Psyllid ID: psy4350

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------
Protein Sequence
MLKDRDDSSSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSFLYDKQGAASEPLLTG
Secondary Structure (PSIPRED)
cccccccccccccccccccccccccccccEEEEEccccccccccccccccccccccccEEEEccccccHHHHHHHHHcccccccccccHHHHHHHcccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccccccccccHHHHHHHHHHcHHHHHHHHcHHHHHcccccccEEEEccccEEEHHHHHHHHccHHccccccccHccEEEHcccccccccccc
Coil and Loop (DISEMBL)
mlkdrddssspcpeeksscggcgqpiIDRFYLLAVDRQWhlgclqcahchvplhselscfsrhgniyckqdffrysqarypdlpipktLVSFLYdkqgaaseplltg
Flexible Loop (DISEMBL)
mlkdrddssspcpeeksscggcgqPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSFLYDKQGAASEPLLTG
Low Complexity Region (SEG)
MLKDRddssspcpeeksscGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSFLYDKQGAASEPLLTG
Disordered region (IsUnstruct)
******************CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSFLYD************
Disordered Region (DISOPRED)
*********************CGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSFLYDKQGAA*******
Disordered Region (DISEMBL)
*******************GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSFLYDKQGAASEPLLTG
Disordered Region (DISPRO)
****************SSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSFLYDKQG*********
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLKDRDDSSSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSFLYDKQGAASEPLLTG
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	107	2.2.26 [Sep-21-2011]
Q68EY3	331	LIM/homeobox protein Lhx9	N/A	N/A	0.626	0.202	0.567	6e-19
A0JNI8	397	LIM/homeobox protein Lhx9	yes	N/A	0.682	0.183	0.540	2e-18
Q80W90	388	LIM/homeobox protein Lhx9	yes	N/A	0.682	0.188	0.540	3e-18
Q9NQ69	397	LIM/homeobox protein Lhx9	yes	N/A	0.682	0.183	0.540	3e-18
Q9WUH2	397	LIM/homeobox protein Lhx9	yes	N/A	0.682	0.183	0.540	3e-18
A2I8Z7	377	LIM/homeobox protein Lhx9	N/A	N/A	0.607	0.172	0.569	3e-18
Q1LWV4	396	LIM/homeobox protein Lhx9	yes	N/A	0.607	0.164	0.569	5e-18
A2PZF9	379	LIM/homeobox protein Lhx9	N/A	N/A	0.579	0.163	0.580	5e-18
Q90881	397	LIM/homeobox protein Lhx9	yes	N/A	0.682	0.183	0.513	6e-18
Q9Z0S2	406	LIM/homeobox protein Lhx2	no	N/A	0.663	0.174	0.52	9e-18

>sp|Q68EY3|LHX9_XENLA LIM/homeobox protein Lhx9 OS=Xenopus laevis GN=lhx9 PE=2 SV=1

 Score = 92.8 bits (229), Expect = 6e-19,   Method: Compositional matrix adjust.
 Identities = 38/67 (56%), Positives = 52/67 (77%)

Query: 13  PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
           PE+ + C GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+D+
Sbjct: 67  PEKPTLCAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLTLESELTCFAKDGSIYCKEDY 126

Query: 73  FRYSQAR 79
           +R+S  R
Sbjct: 127 YRFSVKR 133

May be involved in gonadal development.
Xenopus laevis (taxid: 8355)

>sp|A0JNI8|LHX9_BOVIN LIM/homeobox protein Lhx9 OS=Bos taurus GN=LHX9 PE=2 SV=2

 Score = 90.9 bits (224), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 40/74 (54%), Positives = 53/74 (71%), Gaps = 1/74 (1%)

Query: 2   LKDRDDSSSP-CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCF 60
           L  RD    P  PE+ + C GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF
Sbjct: 53  LNGRDAGMPPLSPEKPALCAGCGGKIADRYYLLAVDKQWHLRCLKCCECKLALESELTCF 112

Query: 61  SRHGNIYCKQDFFR 74
           ++ G+IYCK+D++R
Sbjct: 113 AKDGSIYCKEDYYR 126

Involved in gonadal development.

Bos taurus (taxid: 9913)

>sp|Q80W90|LHX9_RAT LIM/homeobox protein Lhx9 OS=Rattus norvegicus GN=Lhx9 PE=2 SV=1

 Score = 90.5 bits (223), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 40/74 (54%), Positives = 53/74 (71%), Gaps = 1/74 (1%)

Query: 2   LKDRDDSSSP-CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCF 60
           L  RD    P  PE+ + C GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF
Sbjct: 44  LNGRDAGMPPLSPEKPALCAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCF 103

Query: 61  SRHGNIYCKQDFFR 74
           ++ G+IYCK+D++R
Sbjct: 104 AKDGSIYCKEDYYR 117

Involved in gonadal development.

Rattus norvegicus (taxid: 10116)

>sp|Q9NQ69|LHX9_HUMAN LIM/homeobox protein Lhx9 OS=Homo sapiens GN=LHX9 PE=1 SV=3

 Score = 90.5 bits (223), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 40/74 (54%), Positives = 53/74 (71%), Gaps = 1/74 (1%)

Query: 2   LKDRDDSSSP-CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCF 60
           L  RD    P  PE+ + C GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF
Sbjct: 53  LNGRDAGMPPLSPEKPALCAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCF 112

Query: 61  SRHGNIYCKQDFFR 74
           ++ G+IYCK+D++R
Sbjct: 113 AKDGSIYCKEDYYR 126

Involved in gonadal development.

Homo sapiens (taxid: 9606)

>sp|Q9WUH2|LHX9_MOUSE LIM/homeobox protein Lhx9 OS=Mus musculus GN=Lhx9 PE=1 SV=3

 Score = 90.1 bits (222), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 40/74 (54%), Positives = 53/74 (71%), Gaps = 1/74 (1%)

Query: 2   LKDRDDSSSP-CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCF 60
           L  RD    P  PE+ + C GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF
Sbjct: 53  LNGRDAGMPPLSPEKPALCAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCF 112

Query: 61  SRHGNIYCKQDFFR 74
           ++ G+IYCK+D++R
Sbjct: 113 AKDGSIYCKEDYYR 126

Involved in gonadal development.

Mus musculus (taxid: 10090)

>sp|A2I8Z7|LHX9_ASTFA LIM/homeobox protein Lhx9 OS=Astyanax fasciatus GN=lhx9 PE=2 SV=1

 Score = 90.1 bits (222), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 37/65 (56%), Positives = 50/65 (76%)

Query: 10  SPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK 69
           S  PE+ + C GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK
Sbjct: 43  SVSPEKPALCAGCGSKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCK 102

Query: 70  QDFFR 74
           +D++R
Sbjct: 103 EDYYR 107

May be involved in gonadal development.

Astyanax fasciatus (taxid: 223369)

>sp|Q1LWV4|LHX9_DANRE LIM/homeobox protein Lhx9 OS=Danio rerio GN=lhx9 PE=2 SV=1

 Score = 89.7 bits (221), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 37/65 (56%), Positives = 50/65 (76%)

Query: 10  SPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK 69
           S  PE+ + C GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK
Sbjct: 62  SMSPEKPALCAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCK 121

Query: 70  QDFFR 74
           +D++R
Sbjct: 122 EDYYR 126

May be involved in gonadal development.

Danio rerio (taxid: 7955)

>sp|A2PZF9|LHX9_GLARU LIM/homeobox protein Lhx9 OS=Glandirana rugosa GN=lhx9 PE=2 SV=1

 Score = 89.7 bits (221), Expect = 5e-18,   Method: Compositional matrix adjust.
 Identities = 36/62 (58%), Positives = 49/62 (79%)

Query: 13  PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
           PE+ + C GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+D+
Sbjct: 47  PEKPTLCAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDY 106

Query: 73  FR 74
           +R
Sbjct: 107 YR 108

May be involved in gonadal development.

Glandirana rugosa (taxid: 8410)

>sp|Q90881|LHX9_CHICK LIM/homeobox protein Lhx9 OS=Gallus gallus GN=LHX9 PE=2 SV=2

 Score = 89.4 bits (220), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 38/74 (51%), Positives = 54/74 (72%), Gaps = 1/74 (1%)

Query: 2   LKDRDDSSSP-CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCF 60
           +  R+ +  P  PE+ + C GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF
Sbjct: 53  MNGRETNMPPMSPEKPALCAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCF 112

Query: 61  SRHGNIYCKQDFFR 74
           ++ G+IYCK+D++R
Sbjct: 113 AKDGSIYCKEDYYR 126

May be involved in gonadal development.

Gallus gallus (taxid: 9031)

>sp|Q9Z0S2|LHX2_MOUSE LIM/homeobox protein Lhx2 OS=Mus musculus GN=Lhx2 PE=1 SV=1

 Score = 89.0 bits (219), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 39/75 (52%), Positives = 52/75 (69%), Gaps = 4/75 (5%)

Query: 4   DRDDSSSPCPEEKSS----CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSC 59
           DR D+ +  P   S     C GCG  I DR+YLLAVD+QWH+ CL+C  C + L SEL+C
Sbjct: 34  DRGDTETTMPSISSDRAALCAGCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTC 93

Query: 60  FSRHGNIYCKQDFFR 74
           FS+ G+IYCK+D++R
Sbjct: 94  FSKDGSIYCKEDYYR 108

Acts as a transcriptional activator. Stimulates the promoter of the alpha-glycoprotein gene. Transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types.

Mus musculus (taxid: 10090)

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	107
242023961	383	LIM/homeobox protein Lhx2, putative [Ped	0.691	0.193	0.546	8e-19
241753309	357	lim homeobox protein, putative [Ixodes s	0.719	0.215	0.532	2e-18
357622661	359	apterous [Danaus plexippus]	0.682	0.203	0.608	2e-18
328925124	349	apterous B alpha [Bombyx mori]	0.682	0.209	0.594	2e-18
193575711	356	PREDICTED: LIM/homeobox protein Lhx2-lik	0.579	0.174	0.646	4e-18
345132129	420	apterous [Neanthes arenaceodentata]	0.560	0.142	0.616	6e-18
143347140	280	Lhx2 [Platynereis dumerilii]	0.607	0.232	0.584	2e-17
225543484	361	apterous [Tribolium castaneum] gi|224459	0.691	0.204	0.517	2e-17
148224455	331	LIM/homeobox protein Lhx9 [Xenopus laevi	0.626	0.202	0.567	3e-17
410929509	417	PREDICTED: LIM/homeobox protein Lhx2-lik	0.663	0.170	0.52	3e-17

>gi|242023961|ref|XP_002432399.1| LIM/homeobox protein Lhx2, putative [Pediculus humanus corporis] gi|212517822|gb|EEB19661.1| LIM/homeobox protein Lhx2, putative [Pediculus humanus corporis]

 Score = 97.8 bits (242), Expect = 8e-19,   Method: Compositional matrix adjust.
 Identities = 47/86 (54%), Positives = 58/86 (67%), Gaps = 12/86 (13%)

Query: 1  MLKDRD------DSSSPCPEEKSS------CGGCGQPIIDRFYLLAVDRQWHLGCLQCAH 48
          MLKDRD       ++SPCP    S      C GCG  I+DR+YLLAVDRQWH  CL+C  
Sbjct: 1  MLKDRDAMGPVARAASPCPSGGESASCPTACAGCGGRILDRYYLLAVDRQWHSPCLKCTE 60

Query: 49 CHVPLHSELSCFSRHGNIYCKQDFFR 74
          C  PL +EL+CF+R GNIYCK+D++R
Sbjct: 61 CKSPLDTELTCFARDGNIYCKEDYYR 86

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|241753309|ref|XP_002401118.1| lim homeobox protein, putative [Ixodes scapularis] gi|215508343|gb|EEC17797.1| lim homeobox protein, putative [Ixodes scapularis]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 49/92 (53%), Positives = 59/92 (64%), Gaps = 15/92 (16%)

Query: 4  DRDDSSS----PCPEEKSS-------CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVP 52
          D DDSS+    P P   +S       C  CG PI DRFYLLAV+RQWH  CL+C HC   
Sbjct: 12 DPDDSSTQSLRPSPGSAASPPATAKLCAACGAPIADRFYLLAVERQWHTHCLRCCHCKQQ 71

Query: 53 LHSELSCFSRHGNIYCKQDFFRYSQARYPDLP 84
          L SEL+CF+R GNIYCK+D++    +RYP LP
Sbjct: 72 LDSELTCFARDGNIYCKEDYY----SRYPRLP 99

Source: Ixodes scapularis

Species: Ixodes scapularis

Genus: Ixodes

Family: Ixodidae

Order: Ixodida

Class: Arachnida

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357622661|gb|EHJ74087.1| apterous [Danaus plexippus]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 45/74 (60%), Positives = 53/74 (71%), Gaps = 1/74 (1%)

Query: 1  MLKDRDDSSSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCF 60
          MLK+R+ SS   P     C GCG  I DR+YLLAVDRQWH  CL+C  C +PL SEL+CF
Sbjct: 1  MLKERE-SSEGSPATPDECAGCGGRIQDRYYLLAVDRQWHGACLRCCECRLPLDSELTCF 59

Query: 61 SRHGNIYCKQDFFR 74
          SR GNIYCK D++R
Sbjct: 60 SRDGNIYCKDDYYR 73

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328925124|dbj|BAK19077.1| apterous B alpha [Bombyx mori]

 Score = 96.3 bits (238), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 44/74 (59%), Positives = 54/74 (72%), Gaps = 1/74 (1%)

Query: 1  MLKDRDDSSSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCF 60
          MLK+R+ SS   P     C GCG  I DR+YLLAVDRQWH  CL+C  C +PL +EL+CF
Sbjct: 1  MLKERE-SSEGSPGAPDECAGCGGKIQDRYYLLAVDRQWHGSCLRCCECRLPLDTELTCF 59

Query: 61 SRHGNIYCKQDFFR 74
          SR GNIYCK+D++R
Sbjct: 60 SRDGNIYCKEDYYR 73

Source: Bombyx mori

Species: Bombyx mori

Genus: Bombyx

Family: Bombycidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|193575711|ref|XP_001949543.1| PREDICTED: LIM/homeobox protein Lhx2-like [Acyrthosiphon pisum]

 Score = 95.5 bits (236), Expect = 4e-18,   Method: Compositional matrix adjust.
 Identities = 42/65 (64%), Positives = 52/65 (80%), Gaps = 3/65 (4%)

Query: 13 PEEKSS---CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK 69
          PE+ S+   C GCG+ I DRFYL AVD  WH+GCLQCA C +PL +EL+C+SRHGNIYCK
Sbjct: 14 PEDGSNGACCAGCGRSIDDRFYLSAVDMCWHIGCLQCAECKLPLDTELTCYSRHGNIYCK 73

Query: 70 QDFFR 74
          QD++R
Sbjct: 74 QDYYR 78

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|345132129|gb|AEN75257.1| apterous [Neanthes arenaceodentata]

 Score = 94.7 bits (234), Expect = 6e-18,   Method: Compositional matrix adjust.
 Identities = 37/60 (61%), Positives = 50/60 (83%)

Query: 15  EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
           E + C GCG  IIDR+YLLAVD+QWH+ CL+CA CH+PL SEL+CF++ G I+CK+D++R
Sbjct: 57  EPAPCAGCGGKIIDRYYLLAVDKQWHINCLKCADCHLPLDSELTCFAKDGEIFCKEDYYR 116

Source: Neanthes arenaceodentata

Species: Neanthes arenaceodentata

Genus: Neanthes

Family: Nereididae

Order: Phyllodocida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|143347140|gb|ABO93218.1| Lhx2 [Platynereis dumerilii]

 Score = 93.6 bits (231), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 38/65 (58%), Positives = 52/65 (80%)

Query: 15  EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
           E + C  CG  IIDR+YLLAVD+QWH+ CL+CA CH+PL SEL+CF++ G+IYCK+D++R
Sbjct: 45  EPAPCAACGGKIIDRYYLLAVDKQWHINCLKCADCHLPLDSELTCFAKDGDIYCKEDYYR 104

Query: 75  YSQAR 79
              A+
Sbjct: 105 RFAAK 109

Source: Platynereis dumerilii

Species: Platynereis dumerilii

Genus: Platynereis

Family: Nereididae

Order: Phyllodocida

Class: Polychaeta

Phylum: Annelida

Superkingdom: Eukaryota

>gi|225543484|ref|NP_001139388.1| apterous [Tribolium castaneum] gi|224459214|gb|ACN43342.1| apterous b [Tribolium castaneum]

 Score = 93.2 bits (230), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 44/85 (51%), Positives = 58/85 (68%), Gaps = 11/85 (12%)

Query: 1  MLKDRDDS----SSPCPE-------EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHC 49
          MLK+R+      SSPC         + ++C GCG  I DR+YLLAVDRQWH  CL+C  C
Sbjct: 1  MLKERESIERAISSPCSSLGGSSTLDGTTCAGCGGRIQDRYYLLAVDRQWHASCLKCCEC 60

Query: 50 HVPLHSELSCFSRHGNIYCKQDFFR 74
           +PL +EL+CF+R GNIYCK+D++R
Sbjct: 61 KLPLDTELTCFARDGNIYCKEDYYR 85

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|148224455|ref|NP_001087527.1| LIM/homeobox protein Lhx9 [Xenopus laevis] gi|82198794|sp|Q68EY3.1|LHX9_XENLA RecName: Full=LIM/homeobox protein Lhx9; Short=LIM homeobox protein 9 gi|51258697|gb|AAH80067.1| Lhx9 protein [Xenopus laevis]

 Score = 92.8 bits (229), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 38/67 (56%), Positives = 52/67 (77%)

Query: 13  PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
           PE+ + C GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+D+
Sbjct: 67  PEKPTLCAGCGGKISDRYYLLAVDKQWHLRCLKCCECKLTLESELTCFAKDGSIYCKEDY 126

Query: 73  FRYSQAR 79
           +R+S  R
Sbjct: 127 YRFSVKR 133

Source: Xenopus laevis

Species: Xenopus laevis

Genus: Xenopus

Family: Pipidae

Order: Anura

Class: Amphibia

Phylum: Chordata

Superkingdom: Eukaryota

>gi|410929509|ref|XP_003978142.1| PREDICTED: LIM/homeobox protein Lhx2-like [Takifugu rubripes]

 Score = 92.4 bits (228), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 39/75 (52%), Positives = 55/75 (73%), Gaps = 4/75 (5%)

Query: 4   DRDDSSSPCP----EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSC 59
           D  +S +P P    E  + C GCG+ I+DR+YLLAVD+QWH+ CL+C  C + L SEL+C
Sbjct: 55  DMGESETPLPCLTGERVALCAGCGRKIVDRYYLLAVDKQWHMRCLKCCECKLNLESELTC 114

Query: 60  FSRHGNIYCKQDFFR 74
           FS+ G+IYCK+D++R
Sbjct: 115 FSKDGSIYCKEDYYR 129

Source: Takifugu rubripes

Species: Takifugu rubripes

Genus: Takifugu

Family: Tetraodontidae

Order: Tetraodontiformes

Class: Actinopterygii

Phylum: Chordata

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	107
UNIPROTKB|Q68EY3	331	lhx9 "LIM/homeobox protein Lhx	0.551	0.178	0.593	8.1e-18
UNIPROTKB|H0YM35	147	LHX2 "LIM/homeobox protein Lhx	0.504	0.367	0.611	6.7e-17
UNIPROTKB|E1BSF2	330	LHX9 "LIM/homeobox protein Lhx	0.504	0.163	0.611	9.7e-17
UNIPROTKB|E2R2S6	330	LHX9 "Uncharacterized protein"	0.504	0.163	0.611	9.7e-17
UNIPROTKB|H0YL54	336	LHX9 "LIM/homeobox protein Lhx	0.504	0.160	0.611	1.1e-16
UNIPROTKB|A2I8Z7	377	lhx9 "LIM/homeobox protein Lhx	0.504	0.143	0.611	1.1e-16
UNIPROTKB|Q58CW3	378	LHX9 "LIM homeobox 9" [Bos tau	0.504	0.142	0.611	1.5e-16
UNIPROTKB|A0JNI8	397	LHX9 "LIM/homeobox protein Lhx	0.504	0.136	0.611	1.8e-16
UNIPROTKB|F1S5F5	397	LHX9 "Uncharacterized protein"	0.504	0.136	0.611	1.8e-16
UNIPROTKB|F1NV70	378	LHX9 "LIM/homeobox protein Lhx	0.504	0.142	0.611	1.9e-16

UNIPROTKB|Q68EY3 lhx9 "LIM/homeobox protein Lhx9" [Xenopus laevis (taxid:8355)]

 Score = 217 (81.4 bits), Expect = 8.1e-18, P = 8.1e-18
 Identities = 35/59 (59%), Positives = 47/59 (79%)

Query:    21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQAR 79
             GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+D++R+S  R
Sbjct:    75 GCGGKISDRYYLLAVDKQWHLRCLKCCECKLTLESELTCFAKDGSIYCKEDYYRFSVKR 133

GO:0003714 "transcription corepressor activity" evidence=ISS

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

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

UNIPROTKB|H0YM35 LHX2 "LIM/homeobox protein Lhx2" [Homo sapiens (taxid:9606)]

 Score = 208 (78.3 bits), Expect = 6.7e-17, P = 6.7e-17
 Identities = 33/54 (61%), Positives = 44/54 (81%)

Query:    21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
             GCG  I DR+YLLAVD+QWH+ CL+C  C + L SEL+CFS+ G+IYCK+D++R
Sbjct:    14 GCGGKISDRYYLLAVDKQWHMRCLKCCECKLNLESELTCFSKDGSIYCKEDYYR 67

GO:0008270 "zinc ion binding" evidence=IEA

GO:0000988 "protein binding transcription factor activity" evidence=IEA

GO:0001843 "neural tube closure" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0007498 "mesoderm development" evidence=IEA

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

GO:0021978 "telencephalon regionalization" evidence=IEA

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

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

GO:2000678 "negative regulation of transcription regulatory region DNA binding" evidence=IEA

UNIPROTKB|E1BSF2 LHX9 "LIM/homeobox protein Lhx9" [Gallus gallus (taxid:9031)]

 Score = 208 (78.3 bits), Expect = 9.7e-17, P = 9.7e-17
 Identities = 33/54 (61%), Positives = 44/54 (81%)

Query:    21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
             GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+D++R
Sbjct:    73 GCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 126

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:0005634 "nucleus" evidence=IEA

UNIPROTKB|E2R2S6 LHX9 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 208 (78.3 bits), Expect = 9.7e-17, P = 9.7e-17
 Identities = 33/54 (61%), Positives = 44/54 (81%)

Query:    21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
             GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+D++R
Sbjct:    73 GCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 126

GO:0005634 "nucleus" 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|H0YL54 LHX9 "LIM/homeobox protein Lhx9" [Homo sapiens (taxid:9606)]

 Score = 208 (78.3 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 33/54 (61%), Positives = 44/54 (81%)

Query:    21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
             GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+D++R
Sbjct:    79 GCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 132

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:0005634 "nucleus" evidence=IEA

UNIPROTKB|A2I8Z7 lhx9 "LIM/homeobox protein Lhx9" [Astyanax fasciatus (taxid:223369)]

 Score = 210 (79.0 bits), Expect = 1.1e-16, P = 1.1e-16
 Identities = 33/54 (61%), Positives = 44/54 (81%)

Query:    21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
             GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+D++R
Sbjct:    54 GCGSKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 107

GO:0003714 "transcription corepressor activity" evidence=ISS

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

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

UNIPROTKB|Q58CW3 LHX9 "LIM homeobox 9" [Bos taurus (taxid:9913)]

 Score = 209 (78.6 bits), Expect = 1.5e-16, P = 1.5e-16
 Identities = 33/54 (61%), Positives = 44/54 (81%)

Query:    21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
             GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+D++R
Sbjct:    54 GCGGKIADRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 107

GO:0005634 "nucleus" evidence=IEA

GO:0035262 "gonad morphogenesis" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0008283 "cell proliferation" 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|A0JNI8 LHX9 "LIM/homeobox protein Lhx9" [Bos taurus (taxid:9913)]

 Score = 209 (78.6 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 33/54 (61%), Positives = 44/54 (81%)

Query:    21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
             GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+D++R
Sbjct:    73 GCGGKIADRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 126

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

GO:0003714 "transcription corepressor activity" evidence=ISS

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

GO:0005634 "nucleus" evidence=IEA

GO:0035262 "gonad morphogenesis" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0008283 "cell proliferation" 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|F1S5F5 LHX9 "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 209 (78.6 bits), Expect = 1.8e-16, P = 1.8e-16
 Identities = 33/54 (61%), Positives = 44/54 (81%)

