 5889999999999999999999998766 8999999999999999998864

>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=99.72  E-value=1.9e-18  Score=103.88  Aligned_cols=64  Identities=27%  Similarity=0.558  Sum_probs=57.7

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSG   66 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~   66 (131)
                      .++|.+|+++|.+. .|.++++.||++||+|..|+++|.+..| .+++++||+.||.++|+++|+.
T Consensus        25 ~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c~s   89 (90)
T 2dar_A           25 TPMCAHCNQVIRGP-FLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPSS   89 (90)
T ss_dssp             CCBBSSSCCBCCSC-EEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCCCC
T ss_pred             CCCCccCCCEecce-EEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCCCC
Confidence            46799999999765 6789999999999999999999998766 8999999999999999998863

>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=99.72  E-value=2.6e-18  Score=100.92  Aligned_cols=63  Identities=24%  Similarity=0.423  Sum_probs=56.8

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPS   65 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~   65 (131)
                      .++|.+|+++|.+. .|.++++.||++||+|..|+++|.+..|.++|++||+.||.++++|.++
T Consensus        15 ~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~g~~yC~~cy~~~f~p~~s   77 (79)
T 2cor_A           15 KYICQKCHAIIDEQ-PLIFKNDPYHPDHFNCANCGKELTADARELKGELYCLPCHDKMGVSGPS   77 (79)
T ss_dssp             CCBCTTTCCBCCSC-CCCCSSSCCCTTTSBCSSSCCBCCTTCEEETTEEECHHHHHTTSCCSSC
T ss_pred             CCCCccCCCEecce-EEEECcceeCCCCCEeCCCCCccCCCCEeECCEEeCHHHHHHhCCCCCC
Confidence            46899999999955 5889999999999999999999999878999999999999999987543

>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=99.71  E-value=2.4e-18  Score=101.45  Aligned_cols=64  Identities=34%  Similarity=0.762  Sum_probs=57.8

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-Cc-CCeeecccCcCCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SR-EGKLFCRNDFFRSPVRFPSG   66 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~-~~~~~C~~c~~~~~~~~C~~   66 (131)
                      .++|++|+++|.+. ++.++++.||++||+|+.|+++|.+..| .. +|++||+.||.++|+++|.+
T Consensus        15 ~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~~~C~~   80 (81)
T 2dlo_A           15 LEKCATCSQPILDR-ILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGPSS   80 (81)
T ss_dssp             CCBCTTTCCBCCSC-CEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTTSSSCC
T ss_pred             CCccccCCCeecce-eEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhcCcCCC
Confidence            46899999999875 7899999999999999999999998877 44 78999999999999998864

>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=99.71  E-value=1.9e-18  Score=101.62  Aligned_cols=64  Identities=30%  Similarity=0.809  Sum_probs=58.0

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSG   66 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~   66 (131)
                      .++|++|+++|.+. .|.++++.||++||+|+.|+++|.+..| .+++++||+.||.++++++|.+
T Consensus        15 ~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C~~   79 (80)
T 1x3h_A           15 SPKCGGCNRPVLEN-YLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGPSS   79 (80)
T ss_dssp             SCBCTTTCCBCCSS-CEEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHHHSSSCCC
T ss_pred             CCccccCCCeecce-eEEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHHcCCCCCC
Confidence            46899999999885 6889999999999999999999998655 8999999999999999998864

>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=99.71  E-value=1.4e-18  Score=98.62  Aligned_cols=61  Identities=20%  Similarity=0.571  Sum_probs=54.6

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRF   63 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~   63 (131)
                      .++|++|+++|.+ +++.++|+.||++||+|+.|+++|.+..| .++|++||+.||.++|+++
T Consensus         5 ~~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~k   66 (66)
T 1nyp_A            5 VPICGACRRPIEG-RVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGDV   66 (66)
T ss_dssp             CCEETTTTEECCS-CEECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSCC
T ss_pred             CCCCcccCCEecc-eEEEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHhCCC
Confidence            4689999999995 46889999999999999999999998666 8999999999999888764

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

Probab=99.71  E-value=1.7e-18  Score=101.08  Aligned_cols=64  Identities=20%  Similarity=0.474  Sum_probs=56.1

Q ss_pred             CCccccCCccccC-ceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCC
Q psy4437           2 LISCAGCEKPILD-KFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPS   65 (131)
Q Consensus         2 ~~~C~~C~~~I~~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~   65 (131)
                      ..+|.+|+++|.+ +.++.++|+.||++||+|..|+++|.+..| .++|++||+.||.++++++|.
T Consensus        11 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C~   76 (77)
T 1g47_A           11 SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCWI   76 (77)
T ss_dssp             CCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC--
T ss_pred             CCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcccC
Confidence            4689999999974 556789999999999999999999998666 899999999999999998875

>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=99.71  E-value=4.3e-18  Score=102.52  Aligned_cols=64  Identities=23%  Similarity=0.506  Sum_probs=58.7

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPS   65 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~   65 (131)
                      ..+|.+|+++|.+.+.|.++++.||++||+|+.|+++|.+..| .+++++||+.||.++++++|.
T Consensus        15 ~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~   79 (91)
T 2d8y_A           15 RETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGN   79 (91)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSC
T ss_pred             CCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcC
Confidence            3579999999988778899999999999999999999998655 899999999999999999887

>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=99.69  E-value=1.9e-17  Score=97.82  Aligned_cols=63  Identities=22%  Similarity=0.395  Sum_probs=55.5

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc---CcCCeeecccCcCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF---SREGKLFCRNDFFRSPVRFP   64 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f---~~~~~~~C~~c~~~~~~~~C   64 (131)
                      ..+|.+|+++|.+.+.+.++++.||++||+|+.|+++|.+..|   .++|++||+.||.++++...
T Consensus        15 ~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~   80 (82)
T 2co8_A           15 GDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSGPS   80 (82)
T ss_dssp             SCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCCCC
T ss_pred             CCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcCCC
Confidence            4679999999988777889999999999999999999998765   37999999999999887543

>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=99.69  E-value=3.6e-18  Score=100.70  Aligned_cols=67  Identities=18%  Similarity=0.304  Sum_probs=53.5

Q ss_pred             CeeecccCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCC-eee
Q psy4437          48 GKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREG-KLF  125 (131)
Q Consensus        48 ~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g-~~~  125 (131)
                      +.+||++||.++++++|.+|+++|.               +. +++++++.||++||+|..|+++|..+ ++..++ .+|
T Consensus         2 ~~~yC~~dy~~~~~~~C~~C~~~I~---------------~~-~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~   65 (81)
T 1v6g_A            2 SSGSSGLDYQRLYGTRCFSCDQFIE---------------GE-VVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECM   65 (81)
T ss_dssp             CCCCCCSCGGGSCCCBCTTTCCBCC---------------SC-CEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEE
T ss_pred             CCCcchHHHHhHhCCcCccccCEec---------------cc-eEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEE
Confidence            5689999999999976666666554               22 23899999999999999999999866 666555 579


Q ss_pred             cCCCC
Q psy4437         126 CRNDF  130 (131)
Q Consensus       126 C~~cy  130 (131)
                      |..||
T Consensus        66 C~~C~   70 (81)
T 1v6g_A           66 CQKCS   70 (81)
T ss_dssp             EHHHH
T ss_pred             Chhhh
Confidence            98775

>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=99.69  E-value=5.1e-18  Score=99.76  Aligned_cols=64  Identities=27%  Similarity=0.576  Sum_probs=58.0

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSG   66 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~   66 (131)
                      .++|.+|+++|.+. .|.++++.||++||+|+.|+++|.+..| .+++++||+.||.++++++|+.
T Consensus        15 ~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~s   79 (80)
T 2cuq_A           15 APRCARCSKTLTQG-GVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPSS   79 (80)
T ss_dssp             SCCCTTTCCCCCSC-CEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCSTTC
T ss_pred             CCcCCCCCCEecCc-EEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCCCCC
Confidence            46899999999876 6889999999999999999999988666 8999999999999999998863

>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=7e-18  Score=101.18  Aligned_cols=63  Identities=24%  Similarity=0.537  Sum_probs=56.6

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPS   65 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~   65 (131)
                      ..+|.+|+++|.+. ++.++++.||++||+|..|+++|.+..| .+++++||+.||.++|++++.
T Consensus        25 ~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~~   88 (89)
T 1x64_A           25 MPLCDKCGSGIVGA-VVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSS   88 (89)
T ss_dssp             CCBCTTTCCBCCSC-CEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCCC
T ss_pred             CCCcccCCCEeccc-EEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            46799999999875 6889999999999999999999998544 899999999999999998765

>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=99.69  E-value=1.7e-17  Score=97.63  Aligned_cols=58  Identities=29%  Similarity=0.747  Sum_probs=51.8

Q ss_pred             CCCccccccCCcccccceeeeecCCcccccCccccccccccccceeccCCeeecCCCC
Q psy4437          73 SSMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF  130 (131)
Q Consensus        73 ~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~g~~~C~~cy  130 (131)
                      ......|..|+++|.+.+.+.++++.||++||+|..|+++|.+.|+++||+|||+.||
T Consensus        12 ~~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~g~~yC~~~y   69 (80)
T 2dj7_A           12 IRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEYISKDGVPYCESDY   69 (80)
T ss_dssp             CSSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSSCCEEETTEEECTTHH
T ss_pred             CCCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCCCeEEECCEEECHHHH
Confidence            3445789999999987777799999999999999999999986699999999999987

>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=99.68  E-value=1e-17  Score=96.13  Aligned_cols=61  Identities=26%  Similarity=0.670  Sum_probs=55.0

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRF   63 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~   63 (131)
                      ..+|.+|+++|.+. ++.++++.||++||+|..|+++|.+..| .+++++||+.||.++++++
T Consensus         5 ~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~   66 (70)
T 2d8x_A            5 SSGCHQCGEFIIGR-VIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASG   66 (70)
T ss_dssp             SSBCSSSCCBCCSC-CEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCC
T ss_pred             CCcCccCCCEecce-EEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCC
Confidence            46899999999865 6889999999999999999999999777 7999999999999888764

>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=99.68  E-value=3.2e-18  Score=100.53  Aligned_cols=63  Identities=24%  Similarity=0.490  Sum_probs=56.6

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPS   65 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~   65 (131)
                      ..+|.+|+++|.+. ++.++++.||++||+|..|+++|.+..| .+++++||+.||.+++++++.
T Consensus        15 ~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g~   78 (79)
T 1x62_A           15 LPMCDKCGTGIVGV-FVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSS   78 (79)
T ss_dssp             CCCCSSSCCCCCSS-CEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCCC
T ss_pred             CCccccCCCCccCc-EEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            46899999999886 6889999999999999999999987655 899999999999999988754

>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=99.67  E-value=1.5e-17  Score=112.78  Aligned_cols=69  Identities=20%  Similarity=0.576  Sum_probs=63.4

Q ss_pred             CccccCCccccCceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCcccc
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGL   71 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i   71 (131)
                      .+|.+|+++|.+.+.|.++++.||++||+|+.|+++|.+..| .++|++||+.||.++++++|.+|++++
T Consensus       116 ~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~kc~~C~~~~  185 (192)
T 1b8t_A          116 DGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQGA  185 (192)
T ss_dssp             EECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCCC
T ss_pred             CcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccccCCEEeCHHHHHHhcCCcCCCCCCcc
Confidence            359999999987777889999999999999999999987656 899999999999999999999999885

>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=99.66  E-value=5.2e-17  Score=93.93  Aligned_cols=60  Identities=18%  Similarity=0.419  Sum_probs=53.0

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCC-CCcc-CcCCeeecccCcCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS-DKCF-SREGKLFCRNDFFRSPVR   62 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~-~~~f-~~~~~~~C~~c~~~~~~~   62 (131)
                      .++|++|+++|.+. +|.++++.||++||+|+.|+++|. +..| .+++++||..||.+.++.
T Consensus         5 ~~~C~~C~~~I~~~-~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~   66 (73)
T 1wig_A            5 SSGCDSCEKYITGR-VLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTE   66 (73)
T ss_dssp             CCSCSSSCCCCSSC-CBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSS
T ss_pred             cCCcccCCCEecCe-eEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhcc
Confidence            47899999999885 688999999999999999999998 5555 899999999999877653

>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=99.66  E-value=9.7e-17  Score=94.79  Aligned_cols=58  Identities=24%  Similarity=0.402  Sum_probs=51.1

Q ss_pred             CCccccccCCcccccceeeeecCCcccccCccccccccccccc-ee--ccCCeeecCCCCC
Q psy4437          74 SMLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CF--SREGKLFCRNDFF  131 (131)
Q Consensus        74 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~--~~~g~~~C~~cy~  131 (131)
                      ....+|.+|+++|.+.+.+.++++.||++||+|+.|+++|... |+  ++||++||+.||.
T Consensus        13 ~~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~   73 (82)
T 2co8_A           13 GAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLP   73 (82)
T ss_dssp             CSSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCC
T ss_pred             CCCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHH
Confidence            3457899999999887777899999999999999999999988 65  5799999999984

>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=99.66  E-value=2.6e-17  Score=97.15  Aligned_cols=64  Identities=23%  Similarity=0.543  Sum_probs=56.8

Q ss_pred             CCccccCCccccCc-eeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDK-FLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPS   65 (131)
Q Consensus         2 ~~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~   65 (131)
                      .++|++|+++|... .++.++++.||++||+|..|+++|.+..| .+++++||+.||.+++++++.
T Consensus        15 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~   80 (82)
T 1x63_A           15 SPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPS   80 (82)
T ss_dssp             SCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCS
T ss_pred             CCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCC
Confidence            46899999999853 35889999999999999999999998766 899999999999999988764

>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=99.64  E-value=3.2e-17  Score=103.84  Aligned_cols=59  Identities=36%  Similarity=0.926  Sum_probs=53.0

Q ss_pred             CccccCCccccCceeEeecCCccccCCcccCCCcCcCC--C-CccCcCCeeecccCcCCCCC
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--D-KCFSREGKLFCRNDFFRSPV   61 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~--~-~~f~~~~~~~C~~c~~~~~~   61 (131)
                      ++|.+|+++|.+++++.++++.||++||+|..|+++|.  + .+|.++|++||+.||.++|+
T Consensus        62 ~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           62 KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             SBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             CcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            57999999999988899999999999999999999997  3 45589999999999987764

>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=99.64  E-value=2.8e-17  Score=94.73  Aligned_cols=60  Identities=22%  Similarity=0.585  Sum_probs=53.3

Q ss_pred             CCccccCCccccC-ceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCC
Q psy4437           2 LISCAGCEKPILD-KFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPV   61 (131)
Q Consensus         2 ~~~C~~C~~~I~~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~   61 (131)
                      .++|.+|+++|.+ +.++.++++.||++||+|+.|+++|.+..| .+++++||+.||.+++.
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~~   66 (72)
T 1x61_A            5 SSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLE   66 (72)
T ss_dssp             CCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHHH
T ss_pred             CCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHHc
Confidence            4689999999986 457889999999999999999999988766 89999999999987764

>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=2.5e-16  Score=91.65  Aligned_cols=55  Identities=25%  Similarity=0.692  Sum_probs=45.7

Q ss_pred             cccccCCccccc---ceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCCC
Q psy4437          77 ISCAGCEKPILD---KFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDFF  131 (131)
Q Consensus        77 ~~C~~C~~~I~~---~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy~  131 (131)
                      .+|..|+++|.+   ..++.++++.||++||+|+.|+++|.+. |++++|+|||+.||.
T Consensus         6 ~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~   64 (76)
T 1x68_A            6 SGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGS   64 (76)
T ss_dssp             CCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTC
T ss_pred             CCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhh
Confidence            346666666663   3455999999999999999999999877 899999999999984

>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=99.63  E-value=3.9e-16  Score=98.80  Aligned_cols=56  Identities=36%  Similarity=0.984  Sum_probs=50.6

Q ss_pred             CccccccCCcccccceeeeecCCcccccCccccccccccc--c-ceeccCCeeecCCCC
Q psy4437          75 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--D-KCFSREGKLFCRNDF  130 (131)
Q Consensus        75 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~--~-~~~~~~g~~~C~~cy  130 (131)
                      ...+|.+|+++|.++.++.++++.||++||+|..|+++|.  + .|++++|+|||+.||
T Consensus        60 ~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy  118 (123)
T 2l4z_A           60 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDY  118 (123)
T ss_dssp             SCSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHH
T ss_pred             cCCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHh
Confidence            3478999999999988779999999999999999999997  2 399999999999887