Query:    21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
             GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+D++R
Sbjct:    73 GCGGKIADRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 126

GO:0005634 "nucleus" evidence=IEA

GO:0035262 "gonad morphogenesis" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0008283 "cell proliferation" 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|F1NV70 LHX9 "LIM/homeobox protein Lhx9" [Gallus gallus (taxid:9031)]

 Score = 208 (78.3 bits), Expect = 1.9e-16, P = 1.9e-16
 Identities = 33/54 (61%), Positives = 44/54 (81%)

Query:    21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
             GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+D++R
Sbjct:    54 GCGGKISDRYYLLAVDKQWHLRCLKCCECKLALESELTCFAKDGSIYCKEDYYR 107

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:0005634 "nucleus" evidence=IEA

GO:0008283 "cell proliferation" evidence=IEA

GO:0008584 "male gonad development" evidence=IEA

GO:0008585 "female gonad development" evidence=IEA

GO:0035262 "gonad morphogenesis" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P29673	APTE_DROME	No assigned EC number	0.5573	0.5700	0.1300	yes	N/A
A0JNI8	LHX9_BOVIN	No assigned EC number	0.5405	0.6822	0.1838	yes	N/A
Q90881	LHX9_CHICK	No assigned EC number	0.5135	0.6822	0.1838	yes	N/A
Q9NQ69	LHX9_HUMAN	No assigned EC number	0.5405	0.6822	0.1838	yes	N/A
Q80W90	LHX9_RAT	No assigned EC number	0.5405	0.6822	0.1881	yes	N/A
Q9WUH2	LHX9_MOUSE	No assigned EC number	0.5405	0.6822	0.1838	yes	N/A
Q1LWV4	LHX9_DANRE	No assigned EC number	0.5692	0.6074	0.1641	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

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Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	107
cd09369	54	cd09369, LIM1_Lhx2_Lhx9, The first LIM domain of L	3e-28
cd09469	64	cd09469, LIM1_Lhx2, The first LIM domain of Lhx2	8e-20
cd09470	54	cd09470, LIM1_Lhx9, The first LIM domain of Lhx9	2e-19
cd09373	54	cd09373, LIM1_AWH, The first LIM domain of Arrowhe	2e-17
cd09368	52	cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of L	3e-16
cd09468	52	cd09468, LIM1_Lhx4, The first LIM domain of Lhx4	5e-16
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	3e-15
cd09386	55	cd09386, LIM1_LMO4, The first LIM domain of LMO4 (	5e-15
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	1e-14
cd09467	55	cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b	1e-14
cd09371	53	cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b	1e-14
cd09466	56	cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a	1e-13
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	1e-12
pfam00412	58	pfam00412, LIM, LIM domain	1e-12
cd09366	55	cd09366, LIM1_Isl, The first LIM domain of Isl, a	2e-12
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	3e-11
cd09381	56	cd09381, LIM1_Lhx7_Lhx8, The first LIM domain of L	7e-11
cd09370	52	cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a	3e-10
cd09380	54	cd09380, LIM1_Lhx6, The first LIM domain of Lhx6	3e-10
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	3e-08
cd09388	55	cd09388, LIM1_LMO1_LMO3, The first LIM domain of L	3e-07
cd09384	56	cd09384, LIM1_LMO2, The first LIM domain of LMO2 (	5e-07
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	1e-06
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	1e-06
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	8e-06
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	4e-05
cd09336	53	cd09336, LIM1_Paxillin_like, The first LIM domain	7e-05
cd09409	53	cd09409, LIM3_Paxillin, The third LIM domain of pa	1e-04
cd09410	53	cd09410, LIM3_Leupaxin, The third LIM domain of Le	2e-04
cd09396	53	cd09396, LIM_DA1, The Lim domain of DA1	3e-04
cd09357	63	cd09357, LIM3_Zyxin_like, The third LIM domain of	4e-04
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	4e-04
cd09397	58	cd09397, LIM1_UF1, LIM domain in proteins of unkno	5e-04
cd09356	53	cd09356, LIM2_TRIP6, The second LIM domain of Thyr	5e-04
cd09334	54	cd09334, LIM4_PINCH, The fourth LIM domain of prot	7e-04
cd09340	58	cd09340, LIM1_Testin_like, The first LIM domain of	9e-04
cd09353	60	cd09353, LIM2_Zyxin, The second LIM domain of Zyxi	0.001
cd09393	56	cd09393, LIM3_Lrg1p_like, The third LIM domain of	0.001
cd09363	54	cd09363, LIM3_Enigma_like, The third LIM domain of	0.001
cd09408	52	cd09408, LIM2_Leupaxin, The second LIM domain of L	0.001
cd09326	53	cd09326, LIM_CRP_like, The LIM domains of Cysteine	0.002
cd09406	55	cd09406, LIM1_Leupaxin, The first LIM domain of Le	0.002
cd09337	52	cd09337, LIM2_Paxillin_like, The second LIM domain	0.003
cd09477	54	cd09477, LIM2_TLP, The second LIM domain of thymus	0.004
cd09434	56	cd09434, LIM4_FHL3, The fourth LIM domain of Four	0.004

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

 Score = 97.0 bits (242), Expect = 3e-28
 Identities = 39/54 (72%), Positives = 44/54 (81%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GCG+ I DRFYLLAVDRQWH  CL+C  C +PL SELSCFSR GNIYCK+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|188853 cd09469, LIM1_Lhx2, The first LIM domain of Lhx2

 Score = 75.8 bits (186), Expect = 8e-20
 Identities = 33/54 (61%), Positives = 43/54 (79%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GCG  I DR+YLLAVD+QWH+ CL+C  C + L SEL+CFS+ G+IYCK+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 = 74.3 bits (182), Expect = 2e-19
 Identities = 33/54 (61%), Positives = 43/54 (79%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GCG  I DR+YLLAVD+QWHL CL+C  C + L SEL+CF++ G+IYCK+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|188759 cd09373, LIM1_AWH, The first LIM domain of Arrowhead (AWH)

 Score = 69.3 bits (170), Expect = 2e-17
 Identities = 28/54 (51%), Positives = 34/54 (62%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GCG+PI DRF L    R WH+ CL+C  C  PL  + SCF+R   IYCK 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|188754 cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of Lhx3 and Lhx4 family

 Score = 66.3 bits (162), Expect = 3e-16
 Identities = 27/54 (50%), Positives = 36/54 (66%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          CGGC + I+DRF L  +DR WH  CL+C  C   L  +  CF+R+G++YCK DF
Sbjct: 1  CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTDK--CFARNGHVYCKDDF 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|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4

 Score = 65.8 bits (160), Expect = 5e-16
 Identities = 29/54 (53%), Positives = 36/54 (66%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GC Q I+D+F L  +DR WH  CL+CA C + L     CFSR GN+YCK+DF
Sbjct: 1  CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAER--CFSRAGNVYCKEDF 52

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

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

 Score = 63.6 bits (155), Expect = 3e-15
 Identities = 27/54 (50%), Positives = 35/54 (64%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GC +PI+D+F L  +DR WH  C+QC  C  PL  +  CFSR G +YC+ DF
Sbjct: 1  CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTEK--CFSREGKLYCRNDF 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|188772 cd09386, LIM1_LMO4, The first LIM domain of LMO4 (LIM domain only protein 4)

 Score = 63.2 bits (154), Expect = 5e-15
 Identities = 28/56 (50%), Positives = 37/56 (66%), Gaps = 3/56 (5%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSEL--SCFSRHGNIYCKQDF 72
          C GCG  I+DRF L A+DR WH GCL+C+ C   L  E+  SC+++ G I CK D+
Sbjct: 1  CAGCGGKIVDRFLLHALDRYWHNGCLKCSCCQAQL-GEIGSSCYTKGGMILCKNDY 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|188711 cd08368, LIM, LIM is a small protein-protein interaction domain, containing two zinc fingers

 Score = 62.3 bits (152), Expect = 1e-14
 Identities = 20/54 (37%), Positives = 32/54 (59%), Gaps = 1/54 (1%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GCG+PI  R  L A+ ++WH  C +C+ C  PL  + S + + G  YC++ +
Sbjct: 1  CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGD-SFYEKDGKPYCEKCY 53

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

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

 Score = 62.3 bits (151), Expect = 1e-14
 Identities = 27/54 (50%), Positives = 34/54 (62%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GC Q I+DRF L  +DR WH  CL+C+ C   L  +  CFSR  ++YCK DF
Sbjct: 4  CAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAEK--CFSRGDSVYCKDDF 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|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b

 Score = 62.4 bits (152), Expect = 1e-14
 Identities = 26/54 (48%), Positives = 34/54 (62%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GC +PI DR+ L   +R WH  CLQC+ C  PL +  SC+ R   +YCKQD+
Sbjct: 1  CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPLTT--SCYFRDRKLYCKQDY 52

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

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

 Score = 59.8 bits (145), Expect = 1e-13
 Identities = 28/55 (50%), Positives = 33/55 (60%), Gaps = 2/55 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFF 73
          C GC  PI DRF L   D+ WH  CL+C  C   L  +  CFSR G +YCK+DFF
Sbjct: 4  CAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTDK--CFSRGGQVYCKEDFF 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|188715 cd09329, LIM3_abLIM, The third LIM domain of actin binding LIM (abLIM) proteins

 Score = 57.3 bits (139), Expect = 1e-12
 Identities = 22/54 (40%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GCGQ I +   LLA+D+QWH+ C +C  C   L  E     + G  YC++D+
Sbjct: 1  CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLTGEY--MGKDGKPYCERDY 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|215907 pfam00412, LIM, LIM domain

 Score = 57.4 bits (139), Expect = 1e-12
 Identities = 24/58 (41%), Positives = 33/58 (56%), Gaps = 2/58 (3%)

Query: 19 CGGCGQPIIDRFYLL-AVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRY 75
          C GCG+PI DR  +  A+ + WH  C +CA C  PL      F + G +YCK D+F+ 
Sbjct: 1  CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPL-GPGDFFEKDGKLYCKHDYFKL 57

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

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

 Score = 56.6 bits (137), Expect = 2e-12
 Identities = 25/55 (45%), Positives = 33/55 (60%), Gaps = 1/55 (1%)

Query: 19 CGGCGQPIIDRFYL-LAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GCG  I D++ L +A D +WH  CL+CA C   L    +CF R G  YCK+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|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 53.9 bits (130), Expect = 3e-11
 Identities = 22/55 (40%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 18 SCGGCGQPIIDR-FYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQD 71
           C GCG+PI      L A+ + WH  C +CA C  PL S  + F + G +YCK  
Sbjct: 1  KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPL-SGDTFFEKDGKLYCKDC 54

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

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

 Score = 52.7 bits (126), Expect = 7e-11
 Identities = 21/55 (38%), Positives = 31/55 (56%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFF 73
          C  CG  I+D++ L   D  WH+ CL C+ C   L    SC+ +  +I+CK 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|188756 cd09370, LIM1_Lmx1a, The first LIM domain of Lmx1a

 Score = 51.3 bits (123), Expect = 3e-10
 Identities = 26/54 (48%), Positives = 32/54 (59%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GC + I DRF L   D  WH  CLQCA C  PL +  +CF R   +YCK+D+
Sbjct: 1  CEGCNRVIQDRFLLRVNDSLWHERCLQCASCKEPLET--TCFYRDKKLYCKEDY 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|188766 cd09380, LIM1_Lhx6, The first LIM domain of Lhx6

 Score = 51.2 bits (122), Expect = 3e-10
 Identities = 20/54 (37%), Positives = 31/54 (57%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C  CG  I+DR+ L   +  WH+ CL+C+ C   L    SC+ ++  I+CK 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|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase )

 Score = 45.9 bits (109), Expect = 3e-08
 Identities = 18/55 (32%), Positives = 32/55 (58%), Gaps = 2/55 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFF 73
          C GC   I+D  Y+ A+++ WH  C +C+ C   L +    F + G +YC++D++
Sbjct: 1  CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLSNWY--FEKDGKLYCRKDYW 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|188774 cd09388, LIM1_LMO1_LMO3, The first LIM domain of LMO1 and LMO3 (LIM domain only protein 1 and 3)

 Score = 43.7 bits (103), Expect = 3e-07
 Identities = 21/55 (38%), Positives = 32/55 (58%), Gaps = 1/55 (1%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSC-FSRHGNIYCKQDF 72
          C GC + I DR+ L A+D+ WH  CL+CA C   L    S  +++   I C++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|188770 cd09384, LIM1_LMO2, The first LIM domain of LMO2 (LIM domain only protein 2)

 Score = 42.9 bits (101), Expect = 5e-07
 Identities = 22/57 (38%), Positives = 32/57 (56%), Gaps = 3/57 (5%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSC--FSRHGNIYCKQDFF 73
          CGGC Q I DR++L A+D+ WH  CL C  C   L  E+    + + G   C++D+ 
Sbjct: 1  CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRL-GEVGRRLYYKLGRKLCRRDYL 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|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin like protein family

 Score = 41.6 bits (98), Expect = 1e-06
 Identities = 21/54 (38%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          CGGC +PI++  Y+ A++ QWH  C  C  CH P     S F   G  YC+  +
Sbjct: 1  CGGCNKPILEN-YISALNTQWHPECFVCRECHKPF-INGSFFEHEGLPYCETHY 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|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain Kinase 1)

 Score = 42.2 bits (99), Expect = 1e-06
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFF 73
          C  CGQ I D  YL A++  WH  C +C  C   L      + + G ++CK+D++
Sbjct: 22 CASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHWY--YEKDGRLFCKKDYW 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|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like family

 Score = 39.7 bits (93), Expect = 8e-06
 Identities = 19/50 (38%), Positives = 26/50 (52%), Gaps = 2/50 (4%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYC 68
          C  C Q I   F L+A+ R WH     C+HCH  L +E+      G++YC
Sbjct: 1  CAHCNQVIRGPF-LVALGRSWHPEEFTCSHCHCSL-AEIGFVEEKGSLYC 48

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

 Score = 37.9 bits (88), Expect = 4e-05
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GCG  I D F+   V   WH  C QC+ C   L +    + + G +YC + +
Sbjct: 1  CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLTNWY--YEKDGKLYCHKHY 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|188722 cd09336, LIM1_Paxillin_like, The first LIM domain of the paxillin like protein family

 Score = 37.3 bits (87), Expect = 7e-05
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFF 73
          C  C +PI+ +  + A+ + WH     CA C   L ++ + F R G  YC++D+ 
Sbjct: 1  CAACKKPIVGQV-VTALGKTWHPEHFVCAECKTELGTK-NFFERDGQPYCEKDYH 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|188793 cd09409, LIM3_Paxillin, The third LIM domain of paxillin

 Score = 36.7 bits (85), Expect = 1e-04
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          CGGC + I++  Y+ A++  WH  C  C  C  P     S F   G  YC+  +
Sbjct: 1  CGGCARAILEN-YISALNTLWHPECFVCRECFTPF-VNGSFFEHDGQPYCEAHY 52

The third 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 = 53

>gnl|CDD|188794 cd09410, LIM3_Leupaxin, The third LIM domain of Leupaxin

 Score = 36.3 bits (84), Expect = 2e-04
 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GCG+P+ +  YL A +  WH  C  C+ C  P  ++ S F   G   C+  +
Sbjct: 1  CSGCGRPVKEN-YLSAANGVWHPECFVCSDCLKPF-TDGSFFELDGRPLCELHY 52

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|188782 cd09396, LIM_DA1, The Lim domain of DA1

 Score = 35.3 bits (82), Expect = 3e-04
 Identities = 12/35 (34%), Positives = 16/35 (45%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPL 53
          C GC   I    +L A+   WH  C +C  C  P+
Sbjct: 1  CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPI 35

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|188743 cd09357, LIM3_Zyxin_like, The third LIM domain of Zyxin-like family

 Score = 35.5 bits (82), Expect = 4e-04
 Identities = 19/60 (31%), Positives = 31/60 (51%), Gaps = 9/60 (15%)

Query: 19 CGGCGQPIIDR------FYLLAVDRQWHLGCLQCAHCHVPLHSELS---CFSRHGNIYCK 69
          C  CG+PI+          ++A+DR +H+ C +C  C + L SE     C+   G++ CK
Sbjct: 1  CSVCGEPIMPEPGQDETVRIVALDRSFHVNCYKCEDCGMLLSSEDEGQGCYPLDGHLLCK 60

The third LIM domain of Zyxin like family: This family includes Ajuba, Limd1, WTIP, Zyxin, LPP, and Trip6 LIM proteins. Members of Zyxin family contain three tandem C-terminal LIM domains, and a proline-rich N-terminal region. Zyxin proteins are detected primarily in focal adhesion plaques. They function as scaffolds, participating in the assembly of multiple interactions and signal transduction networks, which regulate cell adhesion, spreading, and motility. They can also shuffle into nucleus. In nucleus, zyxin proteins affect gene transcription by interaction with a variety of nuclear proteins, including several transcription factors, playing regulating roles in cell proliferation, differentiation and apoptosis. 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 = 63

>gnl|CDD|188869 cd09485, LIM_Eplin_alpha_beta, The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

 Score = 35.2 bits (81), Expect = 4e-04
 Identities = 19/54 (35%), Positives = 29/54 (53%), Gaps = 1/54 (1%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C  C + +     L+A  + +H  C +C++C+  L S  +  S HGNIYCK  F
Sbjct: 1  CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKL-SLGTYASLHGNIYCKPHF 53

The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin): Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. 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|188783 cd09397, LIM1_UF1, LIM domain in proteins of unknown function

 Score = 35.3 bits (82), Expect = 5e-04
 Identities = 15/55 (27%), Positives = 19/55 (34%), Gaps = 3/55 (5%)

Query: 19 CGGCGQPIIDRFYLLAVDR---QWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQ 70
          C  CG  I  +           QWH  C  C  C  P    + C+      YC+Q
Sbjct: 1  CRKCGLEIEGKSISSKDGELSGQWHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQ 55

The first Lim domain of a LIM domain containing protein: The functions of the proteins are unknown. The members of this family contain two copies of LIM domain. 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 = 58

>gnl|CDD|188742 cd09356, LIM2_TRIP6, The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6)

 Score = 34.8 bits (80), Expect = 5e-04
 Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C  C +PI++R  L A  + +H  C  C  CH  L          G I+C +DF
Sbjct: 1  CSVCSKPIMERI-LRATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHCIEDF 53

The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. 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|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH

 Score = 34.6 bits (80), Expect = 7e-04
 Identities = 16/54 (29%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          CG C +PI  R  + A+ + WH+    CA C  P       + + G  YC+  +
Sbjct: 3  CGACRRPIEGRV-VTALGKHWHVEHFVCAKCEKPFLG-HRHYEKKGLAYCETHY 54

The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. 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 assem bly of multimeric protein complexes. Length = 54

>gnl|CDD|188726 cd09340, LIM1_Testin_like, The first LIM domain of Testin-like family

 Score = 34.5 bits (80), Expect = 9e-04
 Identities = 19/58 (32%), Positives = 23/58 (39%), Gaps = 12/58 (20%)

Query: 19 CGGCGQPI--------IDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYC 68
          C  C +PI         +R      D  WH GC  C  C+  L  +L  F   G IYC
Sbjct: 1  CEKCKEPINPGEVAVFAERA---GEDACWHPGCFVCETCNELL-VDLIYFYHDGKIYC 54

The first LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. 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 = 58

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

 Score = 34.5 bits (79), Expect = 0.001
 Identities = 18/56 (32%), Positives = 23/56 (41%), Gaps = 1/56 (1%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
          C  C Q I DR  L A  + +H  C  C  C  PL  E     +    +C  D+ R
Sbjct: 1  CAVCDQKITDRM-LKATGKSYHPQCFTCVVCKCPLEGESFIVDQANQPHCVNDYHR 55

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

>gnl|CDD|188779 cd09393, LIM3_Lrg1p_like, The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 33.8 bits (78), Expect = 0.001
 Identities = 20/58 (34%), Positives = 28/58 (48%), Gaps = 10/58 (17%)

Query: 19 CGGCGQPIID---RFYLLAVDRQWHLGCLQCAHCHVPLHSELS---CFSRHGNIYCKQ 70
          C  CG+ I D   +F     D++WHL C  C+ CH  + SELS     ++   I C  
Sbjct: 1  CASCGKSIEDECIKFE----DKRWHLKCFTCSRCHREISSELSDAAFNNKDQRILCSN 54

The third LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

>gnl|CDD|188749 cd09363, LIM3_Enigma_like, The third LIM domain of Enigma-like family

 Score = 33.9 bits (78), Expect = 0.001
 Identities = 22/53 (41%), Positives = 27/53 (50%), Gaps = 4/53 (7%)

Query: 19 CGGCGQPII--DRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK 69
          C GC  PI   DRF L A+   WH  C  CA CHV L  + + +S+     CK
Sbjct: 1  CHGCDFPIEAGDRF-LEALGHTWHDTCFVCAVCHVNLEGQ-TFYSKKDKPLCK 51

The third 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 = 54

>gnl|CDD|188792 cd09408, LIM2_Leupaxin, The second LIM domain of Leupaxin

 Score = 33.6 bits (77), Expect = 0.001
 Identities = 19/54 (35%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C  C  PI+    L A+D+ WH     C+HC      E     R G  YC++DF
Sbjct: 1  CAYCAGPILQNV-LTAMDQTWHPEHFFCSHCGELFGDE-GFLERDGKPYCRRDF 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|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein (CRP) family

 Score = 33.7 bits (78), Expect = 0.002
 Identities = 17/51 (33%), Positives = 23/51 (45%), Gaps = 1/51 (1%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK 69
          C  CG+ +     ++A  + WH  C  CA C+  L S        G IYCK
Sbjct: 1  CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLA-EHDGEIYCK 50

The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. 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|188790 cd09406, LIM1_Leupaxin, The first LIM domain of Leupaxin

 Score = 33.7 bits (77), Expect = 0.002
 Identities = 17/54 (31%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C  C +PI  +  + A+ + WH     C  C   L S    F R+G  YC++D+
Sbjct: 3  CASCQKPIAGQV-VTALGQTWHPEHFVCCQCGKELGSR-PFFERNGQAYCEEDY 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|188723 cd09337, LIM2_Paxillin_like, The second LIM domain of the paxillin like protein family

 Score = 32.7 bits (75), Expect = 0.003
 Identities = 18/54 (33%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C  C  PI+D+  + A+D+ WH     CA C  P   E     + G  YC++D+
Sbjct: 1  CAYCNGPILDKC-VTALDKTWHPEHFFCAQCGKPFGDE-GFHEKDGKPYCREDY 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|188861 cd09477, LIM2_TLP, The second LIM domain of thymus LIM protein (TLP)

 Score = 32.7 bits (74), Expect = 0.004
 Identities = 13/35 (37%), Positives = 20/35 (57%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPL 53
          C GCG+P+     ++++ R WH  CL+C  C   L
Sbjct: 1  CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTL 35

The second LIM domain of thymus LIM protein (TLP): 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. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188818 cd09434, LIM4_FHL3, The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3)

 Score = 32.8 bits (75), Expect = 0.004
 Identities = 15/38 (39%), Positives = 19/38 (50%), Gaps = 3/38 (7%)

Query: 19 CGGCGQPII---DRFYLLAVDRQWHLGCLQCAHCHVPL 53
          C  C +PI       Y+   DRQWH  C +C+ C V L
Sbjct: 1  CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSVSL 38

The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. 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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	107
KOG1701|consensus	468		99.79
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.6
KOG1044|consensus	670		99.58
KOG1701|consensus	468		99.57
KOG4577|consensus	383		99.49
KOG2272|consensus	332		99.46
KOG2272|consensus	332		99.46
KOG1703|consensus	479		99.3
KOG1703|consensus	479		99.12
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.83
KOG1044|consensus	670		98.7
KOG4577|consensus	383		98.53
KOG1700|consensus	200		98.21
KOG1700|consensus	200		98.06
KOG1702|consensus	264		97.88
KOG0490|consensus	235		95.46
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	90.0
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	88.18
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	87.21

>KOG1701|consensus

Probab=99.79  E-value=7.4e-21  Score=134.37  Aligned_cols=91  Identities=19%  Similarity=0.436  Sum_probs=83.3

Q ss_pred             CCCCCCCCCccccccccccCceE-EeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCC
Q psy4350           9 SSPCPEEKSSCGGCGQPIIDRFY-LLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIP   86 (107)
Q Consensus         9 ~~~~~~~~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~   86 (107)
                      ++..+..+..|.+|+|.|+.... +.++++.||..||+|..|++.|.++ .||..++++||+.||.. ..  +|..  |+
T Consensus       267 ~~p~~~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq-~FY~v~~k~~CE~cyq~tle--kC~~--Cg  341 (468)
T KOG1701|consen  267 AEPVEDYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQ-SFYQVDGKPYCEGCYQDTLE--KCNK--CG  341 (468)
T ss_pred             CChhhhhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccc-cccccCCcccchHHHHHHHH--HHhh--hh
Confidence            45566677799999999987654 6999999999999999999999998 89999999999999999 77  8999  99


Q ss_pred             CcchhhhhhhccccCCCC
Q psy4350          87 KTLVSFLYDKQGAASEPL  104 (107)
Q Consensus        87 ~~i~~~~~~~~g~~~~p~  104 (107)
                      ++|+++++++.|++|||.
T Consensus       342 ~~I~d~iLrA~GkayHp~  359 (468)
T KOG1701|consen  342 EPIMDRILRALGKAYHPG  359 (468)
T ss_pred             hHHHHHHHHhcccccCCC
Confidence            999999999999999995

>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=99.60  E-value=1.5e-15  Score=81.77  Aligned_cols=56  Identities=30%  Similarity=0.894  Sum_probs=51.2

Q ss_pred             cccccccccCceEE-eecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-h
Q psy4350          19 CGGCGQPIIDRFYL-LAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-Y   75 (107)
Q Consensus        19 C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~   75 (107)
                      |.+|+++|.+.+.+ .+.++.||+.||+|..|+++|.+. .++..++++||+.||.+ |
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~-~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDG-DFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTS-SEEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCC-eeEeECCEEECHHHHhhhC
Confidence            78999999987765 699999999999999999999988 58999999999999987 5

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

>KOG1044|consensus

Probab=99.58  E-value=5.2e-16  Score=113.42  Aligned_cols=85  Identities=27%  Similarity=0.665  Sum_probs=79.7

Q ss_pred             CCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchhh
Q psy4350          14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVSF   92 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~   92 (107)
                      .++..|++|++.|..+..+.++++.||..||+|..|+..|.+  .+..+++.+||+.||.. |++ +|..  |.+.|+|.
T Consensus       131 ~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g--ey~skdg~pyce~dy~~~fgv-kc~~--c~~fisgk  205 (670)
T KOG1044|consen  131 YGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG--EYMSKDGVPYCEKDYQAKFGV-KCEE--CEKFISGK  205 (670)
T ss_pred             cCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc--eeeccCCCcchhhhhhhhcCe-ehHH--hhhhhhhh
Confidence            467789999999998888899999999999999999999987  48899999999999999 995 9999  99999999


Q ss_pred             hhhhccccCCC
Q psy4350          93 LYDKQGAASEP  103 (107)
Q Consensus        93 ~~~~~g~~~~p  103 (107)
                      ++.+.|+-|||
T Consensus       206 vLqag~kh~HP  216 (670)
T KOG1044|consen  206 VLQAGDKHFHP  216 (670)
T ss_pred             hhhccCcccCc
Confidence            99999999999

>KOG1701|consensus

Probab=99.57  E-value=1.9e-16  Score=112.24  Aligned_cols=86  Identities=24%  Similarity=0.551  Sum_probs=72.3

Q ss_pred             CCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchh
Q psy4350          13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVS   91 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~   91 (107)
                      +....+|..|++.|.+.. +.++|+.||+.||+|..|.+.|.+..+....++++||..||++ |+ ++|+.  |+++|+.
T Consensus       331 q~tlekC~~Cg~~I~d~i-LrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA-PrCs~--C~~PI~P  406 (468)
T KOG1701|consen  331 QDTLEKCNKCGEPIMDRI-LRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA-PRCSV--CGNPILP  406 (468)
T ss_pred             HHHHHHHhhhhhHHHHHH-HHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC-cchhh--ccCCccC
Confidence            345678999999999984 8999999999999999999999988334677899999999999 99 79999  9999974


Q ss_pred             h-------hhhhccccCC
Q psy4350          92 F-------LYDKQGAASE  102 (107)
Q Consensus        92 ~-------~~~~~g~~~~  102 (107)
                      .       -+.++++.||
T Consensus       407 ~~G~~etvRvvamdr~fH  424 (468)
T KOG1701|consen  407 RDGKDETVRVVAMDRDFH  424 (468)
T ss_pred             CCCCcceEEEEEcccccc
Confidence            2       2334566666

>KOG4577|consensus

Probab=99.49  E-value=9.5e-16  Score=104.34  Aligned_cols=83  Identities=39%  Similarity=0.903  Sum_probs=73.8

Q ss_pred             CCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchh--
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVS--   91 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~--   91 (107)
                      ..++|+.|.+.|.+++++.++++.||..|++|+.|..+|..  .++.+++.+||+.+|++ || .+|..  |+..|..  
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d--rCFsR~~s~yCkedFfKrfG-TKCsa--C~~GIpPtq  106 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD--RCFSREGSVYCKEDFFKRFG-TKCSA--CQEGIPPTQ  106 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH--HHhhcCCceeehHHHHHHhC-Ccchh--hcCCCChHH
Confidence            56789999999999998899999999999999999999988  57899999999999999 99 59999  9999964  


Q ss_pred             hhhhhccccCC
Q psy4350          92 FLYDKQGAASE  102 (107)
Q Consensus        92 ~~~~~~g~~~~  102 (107)
                      .+-+++...||
T Consensus       107 VVRkAqd~VYH  117 (383)
T KOG4577|consen  107 VVRKAQDFVYH  117 (383)
T ss_pred             HHHHhhcceee
Confidence            55566666666

>KOG2272|consensus

Probab=99.46  E-value=1e-14  Score=97.86  Aligned_cols=86  Identities=17%  Similarity=0.426  Sum_probs=77.8

Q ss_pred             CCCccccccccccCceE-EeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchhh
Q psy4350          15 EKSSCGGCGQPIIDRFY-LLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVSF   92 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~   92 (107)
                      ....|.+|.....+.+. +...+..||..||.|..|-.++.++ .|++-+|+.||+.+|.. |+ |-|+.  |++.|.|.
T Consensus        11 ~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g-~~~efEgRkYCEhDF~~Lfa-PcC~k--C~EFiiGr   86 (332)
T KOG2272|consen   11 ANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDG-IFYEFEGRKYCEHDFHVLFA-PCCGK--CGEFIIGR   86 (332)
T ss_pred             HHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCc-eeEEecCcccccccchhhhc-hhhcc--cccchhhH
Confidence            34569999988876665 4677889999999999999999988 89999999999999999 99 79999  99999999


Q ss_pred             hhhhccccCCCC
Q psy4350          93 LYDKQGAASEPL  104 (107)
Q Consensus        93 ~~~~~g~~~~p~  104 (107)
                      ++.++.++|||-
T Consensus        87 VikamnnSwHp~   98 (332)
T KOG2272|consen   87 VIKAMNNSWHPA   98 (332)
T ss_pred             HHHhhccccCcc
Confidence            999999999994

>KOG2272|consensus

Probab=99.46  E-value=8.1e-15  Score=98.29  Aligned_cols=84  Identities=20%  Similarity=0.515  Sum_probs=77.5

Q ss_pred             CCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchhhh
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVSFL   93 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~~   93 (107)
                      +.++|..|.++|.++ ++.++|+.||...|+|+.|.++.-+- ..|++.|..||+.+|.+ || ..|..  |+..|-|.+
T Consensus       194 gipiCgaC~rpIeer-vi~amgKhWHveHFvCa~CekPFlGH-rHYEkkGlaYCe~h~~qLfG-~~CF~--C~~~i~G~v  268 (332)
T KOG2272|consen  194 GIPICGACRRPIEER-VIFAMGKHWHVEHFVCAKCEKPFLGH-RHYEKKGLAYCETHYHQLFG-NLCFI--CNRVIGGDV  268 (332)
T ss_pred             CCcccccccCchHHH-HHHHhccccchhheeehhcCCcccch-hhhhhcCchhHHHHHHHHhh-hhhee--cCCccCccH
Confidence            567899999999876 48999999999999999999998776 78999999999999999 99 69999  999999999


Q ss_pred             hhhccccCCC
Q psy4350          94 YDKQGAASEP  103 (107)
Q Consensus        94 ~~~~g~~~~p  103 (107)
                      +.+.++||-|
T Consensus       269 v~al~KawCv  278 (332)
T KOG2272|consen  269 VSALNKAWCV  278 (332)
T ss_pred             HHHhhhhhcc
Confidence            9999999876

>KOG1703|consensus

Probab=99.30  E-value=9.9e-13  Score=96.75  Aligned_cols=85  Identities=26%  Similarity=0.592  Sum_probs=76.8

Q ss_pred             CCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcch--
Q psy4350          14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLV--   90 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~--   90 (107)
                      ...+.|.+|.+.|.+.. |.+.+..||+.||+|..|.+.+... .|+..++.+||+.||.+ +. ++|..  |..++.  
T Consensus       361 ~~~p~C~~C~~~i~~~~-v~a~~~~wH~~cf~C~~C~~~~~~~-~~~~~~~~pyce~~~~~~~~-~~~~~--~~~p~~~~  435 (479)
T KOG1703|consen  361 PFRPNCKRCLLPILEEG-VCALGRLWHPECFVCADCGKPLKNS-SFFESDGEPYCEDHYKKLFT-TKCDY--CKKPVEFG  435 (479)
T ss_pred             hhCccccccCCchHHhH-hhhccCeechhceeeecccCCCCCC-cccccCCccchhhhHhhhcc-ccchh--ccchhHhh
Confidence            45788999999998885 7777999999999999999999887 89999999999999999 98 69999  999987  


Q ss_pred             hhhhhhccccCCC
Q psy4350          91 SFLYDKQGAASEP  103 (107)
Q Consensus        91 ~~~~~~~g~~~~p  103 (107)
                      +..+.++|..||+
T Consensus       436 ~~~ie~~~~~~h~  448 (479)
T KOG1703|consen  436 SRQIEADGSPFHG  448 (479)
T ss_pred             hhHhhccCccccc
Confidence            7889999999886

>KOG1703|consensus

Probab=99.12  E-value=1.3e-10  Score=85.62  Aligned_cols=87  Identities=17%  Similarity=0.331  Sum_probs=78.8

Q ss_pred             CCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchhh
Q psy4350          14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVSF   92 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~   92 (107)
                      ...+.|..|+..|.....+.++++.||+.+|.|..|...+... .+...++++||..||.. +. +.|..  |+++|.+.
T Consensus       301 ~~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~-~~~~~~g~~~c~~~~~~~~~-p~C~~--C~~~i~~~  376 (479)
T KOG1703|consen  301 VTRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDG-GPRELDGKILCHECFHAPFR-PNCKR--CLLPILEE  376 (479)
T ss_pred             cccccccccccCcccceeEeeccccccccceeeccccccccCC-CccccCCCccHHHHHHHhhC-ccccc--cCCchHHh
Confidence            3458899999999884468999999999999999999998877 67888999999999999 88 79999  99999999


Q ss_pred             hhhhccccCCCC
Q psy4350          93 LYDKQGAASEPL  104 (107)
Q Consensus        93 ~~~~~g~~~~p~  104 (107)
                      .+.+.+..|||-
T Consensus       377 ~v~a~~~~wH~~  388 (479)
T KOG1703|consen  377 GVCALGRLWHPE  388 (479)
T ss_pred             HhhhccCeechh
Confidence            999999999984

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

Probab=98.83  E-value=3.7e-09  Score=51.88  Aligned_cols=37  Identities=41%  Similarity=1.068  Sum_probs=32.7

Q ss_pred             ccccccccccCc-eEEeecCcccccccccccccCCCCC
Q psy4350          18 SCGGCGQPIIDR-FYLLAVDRQWHLGCLQCAHCHVPLH   54 (107)
Q Consensus        18 ~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~   54 (107)
                      +|.+|++.|.+. ..+.+.++.||+.||+|..|+.+|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            488999999886 5578899999999999999999885

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.

>KOG1044|consensus

Probab=98.70  E-value=1.2e-08  Score=75.51  Aligned_cols=80  Identities=23%  Similarity=0.458  Sum_probs=64.7

Q ss_pred             CCCCCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCC
Q psy4350           9 SSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPK   87 (107)
Q Consensus         9 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~   87 (107)
                      +........+|.+|.+.-... ++.+.++.||..||+|..|+..|... .|+.+++.        + ++ +  ..  |..
T Consensus         9 s~~~~~~~i~c~~c~~kc~ge-vlrv~d~~fhi~cf~c~~cg~~la~~-gff~k~~~--------~~yg-t--~~--c~~   73 (670)
T KOG1044|consen    9 SPQTGKQGIKCDKCRKKCSGE-VLRVNDNHFHINCFQCKKCGRNLAEG-GFFTKPEN--------RLYG-T--DD--CRA   73 (670)
T ss_pred             CccccccceehhhhCCccccc-eeEeeccccceeeeeccccCCCcccc-cceecccc--------eeec-c--cc--hhh
Confidence            334445567899999988765 68999999999999999999999887 67666554        3 44 2  44  778


Q ss_pred             cchhhhhhhccccCCC
Q psy4350          88 TLVSFLYDKQGAASEP  103 (107)
Q Consensus        88 ~i~~~~~~~~g~~~~p  103 (107)
                      .|.+.++.+.|++|||
T Consensus        74 ~~~gevvsa~gktyh~   89 (670)
T KOG1044|consen   74 FVEGEVVSTLGKTYHP   89 (670)
T ss_pred             hccceeEecccceecc
Confidence            9999999999999998

>KOG4577|consensus

Probab=98.53  E-value=2.8e-08  Score=68.32  Aligned_cols=64  Identities=22%  Similarity=0.449  Sum_probs=53.4

Q ss_pred             CCccccccccccCceEE-eecCcccccccccccccCCCCCCCCce-eccCCeeccHHHHhh-hCCCCC
Q psy4350          16 KSSCGGCGQPIIDRFYL-LAVDRQWHLGCLQCAHCHVPLHSELSC-FSRHGNIYCKQDFFR-YSQARY   80 (107)
Q Consensus        16 ~~~C~~C~~~i~~~~~~-~~~~~~~H~~Cf~C~~C~~~l~~~~~~-~~~~~~~~C~~~y~~-~~~~~C   80 (107)
                      .-+|..|.+.|.+..++ .+.+..||..||.|..|.+.|..+..| ...+.++.|+.+|+. -. +.|
T Consensus        92 GTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~-k~~  158 (383)
T KOG4577|consen   92 GTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQ-KHC  158 (383)
T ss_pred             CCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHh-ccc
Confidence            45799999999988766 788899999999999999999854444 577889999999998 55 455

>KOG1700|consensus

Probab=98.21  E-value=3.7e-07  Score=60.52  Aligned_cols=65  Identities=18%  Similarity=0.452  Sum_probs=55.4

Q ss_pred             CCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCC
Q psy4350          12 CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQ   77 (107)
Q Consensus        12 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~   77 (107)
                      .......|..|++.++..+.+...+..||+.||.|..|.+.|... .+..+++.+||+.+|.. +++
T Consensus         3 ~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~-~~~~~e~~~yc~~~~~~~~~~   68 (200)
T KOG1700|consen    3 FTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLS-GYSEHEGVPYCKNCHVAQFGP   68 (200)
T ss_pred             cccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccc-cccccccccccccchHhhhCc
Confidence            344566899999999988777888999999999999999999876 67789999999998777 773

>KOG1700|consensus

Probab=98.06  E-value=6.2e-07  Score=59.46  Aligned_cols=64  Identities=23%  Similarity=0.565  Sum_probs=55.0

Q ss_pred             CCCCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350          10 SPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR   74 (107)
Q Consensus        10 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~   74 (107)
                      .+.......|..|.+.+++.+.+...+..||..||+|..|+..|... .+....+.++|...+..
T Consensus       102 ~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~-~~~~~~g~l~~~~~~~~  165 (200)
T KOG1700|consen  102 QVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPK-NYAALEGVLYCKHHFAQ  165 (200)
T ss_pred             HhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCc-chhhcCCccccchhhhe
Confidence            34556678899999999998888999999999999999999999987 78888888888776665

>KOG1702|consensus

Probab=97.88  E-value=7.1e-07  Score=58.86  Aligned_cols=59  Identities=19%  Similarity=0.536  Sum_probs=52.2

Q ss_pred             CccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          17 SSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        17 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      ..|..|++.+++.+.+..+++.||..||+|..|+..|... .+-..+.++||..+|.+ .+
T Consensus         5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmK-nyKgy~kkpycn~hYpkq~a   64 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMK-NYKGYDKKPYCNPHYPKQVA   64 (264)
T ss_pred             chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhh-hccccccCCCcCccccccee
Confidence            4578899999998888999999999999999999999877 67778889999999987 54

>KOG0490|consensus

Probab=95.46  E-value=0.0067  Score=40.51  Aligned_cols=76  Identities=41%  Similarity=0.848  Sum_probs=56.1

Q ss_pred             ccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh---hCCCCCCCCCCCCcch--hhhhhh
Q psy4350          22 CGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR---YSQARYPDLPIPKTLV--SFLYDK   96 (107)
Q Consensus        22 C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~---~~~~~C~~~~C~~~i~--~~~~~~   96 (107)
                      |+..|.+...+...+..||..|..|..|...+......+..++..||..+|.+   +. .+|..  |...|.  ..+..+
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~-~rr~r--t~~~~~ql~~ler~   78 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFS-KRCAR--CKFTISQLDELERA   78 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhcc-ccccC--CCCCcCHHHHHHHh
Confidence            66777777666777899999999999999998722234444999999999985   44 68999  888873  344444


Q ss_pred             cccc
Q psy4350          97 QGAA  100 (107)
Q Consensus        97 ~g~~  100 (107)
                      ..+.
T Consensus        79 f~~~   82 (235)
T KOG0490|consen   79 FEKV   82 (235)
T ss_pred             hcCC
Confidence            4444

>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=90.00  E-value=0.13  Score=26.70  Aligned_cols=47  Identities=23%  Similarity=0.469  Sum_probs=32.1

Q ss_pred             ccccCCCCCCCCceeccCCeeccHHHHhhhCCCCCCCCCCCCcchhh-hhhhcccc
Q psy4350          46 CAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSF-LYDKQGAA  100 (107)
Q Consensus        46 C~~C~~~l~~~~~~~~~~~~~~C~~~y~~~~~~~C~~~~C~~~i~~~-~~~~~g~~  100 (107)
                      |..|++++.+........++.|...||      .|..  |+.+|.+. .+..+|+.
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf------~C~~--C~~~l~~~~~~~~~~~~   48 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECF------KCSK--CGKPLNDGDFYEKDGKP   48 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTS------BETT--TTCBTTTSSEEEETTEE
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEcccc------ccCC--CCCccCCCeeEeECCEE
Confidence            677888887663444578888887773      5888  99998765 34444543

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 ....

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=88.18  E-value=0.52  Score=24.78  Aligned_cols=29  Identities=21%  Similarity=0.524  Sum_probs=20.6

Q ss_pred             CCcccccccccc--CceEE-eecCcccccccc
Q psy4350          16 KSSCGGCGQPII--DRFYL-LAVDRQWHLGCL   44 (107)
Q Consensus        16 ~~~C~~C~~~i~--~~~~~-~~~~~~~H~~Cf   44 (107)
                      ..+|..|++.+.  +..++ ..-+..||++|+
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~   36 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW   36 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence            457999999995  33222 456788999887

>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=87.21  E-value=0.47  Score=22.97  Aligned_cols=25  Identities=20%  Similarity=0.481  Sum_probs=17.9

Q ss_pred             cccccccccCceE-EeecCccccccc
Q psy4350          19 CGGCGQPIIDRFY-LLAVDRQWHLGC   43 (107)
Q Consensus        19 C~~C~~~i~~~~~-~~~~~~~~H~~C   43 (107)
                      |..|+.+|.+... +...++.|+.-|
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~fCC   26 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYYFCC   26 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEEEEC
Confidence            6778999976654 477788887443

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	107
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		4e-13
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		8e-13
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		1e-11
1m3v_A	122	Flin4: Fusion Of The Lim Binding Domain Of Ldb1 And		2e-07
2l4z_A	123	Nmr Structure Of Fusion Of Ctip (641-685) To Lmo4-L		2e-07
2dfy_X	195	Crystal Structure Of A Cyclized Protein Fusion Of L		3e-07
1rut_X	188	Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 L		4e-07
2dj7_A	80	Solution Structure Of 3rd Lim Domain Of Actin-Bindi		6e-05
1j2o_A	114	Structure Of Flin2, A Complex Containing The N-Term		9e-05
2xjy_A	131	Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21		2e-04

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

Iteration: 1
 Score = 69.7 bits (169), Expect = 4e-13,   Method: Compositional matrix adjust.
 Identities = 36/73 (49%), Positives = 45/73 (61%), Gaps = 4/73 (5%)
Query: 20  GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRY--SQ 77
            GC Q I+DRF L A+DR WH  CL+C+ CHVPL     CFSR  ++YCK DFF+   ++
Sbjct: 64  AGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAER--CFSRGESVYCKDDFFKRFGTK 121
Query: 78  ARYPDLPIPKTLV 90
                L IP T V
Sbjct: 122 CAACQLGIPPTQV 134

>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 = 68.6 bits (166), Expect = 8e-13,   Method: Compositional matrix adjust.
 Identities = 36/73 (49%), Positives = 45/73 (61%), Gaps = 4/73 (5%)
Query: 20 GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRY--SQ 77
           GC Q I+DRF L A+DR WH  CL+C+ CHVPL     CFSR  ++YCK DFF+   ++
Sbjct: 10 AGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAER--CFSRGESVYCKDDFFKRFGTK 67
Query: 78 ARYPDLPIPKTLV 90
               L IP T V
Sbjct: 68 CAACQLGIPPTQV 80

>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 = 64.3 bits (155), Expect = 1e-11,   Method: Compositional matrix adjust.
 Identities = 28/55 (50%), Positives = 37/55 (67%), Gaps = 2/55 (3%)
Query: 20 GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
           GC Q I+D+F L  +DR WH  CL+CA C + L     CFSR G++YCK+DFF+
Sbjct: 10 AGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADR--CFSRAGSVYCKEDFFK 62

>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 = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR 74
          GCG  I DRF L A+D  WH  CL+C+ C   L     S +++ G I C+ D+ R
Sbjct: 10 GCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 64

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

Iteration: 1
 Score = 50.8 bits (120), Expect = 2e-07,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 21  GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR 74
           GCG  I DRF L A+D  WH  CL+C+ C   L     S +++ G I C+ D+ R
Sbjct: 66  GCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 120

>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 = 50.1 bits (118), Expect = 3e-07,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR 74
          GCG  I DRF L A+D  WH  CL+C+ C   L     S +++ G I C+ D+ R
Sbjct: 8  GCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 62

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

Iteration: 1
 Score = 49.7 bits (117), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 23/55 (41%), Positives = 31/55 (56%), Gaps = 1/55 (1%)
Query: 21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR 74
          GCG  I DRF L A+D  WH  CL+C+ C   L     S +++ G I C+ D+ R
Sbjct: 10 GCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 64

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

Iteration: 1
 Score = 42.4 bits (98), Expect = 6e-05,   Method: Compositional matrix adjust.
 Identities = 21/52 (40%), Positives = 29/52 (55%), Gaps = 2/52 (3%)
Query: 21 GCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          GC + I     LLA+D+QWH+ C +C  C V L  E    S+ G  YC+ D+
Sbjct: 20 GCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEY--ISKDGVPYCESDY 69

>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 = 42.0 bits (97), Expect = 9e-05,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 20 GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPL-HSELSCFSRHGNIYCKQDFFR 74
          GGC Q I DR++L A+D+ WH  CL C  C   L       + + G   C++D+ R
Sbjct: 7  GGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 62

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

Iteration: 1
 Score = 40.4 bits (93), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 21/56 (37%), Positives = 30/56 (53%), Gaps = 1/56 (1%)
Query: 20 GGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPL-HSELSCFSRHGNIYCKQDFFR 74
          GGC Q I DR++L A+D+ WH  CL C  C   L       + + G   C++D+ R
Sbjct: 6  GGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 61

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	107
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	2e-21
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	2e-21
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	4e-20
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	7e-06
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	6e-20
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	2e-06
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	7e-20
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	4e-09
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	9e-20
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	9e-18
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	4e-17
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	5e-07
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	4e-17
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	8e-16
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	5e-07
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	1e-15
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	5e-15
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	8e-13
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	3e-12
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	1e-11
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	1e-11
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	2e-11
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	3e-11
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	4e-08
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	4e-11
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	4e-11
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	7e-11
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	9e-11
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	1e-10
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	2e-10
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	3e-10
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-10
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	5e-10
2cuq_A	80	Four and A half LIM domains 3; structural genomics	7e-10
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	1e-09
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	1e-09
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	1e-09
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	2e-09
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	2e-09
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	3e-09
2co8_A	82	NEDD9 interacting protein with calponin homology a	4e-09
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	5e-09
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	3e-08
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	4e-08
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	8e-08
2cor_A	79	Pinch protein; LIM domain, particularly interestin	9e-08
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	7e-05
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	2e-04