>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=99.63  E-value=5.6e-17  Score=93.26  Aligned_cols=60  Identities=22%  Similarity=0.540  Sum_probs=52.6

Q ss_pred             CCccccCCccccCce-eEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCCCCC
Q psy4437           2 LISCAGCEKPILDKF-LLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPV   61 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~   61 (131)
                      ..+|++|+++|.+.+ ++.++++.||++||+|+.|+++|.+..| .++|++||+.||.++|+
T Consensus        11 ~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B           11 SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             TCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHTC
T ss_pred             CccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhhC
Confidence            568999999998654 5689999999999999999999988655 89999999999977653

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

Probab=99.62  E-value=1.1e-16  Score=90.60  Aligned_cols=58  Identities=28%  Similarity=0.579  Sum_probs=51.0

Q ss_pred             CCccccCCccccC-ceeEeecCCccc--cCCcccCCCcCcCCCCcc-CcCCeeec-ccCcCCC
Q psy4437           2 LISCAGCEKPILD-KFLLNVLERTWH--ADCVRCYDCHHTLSDKCF-SREGKLFC-RNDFFRS   59 (131)
Q Consensus         2 ~~~C~~C~~~I~~-~~~~~~~~~~~H--~~Cf~C~~C~~~l~~~~f-~~~~~~~C-~~c~~~~   59 (131)
                      .++|.+|+++|.+ ++.|.++|+.||  ++||+|+.|+++|.+..| .++|+||| .+||.+.
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 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCTTSCCEEETTEEESSHHHHHTT
T ss_pred             cCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCCCCceEEECCEEecCHHHhhhh
Confidence            4689999999985 367899999999  999999999999998766 89999999 7887543

>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=99.62  E-value=1.9e-16  Score=91.53  Aligned_cols=53  Identities=21%  Similarity=0.528  Sum_probs=44.5

Q ss_pred             cccccCCcccccceeeeecCCcccccCccccccccccc-cc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS-DK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~-~~-~~~~~g~~~C~~cy  130 (131)
                      +.|.+|+++|.+.. +.++++.||++||+|+.|+++|. +. |++.++++||..||
T Consensus         6 ~~C~~C~~~I~~~~-v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~   60 (73)
T 1wig_A            6 SGCDSCEKYITGRV-LEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACR   60 (73)
T ss_dssp             CSCSSSCCCCSSCC-BCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHH
T ss_pred             CCcccCCCEecCee-EEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHC
Confidence            45666666776643 48999999999999999999998 44 88999999999986

>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=1.2e-16  Score=91.52  Aligned_cols=54  Identities=26%  Similarity=0.736  Sum_probs=47.9

Q ss_pred             ccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      ...|..|+++|.+.. +.++++.||++||+|..|+++|.+. |+.++|++||+.||
T Consensus         5 ~~~C~~C~~~I~~~~-~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~   59 (70)
T 2d8x_A            5 SSGCHQCGEFIIGRV-IKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCH   59 (70)
T ss_dssp             SSBCSSSCCBCCSCC-EEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHH
T ss_pred             CCcCccCCCEecceE-EEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHh
Confidence            457888888888654 5999999999999999999999988 88899999999886

>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=99.62  E-value=8.7e-17  Score=94.70  Aligned_cols=64  Identities=20%  Similarity=0.469  Sum_probs=55.4

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCC-Ccc--CcCCeeecccCcCCCCCCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD-KCF--SREGKLFCRNDFFRSPVRFPSG   66 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~f--~~~~~~~C~~c~~~~~~~~C~~   66 (131)
                      .++|++|+++|.+. .+.++++.||++||+|..|+++|.+ ..|  ++++++||+.||.+++++.+++
T Consensus        15 ~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~~sg   81 (81)
T 1x6a_A           15 GEFCHGCSLLMTGP-FMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSGPSSG   81 (81)
T ss_dssp             SCBCTTTCCBCCSC-CBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCTTSCC
T ss_pred             CCcCccCCCCcCce-EEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcCCCCC
Confidence            46899999999954 6889999999999999999999964 556  4899999999999988876653

>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=99.61  E-value=1.4e-16  Score=92.94  Aligned_cols=57  Identities=26%  Similarity=0.691  Sum_probs=51.1

Q ss_pred             CCccccCCccccC----ceeEeecCCccccCCcccCCCcCcCCCCcc-CcCCeeecccCcCC
Q psy4437           2 LISCAGCEKPILD----KFLLNVLERTWHADCVRCYDCHHTLSDKCF-SREGKLFCRNDFFR   58 (131)
Q Consensus         2 ~~~C~~C~~~I~~----~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~f-~~~~~~~C~~c~~~   58 (131)
                      .++|++|+++|.+    ++++.++++.||++||+|+.|+++|.+..| .+++++||+.||.+
T Consensus        15 ~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A           15 AKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHH
T ss_pred             CccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCccEeECCEEEChHHhcc
Confidence            4789999999984    567899999999999999999999998766 89999999999853

>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=99.61  E-value=3.9e-16  Score=90.83  Aligned_cols=54  Identities=28%  Similarity=0.690  Sum_probs=48.3

Q ss_pred             cccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecC-CCC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCR-NDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~-~cy  130 (131)
                      .+|..|+++|.+.+.+.++++.||++||+|..|+++|.+. |++++++|||+ .||
T Consensus        10 ~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy   65 (76)
T 2cu8_A           10 SKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCY   65 (76)
T ss_dssp             CBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHH
T ss_pred             CCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHH
Confidence            5788888888866666999999999999999999999987 89999999999 686

>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=99.60  E-value=1.8e-16  Score=91.28  Aligned_cols=54  Identities=30%  Similarity=0.762  Sum_probs=46.4

Q ss_pred             cccccCCccccc---ceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILD---KFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~---~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      ..|..|+++|.+   ..++.++++.||++||+|+.|+++|.+. |++++|+|||..||
T Consensus         6 ~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~   63 (72)
T 1x4l_A            6 SGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCG   63 (72)
T ss_dssp             CSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHH
T ss_pred             CCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHc
Confidence            567777777774   3556899999999999999999999877 88899999998876

>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=99.60  E-value=1.2e-16  Score=90.62  Aligned_cols=53  Identities=23%  Similarity=0.789  Sum_probs=46.4

Q ss_pred             cccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .+|.+|+++|.+. .+.++++.||++||+|+.|+++|.+. |++++|++||+.||
T Consensus         6 ~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y   59 (66)
T 1nyp_A            6 PICGACRRPIEGR-VVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHY   59 (66)
T ss_dssp             CEETTTTEECCSC-EECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHH
T ss_pred             CCCcccCCEecce-EEEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHH
Confidence            4677888888744 45999999999999999999999887 99999999999886

>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=99.60  E-value=2.1e-16  Score=91.01  Aligned_cols=54  Identities=22%  Similarity=0.661  Sum_probs=46.0

Q ss_pred             cccccCCcccccc-eeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDK-FLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .+|..|+++|.+. .++.++++.||++||+|..|+++|.++ |++++|++||+.||
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy   61 (72)
T 1x4k_A            6 SGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCY   61 (72)
T ss_dssp             CCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHH
T ss_pred             CCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHH
Confidence            4566677777653 455999999999999999999999988 89999999999886

>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=99.59  E-value=3.9e-16  Score=90.81  Aligned_cols=53  Identities=28%  Similarity=0.726  Sum_probs=47.6

Q ss_pred             ccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecC-CCC
Q psy4437          78 SCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCR-NDF  130 (131)
Q Consensus        78 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~-~cy  130 (131)
                      +|.+|+++|.+.+.+.++++.||++||+|..|+++|+++ |++++|++||+ .||
T Consensus         2 ~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy   56 (76)
T 1iml_A            2 KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCY   56 (76)
T ss_dssp             BCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHH
T ss_pred             cCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHH
Confidence            588888888866666999999999999999999999987 89999999999 586

>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=99.59  E-value=2.7e-16  Score=89.88  Aligned_cols=53  Identities=26%  Similarity=0.710  Sum_probs=46.3

Q ss_pred             cccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .+|..|+++|.+.. +.++++.||++||+|+.|+++|.+. |++++++|||+.||
T Consensus         6 ~~C~~C~~~I~~~~-~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy   59 (69)
T 2cur_A            6 SGCVKCNKAITSGG-ITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCY   59 (69)
T ss_dssp             CCCSSSCCCCCTTC-EEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHH
T ss_pred             CCCcccCCEeCcce-EEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHh
Confidence            56777888887654 4999999999999999999999876 89999999998876

>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=99.59  E-value=2.4e-16  Score=92.77  Aligned_cols=55  Identities=16%  Similarity=0.521  Sum_probs=49.1

Q ss_pred             ccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      ..+|..|+++|.+.+.+.+.++.||++||+|+.|+++|... |+++++++||+.||
T Consensus         7 ~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy   62 (81)
T 1a7i_A            7 GNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCY   62 (81)
T ss_dssp             -CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHH
T ss_pred             CCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHH
Confidence            36788999999766667999999999999999999999988 89999999999886

>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=99.59  E-value=3.8e-16  Score=89.89  Aligned_cols=54  Identities=22%  Similarity=0.655  Sum_probs=45.9

Q ss_pred             cccccCCcccccc-eeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDK-FLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .+|..|+++|.+. .++.++++.||++||+|+.|+++|.++ |++++|++||+.||
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy   61 (72)
T 1wyh_A            6 SGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCY   61 (72)
T ss_dssp             CBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHH
T ss_pred             CCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHH
Confidence            4566677777652 555999999999999999999999987 89999999999876

>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=99.58  E-value=5.4e-16  Score=90.95  Aligned_cols=54  Identities=22%  Similarity=0.466  Sum_probs=47.4

Q ss_pred             ccccccCCcccccceeeeecCCcccccCccccccccccccceeccCCeeecCCCC
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF  130 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~g~~~C~~cy  130 (131)
                      ..+|..|+++|.+.. +.++++.||++||+|..|+++|.+.+++++|+|||..||
T Consensus        15 ~~~C~~C~~~I~~~~-v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~g~~yC~~cy   68 (79)
T 2cor_A           15 KYICQKCHAIIDEQP-LIFKNDPYHPDHFNCANCGKELTADARELKGELYCLPCH   68 (79)
T ss_dssp             CCBCTTTCCBCCSCC-CCCSSSCCCTTTSBCSSSCCBCCTTCEEETTEEECHHHH
T ss_pred             CCCCccCCCEecceE-EEECcceeCCCCCEeCCCCCccCCCCEeECCEEeCHHHH
Confidence            367888888888555 499999999999999999999998866999999999886

>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=99.58  E-value=3.6e-16  Score=89.83  Aligned_cols=54  Identities=22%  Similarity=0.667  Sum_probs=44.6

Q ss_pred             cccccCCcccccce-eeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDKF-LLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .+|.+|+++|.+.+ ++.+.++.||++||+|+.|+++|.++ |++++|++||+.||
T Consensus        12 ~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y   67 (72)
T 3f6q_B           12 ATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDF   67 (72)
T ss_dssp             CBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHH
T ss_pred             ccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHH
Confidence            45666666666432 34899999999999999999999988 88999999999886

>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=99.58  E-value=3.9e-16  Score=89.40  Aligned_cols=53  Identities=32%  Similarity=0.744  Sum_probs=46.5

Q ss_pred             cccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .+|..|+++|.+.. +.++++.||++||+|..|+++|.+. |++++++|||+.||
T Consensus         6 ~~C~~C~~~I~~~~-~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy   59 (70)
T 2d8z_A            6 SGCVQCKKPITTGG-VTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCF   59 (70)
T ss_dssp             CBCSSSCCBCCSSE-EESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHH
T ss_pred             CCCcccCCeeccce-EEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHH
Confidence            46778888887655 4999999999999999999999877 88999999998876

>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=99.58  E-value=5.7e-16  Score=89.15  Aligned_cols=54  Identities=22%  Similarity=0.674  Sum_probs=46.2

Q ss_pred             cccccCCccccc-ceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILD-KFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .+|.+|+++|.+ ..++.++++.||++||+|..|+++|.+. |++++++|||+.||
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy   61 (72)
T 1x61_A            6 SGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCY   61 (72)
T ss_dssp             CCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHH
T ss_pred             CCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHH
Confidence            467777777765 3455999999999999999999999876 99999999999886

>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=99.57  E-value=3.1e-16  Score=91.91  Aligned_cols=55  Identities=27%  Similarity=0.648  Sum_probs=49.0

Q ss_pred             CccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          75 MLISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        75 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      ...+|..|+++|.+. ++.++++.||++||+|..|+++|.+. |+++++++||+.||
T Consensus        14 ~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy   69 (79)
T 1x62_A           14 KLPMCDKCGTGIVGV-FVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHA   69 (79)
T ss_dssp             CCCCCSSSCCCCCSS-CEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHH
T ss_pred             CCCccccCCCCccCc-EEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHH
Confidence            346899999999886 45999999999999999999999876 99999999999887

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

Probab=99.56  E-value=8.5e-16  Score=89.51  Aligned_cols=54  Identities=22%  Similarity=0.681  Sum_probs=46.4

Q ss_pred             cccccCCccccc-ceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILD-KFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      ..|.+|+++|.+ ..++.++++.||++||+|..|+++|.++ |++++|++||+.||
T Consensus        12 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y   67 (77)
T 1g47_A           12 ATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDF   67 (77)
T ss_dssp             CBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHH
T ss_pred             CCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHH
Confidence            567777777763 4445899999999999999999999987 89999999999886

>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=99.56  E-value=7.3e-16  Score=92.65  Aligned_cols=55  Identities=27%  Similarity=0.625  Sum_probs=49.6

Q ss_pred             ccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      ...|..|+++|.+.+.+.++++.||++||+|..|+++|..+ |+++++++||+.||
T Consensus        15 ~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y   70 (91)
T 2d8y_A           15 RETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHF   70 (91)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHH
T ss_pred             CCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHH
Confidence            36788888988876667999999999999999999999988 99999999999876

>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=99.56  E-value=7.8e-16  Score=92.34  Aligned_cols=53  Identities=28%  Similarity=0.695  Sum_probs=46.0

Q ss_pred             cccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .+|..|+++|.+..+ .++++.||++||+|..|+++|.+. |++.+|++||+.||
T Consensus        26 ~~C~~C~~~I~~~~v-~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy   79 (90)
T 2dar_A           26 PMCAHCNQVIRGPFL-VALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCY   79 (90)
T ss_dssp             CBBSSSCCBCCSCEE-EETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHH
T ss_pred             CCCccCCCEecceEE-EECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHH
Confidence            567777777765544 899999999999999999999987 88999999999887

>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=99.56  E-value=7.5e-16  Score=96.27  Aligned_cols=55  Identities=33%  Similarity=0.987  Sum_probs=49.8

Q ss_pred             ccccccCCcccccceeeeecCCcccccCcccccccccccc---ceeccCCeeecCCCC
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD---KCFSREGKLFCRNDF  130 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~---~~~~~~g~~~C~~cy  130 (131)
                      ..+|.+|+++|.+..++.++++.||++||+|+.|+++|+.   .|++++|+|||+.||
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y   60 (114)
T 1j2o_A            3 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY   60 (114)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHH
T ss_pred             CCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHH
Confidence            3679999999999877799999999999999999999984   399999999999887

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

Probab=99.56  E-value=5.8e-16  Score=87.53  Aligned_cols=54  Identities=26%  Similarity=0.608  Sum_probs=45.5

Q ss_pred             cccccCCccccc-ceeeeecCCccc--ccCccccccccccccc-eeccCCeeec-CCCC
Q psy4437          77 ISCAGCEKPILD-KFLLNVLERTWH--ADCVRCYDCHHTLSDK-CFSREGKLFC-RNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~-~~~~~~~~~~~H--~~Cf~C~~C~~~l~~~-~~~~~g~~~C-~~cy  130 (131)
                      ..|.+|+++|.+ ...++++++.||  ++||+|+.|+++|.+. |++++|+||| .+||
T Consensus         3 ~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L~~~~f~~~~g~~yC~~~C~   61 (65)
T 2iyb_E            3 VVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECK   61 (65)
T ss_dssp             EECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCTTSCCEEETTEEESSHHHH
T ss_pred             CCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCCCCceEEECCEEecCHHHh
Confidence            357778888875 245599999999  9999999999999887 9999999999 5554