>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 = 80.9 bits (199), Expect = 2e-21
 Identities = 24/66 (36%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 10  SPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPL-HSELSCFSRHGNIYC 68
                    C GCG  I DRF L A+D  WH  CL+C+ C   L     S +++ G I C
Sbjct: 55  GSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILC 114

Query: 69  KQDFFR 74
           + D+ R
Sbjct: 115 RNDYIR 120

>2dj7_A Actin-binding LIM protein 3; LIM domain, Zn binding protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 80

 Score = 79.8 bits (197), Expect = 2e-21
 Identities = 24/70 (34%), Positives = 34/70 (48%), Gaps = 4/70 (5%)

Query: 7  DSSSPCPEEK--SSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHG 64
           SS    + +  S C GC + I     LLA+D+QWH+ C +C  C V L       S+ G
Sbjct: 4  GSSGKPIKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG--EYISKDG 61

Query: 65 NIYCKQDFFR 74
            YC+ D+  
Sbjct: 62 VPYCESDYHA 71

>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 = 79.2 bits (195), Expect = 4e-20
 Identities = 34/67 (50%), Positives = 41/67 (61%), Gaps = 2/67 (2%)

Query: 8   SSSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIY 67
             S    E   C GC Q I+DRF L A+DR WH  CL+C+ CHVPL     CFSR  ++Y
Sbjct: 52  MGSGGTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE--RCFSRGESVY 109

Query: 68  CKQDFFR 74
           CK DFF+
Sbjct: 110 CKDDFFK 116

>2jtn_A LIM domain-binding protein 1, LIM/homeobox protein LHX3; intramolecular (fusion) protein-protein complex, protein binding/transcription complex; NMR {Mus musculus} Length = 182

 Score = 41.4 bits (97), Expect = 7e-06
 Identities = 14/56 (25%), Positives = 20/56 (35%), Gaps = 2/56 (3%)

Query: 19  CGGCGQPI-IDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDF 72
           C  C   I   +    A D  +HL C  C  C   L + +         + CK D+
Sbjct: 122 CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY 177

>2rgt_A Fusion of LIM/homeobox protein LHX3, linker, INSU enhancer protein ISL-1; protein-protein complex, LIM domain, Zn finger, activator, D binding; 2.05A {Mus musculus} PDB: 3mmk_A Length = 169

 Score = 78.3 bits (193), Expect = 6e-20
 Identities = 33/61 (54%), Positives = 40/61 (65%), Gaps = 2/61 (3%)

Query: 14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFF 73
           E   C GC Q I+DRF L A+DR WH  CL+C+ CHVPL     CFSR  ++YCK DFF
Sbjct: 4  PEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAER--CFSRGESVYCKDDFF 61

Query: 74 R 74
          +
Sbjct: 62 K 62

>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 = 43.3 bits (102), Expect = 2e-06
 Identities = 14/58 (24%), Positives = 21/58 (36%), Gaps = 2/58 (3%)

Query: 17  SSCGGCGQPI-IDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDF 72
           + C  C   I   +    A D  +HL C  C  C   L + +         + CK D+
Sbjct: 66  TKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY 123

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

 Score = 77.1 bits (190), Expect = 7e-20
 Identities = 22/57 (38%), Positives = 31/57 (54%), Gaps = 1/57 (1%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPL-HSELSCFSRHGNIYCKQDFFR 74
          CGGC Q I DR++L A+D+ WH  CL C  C   L       + + G   C++D+ R
Sbjct: 5  CGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 61

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

 Score = 49.4 bits (118), Expect = 4e-09
 Identities = 14/65 (21%), Positives = 26/65 (40%), Gaps = 1/65 (1%)

Query: 16  KSSCGGCGQPII-DRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
              C  C + I      +   D+ +HL C +CA C             + +I C+QD + 
Sbjct: 66  DGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYE 125

Query: 75  YSQAR 79
           +++  
Sbjct: 126 WTKIN 130

>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 = 76.6 bits (188), Expect = 9e-20
 Identities = 24/58 (41%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 18 SCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPL-HSELSCFSRHGNIYCKQDFFR 74
           C GCG  I DRF L A+D  WH  CL+C+ C   L     S +++ G I C+ D+ R
Sbjct: 7  RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 64

>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 = 71.6 bits (175), Expect = 9e-18
 Identities = 22/63 (34%), Positives = 33/63 (52%), Gaps = 1/63 (1%)

Query: 18 SCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPL-HSELSCFSRHGNIYCKQDFFRYS 76
          +CGGC Q I DR++L A+D+ WH  CL C  C   L       + + G   C++D+ R  
Sbjct: 5  TCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLG 64

Query: 77 QAR 79
           + 
Sbjct: 65 GSG 67

>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 = 71.6 bits (175), Expect = 4e-17
 Identities = 24/58 (41%), Positives = 32/58 (55%), Gaps = 1/58 (1%)

Query: 18 SCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSE-LSCFSRHGNIYCKQDFFR 74
           C GCG  I DRF L A+D  WH  CL+C+ C   L     S +++ G I C+ D+ R
Sbjct: 7  RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 64

>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 = 44.6 bits (105), Expect = 5e-07
 Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 15  EKSSCGGCGQPI-IDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
              +C  CGQ I      + A    +HL C  C+ C   L         +G+++C+ D 
Sbjct: 68  NSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDR 126

>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 = 68.9 bits (169), Expect = 4e-17
 Identities = 23/70 (32%), Positives = 29/70 (41%), Gaps = 2/70 (2%)

Query: 6  DDSSSPCPEEKSS-CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHG 64
            S   C       C  C QPI+DR  L A+ + +H GC  C  CH  L           
Sbjct: 4  GSSGEGCYVATLEKCATCSQPILDR-ILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATS 62

Query: 65 NIYCKQDFFR 74
           I+C +DF R
Sbjct: 63 QIHCIEDFHR 72

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

 Score = 66.7 bits (163), Expect = 8e-16
 Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 1/60 (1%)

Query: 15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
          EK  C GC + I    Y  A ++ WHL    C  C   L  E      +    CK  + +
Sbjct: 2  EKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGE-IYVMVNDKPVCKPCYVK 60

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

 Score = 43.9 bits (104), Expect = 5e-07
 Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 4/59 (6%)

Query: 19  CGGCGQPI-IDRFYLLAVDRQWHLG--CLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
           C GC   I  +   +   +  WH    C  C+ C   L  +       G ++C  +  +
Sbjct: 66  CQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQ-KFMPVEGMVFCSVECKK 123

>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 = 65.5 bits (160), Expect = 1e-15
 Identities = 17/57 (29%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 19 CGGCGQPII-DRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
          C  C +PI  D   +   +R WH  C +CA C  PL +  +  ++   I C +   R
Sbjct: 8  CVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPL-ANETFVAKDNKILCNKCTTR 63

>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 = 63.2 bits (154), Expect = 5e-15
 Identities = 16/67 (23%), Positives = 24/67 (35%), Gaps = 2/67 (2%)

Query: 8  SSSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIY 67
           S    ++   C  CG  I+   ++   DR  H  C  C  C   L  +   F     IY
Sbjct: 7  GSIGNAQKLPMCDKCGTGIVGV-FVKLRDRHRHPECYVCTDCGTNL-KQKGHFFVEDQIY 64

Query: 68 CKQDFFR 74
          C++    
Sbjct: 65 CEKHARE 71

>1x64_A Alpha-actinin-2 associated LIM protein; LIM domain, PDZ and LIM domain 3, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 89

 Score = 58.3 bits (141), Expect = 8e-13
 Identities = 16/70 (22%), Positives = 27/70 (38%), Gaps = 2/70 (2%)

Query: 5  RDDSSSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHG 64
          +    +   +    C  CG  I+    + A D+  H  C  CA C++ L  +   F   G
Sbjct: 14 KVHGGAGSAQRMPLCDKCGSGIVGA-VVKARDKYRHPECFVCADCNLNL-KQKGYFFVEG 71

Query: 65 NIYCKQDFFR 74
           +YC+     
Sbjct: 72 ELYCETHARA 81

>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 = 56.1 bits (136), Expect = 3e-12
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          CG C +PI  R  + A+ +QWH+    CA C  P       + R G  YC+  +
Sbjct: 8  CGACRRPIEGR-VVNAMGKQWHVEHFVCAKCEKPFLGH-RHYERKGLAYCETHY 59

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

 Score = 55.1 bits (133), Expect = 1e-11
 Identities = 14/56 (25%), Positives = 22/56 (39%), Gaps = 1/56 (1%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
          CG CG+ +     +    R +H  C  C  C   L S  +       +YCK  + +
Sbjct: 10 CGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDST-TVAIHDAEVYCKSCYGK 64

>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 = 54.7 bits (132), Expect = 1e-11
 Identities = 19/56 (33%), Positives = 27/56 (48%), Gaps = 2/56 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
          CGGC +P+++  YL A+D  WH  C  C  C     S  S F   G  +C+  +  
Sbjct: 18 CGGCNRPVLEN-YLSAMDTVWHPECFVCGDCFTSF-STGSFFELDGRPFCELHYHH 71

>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 = 56.2 bits (135), Expect = 3e-11
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 19  CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
           C  CGQ +     ++   + WH  C +CA C   L S  +   + G IYCK  +
Sbjct: 118 CPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLEST-TLADKDGEIYCKGCY 170

>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 = 48.1 bits (114), Expect = 4e-08
 Identities = 13/61 (21%), Positives = 21/61 (34%), Gaps = 1/61 (1%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQA 78
          CG C + +     +      +H  C  C  C   L S  +       IYCK  + +    
Sbjct: 10 CGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDST-TVAVHGDEIYCKSCYGKKYGP 68

Query: 79 R 79
          +
Sbjct: 69 K 69

>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 = 53.7 bits (129), Expect = 4e-11
 Identities = 16/57 (28%), Positives = 21/57 (36%), Gaps = 2/57 (3%)

Query: 19 CGGCGQPI-IDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
          C  C Q I  D   L   DR +H GC +C  C   L  E     +   + C   +  
Sbjct: 18 CAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADE-PFTCQDSELLCNDCYCS 73

>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 = 53.6 bits (129), Expect = 4e-11
 Identities = 15/56 (26%), Positives = 26/56 (46%), Gaps = 2/56 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
          C  C Q I    +L+A+ + WH     CAHC   + + +      G +YC+  + +
Sbjct: 28 CAHCNQVIRGP-FLVALGKSWHPEEFNCAHCKNTM-AYIGFVEEKGALYCELCYEK 81

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

 Score = 52.3 bits (126), Expect = 7e-11
 Identities = 16/58 (27%), Positives = 21/58 (36%), Gaps = 2/58 (3%)

Query: 17 SSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
          S C  C +PI     +   ++ WH  C  C  C   L S     +R    YC   F  
Sbjct: 6  SGCVQCKKPITTGG-VTYREQPWHKECFVCTACRKQL-SGQRFTARDDFAYCLNCFCD 61

>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 = 52.9 bits (127), Expect = 9e-11
 Identities = 18/66 (27%), Positives = 30/66 (45%), Gaps = 1/66 (1%)

Query: 7  DSSSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNI 66
                   + +C  C + +     LLA  + +H+ C +C++C+  L    +  S HG I
Sbjct: 6  SGMKFQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLG-TYASLHGRI 64

Query: 67 YCKQDF 72
          YCK  F
Sbjct: 65 YCKPHF 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 = 52.1 bits (125), Expect = 1e-10
 Identities = 17/60 (28%), Positives = 31/60 (51%), Gaps = 2/60 (3%)

Query: 16 KSSCGGCGQPIIDR-FYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
           S CGGCG+ ++     ++A+DR +H+GC  C+ C   L  +   ++     YC+  +  
Sbjct: 5  SSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQ-HFYAVERRAYCEGCYVA 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 = 51.6 bits (124), Expect = 2e-10
 Identities = 17/60 (28%), Positives = 23/60 (38%), Gaps = 2/60 (3%)

Query: 16 KSSCGGCGQPII-DRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
           S C  CG+ ++     L    + WH  C  C+ C  PL S  S     G  YC   +  
Sbjct: 5  SSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSR-SFVPDKGAHYCVPCYEN 63

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

 Score = 50.8 bits (122), Expect = 3e-10
 Identities = 12/54 (22%), Positives = 18/54 (33%), Gaps = 2/54 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C  C + I     +   D+ WH  C  C  C   L +     +     YC   +
Sbjct: 8  CVKCNKAITSG-GITYQDQPWHADCFVCVTCSKKL-AGQRFTAVEDQYYCVDCY 59

>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 = 50.9 bits (122), Expect = 4e-10
 Identities = 11/57 (19%), Positives = 21/57 (36%), Gaps = 2/57 (3%)

Query: 19 CGGCGQPII-DRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
          C  C + I+     +      WH  C  C  C  P+ ++ S   +    +C   + +
Sbjct: 8  CQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTK-SFIPKDNQNFCVPCYEK 63

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

 Score = 50.5 bits (121), Expect = 5e-10
 Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 2/59 (3%)

Query: 16 KSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
           S C  CG+ II R  + A++  WH  C +C  C   L +++      G   C+    R
Sbjct: 5  SSGCHQCGEFIIGR-VIKAMNNSWHPECFRCDLCQEVL-ADIGFVKNAGRHLCRPCHNR 61

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

 Score = 50.0 bits (120), Expect = 7e-10
 Identities = 16/56 (28%), Positives = 22/56 (39%), Gaps = 2/56 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR 74
          C  C + +     +   D+ WH  CL C  C  PL  +    SR  + YC   F  
Sbjct: 18 CARCSKTLTQG-GVTYRDQPWHRECLVCTGCQTPLAGQ-QFTSRDEDPYCVACFGE 71

>1x4l_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 72

 Score = 49.8 bits (119), Expect = 1e-09
 Identities = 16/57 (28%), Positives = 21/57 (36%), Gaps = 4/57 (7%)

Query: 19 CGGCGQPIIDRF---YLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GC  PI       Y+   +RQWH  C  C  C + L       +   +I C    
Sbjct: 8  CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGR-GFLTERDDILCPDCG 63

>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 = 49.7 bits (119), Expect = 1e-09
 Identities = 13/55 (23%), Positives = 21/55 (38%), Gaps = 1/55 (1%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFF 73
          C  C + +     + ++ + WH  CL+C  C   L S        G  YC    +
Sbjct: 3  CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSG-GHAEHEGKPYCNHPCY 56

>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 = 49.3 bits (118), Expect = 1e-09
 Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 2/58 (3%)

Query: 16 KSSCGGCGQPII-DRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
           ++C  C          + +    +H  C  CA C          +   G  YC+ DF
Sbjct: 11 SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDF 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 = 48.9 bits (117), Expect = 2e-09
 Identities = 12/58 (20%), Positives = 19/58 (32%), Gaps = 2/58 (3%)

Query: 16 KSSCGGCGQPII-DRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
           ++C  C          + +    +H  C  CA C          +   G  YC+ DF
Sbjct: 11 SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDF 67

>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 = 48.7 bits (116), Expect = 2e-09
 Identities = 15/55 (27%), Positives = 25/55 (45%), Gaps = 4/55 (7%)

Query: 19 CGGCGQPIIDRF---YLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQ 70
          C  C +PI       ++   D QWH  C  C  C V L  +    +++  I+C++
Sbjct: 8  CVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGK-GFLTQNKEIFCQK 61

>1x63_A Skeletal muscle LIM-protein 1; LIM domain, four and A half LIM domains protein 1, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 82

 Score = 48.5 bits (116), Expect = 3e-09
 Identities = 13/58 (22%), Positives = 22/58 (37%), Gaps = 2/58 (3%)

Query: 16 KSSCGGCGQPII-DRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
             C GC + I+     +      WH  C  C++C   + +  S F +  + YC    
Sbjct: 15 SPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTG-SFFPKGEDFYCVTCH 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 = 48.4 bits (115), Expect = 4e-09
 Identities = 13/66 (19%), Positives = 18/66 (27%), Gaps = 1/66 (1%)

Query: 8  SSSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNI 66
                     C  CG+ +     L      +H  C +C  C   L           G+ 
Sbjct: 7  GQHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHF 66

Query: 67 YCKQDF 72
          YC Q  
Sbjct: 67 YCLQHL 72

>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 = 47.8 bits (114), Expect = 5e-09
 Identities = 11/55 (20%), Positives = 21/55 (38%), Gaps = 1/55 (1%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFF 73
          C  C + +     + ++ + WH  CL+C  C   L          G  +C +  +
Sbjct: 12 CPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPG-GHAEHDGKPFCHKPCY 65

>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 = 46.3 bits (110), Expect = 3e-08
 Identities = 12/52 (23%), Positives = 19/52 (36%), Gaps = 1/52 (1%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQ 70
          C  C Q I     + A+ + +H  C  CA C +P               C++
Sbjct: 18 CFSCDQFIEGE-VVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQK 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 = 45.5 bits (108), Expect = 4e-08
 Identities = 12/62 (19%), Positives = 24/62 (38%), Gaps = 2/62 (3%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFRYSQ 77
          C GC   +    +++A + ++H  C  C  C V +   +     +H  +YC +       
Sbjct: 18 CHGCSLLMTGP-FMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVS 76

Query: 78 AR 79
            
Sbjct: 77 GP 78

>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 = 44.8 bits (106), Expect = 8e-08
 Identities = 14/58 (24%), Positives = 19/58 (32%), Gaps = 5/58 (8%)

Query: 19 CGGCGQPII----DRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          C GC  PI         +    + WH  C  C  C V L ++         +YC    
Sbjct: 18 CAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANK-RFVFHQEQVYCPDCA 74

>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 = 44.8 bits (106), Expect = 9e-08
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 3/57 (5%)

Query: 16 KSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDF 72
          K  C  C   I ++  L+  +  +H     CA+C   L ++       G +YC    
Sbjct: 15 KYICQKCHAIIDEQ-PLIFKNDPYHPDHFNCANCGKELTAD--ARELKGELYCLPCH 68

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

 Score = 37.4 bits (86), Expect = 7e-05
 Identities = 12/54 (22%), Positives = 20/54 (37%), Gaps = 1/54 (1%)

Query: 17 SSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQ 70
          S C  C + I  R  L A ++ +H  C  C  C          + +  +I+   
Sbjct: 6  SGCDSCEKYITGRV-LEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPA 58

>2iyb_E Testin, TESS, TES; LIM domain, SH3-binding, tumour supressor LIM domain EVH1 DO cell motility, phosphorylation, cytoskeleton; 2.35A {Homo sapiens} Length = 65

 Score = 35.6 bits (82), Expect = 2e-04
 Identities = 12/54 (22%), Positives = 19/54 (35%), Gaps = 4/54 (7%)

Query: 19 CGGCGQPI-IDRFYLLAVDRQWHL--GCLQCAHCHVPLHSELSCFSRHGNIYCK 69
          C GC   I  +   +   +  WH    C  C+ C   L  +       G ++C 
Sbjct: 5  CQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQ-KFMPVEGMVFCS 57

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	107
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.87
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.85
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.84
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.82
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.81
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.79
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.78
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.77
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.76
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.76
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.76
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.76
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.73
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.73
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.73
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.73
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.73
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.72
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.72
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.72
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.7
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.7
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.7
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.69
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.69
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.69
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.68
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.68
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.67
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.67
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.67
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.67
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.67
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.66
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.65
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.65
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.61
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.6
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.6
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.59
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.57
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.55
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.43
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.33
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.31
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.28
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.16
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.12
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.44
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	98.41
2cuq_A	80	Four and A half LIM domains 3; structural genomics	98.38
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	98.36
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	98.33
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	98.32
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	98.28
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	98.25
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	98.19
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	98.16
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	96.59
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	96.45
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	95.07
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	94.97
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	94.97
2cor_A	79	Pinch protein; LIM domain, particularly interestin	94.94
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	94.88
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	94.81
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	94.8
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	94.62
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	94.57
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	94.55
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	94.5
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	94.35
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	94.06
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	93.88
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	93.57
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	93.35
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	93.14
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	92.75
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	92.71
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	91.64
2co8_A	82	NEDD9 interacting protein with calponin homology a	90.35
2cs3_A	93	Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, s	90.05
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	90.02
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	89.48
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	85.52
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	82.97
3nw0_A	238	Non-structural maintenance of chromosomes element	80.89

>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=99.87  E-value=1.3e-22  Score=119.95  Aligned_cols=88  Identities=25%  Similarity=0.431  Sum_probs=79.2

Q ss_pred             CCCCCccccccccccC-ceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcch
Q psy4350          13 PEEKSSCGGCGQPIID-RFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLV   90 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~   90 (107)
                      +.+.++|.+|+++|.. .+.+.++++.||+.||+|..|+++|.+. .|+.+++++||+.||.+ |+ ++|..  |+++|.
T Consensus         2 s~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~cy~~~~~-~~C~~--C~~~I~   77 (101)
T 2cup_A            2 SSGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANE-TFVAKDNKILCNKCTTREDS-PKCKG--CFKAIV   77 (101)
T ss_dssp             CSCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSS-CCEEETTEEECHHHHTTCCC-CBCSS--SCCBCC
T ss_pred             CCCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcC-eeECcCCEEEChhHhhhhcC-Ccccc--CCCccc
Confidence            3457889999999974 6678999999999999999999999776 78999999999999999 99 79999  999998


Q ss_pred             --hhhhhhccccCCCC
Q psy4350          91 --SFLYDKQGAASEPL  104 (107)
Q Consensus        91 --~~~~~~~g~~~~p~  104 (107)
                        +..+++.|+.|||-
T Consensus        78 ~~~~~~~a~~~~~H~~   93 (101)
T 2cup_A           78 AGDQNVEYKGTVWHKD   93 (101)
T ss_dssp             SSSCEEESSSCEEETT
T ss_pred             cCCeEEEeCCcchHHh
Confidence              56889999999983

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

Probab=99.85  E-value=4.1e-22  Score=121.98  Aligned_cols=84  Identities=20%  Similarity=0.360  Sum_probs=77.6

Q ss_pred             CCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcch--h
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLV--S   91 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~--~   91 (107)
                      ..++|.+|+++|.+++.+.++++.||+.||+|..|+++|.+. .|+.+++++||+.||.+ |+ ++|..  |+++|.  +
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~f~~~~g~~yC~~cy~~~~~-~~C~~--C~~~I~~~~   77 (126)
T 2xqn_T            2 EKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGE-IYVMVNDKPVCKPCYVKNHA-VVCQG--CHNAIDPEV   77 (126)
T ss_dssp             CCCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTS-EEEEETTEEEEHHHHHHHSC-CBCTT--TCSBCCTTS
T ss_pred             cCCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcC-EEEeECCEEechHHhCcCcC-ccCcc--cCCcCCcCc
Confidence            357899999999987778999999999999999999999887 79999999999999999 99 79999  999999  4


Q ss_pred             hhhhhccccCC
Q psy4350          92 FLYDKQGAASE  102 (107)
Q Consensus        92 ~~~~~~g~~~~  102 (107)
                      ..+++.|+.||
T Consensus        78 ~~~~a~~~~~H   88 (126)
T 2xqn_T           78 QRVTYNNFSWH   88 (126)
T ss_dssp             CEEEETTEEEE
T ss_pred             eEEECCCCEee
Confidence            67889999999

>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=99.84  E-value=2.1e-21  Score=118.43  Aligned_cols=85  Identities=29%  Similarity=0.584  Sum_probs=74.8

Q ss_pred             CCCCCccccccccccCceEEeecCcccccccccccccCCCCCC-CCceeccCCeeccHHHHhh-hCCC--CCCCCCCCCc
Q psy4350          13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR-YSQA--RYPDLPIPKT   88 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~~-~~~~--~C~~~~C~~~   88 (107)
                      +...++|.+|+++|.+.+++.++++.||+.||+|..|+.+|.+ ...|+.+++++||+.||.+ |+ +  +|..  |+++
T Consensus         2 s~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~-~~~~C~~--C~~~   78 (122)
T 1m3v_A            2 SLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG-NSGAGGS--GGHM   78 (122)
T ss_dssp             CSCCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHC-CCCSSSC--SSCC
T ss_pred             CCCCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcC-CCCcccc--CCCC
Confidence            3457889999999999877899999999999999999999973 2268899999999999999 99 7  9999  9999