>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=1.1e-15  Score=91.45  Aligned_cols=54  Identities=28%  Similarity=0.680  Sum_probs=48.5

Q ss_pred             ccccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      ..+|..|+++|.+.. +.++++.||++||+|..|+++|..+ |+++++++||+.||
T Consensus        25 ~~~C~~C~~~I~~~~-~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y   79 (89)
T 1x64_A           25 MPLCDKCGSGIVGAV-VKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHA   79 (89)
T ss_dssp             CCBCTTTCCBCCSCC-EESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHH
T ss_pred             CCCcccCCCEecccE-EEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHH
Confidence            467999999998854 5999999999999999999999987 99999999999887

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

Probab=99.51  E-value=2.8e-15  Score=95.07  Aligned_cols=54  Identities=24%  Similarity=0.631  Sum_probs=48.8

Q ss_pred             cccccCCcccccceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .+|.+|+++|.++.++.++|+.||++||+|+.|+++|++. |+++||+|||+.||
T Consensus         4 ~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy   58 (126)
T 2xqn_T            4 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCY   58 (126)
T ss_dssp             CBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHH
T ss_pred             CCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHh
Confidence            5688888888877677999999999999999999999987 89999999999886

>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=99.51  E-value=4.5e-15  Score=90.69  Aligned_cols=54  Identities=31%  Similarity=0.773  Sum_probs=47.7

Q ss_pred             cccccCCcccc-cceeeeecCCcccccCccccccccccccc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPIL-DKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .+|.+|+++|. +..++.++++.||++||+|..|+++|.+. |++++|++||+.||
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy   61 (101)
T 2cup_A            6 SGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCT   61 (101)
T ss_dssp             CBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHH
T ss_pred             CcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHh
Confidence            57888888886 36666999999999999999999999877 89999999999887

>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=99.51  E-value=2.1e-15  Score=95.29  Aligned_cols=54  Identities=37%  Similarity=1.033  Sum_probs=48.2

Q ss_pred             cccccCCcccccceeeeecCCcccccCccccccccccc--cc-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLS--DK-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~--~~-~~~~~g~~~C~~cy  130 (131)
                      .+|..|+++|.++.++.++++.||++||+|+.|+++|+  +. |++++|+|||+.||
T Consensus         6 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy   62 (122)
T 1m3v_A            6 KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDY   62 (122)
T ss_dssp             CCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHH
T ss_pred             CCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHH
Confidence            57888888888887669999999999999999999997  23 99999999999887

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

Probab=99.48  E-value=9e-15  Score=93.28  Aligned_cols=54  Identities=31%  Similarity=0.981  Sum_probs=48.8

Q ss_pred             cccccCCcccccceeeeecCCcccccCcccccccccccc--c-eeccCCeeecCCCC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSD--K-CFSREGKLFCRNDF  130 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~--~-~~~~~g~~~C~~cy  130 (131)
                      .+|..|+++|.++.++.++++.||++||+|+.|+++|+.  . |+.+||+|||+.||
T Consensus         3 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y   59 (131)
T 2xjy_A            3 LTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY   59 (131)
T ss_dssp             CBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHH
T ss_pred             ccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCch
Confidence            579999999998877799999999999999999999963  3 89999999999886

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

Probab=99.47  E-value=2.2e-14  Score=96.36  Aligned_cols=55  Identities=47%  Similarity=1.284  Sum_probs=50.2

Q ss_pred             ccccccCCcccccceeeeecCCcccccCccccccccccccceeccCCeeecCCCC
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF  130 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~g~~~C~~cy  130 (131)
                      ...|..|+++|.++.++.++++.||++||+|+.|+++|.+..|.++|+|||+.||
T Consensus        60 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~g~~yC~~~y  114 (182)
T 2jtn_A           60 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDF  114 (182)
T ss_dssp             CCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCEEETTEEECHHHH
T ss_pred             CCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCceeECCEeeecCcc
Confidence            4789999999999877799999999999999999999998866899999998886

>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=99.45  E-value=6.6e-14  Score=94.47  Aligned_cols=97  Identities=19%  Similarity=0.393  Sum_probs=63.7

Q ss_pred             ccccCCccccCc-eeEeecCCccccCCcccCCCcCcCC-CCcc-CcCCeeecccCcCCCCCCCCCCCccccCCCCccccc
Q psy4437           4 SCAGCEKPILDK-FLLNVLERTWHADCVRCYDCHHTLS-DKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCA   80 (131)
Q Consensus         4 ~C~~C~~~I~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~-~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~   80 (131)
                      +|.+|+++|.+. .++.++++.||++||+|..|+++|. +..| .+++++||..||.+.++++|.+.+........    
T Consensus        71 ~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~~~~~~~g~~~~~~~~----  146 (188)
T 1rut_X           71 ACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHLNSGGSGGSGGS----  146 (188)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC-------------------
T ss_pred             ccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhcccccccCCCCccccc----
Confidence            699999999864 4678999999999999999999996 4555 89999999999999999988776653211000    


Q ss_pred             cCCcccccceeeeecCCcccccCccc
Q psy4437          81 GCEKPILDKFLLNVLERTWHADCVRC  106 (131)
Q Consensus        81 ~C~~~I~~~~~~~~~~~~~H~~Cf~C  106 (131)
                      .=+..+.+.  ...++..+|+...+.
T Consensus       147 ~~~v~vvge--p~l~g~~~~~~~~r~  170 (188)
T 1rut_X          147 GGDVMVVGE--PTLMGGEFGDEDERL  170 (188)
T ss_dssp             -CCCEECCC--CEETTCCCCCTTEEE
T ss_pred             CCcccccCC--CcccCCCCCCCCCce
Confidence            000001111  166778888877765

>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=99.44  E-value=3.3e-14  Score=83.53  Aligned_cols=59  Identities=22%  Similarity=0.512  Sum_probs=49.4

Q ss_pred             CCccccCCccccCceeEeecCCccccCCcccCCCcCcCCCC-ccCcCC-eeecccCcCCCCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDK-CFSREG-KLFCRNDFFRSPV   61 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~f~~~~-~~~C~~c~~~~~~   61 (131)
                      .++|++|+++|.+. ++.++++.||++||+|..|+++|.+. .|..++ .+||..||.+.+.
T Consensus        15 ~~~C~~C~~~I~~~-~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~   75 (81)
T 1v6g_A           15 GTRCFSCDQFIEGE-VVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSV   75 (81)
T ss_dssp             CCBCTTTCCBCCSC-CEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSS
T ss_pred             CCcCccccCEeccc-eEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCC
Confidence            46899999999864 78999999999999999999999864 555554 5799999977654

>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=99.44  E-value=2.2e-14  Score=95.28  Aligned_cols=55  Identities=47%  Similarity=1.284  Sum_probs=49.5

Q ss_pred             ccccccCCcccccceeeeecCCcccccCccccccccccccceeccCCeeecCCCC
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDF  130 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~g~~~C~~cy  130 (131)
                      ...|.+|+++|.++.++.++|+.||++||+|+.|+++|++..+++||++||+.||
T Consensus         6 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~g~~yC~~~y   60 (169)
T 2rgt_A            6 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGESVYCKDDF   60 (169)
T ss_dssp             -CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCCEESSSCEECHHHH
T ss_pred             CCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCCcccCCeeeecccc
Confidence            3689999999998877799999999999999999999998866899999998886

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

Probab=98.68  E-value=5e-09  Score=50.15  Aligned_cols=30  Identities=33%  Similarity=0.713  Sum_probs=27.9

Q ss_pred             CCCccccCCccccCceeEeecCCccccCCc
Q psy4437           1 MLISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         1 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      |..+|..|++.|+..+.+.++|+.||..||
T Consensus         2 m~~~C~~C~k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            2 MNPNCARCGKIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             CCCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCCcCCccCCEEecceeEEECCeEecccCC
Confidence            788999999999988888899999999998

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

Probab=98.40  E-value=1.3e-07  Score=45.11  Aligned_cols=28  Identities=32%  Similarity=0.749  Sum_probs=25.5

Q ss_pred             cccccCCcccccceeeeecCCcccccCc
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      ..|+.|++.|+..+.+.+.|+.||..||
T Consensus         4 ~~C~~C~k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            4 PNCARCGKIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             CBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CcCCccCCEEecceeEEECCeEecccCC
Confidence            4799999999988888999999999998

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=90.51  E-value=0.63  Score=27.94  Aligned_cols=68  Identities=18%  Similarity=0.307  Sum_probs=37.3

Q ss_pred             CccccCCccccCceeEeec--CCccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccCCCCccccc
Q psy4437           3 ISCAGCEKPILDKFLLNVL--ERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSSSMLISCA   80 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~--~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~~~~~~C~   80 (131)
                      ..|..|+..=....+|.-.  ++.||..|+.=..  .+      ...+.-+|.+|.      .|..|++.-....+..|.
T Consensus         8 ~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~--~~------~~~~~W~C~~C~------~C~~C~~~~~~~~ll~Cd   73 (111)
T 2ysm_A            8 ANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAV--TP------LKRAGWQCPECK------VCQNCKQSGEDSKMLVCD   73 (111)
T ss_dssp             SCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCC--CT------TTSTTCCCTTTC------CCTTTCCCSCCTTEEECS
T ss_pred             CCCcCCCCCCCCcCCeECCCCCCCcChHHhCCcc--cc------ccccCccCCcCC------cccccCccCCCCCeeECC
Confidence            3577777652212223222  5788988865321  11      234556676664      566777665555566666


Q ss_pred             cCCc
Q psy4437          81 GCEK   84 (131)
Q Consensus        81 ~C~~   84 (131)
                      .|.+
T Consensus        74 ~C~~   77 (111)
T 2ysm_A           74 TCDK   77 (111)
T ss_dssp             SSCC
T ss_pred             CCCc
Confidence            6654

>2kwj_A Zinc finger protein DPF3; acetyl-lysine, transcription regulation, nucleus, metal BIND protein; HET: ALY; NMR {Homo sapiens} PDB: 2kwk_A 2kwn_A* 2kwo_A*

Probab=89.83  E-value=0.14  Score=31.25  Aligned_cols=71  Identities=20%  Similarity=0.282  Sum_probs=38.4

Q ss_pred             CccccCCcccc-------CceeEeec--CCccccCCcccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccCC
Q psy4437           3 ISCAGCEKPIL-------DKFLLNVL--ERTWHADCVRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLSS   73 (131)
Q Consensus         3 ~~C~~C~~~I~-------~~~~~~~~--~~~~H~~Cf~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~~   73 (131)
                      ..|..|...-.       ++++|.-.  ++.||+.|+.=.     +......+.+.-+|.+|.      .|..|++.-.+
T Consensus         2 ~~C~~C~~~~~~n~k~g~~~~Li~C~~C~~~~H~~Cl~~~-----~~~~~~~~~~~W~C~~C~------~C~~C~~~~~~   70 (114)
T 2kwj_A            2 SYCDFCLGGSNMNKKSGRPEELVSCADCGRSGHPTCLQFT-----LNMTEAVKTYKWQCIECK------SCILCGTSEND   70 (114)
T ss_dssp             CCCSSSCCBTTBCTTTCCCCCCEECSSSCCEECTTTTTCC-----HHHHHHHHHTTCCCGGGC------CCTTTTCCTTT
T ss_pred             CcCccCCCCccccccCCCCCCCeEeCCCCCccchhhCCCh-----hhhhhccCCCccCccccC------ccCcccccCCC
Confidence            56778866431       12344444  678888876311     000001234556676662      57777776555


Q ss_pred             CCccccccCCc
Q psy4437          74 SMLISCAGCEK   84 (131)
Q Consensus        74 ~~~~~C~~C~~   84 (131)
                      +.+..|..|.+
T Consensus        71 ~~ll~Cd~C~~   81 (114)
T 2kwj_A           71 DQLLFCDDCDR   81 (114)
T ss_dssp             TTEEECSSSCC
T ss_pred             CceEEcCCCCc
Confidence            66666666643

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=87.02  E-value=0.1  Score=31.94  Aligned_cols=23  Identities=17%  Similarity=0.613  Sum_probs=15.1

Q ss_pred             ecCCcccccCc--------cccccccccccc
Q psy4437          94 VLERTWHADCV--------RCYDCHHTLSDK  116 (131)
Q Consensus        94 ~~~~~~H~~Cf--------~C~~C~~~l~~~  116 (131)
                      .=|..||..|.        .|..|..++...
T Consensus        96 ~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~  126 (133)
T 4ap4_A           96 ECGHVFCSQCLRDSLKNANTCPTCRKKINHK  126 (133)
T ss_dssp             TTSBEEEHHHHHHHHHHCSBCTTTCCBCCGG
T ss_pred             CCCChhhHHHHHHHHHcCCCCCCCCCcCChh
Confidence            34666776664        577888777654

>2e6s_A E3 ubiquitin-protein ligase UHRF2; PHD domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=85.03  E-value=1.5  Score=24.71  Aligned_cols=47  Identities=17%  Similarity=0.249  Sum_probs=25.1

Q ss_pred             cCCeeecccCcCCCC----CCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCcc
Q psy4437          46 REGKLFCRNDFFRSP----VRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCVR  105 (131)
Q Consensus        46 ~~~~~~C~~c~~~~~----~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf~  105 (131)
                      +.+.++|..|-.+..    .-.|..|++.-.++.+..|..|.             +.||..|..
T Consensus         7 ~~~~~~c~~C~~~~~w~C~~c~C~vC~~~~~~~~ll~CD~C~-------------~~yH~~Cl~   57 (77)
T 2e6s_A            7 GRNDTECDLCGGDPEKKCHSCSCRVCGGKHEPNMQLLCDECN-------------VAYHIYCLN   57 (77)
T ss_dssp             CCCCCCCTTTCSCSSSCCSSSSCSSSCCCCCSTTEEECSSSC-------------CEEETTSSS
T ss_pred             ccCCccChhhcCCCCeECCCCCCcCcCCcCCCCCEEEcCCCC-------------ccccccccC
Confidence            345667766654321    12455565554455555555553             457877754

>1bor_A Transcription factor PML; proto-oncogene, nuclear bodies (PODS), leukemia, transcription regulation; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=82.55  E-value=2.8  Score=21.52  Aligned_cols=40  Identities=13%  Similarity=0.125  Sum_probs=22.1

Q ss_pred             cccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccc
Q psy4437          30 VRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVG   70 (131)
Q Consensus        30 f~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~   70 (131)
                      +.|..|...+.+.....=|..||..|..+ ....|..|.+.
T Consensus         7 ~~C~IC~~~~~~p~~l~CgH~fC~~Ci~~-~~~~CP~Cr~~   46 (56)
T 1bor_A            7 LRCQQCQAEAKCPKLLPCLHTLCSGCLEA-SGMQCPICQAP   46 (56)
T ss_dssp             SSCSSSCSSCBCCSCSTTSCCSBTTTCSS-SSSSCSSCCSS
T ss_pred             CCceEeCCccCCeEEcCCCCcccHHHHcc-CCCCCCcCCcE
Confidence            56777776665533334466777777655 23344444443

>1jm7_B BARD1, BRCA1-associated ring domain protein 1; ring finger, zinc-binding protein, heterodimer, ubiquitin ligase, antitumor; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=80.38  E-value=2.7  Score=25.14  Aligned_cols=43  Identities=19%  Similarity=0.229  Sum_probs=30.0

Q ss_pred             cccCCCcCcCCCCccC-cCCeeecccCcCCCCCCCCCCCccccC
Q psy4437          30 VRCYDCHHTLSDKCFS-REGKLFCRNDFFRSPVRFPSGCGVGLS   72 (131)
Q Consensus        30 f~C~~C~~~l~~~~f~-~~~~~~C~~c~~~~~~~~C~~c~~~i~   72 (131)
                      +.|..|...+.+.... .=|..||..|..+.....|..|..++.
T Consensus        23 ~~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~~~CP~Cr~~~~   66 (117)
T 1jm7_B           23 LRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAW   66 (117)
T ss_dssp             TSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTTTBCSSSCCBCS
T ss_pred             CCCCCCChHhhCccEeCCCCCHHHHHHHHHHhcCCCcCCCCcCc
Confidence            7788888777654444 568888988887665556666666654

---

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	131
d1j2oa1	30	g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus m	9e-10
d1j2oa1	30	g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus m	9e-10
d1rutx1	30	g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus m	2e-08
d1rutx1	30	g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus m	2e-08
d2dara2	45	g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, En	0.003

>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 = 48.2 bits (115), Expect = 9e-10
 Identities = 11/29 (37%), Positives = 20/29 (68%)

Query: 1  MLISCAGCEKPILDKFLLNVLERTWHADC 29
           L++C GC++ I D++ L  +++ WH DC
Sbjct: 2  SLLTCGGCQQNIGDRYFLKAIDQYWHEDC 30

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]} Length = 30

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 48.2 bits (115), Expect = 9e-10
 Identities = 11/29 (37%), Positives = 20/29 (68%)

Query: 75  MLISCAGCEKPILDKFLLNVLERTWHADC 103
            L++C GC++ I D++ L  +++ WH DC
Sbjct: 2   SLLTCGGCQQNIGDRYFLKAIDQYWHEDC 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 = 44.7 bits (106), Expect = 2e-08
 Identities = 12/26 (46%), Positives = 17/26 (65%)

Query: 5  CAGCEKPILDKFLLNVLERTWHADCV 30
          CAGC   I D+FLL  ++  WH+ C+
Sbjct: 5  CAGCGGKIADRFLLYAMDSYWHSRCL 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 = 44.7 bits (106), Expect = 2e-08
 Identities = 12/26 (46%), Positives = 17/26 (65%)

Query: 79  CAGCEKPILDKFLLNVLERTWHADCV 104
           CAGC   I D+FLL  ++  WH+ C+
Sbjct: 5   CAGCGGKIADRFLLYAMDSYWHSRCL 30

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]} Length = 45

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 5, Enigma
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 31.6 bits (72), Expect = 0.003
 Identities = 9/38 (23%), Positives = 14/38 (36%), Gaps = 1/38 (2%)

Query: 66  GCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADC 103
                 +      CA C + I   F L  L ++WH + 
Sbjct: 8   RAEHIPAGKRTPMCAHCNQVIRGPF-LVALGKSWHPEE 44

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	131
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.26
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.07
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.99
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.95
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.94
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.9
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.9
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.89
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.86
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.85
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.85
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.84
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.84
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.82
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.69
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.69
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.67
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.61
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.6
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.59
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.56
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.56
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.5
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.48
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.48
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.47
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.46
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.42
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.42
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.41
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.4
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.39
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	98.39
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.36
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	98.34
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.31
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.3
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	98.26
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.26
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.26
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	98.25
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.25
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.23
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.21
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.19
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.13
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.12
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.12
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	98.12
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.12
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	98.11
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	98.11
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	98.09
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.06
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.05
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.01
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.96
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.94
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.9
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.89
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.87
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.83
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.83
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.8
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	97.8
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	97.8
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.79
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.77
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.75
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.72
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.72
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.71
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.71
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.71
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.69
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.68
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.68
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	97.66
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.65
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.64
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.62
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.59
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.53
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.52
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.51
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.49
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	97.46
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.45
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.45
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.37
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.3
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.29
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.22
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.2
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.15
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.12
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.92
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.81
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	96.79
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	96.78
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.68
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	96.67
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.63
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.54
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	96.36
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	96.33
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.32
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.26
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.15
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.08
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	96.01
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.81
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	95.76
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	95.64
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	95.57
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.45
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	95.33
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.29
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	95.04
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.0
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	94.92
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	93.5
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	91.59
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	91.31
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	90.69
d2co8a1	33	Nedd9 interacting protein with calponin homology,	90.47
d1bora_	56	Acute promyelocytic leukaemia proto-oncoprotein PM	87.49
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	83.63
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	82.83
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	82.52

>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=99.26  E-value=1.3e-12  Score=62.92  Aligned_cols=35  Identities=23%  Similarity=0.636  Sum_probs=27.7

Q ss_pred             cCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCc
Q psy4437          54 NDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        54 ~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      +||.++|+++|.+|+++|.+.               . ++|+|++||++||
T Consensus         1 ~DY~~~fapkC~~C~~~I~g~---------------~-v~Al~~~wHpeCF   35 (35)
T d1x3ha1           1 KDFLAMFSPKCGGCNRPVLEN---------------Y-LSAMDTVWHPECF   35 (35)
T ss_dssp             CCCCCCCSCBCTTTCCBCCSS---------------C-EEETTEEECTTTC
T ss_pred             CcHHHHhChhhhhcCCcccch---------------h-eeecCCccCcccC
Confidence            478999998777777766543               2 3999999999998

>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=99.07  E-value=3.3e-11  Score=57.94  Aligned_cols=28  Identities=32%  Similarity=1.099  Sum_probs=25.8

Q ss_pred             CCccccCCccccCceeEeecCCccccCCc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      .++|++|+++|.+. +|+|+|+.||++||
T Consensus         8 apkC~~C~~~I~g~-~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           8 SPKCGGCNRPVLEN-YLSAMDTVWHPECF   35 (35)
T ss_dssp             SCBCTTTCCBCCSS-CEEETTEEECTTTC
T ss_pred             ChhhhhcCCcccch-heeecCCccCcccC
Confidence            58999999999887 68899999999998

>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=98.99  E-value=1.5e-10  Score=52.68  Aligned_cols=29  Identities=38%  Similarity=1.146  Sum_probs=27.2

Q ss_pred             CCCccccCCccccCceeEeecCCccccCC
Q psy4437           1 MLISCAGCEKPILDKFLLNVLERTWHADC   29 (131)
Q Consensus         1 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~C   29 (131)
                      ++..|++|+++|.+++++.++++.||.+|
T Consensus         2 ~~~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             CCBCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             CCcccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            56789999999999999999999999987

>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=98.95  E-value=3.1e-10  Score=53.14  Aligned_cols=35  Identities=14%  Similarity=0.356  Sum_probs=28.4

Q ss_pred             cCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCc
Q psy4437          54 NDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        54 ~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      .||.++|+++|..|+++|..+++                +..++.||.+||
T Consensus         1 PCyE~kfa~~C~~Ckk~It~GGv----------------tY~dqpWHkeCF   35 (35)
T d2cuqa2           1 PCYENKFAPRCARCSKTLTQGGV----------------TYRDQPWHRECL   35 (35)
T ss_dssp             CCCCCCSSCCCTTTCCCCCSCCE----------------ESSSSEECTTTC
T ss_pred             CchHHHHHHHHhhcCCccccCce----------------eecCCcchhhhC
Confidence            47899999877777777665544                899999999998

>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=98.94  E-value=3.4e-10  Score=54.55  Aligned_cols=37  Identities=19%  Similarity=0.259  Sum_probs=31.4

Q ss_pred             cCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccCc
Q psy4437          54 NDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        54 ~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      +||.+.++++|.+|.++|.+++..+              .+.|++||.+||
T Consensus         1 kCy~~~~a~~C~~C~k~I~~G~k~v--------------eykg~~WHe~CF   37 (37)
T d1x63a1           1 KCTTREDSPKCKGCFKAIVAGDQNV--------------EYKGTVWHKDCF   37 (37)
T ss_dssp             CCCSCCCSCBCSSSCCBCCSSSCEE--------------ECSSCEEETTTC
T ss_pred             CccccccCcccccCCCccCCCCeEe--------------EeCCccchhccC
Confidence            4788999999888888888766543              999999999998

>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=98.90  E-value=3.6e-10  Score=56.23  Aligned_cols=28  Identities=29%  Similarity=0.622  Sum_probs=25.3

Q ss_pred             CCccccCCccccCceeEeecCCccccCCc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      .++|++|+++|.+. .|.++|+.||+++|
T Consensus        18 ~P~C~~C~~pI~g~-~vtAlgk~WHPEhF   45 (45)
T d2dara2          18 TPMCAHCNQVIRGP-FLVALGKSWHPEEF   45 (45)
T ss_dssp             CCBBSSSCCBCCSC-EEEETTEEECTTTC
T ss_pred             CeeccccCCcccCc-eeeecCCccCcCCC
Confidence            36799999999888 58899999999998

>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=98.90  E-value=1.8e-10  Score=51.58  Aligned_cols=30  Identities=33%  Similarity=0.713  Sum_probs=28.7

Q ss_pred             CCCccccCCccccCceeEeecCCccccCCc
Q psy4437           1 MLISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         1 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      |++.|++|++.++..+.++-+++.||..||
T Consensus         1 Mn~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           1 MNPNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CCCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCCcccccCCccccHHHhhhhHHHHhhccC
Confidence            899999999999999889999999999998

>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=98.89  E-value=5.1e-10  Score=52.62  Aligned_cols=28  Identities=39%  Similarity=0.990  Sum_probs=25.8

Q ss_pred             ccccccCCcccccceeeeecCCcccccCc
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      +..|..|+++|.++.+ .|.|+.|||+||
T Consensus         8 lEkC~~C~~~I~driL-rA~Gk~yHP~CF   35 (35)
T d2dloa1           8 LEKCATCSQPILDRIL-RAMGKAYHPGCF   35 (35)
T ss_dssp             CCBCTTTCCBCCSCCE-EETTEEECTTTC
T ss_pred             HHHHHHhchHHHHHHH-HHhCCCCCCCCC
Confidence            4689999999999988 999999999998

>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=98.86  E-value=5.8e-10  Score=52.43  Aligned_cols=28  Identities=39%  Similarity=1.011  Sum_probs=26.1

Q ss_pred             CCccccCCccccCceeEeecCCccccCCc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      +.+|..|+++|.+. ++.|+|+.|||.||
T Consensus         8 lEkC~~C~~~I~dr-iLrA~Gk~yHP~CF   35 (35)
T d2dloa1           8 LEKCATCSQPILDR-ILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCBCTTTCCBCCSC-CEEETTEEECTTTC
T ss_pred             HHHHHHhchHHHHH-HHHHhCCCCCCCCC
Confidence            56899999999998 79999999999998

>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=98.85  E-value=9.6e-11  Score=56.18  Aligned_cols=33  Identities=24%  Similarity=0.577  Sum_probs=30.4

Q ss_pred             cccCCCcCcCCCCcc-CcCCeeecccCcCCCCCC
Q psy4437          30 VRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVR   62 (131)
Q Consensus        30 f~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~   62 (131)
                      |+|+.|+++|.+..| +++|+|||+.||.++|+|
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhcCC
Confidence            789999999998766 999999999999998875

>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=98.84  E-value=7.6e-10  Score=50.47  Aligned_cols=29  Identities=41%  Similarity=1.012  Sum_probs=26.8

Q ss_pred             CCccccCCccccCceeEeecCCccccCCc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      ...|++|+++|.|++++.++++.||..|+
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            46799999999999999999999999985

>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=98.84  E-value=7.7e-10  Score=55.02  Aligned_cols=30  Identities=30%  Similarity=0.618  Sum_probs=26.6

Q ss_pred             CCccccccCCcccccceeeeecCCcccccCc
Q psy4437          74 SMLISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        74 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      ...++|..|+++|.+..+ +|+|+.|||++|
T Consensus        16 ~r~P~C~~C~~pI~g~~v-tAlgk~WHPEhF   45 (45)
T d2dara2          16 KRTPMCAHCNQVIRGPFL-VALGKSWHPEEF   45 (45)
T ss_dssp             TCCCBBSSSCCBCCSCEE-EETTEEECTTTC
T ss_pred             CCCeeccccCCcccCcee-eecCCccCcCCC
Confidence            345789999999998888 999999999998

>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=98.82  E-value=8.3e-10  Score=50.08  Aligned_cols=30  Identities=27%  Similarity=0.645  Sum_probs=28.2

Q ss_pred             CCCccccCCccccCceeEeecCCccccCCc
Q psy4437           1 MLISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         1 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      |.+.|.+|+++++..+.+..+|+.||..|+
T Consensus         1 M~~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           1 MASKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CCCBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CCCcCCCCCCceeeHHhhccCCcccccccC
Confidence            899999999999998889999999999985

>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=98.69  E-value=2.3e-09  Score=48.83  Aligned_cols=27  Identities=26%  Similarity=0.864  Sum_probs=24.1

Q ss_pred             CCccccCCccccCceeEeecCCccccCC
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADC   29 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~C   29 (131)
                      .++|+.|++||.++ +|.++|+.||+++
T Consensus         5 ~p~C~~C~~PI~~~-~vtAlgk~WHpEH   31 (31)
T d1u5sb1           5 VPICGACRRPIEGR-VVNAMGKQWHVEH   31 (31)
T ss_dssp             CCEETTTTEECCSC-EECCTTSBEETTT
T ss_pred             CcchhhcCCchhhh-HhhhhccccCCCC
Confidence            47899999999886 7999999999974

>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=98.69  E-value=7.5e-10  Score=52.98  Aligned_cols=27  Identities=26%  Similarity=0.826  Sum_probs=25.4

Q ss_pred             ccccccccccccc-eeccCCeeecCCCC
Q psy4437         104 VRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       104 f~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      |+|+.|+++|+++ |+++||+|||+.||
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y   28 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDF   28 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHH
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhH
Confidence            7899999999988 99999999999887

>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=98.67  E-value=5.2e-09  Score=48.76  Aligned_cols=29  Identities=34%  Similarity=0.793  Sum_probs=26.6

Q ss_pred             CCccccCCccccCceeEeecCCccccCCc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      +..|++|++.|..+..+.++++.||.+||
T Consensus         8 ~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           8 PSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             CccccccchhhhCCceeeeeecceeeeeC
Confidence            46799999999988889999999999998

>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=98.61  E-value=2.6e-09  Score=48.47  Aligned_cols=31  Identities=23%  Similarity=0.633  Sum_probs=27.9

Q ss_pred             ccCCCcCcCCCCccCcCCeeecccCcCCCCC
Q psy4437          31 RCYDCHHTLSDKCFSREGKLFCRNDFFRSPV   61 (131)
Q Consensus        31 ~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~   61 (131)
                      +|..|++.|.+++..+||.|||+.||+.+|+
T Consensus         1 kC~~C~~vL~gEYm~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVILTGEYISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBCSSCCEEETTEEECTTHHHHHTT
T ss_pred             CccccCccccceeecCCCCcccHHHHHHhcC
Confidence            5899999999998899999999999987663

>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=98.60  E-value=1.6e-08  Score=45.81  Aligned_cols=28  Identities=39%  Similarity=1.203  Sum_probs=26.0

Q ss_pred             ccccccCCcccccceeeeecCCcccccC
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADC  103 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~C  103 (131)
                      ...|++|+++|.++.++.+.++.||.+|
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            3579999999999999999999999987

>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=98.59  E-value=3.5e-09  Score=53.94  Aligned_cols=41  Identities=22%  Similarity=0.594  Sum_probs=36.2

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCcccc
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGL   71 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i   71 (131)
                      +|..|++.|++... ++|++|||+.||.++|+|+..+.+...
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~g~G~ga   42 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQGA   42 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCccCcccCc
Confidence            58999999998665 899999999999999999988877543

>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=98.56  E-value=1.8e-08  Score=45.85  Aligned_cols=28  Identities=43%  Similarity=1.056  Sum_probs=26.1

Q ss_pred             cccccCCcccccceeeeecCCcccccCc
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      ..|++|+++|.++.++.+.++.||.+|.
T Consensus         3 ~~CaGC~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           3 KRCAGCGGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CBBTTTCCBCCCSEEEEETTEEECGGGC
T ss_pred             cccCCCCCccchhhhhccchhhhhhhhC
Confidence            4799999999999999999999999984

>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=98.56  E-value=2.3e-08  Score=46.50  Aligned_cols=31  Identities=32%  Similarity=0.702  Sum_probs=27.6

Q ss_pred             CCccccccCCcccccceeeeecCCcccccCc
Q psy4437          74 SMLISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        74 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      .....|..|++.|.+.+.+.|+++.||.+||
T Consensus         6 ~g~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           6 RGPSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             cCCccccccchhhhCCceeeeeecceeeeeC
Confidence            4456899999999998888999999999998

>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=5.5e-09  Score=48.07  Aligned_cols=31  Identities=29%  Similarity=0.565  Sum_probs=27.4

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcCCCCC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFFRSPV   61 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~   61 (131)
                      .|..|.++|.++.| .+|++|||.+||..+|+
T Consensus         1 ~C~~C~~~L~GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQLSGQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBCTTSCCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCccccCceeeecCCCeehHHhhHhhcC
Confidence            48899999999999 89999999999976653