Q ss_pred             chhhhhhhcccc
Q psy4350          89 LVSFLYDKQGAA  100 (107)
Q Consensus        89 i~~~~~~~~g~~  100 (107)
                      |.+..+++.|+.
T Consensus        79 I~~~~~~~~g~~   90 (122)
T 1m3v_A           79 GSGGDVMVVGEP   90 (122)
T ss_dssp             SCCEESSSSSSS
T ss_pred             cCchheEEcCCc
Confidence            998777777753

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

Probab=99.82  E-value=8.1e-21  Score=116.85  Aligned_cols=85  Identities=27%  Similarity=0.621  Sum_probs=76.3

Q ss_pred             CCccccccccccCceEEeecCcccccccccccccCCCCCC-CCceeccCCeeccHHHHhh-hCCC--CCCCCCCCCcchh
Q psy4350          16 KSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR-YSQA--RYPDLPIPKTLVS   91 (107)
Q Consensus        16 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~~-~~~~--~C~~~~C~~~i~~   91 (107)
                      .++|.+|+++|.+.+.+.++++.||+.||+|..|+.+|.. ...|+.+++++||+.||.+ |+ +  +|..  |+++|.+
T Consensus         2 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~-~~~~C~~--C~~~I~~   78 (131)
T 2xjy_A            2 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFG-QDGLCAS--CDKRIRA   78 (131)
T ss_dssp             CCBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHC-CCEECTT--TCCEECT
T ss_pred             cccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCC-CccChhh--cCCccCc
Confidence            4689999999999877899999999999999999999963 2278999999999999999 99 6  8999  9999986


Q ss_pred             --hhhhhccccCCC
Q psy4350          92 --FLYDKQGAASEP  103 (107)
Q Consensus        92 --~~~~~~g~~~~p  103 (107)
                        .++.+.|+.|||
T Consensus        79 ~e~~~~a~~~~~H~   92 (131)
T 2xjy_A           79 YEMTMRVKDKVYHL   92 (131)
T ss_dssp             TSEEEEETTEEEEG
T ss_pred             cceeEeeCCceECc
Confidence              567889999997

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

Probab=99.81  E-value=4.7e-20  Score=119.21  Aligned_cols=87  Identities=37%  Similarity=0.776  Sum_probs=77.6

Q ss_pred             CCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcch
Q psy4350          12 CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLV   90 (107)
Q Consensus        12 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~   90 (107)
                      .+...++|.+|+++|.+.+++.++++.||+.||+|..|+++|.+. .| .+++++||+.||.+ |+ ++|..  |+++|.
T Consensus        56 ~~~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~-~f-~~~g~~yC~~~y~~~f~-~kC~~--C~~~I~  130 (182)
T 2jtn_A           56 GTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAER-CF-SRGESVYCKDDFFKRFG-TKCAA--CQLGIP  130 (182)
T ss_dssp             CCCSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSC-CE-EETTEEECHHHHHHTTS-CCCTT--TCCCCC
T ss_pred             CCCCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCC-ce-eECCEeeecCccccccc-ccccc--CCCccC
Confidence            456678999999999998778999999999999999999999886 44 78999999999999 99 79999  999998


Q ss_pred             h--hhhhhccccCCC
Q psy4350          91 S--FLYDKQGAASEP  103 (107)
Q Consensus        91 ~--~~~~~~g~~~~p  103 (107)
                      +  .++.+.++.|||
T Consensus       131 ~~~~v~~a~~~~~H~  145 (182)
T 2jtn_A          131 PTQVVRRAQDFVYHL  145 (182)
T ss_dssp             SSCCCCEETTEECCT
T ss_pred             CCceEEecCCCCEEe
Confidence            6  355788999997

>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=99.79  E-value=3.6e-20  Score=120.32  Aligned_cols=87  Identities=30%  Similarity=0.707  Sum_probs=77.1

Q ss_pred             CCCCccccccccccCceEEeecCcccccccccccccCCCCCC-CCceeccCCeeccHHHHhh-hCCC--CCCCCCCCCcc
Q psy4350          14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR-YSQA--RYPDLPIPKTL   89 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~~-~~~~--~C~~~~C~~~i   89 (107)
                      ...+.|.+|+++|.+.+++.++++.||+.||+|..|+++|.. ...|+.+++++||+.||.+ |+ +  +|..  |+++|
T Consensus         3 l~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~-~~~~C~~--C~~~I   79 (188)
T 1rut_X            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG-NSGACSA--CGQSI   79 (188)
T ss_dssp             -CCCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHS-CCEECTT--TCCEE
T ss_pred             CCCCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccc-cCCcccc--CCCcc
Confidence            456789999999999877899999999999999999999975 2278999999999999999 99 5  6999  99999


Q ss_pred             hh--hhhhhccccCCC
Q psy4350          90 VS--FLYDKQGAASEP  103 (107)
Q Consensus        90 ~~--~~~~~~g~~~~p  103 (107)
                      .+  .++.+.|+.|||
T Consensus        80 ~~~e~~i~a~~~~~H~   95 (188)
T 1rut_X           80 PASELVMRAQGNVYHL   95 (188)
T ss_dssp             CTTSEEEEETTEEECG
T ss_pred             ccCcEEEEcCCCEEeC
Confidence            85  467789999997

>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=99.78  E-value=6.2e-20  Score=117.42  Aligned_cols=85  Identities=39%  Similarity=0.823  Sum_probs=74.0

Q ss_pred             CCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchhh
Q psy4350          14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVSF   92 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~   92 (107)
                      .+.+.|.+|+++|.+.+++.++++.||+.||+|..|+.+|.+. . +.+++++||+.||.+ |+ ++|..  |+++|.+.
T Consensus         4 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~-~-f~~~g~~yC~~~y~~~f~-~~C~~--C~~~I~~~   78 (169)
T 2rgt_A            4 PEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAER-C-FSRGESVYCKDDFFKRFG-TKCAA--CQLGIPPT   78 (169)
T ss_dssp             ---CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSC-C-EESSSCEECHHHHHHHHS-CBCTT--TCCBCCTT
T ss_pred             CCCCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCC-C-cccCCeeeeccccccccc-ccccc--cccccCCC
Confidence            3567899999999988778999999999999999999999886 4 478999999999999 99 79999  99999863


Q ss_pred             --hhhhccccCCC
Q psy4350          93 --LYDKQGAASEP  103 (107)
Q Consensus        93 --~~~~~g~~~~p  103 (107)
                        ++.+.|+.||+
T Consensus        79 ~~v~~a~~~~~H~   91 (169)
T 2rgt_A           79 QVVRRAQDFVYHL   91 (169)
T ss_dssp             SEEEEETTEEEEG
T ss_pred             cEEEEcCCceEee
Confidence              45788888886

>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=99.77  E-value=2.5e-19  Score=116.69  Aligned_cols=88  Identities=18%  Similarity=0.331  Sum_probs=77.2

Q ss_pred             CCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCC------------
Q psy4350          13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQAR------------   79 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~------------   79 (107)
                      ..+.++|.+|++.|.+.+.+.++++.||+.||+|..|+.+|... .|+.+++++||+.||.+ |+ ++            
T Consensus         4 ~~~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~cy~~~f~-~~c~~c~~~~g~~~   81 (192)
T 1b8t_A            4 WGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDST-TVAVHGDEIYCKSCYGKKYG-PKGKGKGMGAGTLS   81 (192)
T ss_dssp             CCCCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSS-SEEEETTEEEEHHHHHHHHS-CCCCCCCCCCCCCC
T ss_pred             CCCCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCC-eeEecCCEeeChhhhHhhcC-ccccccccccccEe
Confidence            45568899999999877778999999999999999999999887 78999999999999999 98 45            


Q ss_pred             ------------------------------------CCCCCCCCcch-hhhhhhccccCCCC
Q psy4350          80 ------------------------------------YPDLPIPKTLV-SFLYDKQGAASEPL  104 (107)
Q Consensus        80 ------------------------------------C~~~~C~~~i~-~~~~~~~g~~~~p~  104 (107)
                                                          |..  |+++|. +..+++.|+.||+-
T Consensus        82 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~C~~--C~~~I~~~~~v~a~~~~~H~~  141 (192)
T 1b8t_A           82 TDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPR--CGQAVYAAEKVIGAGKSWHKS  141 (192)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECTT--TSCEECSSSCEEETTEEECTT
T ss_pred             cCCCcccccccccccccCCCCcCccccccccCCCCcCCC--CCCEecCcEEEecCCCccchh
Confidence                                                778  999997 45677889999973

>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=99.76  E-value=6.8e-19  Score=98.99  Aligned_cols=70  Identities=19%  Similarity=0.446  Sum_probs=63.9

Q ss_pred             CccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccH-HHHhh-hCCCCCCCCCCCCcch
Q psy4350          17 SSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK-QDFFR-YSQARYPDLPIPKTLV   90 (107)
Q Consensus        17 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~-~~y~~-~~~~~C~~~~C~~~i~   90 (107)
                      ++|.+|+++|.+.+.+.++++.||+.||+|..|+++|.+. .|+.+++++||+ .||.+ |+ ++|..  |++.+.
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 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSG-GHAEHEGKPYCNHPCYSAMFG-PKGFG--RGGAES   72 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTT-TEEEETTEEEETTTHHHHHSS-CCCSS--CCCSSS
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCC-ceECcCCeEeeCHHHHHHHhC-ccCCC--cCCcee
Confidence            4799999999966778999999999999999999999887 788999999999 69999 99 79999  997765

>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=99.76  E-value=1.1e-18  Score=98.20  Aligned_cols=72  Identities=19%  Similarity=0.462  Sum_probs=63.7

Q ss_pred             CCCCCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccH-HHHhh-hCCCCCCC
Q psy4350           9 SSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCK-QDFFR-YSQARYPD   82 (107)
Q Consensus         9 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~-~~y~~-~~~~~C~~   82 (107)
                      ++..+...++|.+|+++|.+.+.+.++++.||+.||+|..|+++|.+. .|+.+++++||+ .||.+ |+ ++|..
T Consensus         2 s~~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~cy~~~f~-~kc~g   75 (76)
T 2cu8_A            2 SSGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPG-GHAEHDGKPFCHKPCYATLFG-SGPSS   75 (76)
T ss_dssp             CCSCCCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTT-SCEEETTEEECTTTHHHHHSC-SSCSC
T ss_pred             ccccCCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCC-ceEeECCEEecchHHHHHhcc-cccCC
Confidence            345566788999999999977778999999999999999999999877 788999999999 79999 99 68864

>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=99.76  E-value=1.5e-18  Score=98.58  Aligned_cols=69  Identities=32%  Similarity=0.715  Sum_probs=61.5

Q ss_pred             CCCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          11 PCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        11 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      +...+.++|.+|++.|++.+.+.++++.||+.||+|..|+.+|.+  .|+.+++++||+.||.+ |+ ++|+.
T Consensus        10 ~~~~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~--~~~~~~g~~yC~~~y~~~fg-~~C~~   79 (80)
T 2dj7_A           10 IKIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG--EYISKDGVPYCESDYHAQFG-SGPSS   79 (80)
T ss_dssp             CCCSSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS--CCEEETTEEECTTHHHHHTT-CCSTT
T ss_pred             cCCCCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC--CeEEECCEEECHHHHHHHcC-CCCCC
Confidence            345678899999999997777999999999999999999999985  47899999999999999 99 68874

>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=99.76  E-value=3.3e-19  Score=101.41  Aligned_cols=73  Identities=21%  Similarity=0.449  Sum_probs=55.6

Q ss_pred             CCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcc
Q psy4350          13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTL   89 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i   89 (107)
                      ..+.++|..|+++|.+.+.+.+.++.||+.||+|..|+++|... .|+.+++++||+.||.+ |+ ++|..  |+...
T Consensus         4 ~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~cy~~~f~-~~c~g--cg~g~   77 (81)
T 1a7i_A            4 WGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDST-TVAIHDAEVYCKSCYGKKYG-PKGYG--YGQGA   77 (81)
T ss_dssp             ----CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSS-CCEEETTEEECSHHHHHHCC-------------
T ss_pred             CCCCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCC-CeEeeCCEEECHHHHHHHhC-Ccccc--cCCcc
Confidence            45678999999999877778999999999999999999999887 68899999999999999 99 79999  98653

>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=5.8e-18  Score=93.47  Aligned_cols=65  Identities=22%  Similarity=0.490  Sum_probs=59.0

Q ss_pred             CCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCC
Q psy4350          14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYP   81 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~   81 (107)
                      .+.++|..|++.|.+. .+.++++.||+.||+|..|+++|.+. .|+.+++++||+.||.+ |+ ++|.
T Consensus         3 ~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~cy~~~f~-~~C~   68 (69)
T 2cur_A            3 SGSSGCVKCNKAITSG-GITYQDQPWHADCFVCVTCSKKLAGQ-RFTAVEDQYYCVDCYKNFVS-GPSS   68 (69)
T ss_dssp             CCCCCCSSSCCCCCTT-CEEETTEEECTTTTBCTTTCCBCTTS-CEEECSSCEEEHHHHHHHHT-CSCC
T ss_pred             CCcCCCcccCCEeCcc-eEEECccccccCcCEECCCCCCCCCC-ccEeECCEEECHHHhHHHhc-CCCC
Confidence            4668899999999876 48999999999999999999999876 78999999999999999 99 6886

>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=99.73  E-value=3.3e-18  Score=96.16  Aligned_cols=69  Identities=23%  Similarity=0.533  Sum_probs=61.6

Q ss_pred             CCCCccccccccccC---ceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCC
Q psy4350          14 EEKSSCGGCGQPIID---RFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIP   86 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~---~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~   86 (107)
                      ...++|.+|+++|.+   .+.+.++++.||+.||+|..|+++|.+. .|+.+++++||+.||.+ |+ ++|+.  ++
T Consensus         3 ~~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~-~f~~~~g~~yC~~cy~~~f~-~~C~~--~s   75 (76)
T 1x68_A            3 SGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGK-GFLTQNKEIFCQKCGSGMDT-DISGP--SS   75 (76)
T ss_dssp             TCCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSS-CEEEETTEEEETTTTCCCCC-CSSSS--SC
T ss_pred             ccCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCC-ceEeECCEEECHHHhhhhhC-CcCCC--CC
Confidence            356789999999995   4568999999999999999999999876 78999999999999999 99 79988  64

>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=99.73  E-value=5.7e-18  Score=93.70  Aligned_cols=67  Identities=24%  Similarity=0.548  Sum_probs=60.0

Q ss_pred             CCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      +...++|.+|+++|.+.. +.++++.||+.||+|..|+++|.+. .|+.+++++||+.||.+ |+ ++|..
T Consensus         2 ~~~~~~C~~C~~~I~~~~-~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~cy~~~f~-~~c~~   69 (70)
T 2d8z_A            2 SSGSSGCVQCKKPITTGG-VTYREQPWHKECFVCTACRKQLSGQ-RFTARDDFAYCLNCFCDLYA-SGPSS   69 (70)
T ss_dssp             CCCCCBCSSSCCBCCSSE-EESSSSEEETTTSBCSSSCCBCTTS-CCEESSSSEECHHHHHHHTC-CCCTT
T ss_pred             CCCCCCCcccCCeeccce-EEECccccCCCCCccCCCCCcCCcC-ceEeeCCeEECHHHHHHHhc-cccCC
Confidence            346788999999998764 8999999999999999999999877 78899999999999999 99 68864

>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=99.73  E-value=5.6e-18  Score=102.08  Aligned_cols=69  Identities=32%  Similarity=0.679  Sum_probs=61.4

Q ss_pred             CCCccccccccccCceEEeecCcccccccccccccCCCCCC-CCceeccCCeeccHHHHhh-hCCCCCCCCCCC
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR-YSQARYPDLPIP   86 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~   86 (107)
                      ..++|.+|+++|.+.+.+.++++.||+.||+|..|+++|.. ...|+.+++++||+.||.+ |+ ++|..  |.
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~-~~c~~--c~   72 (114)
T 1j2o_A            2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGG-SGGHM--GS   72 (114)
T ss_dssp             CCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHT-SCCSS--CB
T ss_pred             cCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhC-cccCc--CC
Confidence            35789999999999877899999999999999999999975 2268999999999999999 99 68877  64

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

Probab=99.73  E-value=8.9e-18  Score=93.34  Aligned_cols=66  Identities=26%  Similarity=0.599  Sum_probs=59.7

Q ss_pred             CCCccccccccccCc-eEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          15 EKSSCGGCGQPIIDR-FYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      ..++|..|+++|.+. +.+.++++.||+.||+|..|+++|... .|+.+++++||+.||.+ |+ ++|+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~cy~~~f~-~~C~~   71 (72)
T 1wyh_A            4 GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSR-SFVPDKGAHYCVPCYENKFA-SGPSS   71 (72)
T ss_dssp             CCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTS-CEEEETTEEEEHHHHHHHTS-CCCCC
T ss_pred             cCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCC-ccCCcCCeEECHHHHHHHcc-CcCCC
Confidence            467899999999964 668999999999999999999999887 78899999999999999 99 78874

>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=99.72  E-value=1.3e-17  Score=92.71  Aligned_cols=66  Identities=18%  Similarity=0.495  Sum_probs=59.7

Q ss_pred             CCCccccccccccCc-eEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          15 EKSSCGGCGQPIIDR-FYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      ..++|..|++.|.+. ..+.++++.||+.||+|..|+++|.+. .|+.+++++||+.||.+ |+ ++|+.
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~cy~~~f~-~~C~~   71 (72)
T 1x4k_A            4 GSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTK-SFIPKDNQNFCVPCYEKQHA-SGPSS   71 (72)
T ss_dssp             CCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSS-SEEEETTEEEEHHHHHHHTS-SCCCC
T ss_pred             cCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCC-ccCccCCeEECHHHHhHHhC-CCCCC
Confidence            457899999999975 468999999999999999999999887 78999999999999999 99 68874

>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=1.2e-17  Score=96.69  Aligned_cols=68  Identities=22%  Similarity=0.587  Sum_probs=60.5

Q ss_pred             CCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          12 CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        12 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      .....++|.+|++.|.+. .+.++++.||+.||+|..|++.|.+. .|+.+++++||+.||.+ |+ ++|+.
T Consensus        21 ~~~~~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~~-~f~~~~g~~yC~~cy~~~f~-~~c~s   89 (90)
T 2dar_A           21 AGKRTPMCAHCNQVIRGP-FLVALGKSWHPEEFNCAHCKNTMAYI-GFVEEKGALYCELCYEKFFA-SGPSS   89 (90)
T ss_dssp             TTTCCCBBSSSCCBCCSC-EEEETTEEECTTTCBCSSSCCBCSSS-CBEESSSCEECHHHHHHHTS-CCCCC
T ss_pred             CCCCCCCCccCCCEecce-EEEECCccccccCCccCCCCCCCCCC-EeEeECCEEECHHHHHHHcC-CCCCC
Confidence            345678899999999765 58899999999999999999999877 78899999999999999 99 78874

>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=99.72  E-value=1e-17  Score=93.22  Aligned_cols=65  Identities=26%  Similarity=0.611  Sum_probs=57.8

Q ss_pred             CCCCccccccccccC---ceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCC
Q psy4350          14 EEKSSCGGCGQPIID---RFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARY   80 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~---~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C   80 (107)
                      .+.++|.+|+++|.+   ...+.++++.||+.||+|..|+++|.+. .|+.+++++||+.||.+ |+ |++
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~-~f~~~~g~~yC~~c~~~~~~-p~~   71 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGR-GFLTERDDILCPDCGKDISG-PSS   71 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTS-CCEECSSSEECHHHHHTCCC-SSC
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCC-ccEeECCEEEChhHcCcccC-CCC
Confidence            467889999999985   4568999999999999999999999876 78889999999999999 99 565

>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=99.70  E-value=5.8e-17  Score=93.97  Aligned_cols=67  Identities=27%  Similarity=0.601  Sum_probs=61.0

Q ss_pred             CCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      ....+|..|++.|.+.+.+.++++.||+.||+|..|.++|... .|+.+++++||+.||.+ |+ ++|.-
T Consensus        13 ~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~~f~-~kc~~   80 (91)
T 2d8y_A           13 PARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLG-TYASLHGRIYCKPHFNQLFK-SKGNY   80 (91)
T ss_dssp             SSSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTT-TCCCSSSCCCCHHHHHHHSC-CCSCC
T ss_pred             CCCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCC-CcEeECCEEECHHHHHHHhC-CCcCc
Confidence            4578899999999987778999999999999999999999887 68899999999999999 99 68874

>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=99.70  E-value=4.5e-17  Score=90.09  Aligned_cols=66  Identities=26%  Similarity=0.560  Sum_probs=58.5

Q ss_pred             CCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCC
Q psy4350          13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYP   81 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~   81 (107)
                      +++..+|..|++.|.+. .+.++++.||++||+|..|+++|.+. .|+.+++++||+.||.+ |+ ++.+
T Consensus         2 s~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~-~f~~~~g~~yC~~c~~~~~~-~~~~   68 (70)
T 2d8x_A            2 SSGSSGCHQCGEFIIGR-VIKAMNNSWHPECFRCDLCQEVLADI-GFVKNAGRHLCRPCHNREKA-SGPS   68 (70)
T ss_dssp             CCCSSBCSSSCCBCCSC-CEEETTEEECTTTSBCSSSCCBCSSS-CCEEETTEEECHHHHHHHHC-CCSC
T ss_pred             CCCCCcCccCCCEecce-EEEECcccccccCCEeCCCCCcCCCC-ccEeECCeEECHHHhhhhcC-CCCC
Confidence            35678999999999975 58999999999999999999999987 68889999999999999 98 4544

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

Probab=99.70  E-value=1.9e-17  Score=93.09  Aligned_cols=68  Identities=18%  Similarity=0.448  Sum_probs=58.1

Q ss_pred             CCCCCCccccccccccC-ceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCC
Q psy4350          12 CPEEKSSCGGCGQPIID-RFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYP   81 (107)
Q Consensus        12 ~~~~~~~C~~C~~~i~~-~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~   81 (107)
                      ......+|.+|++.|.+ ..++.+.++.||+.||+|..|+++|... .|+.+++++||+.||.+ |+ ++|.
T Consensus         7 ~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~~f~-~~C~   76 (77)
T 1g47_A            7 NALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDFQMLFA-PCWI   76 (77)
T ss_dssp             SCCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGG-CSEEETTEEECHHHHHHHCC-CC--
T ss_pred             cCCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCC-CeEeECCeEeCHHHHHHHhh-cccC
Confidence            33456889999999985 4447899999999999999999999887 68899999999999999 99 6885

>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=99.69  E-value=1.7e-17  Score=93.90  Aligned_cols=69  Identities=23%  Similarity=0.490  Sum_probs=59.8

Q ss_pred             CCCCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCC
Q psy4350          10 SPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYP   81 (107)
Q Consensus        10 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~   81 (107)
                      .+.....++|.+|++.|.+. .+.++++.||+.||+|..|++.|.+. .|+.+++++||+.||.+ |+ +++.
T Consensus         9 ~~~~~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~cy~~~~~-p~g~   78 (79)
T 1x62_A            9 IGNAQKLPMCDKCGTGIVGV-FVKLRDRHRHPECYVCTDCGTNLKQK-GHFFVEDQIYCEKHARERVS-GPSS   78 (79)
T ss_dssp             CCCCCCCCCCSSSCCCCCSS-CEECSSCEECTTTTSCSSSCCCHHHH-CCEESSSCEECHHHHHHHHS-SCCC
T ss_pred             CCCCCCCCccccCCCCccCc-EEEECcceeCcCcCeeCCCCCCCCCC-CeEeECCEEECHHHHHHHhC-CCCC
Confidence            33456678999999999986 58999999999999999999999765 68889999999999999 99 5643

>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=7.3e-17  Score=93.18  Aligned_cols=67  Identities=25%  Similarity=0.553  Sum_probs=58.8

Q ss_pred             CCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCC
Q psy4350          12 CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYP   81 (107)
Q Consensus        12 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~   81 (107)
                      ......+|.+|++.|.+. .+.++++.||+.||+|..|++.|... .|+.+++++||+.||.+ |+ +++.
T Consensus        21 ~~~~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~~f~-p~~~   88 (89)
T 1x64_A           21 SAQRMPLCDKCGSGIVGA-VVKARDKYRHPECFVCADCNLNLKQK-GYFFVEGELYCETHARARTS-GPSS   88 (89)
T ss_dssp             CCCSCCBCTTTCCBCCSC-CEESSSCEECTTTCCCSSSCCCTTTS-CCEEETTEEECHHHHHHHSS-SCCC
T ss_pred             CCCcCCCcccCCCEeccc-EEEECCceECccCCEecCCCCCCCCC-CeEeECCEEECHHHHHHHhC-CCCC
Confidence            335567899999999985 48999999999999999999999887 68888999999999999 99 5664