>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=98.47  E-value=4.3e-08  Score=47.00  Aligned_cols=29  Identities=31%  Similarity=0.685  Sum_probs=25.4

Q ss_pred             CCccccCCcccc-CceeEeecCCccccCCc
Q psy4437           2 LISCAGCEKPIL-DKFLLNVLERTWHADCV   30 (131)
Q Consensus         2 ~~~C~~C~~~I~-~~~~~~~~~~~~H~~Cf   30 (131)
                      .++|.+|+++|. +...|++.|+.||..||
T Consensus         8 a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           8 SPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             SCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             CcccccCCCccCCCCeEeEeCCccchhccC
Confidence            578999999995 45569999999999998

>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=98.46  E-value=2.3e-08  Score=45.40  Aligned_cols=26  Identities=27%  Similarity=0.852  Sum_probs=22.2

Q ss_pred             cccccCCcccccceeeeecCCcccccC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADC  103 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~C  103 (131)
                      ++|..|++||.++.+ +|+|+.||+++
T Consensus         6 p~C~~C~~PI~~~~v-tAlgk~WHpEH   31 (31)
T d1u5sb1           6 PICGACRRPIEGRVV-NAMGKQWHVEH   31 (31)
T ss_dssp             CEETTTTEECCSCEE-CCTTSBEETTT
T ss_pred             cchhhcCCchhhhHh-hhhccccCCCC
Confidence            578888888888666 99999999974

>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=98.42  E-value=9.3e-09  Score=46.67  Aligned_cols=30  Identities=27%  Similarity=0.511  Sum_probs=26.8

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcCCCC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFFRSP   60 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~   60 (131)
                      .|..|+++|+++.| ++|.+|||.+||-.+|
T Consensus         1 vCt~Ck~~LaGqrFTSrde~pYC~~Cfg~Lf   31 (32)
T d2cuqa1           1 VCTGCQTPLAGQQFTSRDEDPYCVACFGELF   31 (32)
T ss_dssp             BCSSSCCBCTTCCEEECSSSEEEHHHHHHHT
T ss_pred             CccccCccccCCccccCCCCccHHHHhHhhc
Confidence            48899999999999 8999999999986654

>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=98.41  E-value=6.3e-08  Score=47.11  Aligned_cols=34  Identities=24%  Similarity=0.389  Sum_probs=26.4

Q ss_pred             cCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccC
Q psy4437          54 NDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADC  103 (131)
Q Consensus        54 ~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~C  103 (131)
                      .||+++|+.+|..|.+.|.+.                ++.|.+++|||.|
T Consensus         8 ~DYq~~fG~~C~~C~~~ItG~----------------V~~Ag~~~yHP~C   41 (41)
T d1v6ga1           8 LDYQRLYGTRCFSCDQFIEGE----------------VVSALGKTYHPDC   41 (41)
T ss_dssp             SCGGGSCCCBCTTTCCBCCSC----------------CEEETTEEECTTT
T ss_pred             ccHHHHhCcccccccCEeeee----------------eeEecCcccCCCC
Confidence            578999998777777766542                2399999999987

>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=98.40  E-value=3.3e-08  Score=44.75  Aligned_cols=26  Identities=27%  Similarity=0.851  Sum_probs=24.4

Q ss_pred             cccccccccccceeccCCeeecCCCC
Q psy4437         105 RCYDCHHTLSDKCFSREGKLFCRNDF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~~~~~~g~~~C~~cy  130 (131)
                      +|..|++.|.++|..+||.|||+.+|
T Consensus         1 kC~~C~~vL~gEYm~kdG~PyCe~DY   26 (31)
T d2dj7a1           1 KCQTCSVILTGEYISKDGVPYCESDY   26 (31)
T ss_dssp             BCSSSCCBCSSCCEEETTEEECTTHH
T ss_pred             CccccCccccceeecCCCCcccHHHH
Confidence            58899999999999999999999987

>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=98.39  E-value=8.2e-08  Score=44.75  Aligned_cols=28  Identities=25%  Similarity=0.711  Sum_probs=24.5

Q ss_pred             CCccccCCccccCceeEeecCCccccCCc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      +.+|..|+++|+.+ -|...++.||.+||
T Consensus         8 a~~C~~Ckk~It~G-GvtY~dqpWHkeCF   35 (35)
T d2cuqa2           8 APRCARCSKTLTQG-GVTYRDQPWHRECL   35 (35)
T ss_dssp             SCCCTTTCCCCCSC-CEESSSSEECTTTC
T ss_pred             HHHHhhcCCccccC-ceeecCCcchhhhC
Confidence            56899999999776 37789999999998

>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=98.36  E-value=1.5e-07  Score=44.68  Aligned_cols=31  Identities=23%  Similarity=0.246  Sum_probs=27.8

Q ss_pred             CCccccccCCcccccceeeeecCCcccccCc
Q psy4437          74 SMLISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        74 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      +....|..|+|.++..+.+.+.|+.||.+||
T Consensus         6 g~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           6 GAGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CSSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CCCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            4457899999999998888999999999998

>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=98.31  E-value=1.5e-07  Score=41.91  Aligned_cols=28  Identities=32%  Similarity=0.749  Sum_probs=25.3

Q ss_pred             cccccCCcccccceeeeecCCcccccCc
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      +.|++|++.+++.+.+.-.++.||..||
T Consensus         3 ~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           3 PNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CcccccCCccccHHHhhhhHHHHhhccC
Confidence            4689999999998888999999999998

>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=98.30  E-value=2.5e-07  Score=43.74  Aligned_cols=29  Identities=21%  Similarity=0.472  Sum_probs=26.7

Q ss_pred             ccccccCCcccccceeeeecCCcccccCc
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      ...|..|+|.++..+.+.+.|+.||..||
T Consensus         7 ~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           7 RETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CcccccCCCEEeeeeeEecCCeehhhccC
Confidence            36899999999998888999999999998

>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=98.26  E-value=1.9e-07  Score=41.34  Aligned_cols=26  Identities=46%  Similarity=1.083  Sum_probs=22.7

Q ss_pred             cccCCccccC---ceeEeecCCccccCCc
Q psy4437           5 CAGCEKPILD---KFLLNVLERTWHADCV   30 (131)
Q Consensus         5 C~~C~~~I~~---~~~~~~~~~~~H~~Cf   30 (131)
                      |++|.+||++   ...|+..++.||.+||
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            7899999963   5669999999999998

>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=98.26  E-value=4e-08  Score=45.33  Aligned_cols=26  Identities=31%  Similarity=0.784  Sum_probs=23.7

Q ss_pred             cccccccccccc-eeccCCeeecCCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .|..|.+|+.++ |++.||+|||+.+|
T Consensus         1 VC~~C~~PF~~~~Fy~~~g~PyCe~Hy   27 (32)
T d1x3ha2           1 VCGDCFTSFSTGSFFELDGRPFCELHY   27 (32)
T ss_dssp             BCSSSCCBSCSSCCEESSSCEECHHHH
T ss_pred             CcCccCCcCCCCCeEeECCccchHHhh
Confidence            488999999988 99999999999876

>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=98.26  E-value=1.9e-07  Score=42.17  Aligned_cols=28  Identities=25%  Similarity=0.654  Sum_probs=25.3

Q ss_pred             cccccCCcccccceeeeecCCcccccCc
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      ..|++|+|+++..+.++..|+.||+.|+
T Consensus         3 ~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           3 SKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CcCCCCCCceeeHHhhccCCcccccccC
Confidence            4799999999998888999999999884

>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=98.25  E-value=2.1e-07  Score=41.17  Aligned_cols=26  Identities=46%  Similarity=1.083  Sum_probs=19.3

Q ss_pred             cccCCcccc---cceeeeecCCcccccCc
Q psy4437          79 CAGCEKPIL---DKFLLNVLERTWHADCV  104 (131)
Q Consensus        79 C~~C~~~I~---~~~~~~~~~~~~H~~Cf  104 (131)
                      |..|.+||.   +...+.+.++.||.+||
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            455666665   34556999999999998

>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=98.25  E-value=2.3e-07  Score=46.11  Aligned_cols=29  Identities=17%  Similarity=0.507  Sum_probs=27.0

Q ss_pred             ccccccCCcccccceeeeecCCcccccCc
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      ...|.+|+|.++..+.+.+.|+.||..||
T Consensus        15 ~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          15 SDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             CCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            47899999999998888999999999998

>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=98.23  E-value=8.8e-08  Score=42.49  Aligned_cols=28  Identities=25%  Similarity=0.827  Sum_probs=25.6

Q ss_pred             cccCCCcCcCCCCcc-CcCCeeecccCcC
Q psy4437          30 VRCYDCHHTLSDKCF-SREGKLFCRNDFF   57 (131)
Q Consensus        30 f~C~~C~~~l~~~~f-~~~~~~~C~~c~~   57 (131)
                      |+|+.|++.|.+... .+||++||+.||-
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cya   29 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCYA   29 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeeee
Confidence            799999999999877 7999999999984

>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=98.21  E-value=1.9e-07  Score=42.64  Aligned_cols=28  Identities=25%  Similarity=0.522  Sum_probs=23.0

Q ss_pred             CCCCCccccCCCCccccccCCcccccceeeeecCCcccccCc
Q psy4437          63 FPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        63 ~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      .|++|++.|.+.++++              .+.+..||++||
T Consensus         4 ~Ca~C~~~I~~~e~Vm--------------RA~~~VyHl~CF   31 (31)
T d1rutx3           4 ACSACGQSIPASELVM--------------RAQGNVYHLKCF   31 (31)
T ss_dssp             ECTTTCCEECTTSEEE--------------EETTEEECGGGC
T ss_pred             ccccccCcCChhHhhe--------------ecccceeeeccC
Confidence            4777777777777765              999999999998

>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=43.11  Aligned_cols=29  Identities=21%  Similarity=0.472  Sum_probs=26.7

Q ss_pred             CCccccCCccccCceeEeecCCccccCCc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      ..+|..|++.++..+.+.+.|+.||..||
T Consensus         7 ~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           7 RETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CcccccCCCEEeeeeeEecCCeehhhccC
Confidence            35799999999998889999999999998

>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=98.13  E-value=3.7e-07  Score=45.31  Aligned_cols=28  Identities=18%  Similarity=0.549  Sum_probs=26.1

Q ss_pred             CccccCCccccCceeEeecCCccccCCc
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      ..|..|++.++..+.+.+.|+.||..||
T Consensus        16 ~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          16 DGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             EECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             CcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            5699999999998889999999999998

>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=98.12  E-value=1e-07  Score=42.29  Aligned_cols=27  Identities=26%  Similarity=0.822  Sum_probs=24.7

Q ss_pred             ccccccccccccc-eeccCCeeecCCCC
Q psy4437         104 VRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       104 f~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      |+|+.|++.|.+. ...+||.+||+.||
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cy   28 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCY   28 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeee
Confidence            7899999999888 78899999999876

>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=98.12  E-value=1.1e-07  Score=43.61  Aligned_cols=26  Identities=31%  Similarity=0.653  Sum_probs=23.4

Q ss_pred             cccccccccccc-eeccCCeeecCCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .|..|+++|++. |+++|++|||.+||
T Consensus         1 ~C~~C~~~L~GQry~~rd~~PyC~~Cf   27 (32)
T d2d8za2           1 VCTACRKQLSGQRFTARDDFAYCLNCF   27 (32)
T ss_dssp             BCSSSCCBCTTSCCEESSSSEECHHHH
T ss_pred             CcccCCccccCceeeecCCCeehHHhh
Confidence            378899999998 99999999998886

>d1x68a1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.12  E-value=5.6e-07  Score=39.72  Aligned_cols=25  Identities=28%  Similarity=0.813  Sum_probs=17.8

Q ss_pred             ccCCcccc---cceeeeecCCcccccCc
Q psy4437          80 AGCEKPIL---DKFLLNVLERTWHADCV  104 (131)
Q Consensus        80 ~~C~~~I~---~~~~~~~~~~~~H~~Cf  104 (131)
                      ..|.|||.   +...+.+.++.||.+||
T Consensus         2 ~~C~kPItg~gG~k~isFedR~WH~~CF   29 (29)
T d1x68a1           2 VACSKPISGLTGAKFICFQDSQWHSECF   29 (29)
T ss_dssp             TTTCCCCCTTTTCCEEEETTEEEEGGGC
T ss_pred             ccccccccccCCceEEEeehhhcccccC
Confidence            34445443   34556999999999998

>d1imla2 g.39.1.3 (A:29-76) Cysteine-rich (intestinal) protein, CRP, CRIP {Rat (Rattus rattus) [TaxId: 10117]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=98.12  E-value=1.9e-07  Score=46.86  Aligned_cols=36  Identities=25%  Similarity=0.410  Sum_probs=31.2

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeec-ccCcCCCCCCCCCC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFC-RNDFFRSPVRFPSG   66 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C-~~c~~~~~~~~C~~   66 (131)
                      +|..|++.|++... ++|++||| +.||.++|+|+-.+
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FGPkG~g   38 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFG   38 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSS
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccCCCccc
Confidence            58899999999777 89999999 67999999987444

>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=98.11  E-value=7.6e-07  Score=43.54  Aligned_cols=29  Identities=17%  Similarity=0.530  Sum_probs=26.4

Q ss_pred             CCCccccCCccccCceeEeecCCccccCCc
Q psy4437           1 MLISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         1 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      +++.|.+|+.-|.+. +|.+.++.+|++||
T Consensus        17 kLP~CdkCg~GIVG~-~VK~rDK~rHPeCf   45 (45)
T d1x64a1          17 RMPLCDKCGSGIVGA-VVKARDKYRHPECF   45 (45)
T ss_dssp             SCCBCTTTCCBCCSC-CEESSSCEECTTTC
T ss_pred             cCccccccCCCcEEE-EEEeccccCCCCCC
Confidence            478999999999888 68899999999998

>d1x68a1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.11  E-value=4.8e-07  Score=39.93  Aligned_cols=26  Identities=31%  Similarity=0.929  Sum_probs=22.6

Q ss_pred             cccCCcccc---CceeEeecCCccccCCc
Q psy4437           5 CAGCEKPIL---DKFLLNVLERTWHADCV   30 (131)
Q Consensus         5 C~~C~~~I~---~~~~~~~~~~~~H~~Cf   30 (131)
                      |.+|.+||+   +...|+..++.||.+||
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            789999995   35679999999999998

>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=98.09  E-value=1.1e-06  Score=40.33  Aligned_cols=28  Identities=25%  Similarity=0.627  Sum_probs=25.8

Q ss_pred             CCccccCCccccCceeEeecCCccccCCc
Q psy4437           2 LISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         2 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      ++.|.+|+.-|.+. ++.+.++.+||+||
T Consensus         8 lp~CdkCg~GIVG~-~VK~rDk~rHPeCf   35 (35)
T d1x62a2           8 LPMCDKCGTGIVGV-FVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCSSSCCCCCSS-CEECSSCEECTTTT
T ss_pred             CccccccCCCcEeE-EEEeccccCCCCCC
Confidence            68899999999888 68899999999997

>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=98.06  E-value=7.5e-07  Score=42.22  Aligned_cols=28  Identities=25%  Similarity=0.328  Sum_probs=26.0

Q ss_pred             CccccCCccccCceeEeecCCccccCCc
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      .+|..|++.++.-+.+.+.|+.||.+||
T Consensus         9 ~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           9 DLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CcccccCCEEeeeeEEEecCcEeccccC
Confidence            5799999999988889999999999998

>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=98.05  E-value=1.8e-07  Score=42.36  Aligned_cols=26  Identities=27%  Similarity=0.628  Sum_probs=23.6

Q ss_pred             cccccccccccc-eeccCCeeecCCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .|+.|+++|.+. |..+|++|||.+||
T Consensus         1 vCt~Ck~~LaGqrFTSrde~pYC~~Cf   27 (32)
T d2cuqa1           1 VCTGCQTPLAGQQFTSRDEDPYCVACF   27 (32)
T ss_dssp             BCSSSCCBCTTCCEEECSSSEEEHHHH
T ss_pred             CccccCccccCCccccCCCCccHHHHh
Confidence            488999999998 99999999998886

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.01  E-value=2.2e-07  Score=42.81  Aligned_cols=29  Identities=28%  Similarity=0.717  Sum_probs=25.2

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcCCC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFFRS   59 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~   59 (131)
                      +|..|.+++.+..| +.||+|||+.+|+++
T Consensus         1 VC~~C~~PF~~~~Fy~~~g~PyCe~HyH~~   30 (32)
T d1x3ha2           1 VCGDCFTSFSTGSFFELDGRPFCELHYHHR   30 (32)
T ss_dssp             BCSSSCCBSCSSCCEESSSCEECHHHHHHH
T ss_pred             CcCccCCcCCCCCeEeECCccchHHhhhhh
Confidence            58999999998766 999999999998754

>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=97.96  E-value=4.9e-07  Score=44.33  Aligned_cols=33  Identities=27%  Similarity=0.574  Sum_probs=29.7

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRF   63 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~   63 (131)
                      +|+.|+..|+...| +.+|.+||+.+|.++|.++
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~k   34 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK   34 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhh
Confidence            68999999999888 8999999999999888764

>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=97.94  E-value=2.2e-06  Score=36.97  Aligned_cols=26  Identities=27%  Similarity=0.782  Sum_probs=22.1

Q ss_pred             cccCCcccc-CceeEeecCCccccCCc
Q psy4437           5 CAGCEKPIL-DKFLLNVLERTWHADCV   30 (131)
Q Consensus         5 C~~C~~~I~-~~~~~~~~~~~~H~~Cf   30 (131)
                      |..|.+.|. +...++..|.+||..||
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            788999994 45568899999999998

>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=97.90  E-value=7e-07  Score=47.77  Aligned_cols=40  Identities=18%  Similarity=0.444  Sum_probs=34.9

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccc
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVG   70 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~   70 (131)
                      .|..|++.|++... +++++|||+.||.++|+|+-.+-+..
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG~G~G~g   41 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMG   41 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCccccccc
Confidence            48899999999887 89999999999999999987776644

>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=97.89  E-value=2.8e-06  Score=36.57  Aligned_cols=26  Identities=27%  Similarity=0.778  Sum_probs=21.9

Q ss_pred             cccCCcccc-CceeEeecCCccccCCc
Q psy4437           5 CAGCEKPIL-DKFLLNVLERTWHADCV   30 (131)
Q Consensus         5 C~~C~~~I~-~~~~~~~~~~~~H~~Cf   30 (131)
                      |..|.+.|. +...+...|.+||..||
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            778999984 45568889999999998

>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=97.87  E-value=3.7e-06  Score=36.09  Aligned_cols=26  Identities=38%  Similarity=0.852  Sum_probs=21.5

Q ss_pred             cccCCcccc-CceeEeecCCccccCCc
Q psy4437           5 CAGCEKPIL-DKFLLNVLERTWHADCV   30 (131)
Q Consensus         5 C~~C~~~I~-~~~~~~~~~~~~H~~Cf   30 (131)
                      |..|.+||. +..-+...++.||..||
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            678999994 44457889999999998

>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=97.83  E-value=4.4e-06  Score=40.41  Aligned_cols=26  Identities=31%  Similarity=0.805  Sum_probs=23.1

Q ss_pred             CccccCCccccCceeEeecCCccccCC
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADC   29 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~C   29 (131)
                      .+|..|++.|.+. ++.|.++.|||+|
T Consensus        16 ~~C~~C~~~ItG~-V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          16 TRCFSCDQFIEGE-VVSALGKTYHPDC   41 (41)
T ss_dssp             CBCTTTCCBCCSC-CEEETTEEECTTT
T ss_pred             cccccccCEeeee-eeEecCcccCCCC
Confidence            5799999999655 7889999999987

>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=97.83  E-value=3.6e-06  Score=36.31  Aligned_cols=26  Identities=27%  Similarity=0.772  Sum_probs=17.3

Q ss_pred             cccCCccccc-ceeeeecCCcccccCc
Q psy4437          79 CAGCEKPILD-KFLLNVLERTWHADCV  104 (131)
Q Consensus        79 C~~C~~~I~~-~~~~~~~~~~~H~~Cf  104 (131)
                      |..|.+.|.+ ...+...|..||..||
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            3445555543 1223899999999998

>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=97.80  E-value=8.2e-06  Score=37.33  Aligned_cols=28  Identities=29%  Similarity=0.686  Sum_probs=22.0

Q ss_pred             ccccccCCcccccceeeeecCCcccccCc
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      ++.|.+|+.-|.+..+ .+.++.+||+||
T Consensus         8 lp~CdkCg~GIVG~~V-K~rDk~rHPeCf   35 (35)
T d1x62a2           8 LPMCDKCGTGIVGVFV-KLRDRHRHPECY   35 (35)
T ss_dssp             CCCCSSSCCCCCSSCE-ECSSCEECTTTT
T ss_pred             CccccccCCCcEeEEE-EeccccCCCCCC
Confidence            4566667666666666 999999999998

>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=97.80  E-value=1.3e-06  Score=39.94  Aligned_cols=27  Identities=19%  Similarity=0.707  Sum_probs=24.5

Q ss_pred             ccccccccccccc-eeccCCeeecCCCC
Q psy4437         104 VRCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       104 f~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      |.|+.|.+|+-+. .++++|..||+.+|
T Consensus         1 FvCA~CekPF~G~rhyE~~g~ayCe~Hy   28 (35)
T d1u5sb2           1 FVCAKCEKPFLGHRHYERKGLAYCETHY   28 (35)
T ss_dssp             CBCTTTCCBCSSSCCEEETTEEECHHHH
T ss_pred             CcccccCCccCCchhhhhcCchHHHHHH
Confidence            7899999999877 89999999998876

>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=97.80  E-value=1.3e-05  Score=36.66  Aligned_cols=34  Identities=21%  Similarity=0.537  Sum_probs=24.5

Q ss_pred             cCcCCCCCCCCCCCccccCCCCccccccCCcccccceeeeecCCcccccC
Q psy4437          54 NDFFRSPVRFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADC  103 (131)
Q Consensus        54 ~c~~~~~~~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~C  103 (131)
                      ++|..+|+..|.+|++.|.+-                ++.|.+..|||+|
T Consensus         1 kdYw~kfge~C~~C~~~itGp----------------vMvAG~~K~HPEC   34 (34)
T d1x6aa1           1 KDYWGKFGEFCHGCSLLMTGP----------------FMVAGEFKYHPEC   34 (34)
T ss_dssp             CCSSCCSSCBCTTTCCBCCSC----------------CBCCTTCCBCTTS
T ss_pred             CcHHHHHHHHhhhhHhhcccc----------------eeeecccccCCCC
Confidence            367788887777777655432                2288999999997

>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=97.79  E-value=2.1e-06  Score=38.32  Aligned_cols=27  Identities=22%  Similarity=0.637  Sum_probs=24.7

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFF   57 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~   57 (131)
                      .|+.|+++|+++.| ..++++||-+||.
T Consensus         1 vC~~C~K~Lag~rFTa~eDq~yCVdCYK   28 (31)
T d2cura1           1 VCVTCSKKLAGQRFTAVEDQYYCVDCYK   28 (31)
T ss_dssp             BCTTTCCBCTTSCEEECSSCEEEHHHHH
T ss_pred             CcccccchhcCceeEEecceEEEeeeec
Confidence            48999999999999 7999999999984

>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=97.77  E-value=6.3e-06  Score=35.44  Aligned_cols=26  Identities=27%  Similarity=0.768  Sum_probs=17.7

Q ss_pred             cccCCccccc-ceeeeecCCcccccCc
Q psy4437          79 CAGCEKPILD-KFLLNVLERTWHADCV  104 (131)
Q Consensus        79 C~~C~~~I~~-~~~~~~~~~~~H~~Cf  104 (131)
                      |..|.|.|.+ ...+...|.+||..||
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            4455555554 2234899999999998

>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=97.75  E-value=1.4e-06  Score=39.57  Aligned_cols=31  Identities=19%  Similarity=0.584  Sum_probs=27.3

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcCCCCC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFFRSPV   61 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~   61 (131)
                      .|..|.++|..+.| .+++..||..||.++|+
T Consensus         1 ~C~~C~qPIGtksfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           1 ICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CCSSSCCCCCSSSEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCcccccccccCCCCceEeecchhhcC
Confidence            37899999999999 79999999999987764

>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=97.72  E-value=7.5e-06  Score=37.17  Aligned_cols=28  Identities=18%  Similarity=0.592  Sum_probs=23.9

Q ss_pred             CccccCCccccCc-eeEeecCCccccCCc
Q psy4437           3 ISCAGCEKPILDK-FLLNVLERTWHADCV   30 (131)
Q Consensus         3 ~~C~~C~~~I~~~-~~~~~~~~~~H~~Cf   30 (131)
                      ..|++|++.|... .+..+.++.||.+||
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            4699999999765 457889999999998

>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=97.72  E-value=6.5e-06  Score=35.85  Aligned_cols=27  Identities=19%  Similarity=0.581  Sum_probs=23.5

Q ss_pred             cccccCCcccccceeeeecCCcccccC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADC  103 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~C  103 (131)
                      ..|++|++.++..+.+.-.|+.||..|
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            368999999998888788999999987

>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=97.71  E-value=8.2e-06  Score=34.98  Aligned_cols=26  Identities=35%  Similarity=0.788  Sum_probs=19.8

Q ss_pred             cccCCccccc-ceeeeecCCcccccCc
Q psy4437          79 CAGCEKPILD-KFLLNVLERTWHADCV  104 (131)
Q Consensus        79 C~~C~~~I~~-~~~~~~~~~~~H~~Cf  104 (131)
                      |..|.+||.. ..-+...++.||..||
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            5677888863 3334899999999998

>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=97.71  E-value=8.8e-06  Score=36.24  Aligned_cols=26  Identities=35%  Similarity=0.769  Sum_probs=22.6

Q ss_pred             cccccCCcccccceeeeecCCcccccC
Q psy4437          77 ISCAGCEKPILDKFLLNVLERTWHADC  103 (131)
Q Consensus        77 ~~C~~C~~~I~~~~~~~~~~~~~H~~C  103 (131)
                      .-|..|++.|.++.+ .+.+++|||.|
T Consensus         6 sgC~~C~~~ItGkVL-EAG~khYHP~C   31 (32)
T d1wiga1           6 SGCDSCEKYITGRVL-EAGEKHYHPSC   31 (32)
T ss_dssp             CSCSSSCCCCSSCCB-CCSSCCBCTTT
T ss_pred             chhhhhhhhhhhhhh-hccccccCCCC
Confidence            458888888888877 99999999987

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.71  E-value=7.1e-06  Score=35.72  Aligned_cols=27  Identities=19%  Similarity=0.581  Sum_probs=23.8

Q ss_pred             CccccCCccccCceeEeecCCccccCC
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADC   29 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~C   29 (131)
                      .+|.+|++.++..+.|.-.|++||..|
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            469999999999888878899999987

>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=97.69  E-value=1.4e-05  Score=38.98  Aligned_cols=30  Identities=17%  Similarity=0.495  Sum_probs=24.2

Q ss_pred             CCccccccCCcccccceeeeecCCcccccCc
Q psy4437          74 SMLISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        74 ~~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      +.++.|.+|+.-|.+..+ .+.++.+|++||
T Consensus        16 QkLP~CdkCg~GIVG~~V-K~rDK~rHPeCf   45 (45)
T d1x64a1          16 QRMPLCDKCGSGIVGAVV-KARDKYRHPECF   45 (45)
T ss_dssp             CSCCBCTTTCCBCCSCCE-ESSSCEECTTTC
T ss_pred             ccCccccccCCCcEEEEE-EeccccCCCCCC
Confidence            345677777777777776 999999999998

>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=97.68  E-value=3.5e-06  Score=38.26  Aligned_cols=30  Identities=27%  Similarity=0.574  Sum_probs=24.5

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeeccc-CcCCCC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRN-DFFRSP   60 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~-c~~~~~   60 (131)
                      +|..|++.|+.... +++|+|||.. ||..+|
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~PCY~aLF   32 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHKPCYATLF   32 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTTTHHHHHS
T ss_pred             CchhcccccCCCCccccCCCcCcCcchHHhhc
Confidence            58899999998766 8999999975 775444

>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=97.68  E-value=1.1e-05  Score=34.83  Aligned_cols=28  Identities=18%  Similarity=0.489  Sum_probs=25.2

Q ss_pred             CccccCCccccCceeEeecCCccccCCc
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      .+|+.|.+.++-.+-|...|++||..||
T Consensus         1 nkcg~c~ktvy~aeevqc~grsfhk~cf   28 (28)
T d1a7ia1           1 NKCGACGRTVYHAEEVQCDGRSFHRCCF   28 (28)
T ss_dssp             CBCSSSCCBCSSTTEEEETTEEEESSSE
T ss_pred             CccccccceEeeeeeeeecCceeccccC
Confidence            3799999999888778899999999997

>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=97.66  E-value=2.8e-06  Score=38.85  Aligned_cols=32  Identities=16%  Similarity=0.485  Sum_probs=28.2

Q ss_pred             cccCCCcCcCCCC-ccCcCCeeecccCcCCCCC
Q psy4437          30 VRCYDCHHTLSDK-CFSREGKLFCRNDFFRSPV   61 (131)
Q Consensus        30 f~C~~C~~~l~~~-~f~~~~~~~C~~c~~~~~~   61 (131)
                      |+|+.|.+++-+. .|++.|..||+.+|.++|+
T Consensus         1 FvCA~CekPF~G~rhyE~~g~ayCe~Hy~qLfg   33 (35)
T d1u5sb2           1 FVCAKCEKPFLGHRHYERKGLAYCETHYNQLFG   33 (35)
T ss_dssp             CBCTTTCCBCSSSCCEEETTEEECHHHHHHHCS
T ss_pred             CcccccCCccCCchhhhhcCchHHHHHHHHHhc
Confidence            7899999999884 5699999999999988775

>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=97.65  E-value=6.7e-06  Score=37.31  Aligned_cols=26  Identities=31%  Similarity=0.750  Sum_probs=22.5

Q ss_pred             cccccccccccc-eeccCCeeecCC-CC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRN-DF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~-cy  130 (131)
                      +|..|++.|+.+ ..+.+|+|||.. ||
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~PCY   28 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHKPCY   28 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTTTHH
T ss_pred             CchhcccccCCCCccccCCCcCcCcchH
Confidence            588999999988 899999999965 54

>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=97.64  E-value=2.8e-06  Score=38.48  Aligned_cols=26  Identities=23%  Similarity=0.667  Sum_probs=23.2

Q ss_pred             cccccccccccc-eeccCCeeecCCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .|+.|+++|... |++.+|++||+.||
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cy   27 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCY   27 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHH
T ss_pred             CcccccccHhhcceeeecCcEeHHHHH
Confidence            488999999887 99999999999876

>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=97.62  E-value=3.4e-06  Score=42.63  Aligned_cols=26  Identities=23%  Similarity=0.843  Sum_probs=23.5

Q ss_pred             cccccccccccc-eeccCCeeecCCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      +|+.|++.|++. ..+.|++|||+.||
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY   27 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCY   27 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHH
T ss_pred             ChhhcCCccCCCcccccCCcccchhhh
Confidence            589999999988 88899999999886

>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=97.59  E-value=3e-06  Score=38.37  Aligned_cols=31  Identities=19%  Similarity=0.532  Sum_probs=27.1

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcCCCCC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFFRSPV   61 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~   61 (131)
                      .|..|.+++..+.| .+++..||..||.++|+
T Consensus         1 ~C~~C~qPIGtkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           1 LCSGCEQPLGSRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             BCTTTCCBTTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCcccccccccCCCcEEEEeccccccC
Confidence            37899999999999 79999999999987764

>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=97.53  E-value=4.3e-06  Score=37.46  Aligned_cols=29  Identities=14%  Similarity=0.551  Sum_probs=25.4

Q ss_pred             cCCCcCcCCCCcc-CcCCeeecccCcCCCC
Q psy4437          32 CYDCHHTLSDKCF-SREGKLFCRNDFFRSP   60 (131)
Q Consensus        32 C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~   60 (131)
                      |-.|++.|.+... .+++++||+.||-+++
T Consensus         2 C~~C~K~LdStTva~h~~eiYCKsCygkky   31 (32)
T d1a7ia2           2 CMVCRKNLDSTTVAIHDAEVYCKSCYGKKY   31 (32)
T ss_dssp             CSSSCCEECSSCCEEETTEEECSHHHHHHC
T ss_pred             chhhhhccCcceeeeecceEEehhhccccC
Confidence            6789999999877 8999999999997665