>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=99.69  E-value=3.4e-17  Score=89.61  Aligned_cols=60  Identities=30%  Similarity=0.794  Sum_probs=55.0

Q ss_pred             CCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      ..++|.+|+++|.+. .+.++++.||+.||+|..|+++|.+. .|+.+++++||+.||.+ |+
T Consensus         4 ~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~~f~   64 (66)
T 1nyp_A            4 GVPICGACRRPIEGR-VVNAMGKQWHVEHFVCAKCEKPFLGH-RHYERKGLAYCETHYNQLFG   64 (66)
T ss_dssp             CCCEETTTTEECCSC-EECCTTSBEETTTCBCTTTCCBCSSS-CCEEETTEEECHHHHHHHCS
T ss_pred             CCCCCcccCCEecce-EEEECccccccCcCEECCCCCCCCCC-ceEeECCcEECHHHHHHHhC
Confidence            467899999999954 68999999999999999999999876 78999999999999999 98

>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=99.68  E-value=6.1e-17  Score=89.96  Aligned_cols=66  Identities=27%  Similarity=0.754  Sum_probs=57.9

Q ss_pred             CCCCccccccccccCc-eEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          14 EEKSSCGGCGQPIIDR-FYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      .+.++|.+|++.|.+. ..+.++++.||+.||+|..|+++|.+. .|+.+++++||+.||.+ |+  +|..
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~cy~~~~~--~~~~   70 (72)
T 1x61_A            3 SGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQ-HFYAVERRAYCEGCYVATLE--SGPS   70 (72)
T ss_dssp             SCCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTS-CEEESSSCEEEHHHHHHHHH--TCSS
T ss_pred             CCCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcC-cCEeeCCeEECHHHHHHHHc--cCCC
Confidence            4578899999999864 468999999999999999999999766 78999999999999999 87  5554

>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=99.68  E-value=5.1e-17  Score=105.72  Aligned_cols=71  Identities=24%  Similarity=0.626  Sum_probs=65.1

Q ss_pred             CCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcc
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTL   89 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i   89 (107)
                      +.++|.+|++.|.+.+.+.++++.||+.||+|..|+++|... .|+.+++++||+.||.+ |+ ++|..  |++++
T Consensus       114 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~cy~~~f~-~kc~~--C~~~~  185 (192)
T 1b8t_A          114 GSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLEST-TLADKDGEIYCKGCYAKNFG-PKGFG--FGQGA  185 (192)
T ss_dssp             CCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSS-SEEEETTEEEEHHHHHHHTC-CCCCC--CCCCC
T ss_pred             CCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCC-cccccCCEEeCHHHHHHhcC-CcCCC--CCCcc
Confidence            356799999999977778999999999999999999999877 68899999999999999 99 79999  99985

>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=99.67  E-value=7.8e-17  Score=91.22  Aligned_cols=64  Identities=28%  Similarity=0.820  Sum_probs=58.4

Q ss_pred             CCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          16 KSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        16 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      .++|.+|+++|.+. .+.++++.||+.||+|..|+++|.+. .++.+++++||+.||.+ |+ ++|+.
T Consensus        15 ~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~~y~~~f~-~~C~~   79 (80)
T 1x3h_A           15 SPKCGGCNRPVLEN-YLSAMDTVWHPECFVCGDCFTSFSTG-SFFELDGRPFCELHYHHRRG-SGPSS   79 (80)
T ss_dssp             SCBCTTTCCBCCSS-CEEETTEEECTTTCBCSSSCCBSCSS-CCEESSSCEECHHHHHHHHS-SSCCC
T ss_pred             CCccccCCCeecce-eEEECCCeEecCcCChhhCCCCCCCC-cEEeECCEEECHHHHHHHcC-CCCCC
Confidence            57899999999985 48999999999999999999999887 68889999999999999 99 68874

>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=99.67  E-value=4.6e-17  Score=92.80  Aligned_cols=66  Identities=21%  Similarity=0.413  Sum_probs=57.9

Q ss_pred             CCCCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCcee--ccCCeeccHHHHhh-hC
Q psy4350          10 SPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCF--SRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        10 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~--~~~~~~~C~~~y~~-~~   76 (107)
                      .+...+..+|.+|++.|++.+.+.++++.||..||+|..|++.|... .|.  .+++++||+.||.+ |+
T Consensus         9 ~~~~~~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~-~~~~~~~~g~~yC~~~y~~~~~   77 (82)
T 2co8_A            9 HQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPG-GYEQHPGDGHFYCLQHLPQTDS   77 (82)
T ss_dssp             CCCCCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTT-SEECCTTTCCCEETTTCCCCCC
T ss_pred             CcCCCCCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCC-ceeEeCcCCEEEChHHHHhhhc
Confidence            44556778999999999887778899999999999999999999887 555  57999999999998 77

>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=99.67  E-value=1.1e-16  Score=90.66  Aligned_cols=65  Identities=25%  Similarity=0.575  Sum_probs=58.9

Q ss_pred             CCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      ..++|.+|+++|.+. .+.++++.||+.||+|..|+++|.+. .|+.+++++||+.||.+ |+ ++|+.
T Consensus        14 ~~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~cy~~~f~-~~c~s   79 (80)
T 2cuq_A           14 FAPRCARCSKTLTQG-GVTYRDQPWHRECLVCTGCQTPLAGQ-QFTSRDEDPYCVACFGELFA-SGPSS   79 (80)
T ss_dssp             SSCCCTTTCCCCCSC-CEESSSSEECTTTCBCSSSCCBCTTC-CEEECSSSEEEHHHHHHHTT-CSTTC
T ss_pred             cCCcCCCCCCEecCc-EEEECCchhhhhhCCcccCCCcCCCC-eeEeECCEEECHHHHHHHcC-CCCCC
Confidence            457899999999886 58999999999999999999999876 78999999999999999 99 68874

>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=99.67  E-value=8e-17  Score=98.26  Aligned_cols=64  Identities=38%  Similarity=0.903  Sum_probs=56.5

Q ss_pred             CCCCCccccccccccCceEEeecCcccccccccccccCCCCCC-CCceeccCCeeccHHHHhh-hC
Q psy4350          13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      ....++|.+|+++|.+.+++.++++.||+.||+|..|+++|.. ...|+.+++++||+.||.+ ||
T Consensus        58 ~~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           58 GLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             CSSCSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             CccCCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            3456789999999999877899999999999999999999962 2268999999999999998 86

>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=99.67  E-value=1.2e-16  Score=90.73  Aligned_cols=65  Identities=32%  Similarity=0.712  Sum_probs=57.7

Q ss_pred             CCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceecc-CCeeccHHHHhh-hCCCCCCC
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSR-HGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~-~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      ..++|.+|+++|.+. .+.++++.||+.||+|..|+++|.+. .|... ++++||+.||.+ |+ ++|+.
T Consensus        14 ~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~~-~f~~~~~g~~yC~~cy~~~f~-~~C~~   80 (81)
T 2dlo_A           14 TLEKCATCSQPILDR-ILRAMGKAYHPGCFTCVVCHRGLDGI-PFTVDATSQIHCIEDFHRKFA-SGPSS   80 (81)
T ss_dssp             SCCBCTTTCCBCCSC-CEEETTEEECTTTCBCSSSCCBCTTS-CEECCTTCCCEEHHHHHHHTT-SSSCC
T ss_pred             CCCccccCCCeecce-eEEECCccccHHhcCcccCCCccCCC-eeEECCCCEEECHHHHHHHhc-CcCCC
Confidence            567899999999976 58999999999999999999999876 67655 789999999999 99 68875

>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=99.66  E-value=2.6e-16  Score=89.09  Aligned_cols=66  Identities=20%  Similarity=0.337  Sum_probs=57.2

Q ss_pred             CCCCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCC
Q psy4350          12 CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYP   81 (107)
Q Consensus        12 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~   81 (107)
                      ...+.++|.+|++.|.+. .+.++++.||+.||+|..|+++|.+. .| .+++++||+.||.+ |+ |.+.
T Consensus        11 ~~~~~~~C~~C~~~I~~~-~v~a~~~~~H~~CF~C~~C~~~L~~~-~f-~~~g~~yC~~cy~~~f~-p~~s   77 (79)
T 2cor_A           11 RGLGKYICQKCHAIIDEQ-PLIFKNDPYHPDHFNCANCGKELTAD-AR-ELKGELYCLPCHDKMGV-SGPS   77 (79)
T ss_dssp             CCCCCCBCTTTCCBCCSC-CCCCSSSCCCTTTSBCSSSCCBCCTT-CE-EETTEEECHHHHHTTSC-CSSC
T ss_pred             hccCCCCCccCCCEecce-EEEECcceeCCCCCEeCCCCCccCCC-CE-eECCEEeCHHHHHHhCC-CCCC
Confidence            445678899999999965 48999999999999999999999876 44 88999999999999 98 5654

>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=99.65  E-value=5.7e-17  Score=92.22  Aligned_cols=66  Identities=26%  Similarity=0.571  Sum_probs=58.6

Q ss_pred             CCCcccccccccc-CceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          15 EKSSCGGCGQPII-DRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        15 ~~~~C~~C~~~i~-~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      ..++|..|+++|. +..++.++++.||+.||+|..|+++|.+. .|+.+++++||+.||.+ |+ ++|..
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~f~~~~~~~~C~~c~~~~~~-~~C~~   81 (82)
T 2ehe_A           14 FANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADE-PFTCQDSELLCNDCYCSAFS-SGPSS   81 (82)
T ss_dssp             CSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSC-CEEEETTEEEETTTSSCCGG-GSSCC
T ss_pred             cCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCC-ccEeeCCEEECHHHHhhhcC-CCCCC
Confidence            4568999999998 45557889999999999999999999877 78999999999999999 99 68874

>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=99.65  E-value=2.4e-16  Score=89.58  Aligned_cols=66  Identities=20%  Similarity=0.531  Sum_probs=58.2

Q ss_pred             CCCccccccccccCce-EEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          15 EKSSCGGCGQPIIDRF-YLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      ..++|.+|++.|.+.+ .+.++++.||+.||+|..|+++|... .|+.+++++||+.||.+ |+ +++..
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~~~~~~~~~yC~~cy~~~f~-~~~~~   81 (82)
T 1x63_A           14 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTG-SFFPKGEDFYCVTCHETKFA-SGPSS   81 (82)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTS-CEEEETTEEEEHHHHHHHTS-CCCSC
T ss_pred             cCCcCccCCcccccCceEEEECccccccccCchhhCCCccCCC-ccEeeCCEEECHHHHHHHhC-CCCCC
Confidence            3578999999998543 48999999999999999999999887 78899999999999999 99 57653

>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=99.61  E-value=5.4e-16  Score=85.84  Aligned_cols=62  Identities=19%  Similarity=0.501  Sum_probs=55.1

Q ss_pred             CCCCccccccccccCceE-EeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          14 EEKSSCGGCGQPIIDRFY-LLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      ....+|.+|++.|.+.+. +.+.++.||+.||+|..|+++|... .++.+++++||+.||.+ |+
T Consensus         9 ~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B            9 SASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             CTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGG-CCEEETTEEECHHHHHHHTC
T ss_pred             cCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCC-CeEeECCeEeCHHHHHHhhC
Confidence            456789999999997654 5799999999999999999999887 68899999999999998 75

>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=99.60  E-value=6.4e-16  Score=86.20  Aligned_cols=62  Identities=19%  Similarity=0.378  Sum_probs=54.7

Q ss_pred             CCCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      ...++|.+|+++|.+. .+.++++.||+.||+|..|+++|.....|+..++++||..||.+ ++
T Consensus         3 ~~~~~C~~C~~~I~~~-~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~   65 (73)
T 1wig_A            3 SGSSGCDSCEKYITGR-VLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAART   65 (73)
T ss_dssp             CSCCSCSSSCCCCSSC-CBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSS
T ss_pred             cCcCCcccCCCEecCe-eEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhc
Confidence            4567899999999985 48999999999999999999999833378899999999999998 66

>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=99.59  E-value=1.9e-15  Score=85.68  Aligned_cols=65  Identities=20%  Similarity=0.474  Sum_probs=55.4

Q ss_pred             CCCccccccccccCceEEeecCcccccccccccccCCCCCCCCcee-ccCCeeccHHHHhh-hCCCCCC
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCF-SRHGNIYCKQDFFR-YSQARYP   81 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~-~~~~~~~C~~~y~~-~~~~~C~   81 (107)
                      ..++|.+|+++|.+. .+.++++.||+.||+|..|+++|.....|. .+++++||+.||.+ |+ +.++
T Consensus        14 ~~~~C~~C~~~I~~~-~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~-~~~s   80 (81)
T 1x6a_A           14 FGEFCHGCSLLMTGP-FMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVS-GPSS   80 (81)
T ss_dssp             SSCBCTTTCCBCCSC-CBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHC-TTSC
T ss_pred             cCCcCccCCCCcCce-EEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhc-CCCC
Confidence            456899999999954 589999999999999999999997533676 58999999999999 99 4554

>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=99.57  E-value=3.2e-15  Score=83.90  Aligned_cols=59  Identities=24%  Similarity=0.595  Sum_probs=52.8

Q ss_pred             CCCccccccccccC----ceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350          15 EKSSCGGCGQPIID----RFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR   74 (107)
Q Consensus        15 ~~~~C~~C~~~i~~----~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~   74 (107)
                      ..++|.+|+++|.+    .+.+.++++.||+.||+|..|+++|.+. .|+.+++++||+.||.+
T Consensus        14 ~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~-~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A           14 VAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANK-RFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTS-CCCEETTEECCHHHHHH
T ss_pred             hCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCC-ccEeECCEEEChHHhcc
Confidence            35789999999994    4668999999999999999999999877 78899999999999964

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

Probab=99.55  E-value=3.6e-15  Score=81.33  Aligned_cols=58  Identities=22%  Similarity=0.501  Sum_probs=51.9

Q ss_pred             CCccccccccccCc-eEEeecCcccc--cccccccccCCCCCCCCceeccCCeecc-HHHHhh
Q psy4350          16 KSSCGGCGQPIIDR-FYLLAVDRQWH--LGCLQCAHCHVPLHSELSCFSRHGNIYC-KQDFFR   74 (107)
Q Consensus        16 ~~~C~~C~~~i~~~-~~~~~~~~~~H--~~Cf~C~~C~~~l~~~~~~~~~~~~~~C-~~~y~~   74 (107)
                      .++|.+|+++|.+. ..+.++++.||  +.||+|..|+++|.+. .|+.+++++|| .+||.+
T Consensus         2 a~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L~~~-~f~~~~g~~yC~~~C~~k   63 (65)
T 2iyb_E            2 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQ-KFMPVEGMVFCSVECKKR   63 (65)
T ss_dssp             CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCTTS-CCEEETTEEESSHHHHHT
T ss_pred             cCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCCCC-ceEEECCEEecCHHHhhh
Confidence            46799999999963 56899999999  9999999999999877 78999999999 889865

>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=99.43  E-value=1.9e-13  Score=77.35  Aligned_cols=61  Identities=20%  Similarity=0.388  Sum_probs=51.0

Q ss_pred             CCCccccccccccCceEEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      ..++|..|++.|.+. .+.++++.||+.||+|..|+++|.....+...++.+||..||.+ ++
T Consensus        14 ~~~~C~~C~~~I~~~-~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~   75 (81)
T 1v6g_A           14 YGTRCFSCDQFIEGE-VVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSV   75 (81)
T ss_dssp             CCCBCTTTCCBCCSC-CEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSS
T ss_pred             hCCcCccccCEeccc-eEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCC
Confidence            356899999999964 58999999999999999999999866345555556899999988 65

>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=99.33  E-value=5.9e-13  Score=86.22  Aligned_cols=64  Identities=23%  Similarity=0.488  Sum_probs=52.4

Q ss_pred             ccccccccccCce-EEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          18 SCGGCGQPIIDRF-YLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        18 ~C~~C~~~i~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      +|..|++.|...+ ++.+.++.||+.||+|..|++.|.....|+..++++||+.||.+ ++ ++|..
T Consensus        71 ~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~-~~~~~  136 (188)
T 1rut_X           71 ACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALI-NGHLN  136 (188)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC------
T ss_pred             ccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhc-ccccc
Confidence            7999999998754 47899999999999999999999643378899999999999999 88 57765

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

Probab=99.31  E-value=1e-12  Score=80.38  Aligned_cols=59  Identities=24%  Similarity=0.541  Sum_probs=51.9

Q ss_pred             ccccccccccCce-EEeecCcccccccccccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          18 SCGGCGQPIIDRF-YLLAVDRQWHLGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        18 ~C~~C~~~i~~~~-~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      +|..|+++|.+.+ .+.+.++.||+.||+|..|+++|.....|+..++++||..||.+ |+
T Consensus        68 ~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~  128 (131)
T 2xjy_A           68 LCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTK  128 (131)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHHHH
T ss_pred             ChhhcCCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHHhh
Confidence            8999999998744 57899999999999999999999543378889999999999998 76

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

Probab=99.28  E-value=3.7e-12  Score=77.44  Aligned_cols=59  Identities=20%  Similarity=0.519  Sum_probs=52.3

Q ss_pred             CCccccccccccCc-eEEeecCcccc--cccccccccCCCCCCCCceeccCCeeccHHHHhh-h
Q psy4350          16 KSSCGGCGQPIIDR-FYLLAVDRQWH--LGCLQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-Y   75 (107)
Q Consensus        16 ~~~C~~C~~~i~~~-~~~~~~~~~~H--~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~   75 (107)
                      .++|.+|+++|.+. ..+.++++.||  +.||+|..|+++|.+. .|+..++++||+.+|.+ |
T Consensus        63 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l~~~-~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           63 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQ-KFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             CCBCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBCTTS-EEEEETTEEESSHHHHHSC
T ss_pred             CccCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCCCCccCCC-eeEeECCEEcchHHhhhhc
Confidence            57899999999863 45899999999  9999999999999876 78889999999988877 5

>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=99.16  E-value=3.9e-11  Score=76.41  Aligned_cols=61  Identities=23%  Similarity=0.441  Sum_probs=51.6

Q ss_pred             CCccccccccccCceE-EeecCcccccccccccccCCCCCCCCce-eccCCeeccHHHHhh-hC
Q psy4350          16 KSSCGGCGQPIIDRFY-LLAVDRQWHLGCLQCAHCHVPLHSELSC-FSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        16 ~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~-~~~~~~~~C~~~y~~-~~   76 (107)
                      .++|..|++.|.+.+. +.+.++.||+.||+|..|++.|..+..| ...++++||+.||.+ +.
T Consensus        65 ~~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~~  128 (169)
T 2rgt_A           65 GTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQ  128 (169)
T ss_dssp             SCBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHHH
T ss_pred             cccccccccccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHhh
Confidence            4689999999987654 5899999999999999999999744355 456899999999998 76

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

Probab=99.12  E-value=5.5e-11  Score=76.55  Aligned_cols=60  Identities=23%  Similarity=0.454  Sum_probs=50.1

Q ss_pred             CCCccccccccccCceE-EeecCcccccccccccccCCCCCCCCcee-ccCCeeccHHHHhh
Q psy4350          15 EKSSCGGCGQPIIDRFY-LLAVDRQWHLGCLQCAHCHVPLHSELSCF-SRHGNIYCKQDFFR   74 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~-~~~~~~~C~~~y~~   74 (107)
                      ..++|..|++.|.+.+. +.+.++.||+.||+|..|++.|..+..|+ ..++++||+.||.+
T Consensus       118 f~~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~  179 (182)
T 2jtn_A          118 FGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYET  179 (182)
T ss_dssp             TSCCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHH
T ss_pred             cccccccCCCccCCCceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHH
Confidence            35789999999987653 57899999999999999999997443554 56899999999976

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

Probab=98.44  E-value=5.2e-08  Score=45.20  Aligned_cols=29  Identities=24%  Similarity=0.731  Sum_probs=26.6

Q ss_pred             CCccccccccccCceEEeecCcccccccc
Q psy4350          16 KSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        16 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      .++|..|++.++.++.+.+.|+.||..||
T Consensus         3 ~~~C~~C~k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            3 NPNCARCGKIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             CCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCcCCccCCEEecceeEEECCeEecccCC
Confidence            35799999999999989999999999997

>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=98.41  E-value=2.3e-08  Score=56.17  Aligned_cols=38  Identities=3%  Similarity=-0.140  Sum_probs=34.5

Q ss_pred             CCeeccHHHHhh-hCCCCCCCCCCCCcch--hhhhhhccccCCC
Q psy4350          63 HGNIYCKQDFFR-YSQARYPDLPIPKTLV--SFLYDKQGAASEP  103 (107)
Q Consensus        63 ~~~~~C~~~y~~-~~~~~C~~~~C~~~i~--~~~~~~~g~~~~p  103 (107)
                      +|++||+.||.+ |+ ++|..  |+++|.  +.++.+.|+.|||
T Consensus         1 ~g~~yC~~~y~~~~~-~~C~~--C~~~I~~~~~~~~a~~~~~H~   41 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFA-NTCAE--CQQLIGHDSRELFYEDRHFHE   41 (82)
T ss_dssp             CCCCCCCCCCCCCCS-CBCTT--TCCBCCSSCCBCCCSSCCCBT
T ss_pred             CCceechhHhCcccC-CcCcc--CCCccccCcEEEEeCCccccc
Confidence            578999999999 99 69999  999998  7888889999998

>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=98.38  E-value=2.9e-08  Score=55.49  Aligned_cols=38  Identities=11%  Similarity=-0.036  Sum_probs=35.1

Q ss_pred             CCeeccHHHHhh-hCCCCCCCCCCCCcchhhhhhhccccCCC
Q psy4350          63 HGNIYCKQDFFR-YSQARYPDLPIPKTLVSFLYDKQGAASEP  103 (107)
Q Consensus        63 ~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~~~~~~g~~~~p  103 (107)
                      +|++||+.||.+ |+ ++|..  |+++|.+..+++.|+.|||
T Consensus         1 gg~~yC~~cy~~~~~-~~C~~--C~~~I~~~~v~a~~~~~H~   39 (80)
T 2cuq_A            1 GSSGSSGPCYENKFA-PRCAR--CSKTLTQGGVTYRDQPWHR   39 (80)
T ss_dssp             CCCCSCCCCCCCCSS-CCCTT--TCCCCCSCCEESSSSEECT
T ss_pred             CCcEEcHHHHccccC-CcCCC--CCCEecCcEEEECCchhhh
Confidence            478999999999 99 79999  9999999889999999997

>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=98.36  E-value=4.5e-08  Score=54.85  Aligned_cols=38  Identities=5%  Similarity=0.013  Sum_probs=34.8

Q ss_pred             CeeccHHHHhh-hCCCCCCCCCCCCcchhhhhhhccccCCCC
Q psy4350          64 GNIYCKQDFFR-YSQARYPDLPIPKTLVSFLYDKQGAASEPL  104 (107)
Q Consensus        64 ~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~~~~~~g~~~~p~  104 (107)
                      +.+||+.||.+ |+ ++|..  |+++|.+..+.+.|+.|||-
T Consensus         2 ~~~yC~~~y~~~~~-~~C~~--C~~~I~~~~~~a~~~~~H~~   40 (81)
T 1x6a_A            2 SSGSSGKDYWGKFG-EFCHG--CSLLMTGPFMVAGEFKYHPE   40 (81)
T ss_dssp             CCCCCCCCSSCCSS-CBCTT--TCCBCCSCCBCCTTCCBCTT
T ss_pred             CCccchhHHhhhcC-CcCcc--CCCCcCceEEEECCceeccc
Confidence            57899999999 99 69999  99999999999999999973

>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=98.33  E-value=3.2e-08  Score=54.93  Aligned_cols=38  Identities=3%  Similarity=-0.015  Sum_probs=34.0

Q ss_pred             CCeeccHHHHhh-hCCCCCCCCCCCCcchh-----hhhhhccccCCC
Q psy4350          63 HGNIYCKQDFFR-YSQARYPDLPIPKTLVS-----FLYDKQGAASEP  103 (107)
Q Consensus        63 ~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~-----~~~~~~g~~~~p  103 (107)
                      ++++||+.||.+ |+ ++|..  |+++|.+     ..+++.|+.|||
T Consensus         1 g~~~yC~~cy~~~~~-~~C~~--C~~~I~~~g~~~~~~~a~~~~~H~   44 (77)
T 2egq_A            1 GSSGSSGDCYKNFVA-KKCAG--CKNPITGFGKGSSVVAYEGQSWHD   44 (77)
T ss_dssp             CCSSCCTTCCCSCCC-CCCSS--SCCCCCCCSSCCCEEEETTEEEET
T ss_pred             CCCeEchhHhchhhC-ccCcc--cCCcccCCCCCceeEEECcceeCc
Confidence            367899999999 99 79999  9999997     778889999997