>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=97.52  E-value=1.9e-05  Score=35.81  Aligned_cols=28  Identities=18%  Similarity=0.434  Sum_probs=25.3

Q ss_pred             CccccCCccccCceeEeecCCccccCCc
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      .+|+.|.+.++-.+-|...|++||..||
T Consensus         8 ~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           8 KKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             EECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             ceeccccceEeeeeeeeecCcccccccC
Confidence            4799999999888778899999999998

>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=97.51  E-value=5.3e-06  Score=38.09  Aligned_cols=31  Identities=29%  Similarity=0.632  Sum_probs=26.5

Q ss_pred             ccCCCcCcCCCCccC--cCCeeecccCcCCCCC
Q psy4437          31 RCYDCHHTLSDKCFS--REGKLFCRNDFFRSPV   61 (131)
Q Consensus        31 ~C~~C~~~l~~~~f~--~~~~~~C~~c~~~~~~   61 (131)
                      +|..|++.|.+..|.  .++++||.++|+++|+
T Consensus         1 tCvvC~~~LDGvPFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           1 TCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             BCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             CeeEcCcccCCCcEEEcCCCCEeehhhhhhhcC
Confidence            488999999999883  6799999999988764

>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=97.49  E-value=2.3e-05  Score=34.82  Aligned_cols=26  Identities=35%  Similarity=0.791  Sum_probs=23.2

Q ss_pred             CccccCCccccCceeEeecCCccccCC
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADC   29 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~C   29 (131)
                      +-|..|.+.|+++ ++++.++.|||.|
T Consensus         6 sgC~~C~~~ItGk-VLEAG~khYHP~C   31 (32)
T d1wiga1           6 SGCDSCEKYITGR-VLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCSSSCCCCSSC-CBCCSSCCBCTTT
T ss_pred             chhhhhhhhhhhh-hhhccccccCCCC
Confidence            4589999999888 7899999999987

>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=97.46  E-value=1.5e-05  Score=39.75  Aligned_cols=26  Identities=31%  Similarity=0.726  Sum_probs=23.0

Q ss_pred             cccccccccccc-eeccCCeeec-CCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFC-RNDF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C-~~cy  130 (131)
                      +|..|++.|+++ ..+.|++||| ..||
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY   28 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCY   28 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHH
T ss_pred             CchhcCcCcCCCChhhcCCcccccccch
Confidence            588999999988 8999999999 6576

>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=97.45  E-value=4.8e-06  Score=40.71  Aligned_cols=26  Identities=35%  Similarity=0.796  Sum_probs=23.5

Q ss_pred             cccccccccccc-eeccCCeeecCCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      +|+.|++.|+.+ |...+|.+||+.||
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf   27 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHF   27 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHH
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHH
Confidence            689999999988 88999999998876

>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=97.45  E-value=8.4e-06  Score=36.86  Aligned_cols=29  Identities=24%  Similarity=0.618  Sum_probs=25.3

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcCCC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFFRS   59 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~   59 (131)
                      .|+.|+.+|.+..| +.+|.+||+.||.+-
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~f   30 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKF   30 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHH
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHh
Confidence            48899999999888 788999999998653

>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=97.37  E-value=2e-05  Score=35.17  Aligned_cols=27  Identities=22%  Similarity=0.650  Sum_probs=24.4

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFF   57 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~   57 (131)
                      .|..|+..|.++.| ..+.+.||+.||.
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi   28 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYV   28 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceee
Confidence            48899999999988 8999999999985

>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=97.30  E-value=1.4e-05  Score=36.19  Aligned_cols=25  Identities=20%  Similarity=0.691  Sum_probs=22.5

Q ss_pred             ccccccccccc-eeccCCeeecCCCC
Q psy4437         106 CYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       106 C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      |..|++||++. |..+++..||..||
T Consensus         2 C~~C~qPIGtksfipk~~~~yCvpCy   27 (32)
T d1x4ka1           2 CHRCQQPIGTKSFIPKDNQNFCVPCY   27 (32)
T ss_dssp             CSSSCCCCCSSSEEEETTEEEEHHHH
T ss_pred             cccccCcccccccccCCCCceEeecc
Confidence            78899999998 88999999998776

>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=97.29  E-value=1.3e-05  Score=35.71  Aligned_cols=26  Identities=19%  Similarity=0.604  Sum_probs=22.0

Q ss_pred             cccccccccccc-eeccCCeeecCCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .|..|+++|++. |...+++.||-+||
T Consensus         1 vC~~C~K~Lag~rFTa~eDq~yCVdCY   27 (31)
T d2cura1           1 VCVTCSKKLAGQRFTAVEDQYYCVDCY   27 (31)
T ss_dssp             BCTTTCCBCTTSCEEECSSCEEEHHHH
T ss_pred             CcccccchhcCceeEEecceEEEeeee
Confidence            378899999888 88899999998776

>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=97.22  E-value=7e-05  Score=33.90  Aligned_cols=29  Identities=17%  Similarity=0.369  Sum_probs=24.8

Q ss_pred             ccccccCCcccccceeeeecCCcccccCc
Q psy4437          76 LISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        76 ~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      ...|..|.+.++-++-+.-.|++||..||
T Consensus         7 g~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           7 GKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CceeccccceEeeeeeeeecCcccccccC
Confidence            35799999999877666999999999998

>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=97.20  E-value=2e-05  Score=35.56  Aligned_cols=25  Identities=20%  Similarity=0.680  Sum_probs=22.4

Q ss_pred             ccccccccccc-eeccCCeeecCCCC
Q psy4437         106 CYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       106 C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      |..|++||++. |..+++..||..||
T Consensus         2 C~~C~qPIGtkSFip~~~~~yCvpCY   27 (32)
T d1wyha1           2 CSGCEQPLGSRSFVPDKGAHYCVPCY   27 (32)
T ss_dssp             CTTTCCBTTTSCEEEETTEEEEHHHH
T ss_pred             cccccCcccccccccCCCcEEEEecc
Confidence            78899999998 88999999998876

>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=97.15  E-value=0.00013  Score=30.66  Aligned_cols=26  Identities=27%  Similarity=0.763  Sum_probs=21.4

Q ss_pred             cccCCccccC-ceeEeecCCccccCCc
Q psy4437           5 CAGCEKPILD-KFLLNVLERTWHADCV   30 (131)
Q Consensus         5 C~~C~~~I~~-~~~~~~~~~~~H~~Cf   30 (131)
                      |++|++.+.+ +.-+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            7899998854 4457789999999997

>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=97.12  E-value=0.00011  Score=31.55  Aligned_cols=27  Identities=19%  Similarity=0.541  Sum_probs=22.6

Q ss_pred             ccccCCcccccceeeeecCCcccccCc
Q psy4437          78 SCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        78 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      .|..|++.++-++-+.-.|++||..||
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            477888888876666899999999997

>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=96.92  E-value=4.8e-05  Score=33.85  Aligned_cols=26  Identities=19%  Similarity=0.655  Sum_probs=23.0

Q ss_pred             cccccccccccc-eeccCCeeecCCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      .|..|+..|.+. |+..+.+.||+.||
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CY   27 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCY   27 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHH
T ss_pred             CeeEeCceecCCcceEeecccccccee
Confidence            377899999988 99999999999887

>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=96.81  E-value=0.00023  Score=31.36  Aligned_cols=28  Identities=32%  Similarity=0.831  Sum_probs=24.1

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcCC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFFR   58 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~~   58 (131)
                      +|..|-.+|..+.| .+|++++|..|..+
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~sr   29 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCTTR   29 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHHTT
T ss_pred             CchhhccccccCcccccCCeEeecccccc
Confidence            58889999999999 79999999887643

>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=96.79  E-value=0.00055  Score=31.28  Aligned_cols=29  Identities=21%  Similarity=0.291  Sum_probs=24.9

Q ss_pred             CccccccCCcccccceeeeecCCcccccCc
Q psy4437          75 MLISCAGCEKPILDKFLLNVLERTWHADCV  104 (131)
Q Consensus        75 ~~~~C~~C~~~I~~~~~~~~~~~~~H~~Cf  104 (131)
                      +..+|..|...|.+..+ .+.+..||+..|
T Consensus         7 Gk~vC~KCh~iIdd~pL-~Fr~d~YHp~HF   35 (35)
T d2cora2           7 GKYICQKCHAIIDEQPL-IFKNDPYHPDHF   35 (35)
T ss_dssp             CCCBCTTTCCBCCSCCC-CCSSSCCCTTTS
T ss_pred             hhHHHHHHHhhhhcCcc-eecCCCCCCCCC
Confidence            34689999999988777 999999999887

>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=96.78  E-value=8.5e-05  Score=39.46  Aligned_cols=25  Identities=16%  Similarity=0.659  Sum_probs=22.7

Q ss_pred             ccccccccccc-eeccCCeeecCCCC
Q psy4437         106 CYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       106 C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      |..|++.|++. ..+.+++|||+.||
T Consensus         2 C~~C~K~LdS~~~~eh~~e~YCk~CY   27 (65)
T d1b8ta2           2 CMVCKKNLDSTTVAVHGDEIYCKSCY   27 (65)
T ss_dssp             CTTTCCBCCSSSEEEETTEEEEHHHH
T ss_pred             chhcCCccCCCccccCCCcccchhhh
Confidence            78899999988 88899999999886

>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=96.68  E-value=0.00017  Score=31.97  Aligned_cols=25  Identities=40%  Similarity=0.886  Sum_probs=21.3

Q ss_pred             cccccccccccc-eeccCCeeecCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRND  129 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~c  129 (131)
                      .|+.|+..|... +|..++++||+.+
T Consensus         1 vC~dCg~NLKqrG~Ffv~~~lyCE~H   26 (31)
T d1x64a2           1 VCADCNLNLKQKGYFFVEGELYCETH   26 (31)
T ss_dssp             CCSSSCCCTTTSCCEEETTEEECHHH
T ss_pred             CccccccChhhcceEEeccEEeehhh
Confidence            388999999877 8889999999864

>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=96.67  E-value=0.00021  Score=31.50  Aligned_cols=29  Identities=21%  Similarity=0.500  Sum_probs=24.8

Q ss_pred             ccCCCcCcCCCCccCcCCeeecccCcCCC
Q psy4437          31 RCYDCHHTLSDKCFSREGKLFCRNDFFRS   59 (131)
Q Consensus        31 ~C~~C~~~l~~~~f~~~~~~~C~~c~~~~   59 (131)
                      .|+.|++.|+....+.+|++||..|..++
T Consensus         1 nC~~CgkeltadArEl~geLyCLpChdKm   29 (31)
T d2cora1           1 NCANCGKELTADARELKGELYCLPCHDKM   29 (31)
T ss_dssp             BCSSSCCBCCTTCEEETTEEECHHHHHTT
T ss_pred             CccccccccchhHHHhcCCEEEEeccccc
Confidence            48899999998877889999999987654

>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=96.63  E-value=0.00058  Score=30.98  Aligned_cols=26  Identities=23%  Similarity=0.554  Sum_probs=21.6

Q ss_pred             CccccCCccccCceeEeecCCccccCC
Q psy4437           3 ISCAGCEKPILDKFLLNVLERTWHADC   29 (131)
Q Consensus         3 ~~C~~C~~~I~~~~~~~~~~~~~H~~C   29 (131)
                      ..|.+|.+.|++. ++.+.+..|||+|
T Consensus         9 e~C~~C~~~itGp-vMvAG~~K~HPEC   34 (34)
T d1x6aa1           9 EFCHGCSLLMTGP-FMVAGEFKYHPEC   34 (34)
T ss_dssp             CBCTTTCCBCCSC-CBCCTTCCBCTTS
T ss_pred             HHhhhhHhhcccc-eeeecccccCCCC
Confidence            5799999988765 5668888999997

>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=96.54  E-value=0.0002  Score=31.87  Aligned_cols=25  Identities=16%  Similarity=0.687  Sum_probs=22.0

Q ss_pred             ccccccccccc-eeccCCeeecCCCC
Q psy4437         106 CYDCHHTLSDK-CFSREGKLFCRNDF  130 (131)
Q Consensus       106 C~~C~~~l~~~-~~~~~g~~~C~~cy  130 (131)
                      |-.|.+.|.+. ..+.++.+||+.||
T Consensus         2 C~~C~K~LdStTva~h~~eiYCKsCy   27 (32)
T d1a7ia2           2 CMVCRKNLDSTTVAIHDAEVYCKSCY   27 (32)
T ss_dssp             CSSSCCEECSSCCEEETTEEECSHHH
T ss_pred             chhhhhccCcceeeeecceEEehhhc
Confidence            66789999888 78899999999886

>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=96.36  E-value=0.00035  Score=30.63  Aligned_cols=25  Identities=16%  Similarity=0.655  Sum_probs=21.4

Q ss_pred             cccccccccccc-eeccCCeeecCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRND  129 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~c  129 (131)
                      +|+.|++.++++ |+.+....||..|
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtc   26 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTC   26 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHH
T ss_pred             CcchhhhhcccccccCCCCcEEEEEe
Confidence            488999999988 9999999998543

>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=96.33  E-value=0.001  Score=30.27  Aligned_cols=28  Identities=21%  Similarity=0.405  Sum_probs=19.6

Q ss_pred             CCCCCCccccCCCCccccccCCcccccceeeeecCCcccccC
Q psy4437          62 RFPSGCGVGLSSSMLISCAGCEKPILDKFLLNVLERTWHADC  103 (131)
Q Consensus        62 ~~C~~c~~~i~~~~~~~C~~C~~~I~~~~~~~~~~~~~H~~C  103 (131)
                      ..|.+|+.++.|.+.+              |...|..||+.|
T Consensus         8 ~~C~RC~~gF~p~Eki--------------VNSnGEl~H~qC   35 (35)
T d1g47a1           8 ATCERCKGGFAPAEKI--------------VNSNGELYHEQC   35 (35)
T ss_dssp             CBCSSSCCBCCSTTTC--------------EEETTEEECTTT
T ss_pred             HHHHHHccCCCchHHh--------------hcCCCccccccC
Confidence            3566666666655543              389999999987

>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=96.32  E-value=0.0016  Score=27.15  Aligned_cols=13  Identities=31%  Similarity=0.833  Sum_probs=11.7

Q ss_pred             eeecCCcccccCc
Q psy4437          92 LNVLERTWHADCV  104 (131)
Q Consensus        92 ~~~~~~~~H~~Cf  104 (131)
                      +.+.++.||..||
T Consensus        15 vvaldrvfhvgcf   27 (27)
T d1x61a1          15 VVALDRVFHVGCF   27 (27)
T ss_dssp             EECSSSEECTTTC
T ss_pred             eEEEeeeEEeccC
Confidence            4899999999997

>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=96.26  E-value=0.00044  Score=30.43  Aligned_cols=25  Identities=28%  Similarity=0.830  Sum_probs=21.6

Q ss_pred             cccccccccccc-eeccCCeeecCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRND  129 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~c  129 (131)
                      +|+.|-.||..+ |..+|++++|.+|
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc   26 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKC   26 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHH
T ss_pred             CchhhccccccCcccccCCeEeeccc
Confidence            588899999988 8899999999654

>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=96.15  E-value=0.00018  Score=31.96  Aligned_cols=25  Identities=32%  Similarity=0.772  Sum_probs=21.0

Q ss_pred             cccccccccccc-eeccCCeeecCCC
Q psy4437         105 RCYDCHHTLSDK-CFSREGKLFCRND  129 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~~~g~~~C~~c  129 (131)
                      .|+.|+..|... +|..++++||+++
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~H   26 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKH   26 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHH
T ss_pred             CccccccChhhcceEEeccEEehhhh
Confidence            388999999876 8888999999864

>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=96.08  E-value=0.0014  Score=29.10  Aligned_cols=25  Identities=32%  Similarity=0.732  Sum_probs=21.2

Q ss_pred             cccccccccccc--eeccCCeeecCCC
Q psy4437         105 RCYDCHHTLSDK--CFSREGKLFCRND  129 (131)
Q Consensus       105 ~C~~C~~~l~~~--~~~~~g~~~C~~c  129 (131)
                      +|+.|...|..+  |...+|.+||+.+
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            488899899877  8889999999864

>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=96.01  E-value=0.002  Score=29.31  Aligned_cols=27  Identities=19%  Similarity=0.537  Sum_probs=21.4

Q ss_pred             CccccCCccccC-ceeEeecCCccccCC
Q psy4437           3 ISCAGCEKPILD-KFLLNVLERTWHADC   29 (131)
Q Consensus         3 ~~C~~C~~~I~~-~~~~~~~~~~~H~~C   29 (131)
                      ..|.+|+..... ..+|...|..||+.|
T Consensus         8 ~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           8 ATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHccCCCchHHhhcCCCccccccC
Confidence            468999988854 456888899999886

>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=95.81  E-value=9.1e-05  Score=33.68  Aligned_cols=30  Identities=33%  Similarity=0.923  Sum_probs=24.5

Q ss_pred             ccCCCcCcCCC---CccCcCCeeecccCcCCCC
Q psy4437          31 RCYDCHHTLSD---KCFSREGKLFCRNDFFRSP   60 (131)
Q Consensus        31 ~C~~C~~~l~~---~~f~~~~~~~C~~c~~~~~   60 (131)
                      +|+-|+..|.+   ..|.+.|.++|+.+|.+.|
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            47788888875   5678999999999997765

>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=95.76  E-value=0.0024  Score=29.07  Aligned_cols=26  Identities=23%  Similarity=0.405  Sum_probs=21.4

Q ss_pred             ccccCCccccCceeEeecCCccccCCc
Q psy4437           4 SCAGCEKPILDKFLLNVLERTWHADCV   30 (131)
Q Consensus         4 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf   30 (131)
                      +|.+|+..|.+.. +...+..||+..|
T Consensus        10 vC~KCh~iIdd~p-L~Fr~d~YHp~HF   35 (35)
T d2cora2          10 ICQKCHAIIDEQP-LIFKNDPYHPDHF   35 (35)
T ss_dssp             BCTTTCCBCCSCC-CCCSSSCCCTTTS
T ss_pred             HHHHHHhhhhcCc-ceecCCCCCCCCC
Confidence            6899999997754 6688999999876

>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=95.64  E-value=0.0006  Score=31.03  Aligned_cols=26  Identities=27%  Similarity=0.621  Sum_probs=21.3

Q ss_pred             cccccccccccc-eec-cCCeeecCCCC
Q psy4437         105 RCYDCHHTLSDK-CFS-REGKLFCRNDF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~-~~~-~~g~~~C~~cy  130 (131)
                      +|..|++.|.+. |.. .++++||-++|
T Consensus         1 tCvvC~~~LDGvPFtvD~~n~i~Cv~Dy   28 (33)
T d2dloa2           1 TCVVCHRGLDGIPFTVDATSQIHCIEDF   28 (33)
T ss_dssp             BCSSSCCBCTTSCEECCTTCCCEEHHHH
T ss_pred             CeeEcCcccCCCcEEEcCCCCEeehhhh
Confidence            478899999988 654 57999998876

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.57  E-value=0.0024  Score=28.13  Aligned_cols=26  Identities=38%  Similarity=0.823  Sum_probs=21.9

Q ss_pred             ccCCCcCcCCCC-ccCcCCeeecccCc
Q psy4437          31 RCYDCHHTLSDK-CFSREGKLFCRNDF   56 (131)
Q Consensus        31 ~C~~C~~~l~~~-~f~~~~~~~C~~c~   56 (131)
                      .|+.|+.+|..+ .|..++.+||+.+.
T Consensus         1 vC~dCg~NLKqrG~Ffv~~~lyCE~HA   27 (31)
T d1x64a2           1 VCADCNLNLKQKGYFFVEGELYCETHA   27 (31)
T ss_dssp             CCSSSCCCTTTSCCEEETTEEECHHHH
T ss_pred             CccccccChhhcceEEeccEEeehhhh
Confidence            489999999986 45899999998764

>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=95.45  E-value=0.0027  Score=29.95  Aligned_cols=27  Identities=19%  Similarity=0.524  Sum_probs=17.6

Q ss_pred             cccCCcccccc-eeeeecCCcccccCcc
Q psy4437          79 CAGCEKPILDK-FLLNVLERTWHADCVR  105 (131)
Q Consensus        79 C~~C~~~I~~~-~~~~~~~~~~H~~Cf~  105 (131)
                      |.+|++...+. +.....+..|||.|-.
T Consensus         2 C~rC~~mF~EGEEMYLQGs~IWHP~C~~   29 (41)
T d1wiga2           2 CVRCGQMFAEGEEMYLQGSSIWHPACRQ   29 (41)
T ss_dssp             CSSSCCCCCSSCCCEEETTEEECTTHHH
T ss_pred             cchhhccccccceeeecCCceeCCcccc
Confidence            56666666542 3336678899998843

>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=95.33  E-value=0.0019  Score=28.34  Aligned_cols=25  Identities=24%  Similarity=0.623  Sum_probs=20.7

Q ss_pred             cccccccccccceeccCCeeecCCC
Q psy4437         105 RCYDCHHTLSDKCFSREGKLFCRND  129 (131)
Q Consensus       105 ~C~~C~~~l~~~~~~~~g~~~C~~c  129 (131)
                      .|+.|++.|+....+..|.+||..|
T Consensus         1 nC~~CgkeltadArEl~geLyCLpC   25 (31)
T d2cora1           1 NCANCGKELTADARELKGELYCLPC   25 (31)
T ss_dssp             BCSSSCCBCCTTCEEETTEEECHHH
T ss_pred             CccccccccchhHHHhcCCEEEEec
Confidence            3788999998888888999999654

>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=95.29  E-value=0.0035  Score=29.50  Aligned_cols=28  Identities=18%  Similarity=0.466  Sum_probs=20.1

Q ss_pred             ccccCCccccCceeEe-ecCCccccCCcc
Q psy4437           4 SCAGCEKPILDKFLLN-VLERTWHADCVR   31 (131)
Q Consensus         4 ~C~~C~~~I~~~~~~~-~~~~~~H~~Cf~   31 (131)
                      .|++|++...+++-+. ..+..|||.|-.
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~IWHP~C~~   29 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSSIWHPACRQ   29 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTEEECTTHHH
T ss_pred             CcchhhccccccceeeecCCceeCCcccc
Confidence            4899999997654443 456789998743

>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=95.04  E-value=0.0014  Score=28.69  Aligned_cols=30  Identities=13%  Similarity=0.469  Sum_probs=22.8

Q ss_pred             ccCCCcCcCCCCcc-CcCCeeecccCcCCCC
Q psy4437          31 RCYDCHHTLSDKCF-SREGKLFCRNDFFRSP   60 (131)
Q Consensus        31 ~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~   60 (131)
                      .|+.|++.+....| .++...||..|...+|
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtche~kf   31 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKF   31 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHT
T ss_pred             CcchhhhhcccccccCCCCcEEEEEeecccc
Confidence            47889888887555 7888999988765443

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.00  E-value=0.0055  Score=27.09  Aligned_cols=26  Identities=35%  Similarity=0.756  Sum_probs=21.3

Q ss_pred             ccCCCcCcCCC-Ccc-CcCCeeecccCc
Q psy4437          31 RCYDCHHTLSD-KCF-SREGKLFCRNDF   56 (131)
Q Consensus        31 ~C~~C~~~l~~-~~f-~~~~~~~C~~c~   56 (131)
                      .|+.|+..|.. ..| ..+|.+||+.+-
T Consensus         1 tC~tC~n~LVPGDRFHyvNG~lfCE~D~   28 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYINGSLFCEHDR   28 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEETTEEEEGGGC
T ss_pred             CcccccccccCCceeEEecCEEEEecCC
Confidence            48899998876 567 799999999875

>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=94.92  E-value=0.0017  Score=29.37  Aligned_cols=27  Identities=19%  Similarity=0.520  Sum_probs=21.3

Q ss_pred             ccccccccccccc--eec-cCCeeecCCCC
Q psy4437         104 VRCYDCHHTLSDK--CFS-REGKLFCRNDF  130 (131)
Q Consensus       104 f~C~~C~~~l~~~--~~~-~~g~~~C~~cy  130 (131)
                      |.|..|+..|+.+  |.. ...++||..||
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy   30 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCH   30 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecch
Confidence            6788999999887  654 45889998776

>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=93.50  E-value=0.031  Score=24.59  Aligned_cols=24  Identities=25%  Similarity=0.704  Sum_probs=19.6

Q ss_pred             ccccccccccc-eeccCCeeecCCC
Q psy4437         106 CYDCHHTLSDK-CFSREGKLFCRND  129 (131)
Q Consensus       106 C~~C~~~l~~~-~~~~~g~~~C~~c  129 (131)
                      |..|+..|.+. |...+..++|++|
T Consensus         2 cgkcsvslvg~gfltq~~~i~c~~c   26 (34)
T d1x68a2           2 CGKCSVSLVGKGFLTQNKEIFCQKC   26 (34)
T ss_dssp             CTTTCCBCSSSCEEEETTEEEETTT
T ss_pred             CccceEEEEeeeeeeccCcEEehhc
Confidence            67788888777 8788889999887

>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=91.59  E-value=0.14  Score=28.69  Aligned_cols=44  Identities=18%  Similarity=0.229  Sum_probs=31.0

Q ss_pred             cccCCCcCcCCCCcc-CcCCeeecccCcCCCCCCCCCCCccccCC
Q psy4437          30 VRCYDCHHTLSDKCF-SREGKLFCRNDFFRSPVRFPSGCGVGLSS   73 (131)
Q Consensus        30 f~C~~C~~~l~~~~f-~~~~~~~C~~c~~~~~~~~C~~c~~~i~~   73 (131)
                      +.|..|...+..... ..=|..||..|..+.....|..|..++..
T Consensus        23 l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~~~CP~Cr~~~~~   67 (97)
T d1jm7b_          23 LRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWI   67 (97)
T ss_dssp             TSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTTTBCSSSCCBCSC
T ss_pred             CCCccCCchhhcCceeCCCCCchhHHHHHHHHhccccccCCcCch
Confidence            678888888876544 34588999999877666566666665544

>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=91.31  E-value=0.067  Score=23.48  Aligned_cols=25  Identities=28%  Similarity=0.658  Sum_probs=19.9

Q ss_pred             cCCCcCcCCCCcc-CcCCeeecccCc
Q psy4437          32 CYDCHHTLSDKCF-SREGKLFCRNDF   56 (131)
Q Consensus        32 C~~C~~~l~~~~f-~~~~~~~C~~c~   56 (131)
                      |-.|+.+|.++.| .....++|.+|-
T Consensus         2 cgkcsvslvg~gfltq~~~i~c~~cg   27 (34)
T d1x68a2           2 CGKCSVSLVGKGFLTQNKEIFCQKCG   27 (34)
T ss_dssp             CTTTCCBCSSSCEEEETTEEEETTTT
T ss_pred             CccceEEEEeeeeeeccCcEEehhcC
Confidence            6678889999888 677788888774

>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=90.69  E-value=0.056  Score=23.68  Aligned_cols=27  Identities=33%  Similarity=0.652  Sum_probs=22.5

Q ss_pred             ccCCCcCcCCCCccC-cCCeeecccCcC
Q psy4437          31 RCYDCHHTLSDKCFS-REGKLFCRNDFF   57 (131)
Q Consensus        31 ~C~~C~~~l~~~~f~-~~~~~~C~~c~~   57 (131)
                      +|..|...|.+..|+ ..|+.+|..|..
T Consensus         1 rC~~C~~~LAD~GFvKnagR~LCrpch~   28 (32)
T d2d8xa1           1 RCDLCQEVLADIGFVKNAGRHLCRPCHN   28 (32)
T ss_dssp             BCSSSCCBCSSSCCEEETTEEECHHHHH
T ss_pred             CchHHHhHHHHhhhhhcccccccchhhh
Confidence            588999999999895 568999988764

>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=90.47  E-value=0.076  Score=23.40  Aligned_cols=26  Identities=27%  Similarity=0.677  Sum_probs=19.1

Q ss_pred             cccccccccccc---eeccCCeeecCCCC
Q psy4437         105 RCYDCHHTLSDK---CFSREGKLFCRNDF  130 (131)
Q Consensus       105 ~C~~C~~~l~~~---~~~~~g~~~C~~cy  130 (131)
                      +|..|...|-.+   ....||.+||..++
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hl   29 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHL   29 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeecc
Confidence            466777778766   35679999998764

>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=87.49  E-value=0.71  Score=22.97  Aligned_cols=42  Identities=12%  Similarity=0.117  Sum_probs=23.0

Q ss_pred             cccCCCcCcCCCCccCcCCeeecccCcCCCCCCCCCCCccccC
Q psy4437          30 VRCYDCHHTLSDKCFSREGKLFCRNDFFRSPVRFPSGCGVGLS   72 (131)
Q Consensus        30 f~C~~C~~~l~~~~f~~~~~~~C~~c~~~~~~~~C~~c~~~i~   72 (131)
                      +.|..|...+.+.....=|..||..|..+ ....|..|.+.+.
T Consensus         7 l~C~IC~~~~~~p~~lpCgH~fC~~Ci~~-~~~~CP~Cr~~~~   48 (56)
T d1bora_           7 LRCQQCQAEAKCPKLLPCLHTLCSGCLEA-SGMQCPICQAPWP   48 (56)
T ss_dssp             SSCSSSCSSCBCCSCSTTSCCSBTTTCSS-SSSSCSSCCSSSS
T ss_pred             CCCcccCcccCCCEEecCCCHHhHHHHHc-CCCcCcCCCCccc
Confidence            46777766665433333466777777643 2444555555443

>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=83.63  E-value=0.24  Score=20.94  Aligned_cols=24  Identities=21%  Similarity=0.679  Sum_probs=16.3

Q ss_pred             cCCCcCcCCCCcc-CcCCeeecccC
Q psy4437          32 CYDCHHTLSDKCF-SREGKLFCRND   55 (131)
Q Consensus        32 C~~C~~~l~~~~f-~~~~~~~C~~c   55 (131)
                      |..|+.+|.+..| ...+.++|.+|
T Consensus         2 c~kcsvslvgrgflterddilc~dc   26 (30)
T d1x4la2           2 CKKCSLSLVGRGFLTERDDILCPDC   26 (30)
T ss_dssp             CSSSCCBCTTSCCEECSSSEECHHH
T ss_pred             cceeeEEEEeeeccccccceecccc
Confidence            6678888888777 44445666654

>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=82.83  E-value=0.26  Score=21.48  Aligned_cols=27  Identities=26%  Similarity=0.765  Sum_probs=20.0

Q ss_pred             ccCCCcCcCCC---CccCcCCeeecccCcC
Q psy4437          31 RCYDCHHTLSD---KCFSREGKLFCRNDFF   57 (131)
Q Consensus        31 ~C~~C~~~l~~---~~f~~~~~~~C~~c~~   57 (131)
                      +|.-|+..|.+   .-|.+.+.++|+.+|.
T Consensus         2 kC~cC~cRLGEVG~tlytk~nliLCkrDYl   31 (33)
T d1j2oa2           2 SCDLCGCRLGEVGRRLYYKLGRKLCRRDYL   31 (33)
T ss_dssp             CCSSSCSCCCCSSSCCCCBTTBCCCHHHHH
T ss_pred             ccccccccccchhhHHHhhcceeeehhhhh
Confidence            56667777765   3457889999998874

>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=82.52  E-value=0.16  Score=23.30  Aligned_cols=31  Identities=23%  Similarity=0.536  Sum_probs=18.0

Q ss_pred             ccccCCcccccceeeeecCCcccccCcccccccccc
Q psy4437          78 SCAGCEKPILDKFLLNVLERTWHADCVRCYDCHHTL  113 (131)
Q Consensus        78 ~C~~C~~~I~~~~~~~~~~~~~H~~Cf~C~~C~~~l  113 (131)
                      .|..|.+|.-....+++.|+.    | .|..|..++
T Consensus         2 vC~vCr~pFP~GDRVTFnGKe----C-~CQ~Cs~p~   32 (40)
T d1v6ga2           2 VCAVCRLPFPPGDRVTFNGKE----C-MCQKCSLPV   32 (40)
T ss_dssp             SCSSSCCCCCSSSCEEEETTE----E-EEHHHHSCC
T ss_pred             cccccCCCCCCCCeEEEcCce----e-ehhhcCCCc
Confidence            467777776655555666654    2 355555554