>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=98.32  E-value=3.7e-08  Score=55.07  Aligned_cols=39  Identities=10%  Similarity=0.162  Sum_probs=35.2

Q ss_pred             CCeeccHHHHhh-hCCCCCCCCCCCCcchhhhhhhccccCCCC
Q psy4350          63 HGNIYCKQDFFR-YSQARYPDLPIPKTLVSFLYDKQGAASEPL  104 (107)
Q Consensus        63 ~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~~~~~~g~~~~p~  104 (107)
                      ++++||+.||.+ |+ ++|..  |+++|.+..+++.|+.|||-
T Consensus         1 gg~~yC~~~y~~~~~-~~C~~--C~~~I~~~~v~a~~~~~H~~   40 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFS-PKCGG--CNRPVLENYLSAMDTVWHPE   40 (80)
T ss_dssp             CCCCCCCCCCCCCCS-CBCTT--TCCBCCSSCEEETTEEECTT
T ss_pred             CCCccchhHHhhhcC-Ccccc--CCCeecceeEEECCCeEecC
Confidence            468999999999 98 79999  99999998889999999973

>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=98.28  E-value=8.5e-08  Score=53.75  Aligned_cols=38  Identities=16%  Similarity=0.150  Sum_probs=34.5

Q ss_pred             CeeccHHHHhh-hCCCCCCCCCCCCcchhhhhhhccccCCCC
Q psy4350          64 GNIYCKQDFFR-YSQARYPDLPIPKTLVSFLYDKQGAASEPL  104 (107)
Q Consensus        64 ~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~~~~~~g~~~~p~  104 (107)
                      +.+||+.||.+ |+ ++|..  |+++|.+..+++.|+.|||-
T Consensus         2 ~~~yC~~dy~~~~~-~~C~~--C~~~I~~~~v~a~~~~wH~~   40 (81)
T 1v6g_A            2 SSGSSGLDYQRLYG-TRCFS--CDQFIEGEVVSALGKTYHPD   40 (81)
T ss_dssp             CCCCCCSCGGGSCC-CBCTT--TCCBCCSCCEEETTEEECTT
T ss_pred             CCCcchHHHHhHhC-CcCcc--ccCEeccceEEECCceeCcc
Confidence            46899999999 99 69999  99999999999999999973

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3

Probab=98.25  E-value=6e-07  Score=52.14  Aligned_cols=36  Identities=19%  Similarity=0.486  Sum_probs=30.9

Q ss_pred             CCCccccccccccCc-eEEeecCcccccccccccccC
Q psy4350          15 EKSSCGGCGQPIIDR-FYLLAVDRQWHLGCLQCAHCH   50 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~-~~~~~~~~~~H~~Cf~C~~C~   50 (107)
                      ..++|..|+++|.+. ..+.++++.||+.||+|..|+
T Consensus        65 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           65 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             CCCBCSSSCCBCCSSSCEEESSSCEEETTTCCCTTCC
T ss_pred             cCCccccCCCccccCCeEEEeCCcchHHhCCCCCCCC
Confidence            457899999999854 358999999999999999885

>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=98.19  E-value=1.1e-07  Score=53.32  Aligned_cols=38  Identities=8%  Similarity=0.121  Sum_probs=32.7

Q ss_pred             CCeeccHHHHhhhCCCCCCCCCCCCcchhhhhhhccccCCC
Q psy4350          63 HGNIYCKQDFFRYSQARYPDLPIPKTLVSFLYDKQGAASEP  103 (107)
Q Consensus        63 ~~~~~C~~~y~~~~~~~C~~~~C~~~i~~~~~~~~g~~~~p  103 (107)
                      ++++||+.||..++ ++|..  |+++|.+..+++.|+.|||
T Consensus         2 ~g~~yC~~~y~~~~-~~C~~--C~~~I~~~~~~a~~~~~H~   39 (81)
T 2dlo_A            2 SSGSSGEGCYVATL-EKCAT--CSQPILDRILRAMGKAYHP   39 (81)
T ss_dssp             CCCCCCCCCCCSSC-CBCTT--TCCBCCSCCEEETTEEECT
T ss_pred             cCCEECHHHhhcCC-Ccccc--CCCeecceeEEECCccccH
Confidence            57889999988655 68999  9999998888889999997

>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=98.16  E-value=1.1e-07  Score=53.36  Aligned_cols=38  Identities=13%  Similarity=-0.021  Sum_probs=33.1

Q ss_pred             CCeeccHHHHhh-hCCCCCCCCCCCCcch--hhhhhhccccCCC
Q psy4350          63 HGNIYCKQDFFR-YSQARYPDLPIPKTLV--SFLYDKQGAASEP  103 (107)
Q Consensus        63 ~~~~~C~~~y~~-~~~~~C~~~~C~~~i~--~~~~~~~g~~~~p  103 (107)
                      ++.+||+.||.+ |+ ++|..  |+++|.  +..+++.|+.|||
T Consensus         1 ~~~~yC~~cy~~~~~-~~C~~--C~~~I~~~~~~~~a~~~~~H~   41 (82)
T 1x63_A            1 GSSGSSGKCTTREDS-PKCKG--CFKAIVAGDQNVEYKGTVWHK   41 (82)
T ss_dssp             CCSCCCCCCCSCCCS-CBCSS--SCCBCCSSSCEEECSSCEEET
T ss_pred             CCCcCchhHHccccC-CcCcc--CCcccccCceEEEECcccccc
Confidence            357899999999 88 69999  999998  6678889999987

>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=96.59  E-value=0.00067  Score=36.86  Aligned_cols=24  Identities=8%  Similarity=0.090  Sum_probs=16.2

Q ss_pred             CCCCCCCCCCcchhhhhhhccccCCC
Q psy4350          78 ARYPDLPIPKTLVSFLYDKQGAASEP  103 (107)
Q Consensus        78 ~~C~~~~C~~~i~~~~~~~~g~~~~p  103 (107)
                      ++|..  |+++|.+..+.+.|+.|||
T Consensus         6 ~~C~~--C~~~I~~~~v~a~~~~wH~   29 (73)
T 1wig_A            6 SGCDS--CEKYITGRVLEAGEKHYHP   29 (73)
T ss_dssp             CSCSS--SCCCCSSCCBCCSSCCBCT
T ss_pred             CCccc--CCCEecCeeEEeCCCCCCC
Confidence            46666  7777766666666666665

>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=96.45  E-value=0.00069  Score=40.44  Aligned_cols=21  Identities=5%  Similarity=-0.015  Sum_probs=17.0

Q ss_pred             CCCCCceeccCCeeccHHHHhh
Q psy4350          53 LHSELSCFSRHGNIYCKQDFFR   74 (107)
Q Consensus        53 l~~~~~~~~~~~~~~C~~~y~~   74 (107)
                      |.+. .|+.+++++||..||.+
T Consensus        92 l~g~-~f~~~~~~~yC~~~~~~  112 (122)
T 1m3v_A           92 LMGG-EFGDEDERLITRLENTQ  112 (122)
T ss_dssp             CCSC-TTCCTTCCCCEECTTTT
T ss_pred             CCCC-ccEecCCEeEccCcchh
Confidence            4344 68889999999999887

>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=95.07  E-value=0.0053  Score=32.60  Aligned_cols=10  Identities=20%  Similarity=0.833  Sum_probs=4.6

Q ss_pred             cccccCCCCC
Q psy4350          45 QCAHCHVPLH   54 (107)
Q Consensus        45 ~C~~C~~~l~   54 (107)
                      +|..|++.+.
T Consensus         7 ~C~~C~~~I~   16 (69)
T 2cur_A            7 GCVKCNKAIT   16 (69)
T ss_dssp             CCSSSCCCCC
T ss_pred             CCcccCCEeC
Confidence            3444554443

>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=94.97  E-value=0.0035  Score=34.05  Aligned_cols=38  Identities=13%  Similarity=0.322  Sum_probs=18.3

Q ss_pred             cccccCCCCCC--CCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchh
Q psy4350          45 QCAHCHVPLHS--ELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVS   91 (107)
Q Consensus        45 ~C~~C~~~l~~--~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~   91 (107)
                      +|..|++++.+  ...+....++.|-    .. |   .|..  |+.+|.+
T Consensus         7 ~C~~C~~~I~~~g~~~~~~a~~~~wH----~~CF---~C~~--C~~~L~~   47 (76)
T 1x68_A            7 GCVACSKPISGLTGAKFICFQDSQWH----SECF---NCGK--CSVSLVG   47 (76)
T ss_dssp             CCTTTCCCCCTTTTCCEEEETTEEEE----GGGC---BCTT--TCCBCSS
T ss_pred             CCccCCCcccCCCCceeEEECCcccC----cccC---Chhh--CCCcCCC
Confidence            45666666653  1123333444431    12 3   3566  6666654

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

Probab=94.97  E-value=0.0018  Score=34.26  Aligned_cols=18  Identities=0%  Similarity=-0.236  Sum_probs=7.6

Q ss_pred             CCCcch--hhhhhhccccCC
Q psy4350          85 IPKTLV--SFLYDKQGAASE  102 (107)
Q Consensus        85 C~~~i~--~~~~~~~g~~~~  102 (107)
                      |+++|.  +..+++.|+.||
T Consensus         8 C~~~I~~~~~~v~a~~~~wH   27 (65)
T 2iyb_E            8 CHNAIDPEVQRVTYNNFSWH   27 (65)
T ss_dssp             TSSEECTTSCEEEETTEEEE
T ss_pred             CCCeeccCceEEEECCCccC
Confidence            444444  233444444444

>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=94.94  E-value=0.0074  Score=33.11  Aligned_cols=24  Identities=4%  Similarity=-0.162  Sum_probs=15.2

Q ss_pred             CCCCCCCCCCcchhhhhhhccccCCC
Q psy4350          78 ARYPDLPIPKTLVSFLYDKQGAASEP  103 (107)
Q Consensus        78 ~~C~~~~C~~~i~~~~~~~~g~~~~p  103 (107)
                      ++|..  |+++|.+..+++.|+.|||
T Consensus        16 ~~C~~--C~~~I~~~~v~a~~~~~H~   39 (79)
T 2cor_A           16 YICQK--CHAIIDEQPLIFKNDPYHP   39 (79)
T ss_dssp             CBCTT--TCCBCCSCCCCCSSSCCCT
T ss_pred             CCCcc--CCCEecceEEEECcceeCC
Confidence            46666  6666666666666666665

>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=94.88  E-value=0.0025  Score=35.84  Aligned_cols=38  Identities=18%  Similarity=0.441  Sum_probs=23.4

Q ss_pred             ccccccCCCCCCCCceeccCCeeccHHHHhhhCCCCCCCCCCCCcchh
Q psy4350          44 LQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVS   91 (107)
Q Consensus        44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~~~~~~C~~~~C~~~i~~   91 (107)
                      -+|..|++.+.+  .+....++.|...||      .|..  |+++|.+
T Consensus        26 ~~C~~C~~~I~~--~~v~a~~~~~H~~CF------~C~~--C~~~L~~   63 (90)
T 2dar_A           26 PMCAHCNQVIRG--PFLVALGKSWHPEEF------NCAH--CKNTMAY   63 (90)
T ss_dssp             CBBSSSCCBCCS--CEEEETTEEECTTTC------BCSS--SCCBCSS
T ss_pred             CCCccCCCEecc--eEEEECCccccccCC------ccCC--CCCCCCC
Confidence            356777777754  344556667665552      4666  7777764

>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=94.80  E-value=0.0024  Score=33.73  Aligned_cols=10  Identities=30%  Similarity=1.006  Sum_probs=5.9

Q ss_pred             cccccCCCCC
Q psy4350          45 QCAHCHVPLH   54 (107)
Q Consensus        45 ~C~~C~~~l~   54 (107)
                      +|..|++.+.
T Consensus         7 ~C~~C~~~I~   16 (66)
T 1nyp_A            7 ICGACRRPIE   16 (66)
T ss_dssp             EETTTTEECC
T ss_pred             CCcccCCEec
Confidence            4556666665

>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=94.62  E-value=0.0056  Score=32.61  Aligned_cols=23  Identities=4%  Similarity=0.057  Sum_probs=12.0

Q ss_pred             CCCCCCCCCcchhhhhhhccccCCC
Q psy4350          79 RYPDLPIPKTLVSFLYDKQGAASEP  103 (107)
Q Consensus        79 ~C~~~~C~~~i~~~~~~~~g~~~~p  103 (107)
                      +|..  |+++|.+..+++.|+.|||
T Consensus         7 ~C~~--C~~~I~~~~~~a~~~~~H~   29 (70)
T 2d8x_A            7 GCHQ--CGEFIIGRVIKAMNNSWHP   29 (70)
T ss_dssp             BCSS--SCCBCCSCCEEETTEEECT
T ss_pred             cCcc--CCCEecceEEEECcccccc
Confidence            4555  5555555445555555554

>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=94.57  E-value=0.0055  Score=32.61  Aligned_cols=11  Identities=27%  Similarity=1.023  Sum_probs=6.1

Q ss_pred             cccccCCCCCC
Q psy4350          45 QCAHCHVPLHS   55 (107)
Q Consensus        45 ~C~~C~~~l~~   55 (107)
                      +|..|++.+.+
T Consensus         7 ~C~~C~~~I~~   17 (70)
T 2d8z_A            7 GCVQCKKPITT   17 (70)
T ss_dssp             BCSSSCCBCCS
T ss_pred             CCcccCCeecc
Confidence            45566666544

>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=94.55  E-value=0.0063  Score=32.53  Aligned_cols=11  Identities=18%  Similarity=0.606  Sum_probs=6.4

Q ss_pred             cccccCCCCCC
Q psy4350          45 QCAHCHVPLHS   55 (107)
Q Consensus        45 ~C~~C~~~l~~   55 (107)
                      +|..|++++..
T Consensus         7 ~C~~C~~~I~~   17 (72)
T 1wyh_A            7 GCSACGETVMP   17 (72)
T ss_dssp             BCSSSCCBCCS
T ss_pred             CCccCCCcccc
Confidence            45666666653

>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=94.50  E-value=0.0088  Score=32.71  Aligned_cols=11  Identities=18%  Similarity=0.622  Sum_probs=5.9

Q ss_pred             cccccCCCCCC
Q psy4350          45 QCAHCHVPLHS   55 (107)
Q Consensus        45 ~C~~C~~~l~~   55 (107)
                      +|..|++.+.+
T Consensus        17 ~C~~C~~~I~~   27 (79)
T 1x62_A           17 MCDKCGTGIVG   27 (79)
T ss_dssp             CCSSSCCCCCS
T ss_pred             ccccCCCCccC
Confidence            45555555543

>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=94.35  E-value=0.0061  Score=32.58  Aligned_cols=38  Identities=8%  Similarity=0.222  Sum_probs=19.1

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchh
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVS   91 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~   91 (107)
                      +|..|++.+...+......++.|-    .. |   .|..  |+++|.+
T Consensus         7 ~C~~C~~~I~~~~~~~~a~~~~~H----~~CF---~C~~--C~~~L~~   45 (72)
T 1x4k_A            7 GCQECKKTIMPGTRKMEYKGSSWH----ETCF---ICHR--CQQPIGT   45 (72)
T ss_dssp             CBSSSCCCCCSSSCEEEETTEEEE----TTTT---CCSS--SCCCCCS
T ss_pred             CCccCCCcccCCceEEEECcCeec----ccCC---cccc--cCCccCC
Confidence            566677766543223333444442    22 3   2555  6666654

>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=94.06  E-value=0.01  Score=31.69  Aligned_cols=11  Identities=36%  Similarity=0.942  Sum_probs=6.1

Q ss_pred             cccccCCCCCC
Q psy4350          45 QCAHCHVPLHS   55 (107)
Q Consensus        45 ~C~~C~~~l~~   55 (107)
                      +|..|++++.+
T Consensus         7 ~C~~C~~~I~~   17 (72)
T 1x4l_A            7 GCAGCTNPISG   17 (72)
T ss_dssp             SBTTTTBCCCC
T ss_pred             CCcCCCccccC
Confidence            45566665553

>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=93.88  E-value=0.0094  Score=32.27  Aligned_cols=10  Identities=20%  Similarity=0.773  Sum_probs=5.4

Q ss_pred             cccccCCCCC
Q psy4350          45 QCAHCHVPLH   54 (107)
Q Consensus        45 ~C~~C~~~l~   54 (107)
                      +|..|++.+.
T Consensus         2 ~C~~C~~~I~   11 (76)
T 1iml_A            2 KCPKCDKEVY   11 (76)
T ss_dssp             BCTTTSSBCC
T ss_pred             cCCCCCCEEE
Confidence            3555555554

>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=93.57  E-value=0.011  Score=31.91  Aligned_cols=13  Identities=15%  Similarity=0.485  Sum_probs=7.9

Q ss_pred             ccccccCCCCCCC
Q psy4350          44 LQCAHCHVPLHSE   56 (107)
Q Consensus        44 f~C~~C~~~l~~~   56 (107)
                      -+|..|++++...
T Consensus        10 ~~C~~C~~~I~~~   22 (76)
T 2cu8_A           10 SKCPKCDKTVYFA   22 (76)
T ss_dssp             CBCTTTCCBCCTT
T ss_pred             CCCcCCCCEeECC
Confidence            3566777776643

>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=93.35  E-value=0.017  Score=32.21  Aligned_cols=12  Identities=17%  Similarity=0.462  Sum_probs=7.6

Q ss_pred             ccccccCCCCCC
Q psy4350          44 LQCAHCHVPLHS   55 (107)
Q Consensus        44 f~C~~C~~~l~~   55 (107)
                      -+|..|++.+.+
T Consensus        26 ~~C~~C~~~I~~   37 (89)
T 1x64_A           26 PLCDKCGSGIVG   37 (89)
T ss_dssp             CBCTTTCCBCCS
T ss_pred             CCcccCCCEecc
Confidence            356677776654

>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=93.14  E-value=0.0052  Score=32.69  Aligned_cols=49  Identities=16%  Similarity=0.337  Sum_probs=31.5

Q ss_pred             ccccccCCCCCCCCceeccCCeeccHHHHhhhCCCCCCCCCCCCcchhh-hhhhcccc
Q psy4350          44 LQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSF-LYDKQGAA  100 (107)
Q Consensus        44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~~~~~~C~~~~C~~~i~~~-~~~~~g~~  100 (107)
                      -+|..|++.+...+......++.|-..||      .|..  |++++.+. .+..+|+.
T Consensus        12 ~~C~~C~~~i~~~e~~~~~~~~~~H~~CF------~C~~--C~~~L~~~~~~~~~g~~   61 (72)
T 3f6q_B           12 ATCERCKGGFAPAEKIVNSNGELYHEQCF------VCAQ--CFQQFPEGLFYEFEGRK   61 (72)
T ss_dssp             CBCTTTCCBCCTTCEEEEETTEEEETTTS------SCTT--TCCCCGGGCCEEETTEE
T ss_pred             ccchhcCccccCCceEEEeCcCeeCcCCC------cccC--CCCCCCCCCeEeECCeE
Confidence            47888888887553444567777766662      5778  88888754 33334443

>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=92.75  E-value=0.028  Score=29.92  Aligned_cols=10  Identities=20%  Similarity=0.564  Sum_probs=5.3

Q ss_pred             cccccCCCCC
Q psy4350          45 QCAHCHVPLH   54 (107)
Q Consensus        45 ~C~~C~~~l~   54 (107)
                      +|..|++++.
T Consensus         7 ~C~~C~~~I~   16 (72)
T 1x61_A            7 GCGGCGEDVV   16 (72)
T ss_dssp             CCSSSCSCCC
T ss_pred             CCccCCCccC
Confidence            4555555554

>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=92.71  E-value=0.024  Score=31.11  Aligned_cols=10  Identities=30%  Similarity=0.893  Sum_probs=5.8

Q ss_pred             cccccCCCCC
Q psy4350          45 QCAHCHVPLH   54 (107)
Q Consensus        45 ~C~~C~~~l~   54 (107)
                      .|..|++.+.
T Consensus        17 ~C~~C~~~I~   26 (80)
T 2dj7_A           17 HCAGCKEEIK   26 (80)
T ss_dssp             CCTTTCCCCS
T ss_pred             CCcCcCCeeC
Confidence            4556666554

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

Probab=91.64  E-value=0.041  Score=29.58  Aligned_cols=12  Identities=17%  Similarity=0.548  Sum_probs=7.4

Q ss_pred             ccccccCCCCCC
Q psy4350          44 LQCAHCHVPLHS   55 (107)
Q Consensus        44 f~C~~C~~~l~~   55 (107)
                      -+|..|++.+..
T Consensus        12 ~~C~~C~~~I~~   23 (77)
T 1g47_A           12 ATCERCKGGFAP   23 (77)
T ss_dssp             CBCSSSCCBCCS
T ss_pred             CCchhcCCccCC
Confidence            356677776653

>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=90.35  E-value=0.089  Score=28.82  Aligned_cols=12  Identities=33%  Similarity=0.398  Sum_probs=7.6

Q ss_pred             ccccccCCCCCC
Q psy4350          44 LQCAHCHVPLHS   55 (107)
Q Consensus        44 f~C~~C~~~l~~   55 (107)
                      -+|..|++.+..
T Consensus        16 ~~C~~C~~~I~~   27 (82)
T 2co8_A           16 DLCALCGEHLYV   27 (82)
T ss_dssp             CBCSSSCCBCCT
T ss_pred             CCCcccCCCccc
Confidence            356777776654

>2cs3_A Protein C14ORF4, MY039 protein; ZF-C3HC4 domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.44.1.3

Probab=90.05  E-value=0.21  Score=27.70  Aligned_cols=38  Identities=16%  Similarity=0.348  Sum_probs=30.7

Q ss_pred             CCCCCCCccccccccccCceEEeecCcccccccccccc
Q psy4350          11 PCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAH   48 (107)
Q Consensus        11 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~   48 (107)
                      ......-.|.-|.+.+.+...+..-...-|+-||.|+.
T Consensus        10 ~~~~a~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr   47 (93)
T 2cs3_A           10 MANSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSR   47 (93)
T ss_dssp             SCSCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHH
T ss_pred             CCCCCeeEeecchhhhccCceeeCCCccCCeeeccccH
Confidence            34556678999999998887678888888999998874

>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=90.02  E-value=0.042  Score=32.73  Aligned_cols=23  Identities=4%  Similarity=-0.064  Sum_probs=11.1

Q ss_pred             CCCCCCCCCcchhhh-hhhccccCCC
Q psy4350          79 RYPDLPIPKTLVSFL-YDKQGAASEP  103 (107)
Q Consensus        79 ~C~~~~C~~~i~~~~-~~~~g~~~~p  103 (107)
                      +|..  |+++|.+.. +.+.|+.|||
T Consensus        63 ~C~~--C~~~I~~~~~v~a~~~~wH~   86 (123)
T 2l4z_A           63 RCAG--CGGKIADRFLLYAMDSYWHS   86 (123)
T ss_dssp             BBSS--SSSBCCSSSEEEETTEEEET
T ss_pred             cCcC--CCCCcCCcEEEEeCCcEEcc
Confidence            4555  555554432 4444555544

>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=89.48  E-value=0.054  Score=29.51  Aligned_cols=10  Identities=20%  Similarity=0.683  Sum_probs=5.4

Q ss_pred             cccccCCCCC
Q psy4350          45 QCAHCHVPLH   54 (107)
Q Consensus        45 ~C~~C~~~l~   54 (107)
                      +|..|++.+.
T Consensus         9 ~C~~C~~~I~   18 (81)
T 1a7i_A            9 KCGACGRTVY   18 (81)
T ss_dssp             BCSSSCCBCS
T ss_pred             cCcCcCcccc
Confidence            4555555554

>2ct0_A Non-SMC element 1 homolog; ring domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=85.52  E-value=1.1  Score=24.25  Aligned_cols=35  Identities=20%  Similarity=0.387  Sum_probs=21.6

Q ss_pred             CCCCCCCCccccccccccCceEEeecCcccccccc
Q psy4350          10 SPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        10 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      +..+.....|.-|...|........-+..||..|+
T Consensus         9 ~~y~~~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci   43 (74)
T 2ct0_A            9 ETYPDAVKICNICHSLLIQGQSCETCGIRMHLPCV   43 (74)
T ss_dssp             CCCSSSSCBCSSSCCBCSSSEECSSSCCEECHHHH
T ss_pred             hhccCCCCcCcchhhHcccCCccCCCCchhhHHHH
Confidence            44556678899999988765322333444555554

>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=82.97  E-value=0.86  Score=25.14  Aligned_cols=49  Identities=12%  Similarity=0.154  Sum_probs=31.7

Q ss_pred             ccccccCCCCCCCCceeccCCeeccHHHHhhhCCCCCCCCCCCCcchhh-hhhhccccC
Q psy4350          44 LQCAHCHVPLHSELSCFSRHGNIYCKQDFFRYSQARYPDLPIPKTLVSF-LYDKQGAAS  101 (107)
Q Consensus        44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~~~~~~C~~~~C~~~i~~~-~~~~~g~~~  101 (107)
                      -+|..|++.+... ......++.|-..||      .|..  |+++|.+. .+..+|+.|
T Consensus        16 ~~C~~C~~~I~~~-~~v~a~~~~~H~~CF------~C~~--C~~~L~~~~~~~~~g~~y   65 (91)
T 2d8y_A           16 ETCVECQKTVYPM-ERLLANQQVFHISCF------RCSY--CNNKLSLGTYASLHGRIY   65 (91)
T ss_dssp             CBCTTTCCBCCTT-SEEECSSSEEETTTC------BCTT--TCCBCCTTTCCCSSSCCC
T ss_pred             CcCccCCCccCCc-eeEEECCCEECCCCC------eeCC--CCCCCCCCCcEeECCEEE
Confidence            4788899888765 344566677766662      4777  88888754 344445444

>3nw0_A Non-structural maintenance of chromosomes element homolog; E3 ligase, Zn, metal binding protein; 2.92A {Homo sapiens}

Probab=80.89  E-value=1  Score=29.84  Aligned_cols=30  Identities=20%  Similarity=0.339  Sum_probs=17.3

Q ss_pred             CCCccccccccccCceEEeecCcccccccc
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      ....|..|+..|..+....--+..||..|+
T Consensus       179 ~i~~C~iC~~iv~~g~~C~~C~~~~H~~C~  208 (238)
T 3nw0_A          179 AVKICNICHSLLIQGQSCETCGIRMHLPCV  208 (238)
T ss_dssp             TCCBCTTTCSBCSSCEECSSSCCEECHHHH
T ss_pred             CCCcCcchhhHHhCCcccCccChHHHHHHH
Confidence            466788888888755322223444555554

---

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	107
d1rutx1	30	g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus m	8e-10
d1j2oa1	30	g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus m	1e-09
d2dj7a2	36	g.39.1.3 (A:8-43) Actin-binding LIM protein 3, abL	2e-06
d2dara2	45	g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, En	0.002
d1x3ha1	35	g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [	0.003

>d1rutx1 g.39.1.3 (X:19-48) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]} Length = 30

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: LIM only 4 (Lmo4)
species: Mouse (Mus musculus) [TaxId: 10090]

 Score = 47.8 bits (114), Expect = 8e-10
 Identities = 15/26 (57%), Positives = 16/26 (61%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGCL 44
          C GCG  I DRF L A+D  WH  CL
Sbjct: 5  CAGCGGKIADRFLLYAMDSYWHSRCL 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 = 47.5 bits (113), Expect = 1e-09
 Identities = 14/26 (53%), Positives = 19/26 (73%)

Query: 18 SCGGCGQPIIDRFYLLAVDRQWHLGC 43
          +CGGC Q I DR++L A+D+ WH  C
Sbjct: 5  TCGGCQQNIGDRYFLKAIDQYWHEDC 30

>d2dj7a2 g.39.1.3 (A:8-43) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 3, abLIM-3
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 39.1 bits (91), Expect = 2e-06
 Identities = 13/28 (46%), Positives = 17/28 (60%)

Query: 17 SSCGGCGQPIIDRFYLLAVDRQWHLGCL 44
          S C GC + I     LLA+D+QWH+ C 
Sbjct: 9  SHCAGCKEEIKHGQSLLALDKQWHVSCF 36

>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 = 31.3 bits (71), Expect = 0.002
 Identities = 9/22 (40%), Positives = 12/22 (54%), Gaps = 1/22 (4%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWH 40
          C  C Q I   F L+A+ + WH
Sbjct: 21 CAHCNQVIRGPF-LVALGKSWH 41

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]} Length = 35

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 30.8 bits (70), Expect = 0.003
 Identities = 12/25 (48%), Positives = 17/25 (68%), Gaps = 1/25 (4%)

Query: 19 CGGCGQPIIDRFYLLAVDRQWHLGC 43
          CGGC +P+++  YL A+D  WH  C
Sbjct: 11 CGGCNRPVLEN-YLSAMDTVWHPEC 34

Homologous Domains Detected by HHsearch

Original result of HHsearch against SCOP70(version1.75) database

ID	Length	Definition	Probability
Query	107
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.79
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.67
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.63
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.61
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.6
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.59
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.58
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.58
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.53
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.5
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.49
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.48
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.47
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.47
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.45
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.44
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.41
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.39
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.37
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.27
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.24
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.21
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.21
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.2
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.2
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.18
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.15
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	98.14
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.13
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.1
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.09
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.05
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	98.0
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.0
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.99
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	97.97
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.94
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.94
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.93
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.93
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.85
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.83
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.82
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.82
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.76
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.74
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.7
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.66
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.65
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.64
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.64
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.48
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.43
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.02
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	96.93
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.91
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.81
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.74
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.69
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.67
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.65
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	96.61
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	96.55
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.37
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.13
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.07
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	95.97
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	95.77
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	95.3
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	95.29
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	94.91
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	94.82
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	94.72
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	94.53
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	94.5
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	94.07
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	93.89
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	92.58
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	92.03
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	91.15
d2cs3a1	80	Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [	87.63
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	83.1
d2gvia2	33	Uncharacterized protein Ta1109 {Thermoplasma acido	82.0

>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=98.79  E-value=1.1e-09  Score=50.94  Aligned_cols=32  Identities=25%  Similarity=0.680  Sum_probs=30.3

Q ss_pred             ccccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          44 LQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      |+|..|++++.+. .|++++|++||+.||.+ |+
T Consensus         1 F~C~~C~~~f~~~-~F~e~~G~pYCe~~Y~~lFA   33 (35)
T d1g47a2           1 FVCAQCFQQFPEG-LFYEFEGRKYCEHDFQMLFA   33 (35)
T ss_dssp             CCCTTTCCCCGGG-CSEEETTEEECHHHHHHHCC
T ss_pred             CCCCCCcCCCCCC-CeEEECCEecChHhHHhhcC
Confidence            7899999999987 89999999999999999 98

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.67  E-value=6.8e-10  Score=51.76  Aligned_cols=31  Identities=13%  Similarity=0.267  Sum_probs=28.8

Q ss_pred             HHhh-hCCCCCCCCCCCCcchhhhhhhccccCCCC
Q psy4350          71 DFFR-YSQARYPDLPIPKTLVSFLYDKQGAASEPL  104 (107)
Q Consensus        71 ~y~~-~~~~~C~~~~C~~~i~~~~~~~~g~~~~p~  104 (107)
                      ||.+ |+ ++|..  |+++|+|..++|.|+.|||-
T Consensus         2 DY~~~fa-pkC~~--C~~~I~g~~v~Al~~~wHpe   33 (35)
T d1x3ha1           2 DFLAMFS-PKCGG--CNRPVLENYLSAMDTVWHPE   33 (35)
T ss_dssp             CCCCCCS-CBCTT--TCCBCCSSCEEETTEEECTT
T ss_pred             cHHHHhC-hhhhh--cCCcccchheeecCCccCcc
Confidence            6788 99 79999  99999999999999999993

>d1x3ha1 g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Leupaxin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.63  E-value=9.7e-09  Score=47.74  Aligned_cols=30  Identities=40%  Similarity=1.072  Sum_probs=26.8

Q ss_pred             CCCCccccccccccCceEEeecCcccccccc
Q psy4350          14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      ...++|.+|+++|.+. .++++++.||+.||
T Consensus         6 ~fapkC~~C~~~I~g~-~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           6 MFSPKCGGCNRPVLEN-YLSAMDTVWHPECF   35 (35)
T ss_dssp             CCSCBCTTTCCBCCSS-CEEETTEEECTTTC
T ss_pred             HhChhhhhcCCcccch-heeecCCccCcccC
Confidence            3578999999999887 49999999999998

>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=98.61  E-value=3e-08  Score=49.03  Aligned_cols=36  Identities=28%  Similarity=0.636  Sum_probs=31.6

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCC
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPD   82 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~   82 (107)
                      +|..|++.|.+. ...++++++||+.||.+ |+ |+...
T Consensus         1 KC~~C~k~Lds~-t~~ehdg~~YCk~CY~k~fG-PKG~g   37 (49)
T d1b8ta4           1 RCAKCGKSLEST-TLADKDGEIYCKGCYAKNFG-PKGFG   37 (49)
T ss_dssp             BCTTTCCBCCSS-SEEEETTEEEEHHHHHHHTC-CCCCC
T ss_pred             ChhhcCCccCCC-cccccCCcccchhhhhhccC-CCccC
Confidence            588999999877 78899999999999999 99 56655

>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=98.60  E-value=1.6e-08  Score=49.00  Aligned_cols=35  Identities=20%  Similarity=0.585  Sum_probs=31.2

Q ss_pred             CCCCCCCCccccccccccCceEEeecCcccccccc
Q psy4350          10 SPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        10 ~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      +....+.++|..|++.++.++.+.+.|+.||..||
T Consensus         9 ~~~~g~~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3           9 AQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCCCCCCEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             ccccCCCCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            44556678999999999999999999999999998

>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=98.59  E-value=8.7e-10  Score=50.57  Aligned_cols=31  Identities=10%  Similarity=0.188  Sum_probs=27.1

Q ss_pred             HHHhh-hCCCCCCCCCCCCcchhhhhhhccccCCCC
Q psy4350          70 QDFFR-YSQARYPDLPIPKTLVSFLYDKQGAASEPL  104 (107)
Q Consensus        70 ~~y~~-~~~~~C~~~~C~~~i~~~~~~~~g~~~~p~  104 (107)
                      .||.. ..  +|..  |+++|++.++++.|++|||.
T Consensus         2 ~Cy~~tlE--kC~~--C~~~I~driLrA~Gk~yHP~   33 (35)
T d2dloa1           2 GCYVATLE--KCAT--CSQPILDRILRAMGKAYHPG   33 (35)
T ss_dssp             CCCCSSCC--BCTT--TCCBCCSCCEEETTEEECTT
T ss_pred             hhHHHHHH--HHHH--hchHHHHHHHHHhCCCCCCC
Confidence            35666 55  8999  99999999999999999995

>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=98.58  E-value=1.7e-08  Score=46.18  Aligned_cols=31  Identities=39%  Similarity=0.873  Sum_probs=27.9

Q ss_pred             CCCCCccccccccccCceEEeecCcccccccc
Q psy4350          13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      +....+|..|+++|.++ ++.+.|+.||+.||
T Consensus         5 ~~tlEkC~~C~~~I~dr-iLrA~Gk~yHP~CF   35 (35)
T d2dloa1           5 VATLEKCATCSQPILDR-ILRAMGKAYHPGCF   35 (35)
T ss_dssp             CSSCCBCTTTCCBCCSC-CEEETTEEECTTTC
T ss_pred             HHHHHHHHHhchHHHHH-HHHHhCCCCCCCCC
Confidence            45678899999999998 48999999999998

>d1b8ta2 g.39.1.3 (A:36-100) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Chicken (Gallus gallus) [TaxId: 9031]

Probab=98.58  E-value=3.3e-08  Score=51.53  Aligned_cols=52  Identities=21%  Similarity=0.341  Sum_probs=40.4

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcchhhhhhhccccC
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLVSFLYDKQGAAS  101 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~~~~~~~~g~~~  101 (107)
                      .|..|.+.|.+. .+..+++++||+.||.+ |+++..+.    ..-.+.+.++.|..+
T Consensus         1 ~C~~C~K~LdS~-~~~eh~~e~YCk~CY~k~fGPkG~G~----G~gag~l~~d~g~~~   53 (65)
T d1b8ta2           1 LCMVCKKNLDST-TVAVHGDEIYCKSCYGKKYGPKGKGK----GMGAGTLSTDKGESL   53 (65)
T ss_dssp             BCTTTCCBCCSS-SEEEETTEEEEHHHHHHHHSCCCCCC----CCCCCCCCCCCCCCC
T ss_pred             CchhcCCccCCC-ccccCCCcccchhhhccccCCCcccc----ccccceeeecccccC
Confidence            478999999887 78999999999999999 99766665    334556666666543

>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=98.53  E-value=3.5e-08  Score=47.64  Aligned_cols=32  Identities=28%  Similarity=0.624  Sum_probs=27.9

Q ss_pred             CCCCCCccccccccccCceEEeecCcccccccc
Q psy4350          12 CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        12 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      .....+.|..|+++|.... +.++|+.||+++|
T Consensus        14 ~~~r~P~C~~C~~pI~g~~-vtAlgk~WHPEhF   45 (45)
T d2dara2          14 AGKRTPMCAHCNQVIRGPF-LVALGKSWHPEEF   45 (45)
T ss_dssp             TTTCCCBBSSSCCBCCSCE-EEETTEEECTTTC
T ss_pred             CCCCCeeccccCCcccCce-eeecCCccCcCCC
Confidence            3456788999999998885 9999999999987

>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=98.50  E-value=4.6e-08  Score=43.36  Aligned_cols=29  Identities=52%  Similarity=1.085  Sum_probs=26.6

Q ss_pred             CCccccccccccCceEEeecCcccccccc
Q psy4350          16 KSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        16 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      ...|++|+++|.+++++.+.++.||..|+
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            46799999999999999999999999884

>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=98.49  E-value=3.1e-08  Score=43.75  Aligned_cols=29  Identities=24%  Similarity=0.574  Sum_probs=26.3

Q ss_pred             CCccccccccccCceEEeecCcccccccc
Q psy4350          16 KSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        16 ~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      .++|++|+++++.++.+..+|+.||..|+
T Consensus         2 ~~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CCBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CCcCCCCCCceeeHHhhccCCcccccccC
Confidence            36799999999999999999999999884

>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=98.48  E-value=1.8e-08  Score=43.97  Aligned_cols=28  Identities=25%  Similarity=0.748  Sum_probs=26.4

Q ss_pred             CccccccccccCceEEeecCcccccccc
Q psy4350          17 SSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        17 ~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      +.|++|++.+++.+.+..+++.||..||
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            5799999999999999999999999997

>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=98.47  E-value=4.6e-08  Score=45.15  Aligned_cols=32  Identities=22%  Similarity=0.557  Sum_probs=29.1

Q ss_pred             CCCCCccccccccccCceEEeecCcccccccc
Q psy4350          13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      .+....|..|++.++..+.+.+.|+.||..||
T Consensus         4 ~p~~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           4 APARETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SSSSCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CCCCcccccCCCEEeeeeeEecCCeehhhccC
Confidence            34567899999999999999999999999998

>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=98.47  E-value=6.4e-08  Score=43.94  Aligned_cols=33  Identities=39%  Similarity=0.816  Sum_probs=29.6

Q ss_pred             CCCCCCccccccccccCceEEeecCcccccccc
Q psy4350          12 CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        12 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      ...++..|++|++.|..+..+.++++.||.+||
T Consensus         4 ~~~g~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           4 KIRGPSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CCSSCSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             cccCCccccccchhhhCCceeeeeecceeeeeC
Confidence            456778899999999998889999999999998

>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=98.44  E-value=5.7e-08  Score=45.01  Aligned_cols=33  Identities=18%  Similarity=0.317  Sum_probs=29.7

Q ss_pred             CCCCCCccccccccccCceEEeecCcccccccc
Q psy4350          12 CPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        12 ~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      .+.+...|..|.+.+++.+.+.+.++.||.+||
T Consensus         4 ~~g~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           4 EAGAGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CCCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             cCCCCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            345678899999999999999999999999998

>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=98.41  E-value=5.3e-08  Score=42.26  Aligned_cols=30  Identities=33%  Similarity=0.774  Sum_probs=27.2

Q ss_pred             ccccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350          44 LQCAHCHVPLHSELSCFSRHGNIYCKQDFFR   74 (107)
Q Consensus        44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~   74 (107)
                      |+|..|++.|.+. ....++|++||+.||.+
T Consensus         1 frca~cgk~lest-t~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLEST-TLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEECSS-CSEEETTEEECHHHHHH
T ss_pred             CccccccCccccc-eeeccCCcEEEeeeeec
Confidence            7899999999887 78999999999999974

>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=98.39  E-value=1.1e-07  Score=42.59  Aligned_cols=31  Identities=26%  Similarity=0.588  Sum_probs=28.1

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      .|..|.++|.++ +|..+++++||..||.. |+
T Consensus         1 ~C~~C~~~L~GQ-ry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQLSGQ-RFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBCTTS-CCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCccccCc-eeeecCCCeehHHhhHhhcC
Confidence            478899999998 89999999999999988 74

>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=98.37  E-value=1.4e-07  Score=41.66  Aligned_cols=28  Identities=50%  Similarity=1.121  Sum_probs=25.7

Q ss_pred             CCccccccccccCceEEeecCccccccc
Q psy4350          16 KSSCGGCGQPIIDRFYLLAVDRQWHLGC   43 (107)
Q Consensus        16 ~~~C~~C~~~i~~~~~~~~~~~~~H~~C   43 (107)
                      ...|++|+++|.+++.+.+.++.||..|
T Consensus         3 ~~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           3 LLTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             CcccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            4579999999999999999999999876

>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=98.27  E-value=2.6e-07  Score=45.14  Aligned_cols=35  Identities=20%  Similarity=0.545  Sum_probs=30.3

Q ss_pred             cccccCCCCCCCCceeccCCeecc-HHHHhh-hCCCCC
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYC-KQDFFR-YSQARY   80 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C-~~~y~~-~~~~~C   80 (107)
                      +|..|++.|... ...++++++|| +.||.+ |+++..
T Consensus         1 kC~~C~K~L~sg-~~aeHdg~pYC~k~CY~~~FGPkG~   37 (48)
T d1imla2           1 KCEKCGKTLTSG-GHAEHEGKPYCNHPCYSAMFGPKGF   37 (48)
T ss_dssp             BCTTTCCBCCTT-TEEEETTEEEETTTHHHHHSSCCCS
T ss_pred             CchhcCcCcCCC-ChhhcCCcccccccchhhccCCCcc
Confidence            588999999887 79999999999 889999 995443

>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=98.24  E-value=2.7e-07  Score=40.69  Aligned_cols=30  Identities=30%  Similarity=0.797  Sum_probs=26.6

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      +|..|++.|.+  .+..++|.+||+.||.. ||
T Consensus         1 kC~~C~~vL~g--EYm~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVILTG--EYISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBCSS--CCEEETTEEECTTHHHHHTT
T ss_pred             CccccCccccc--eeecCCCCcccHHHHHHhcC
Confidence            58899999987  47899999999999998 86

>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=98.21  E-value=8.2e-08  Score=45.50  Aligned_cols=32  Identities=19%  Similarity=0.241  Sum_probs=29.5

Q ss_pred             HHHhh-hCCCCCCCCCCCCcchhhhhhhccccCCCC
Q psy4350          70 QDFFR-YSQARYPDLPIPKTLVSFLYDKQGAASEPL  104 (107)
Q Consensus        70 ~~y~~-~~~~~C~~~~C~~~i~~~~~~~~g~~~~p~  104 (107)
                      .||++ |+ .+|..  |++.|+|.++.+.++.|||-
T Consensus         8 ~DYq~~fG-~~C~~--C~~~ItG~V~~Ag~~~yHP~   40 (41)
T d1v6ga1           8 LDYQRLYG-TRCFS--CDQFIEGEVVSALGKTYHPD   40 (41)
T ss_dssp             SCGGGSCC-CBCTT--TCCBCCSCCEEETTEEECTT
T ss_pred             ccHHHHhC-ccccc--ccCEeeeeeeEecCcccCCC
Confidence            47899 99 59999  99999999999999999994

>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=98.21  E-value=4.3e-07  Score=41.23  Aligned_cols=30  Identities=23%  Similarity=0.595  Sum_probs=26.8

Q ss_pred             CCCCccccccccccCceEEeecCcccccccc
Q psy4350          14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      ..+.+|..|+++|..+. +...++.||..||
T Consensus         6 kfa~~C~~Ckk~It~GG-vtY~dqpWHkeCF   35 (35)
T d2cuqa2           6 KFAPRCARCSKTLTQGG-VTYRDQPWHRECL   35 (35)
T ss_dssp             CSSCCCTTTCCCCCSCC-EESSSSEECTTTC
T ss_pred             HHHHHHhhcCCccccCc-eeecCCcchhhhC
Confidence            35788999999999885 8999999999997

>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=98.20  E-value=6.4e-07  Score=39.54  Aligned_cols=31  Identities=29%  Similarity=0.653  Sum_probs=27.9

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      .|..|+++|.++ .|..++.++||..||-. |+
T Consensus         1 vCt~Ck~~LaGq-rFTSrde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1           1 VCTGCQTPLAGQ-QFTSRDEDPYCVACFGELFA   32 (32)
T ss_dssp             BCSSSCCBCTTC-CEEECSSSEEEHHHHHHHTT
T ss_pred             CccccCccccCC-ccccCCCCccHHHHhHhhcC
Confidence            478899999998 89999999999999987 64

>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=98.18  E-value=6.4e-07  Score=40.18  Aligned_cols=29  Identities=21%  Similarity=0.673  Sum_probs=26.4

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR   74 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~   74 (107)
                      +|..|.++..+. .|+..++++||+.+|..
T Consensus         1 VC~~C~~PF~~~-~Fy~~~g~PyCe~HyH~   29 (32)
T d1x3ha2           1 VCGDCFTSFSTG-SFFELDGRPFCELHYHH   29 (32)
T ss_dssp             BCSSSCCBSCSS-CCEESSSCEECHHHHHH
T ss_pred             CcCccCCcCCCC-CeEeECCccchHHhhhh
Confidence            588999999887 79999999999999986

>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=98.15  E-value=5.9e-07  Score=41.80  Aligned_cols=31  Identities=26%  Similarity=0.614  Sum_probs=26.0

Q ss_pred             CCCCccccccccccCce-EEeecCcccccccc
Q psy4350          14 EEKSSCGGCGQPIIDRF-YLLAVDRQWHLGCL   44 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~-~~~~~~~~~H~~Cf   44 (107)
                      ..+.+|..|+++|.++. .+.+.++.||..||
T Consensus         6 ~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           6 EDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             ccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            35678999999997544 38999999999998

>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=98.13  E-value=1e-06  Score=38.97  Aligned_cols=31  Identities=23%  Similarity=0.686  Sum_probs=27.6

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      .|..|+++|.+. .|...++.+||+.||.+ |+
T Consensus         1 nCa~C~~sL~d~-gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           1 NCAHCKNTMAYI-GFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             BCSSSCCBCSSS-CBEESSSCEECHHHHHHHTS
T ss_pred             CcccccccHhhc-ceeeecCcEeHHHHHHHhcC
Confidence            378899999888 89999999999999998 64

>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=98.10  E-value=3.8e-07  Score=38.98  Aligned_cols=27  Identities=22%  Similarity=0.789  Sum_probs=24.7

Q ss_pred             CccccccccccCceEEeecCccccccc
Q psy4350          17 SSCGGCGQPIIDRFYLLAVDRQWHLGC   43 (107)
Q Consensus        17 ~~C~~C~~~i~~~~~~~~~~~~~H~~C   43 (107)
                      .+|.+|++.++.++.+.-.|++||..|
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            479999999999999999999999876

>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=98.09  E-value=9.2e-08  Score=42.37  Aligned_cols=25  Identities=4%  Similarity=-0.055  Sum_probs=23.7

Q ss_pred             CCCCCCCCCCCcchhhhhhhccccCCC
Q psy4350          77 QARYPDLPIPKTLVSFLYDKQGAASEP  103 (107)
Q Consensus        77 ~~~C~~~~C~~~i~~~~~~~~g~~~~p  103 (107)
                      .|.|+.  |++||.+..+++.|+++||
T Consensus         5 ~p~C~~--C~~PI~~~~vtAlgk~WHp   29 (31)
T d1u5sb1           5 VPICGA--CRRPIEGRVVNAMGKQWHV   29 (31)
T ss_dssp             CCEETT--TTEECCSCEECCTTSBEET
T ss_pred             Ccchhh--cCCchhhhHhhhhccccCC
Confidence            379999  9999999999999999998

>d1u5sb2 g.39.1.3 (B:103-137) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.05  E-value=1.8e-06  Score=38.60  Aligned_cols=32  Identities=25%  Similarity=0.786  Sum_probs=29.3

Q ss_pred             ccccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          44 LQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      |+|..|.++.-+. ..++++|..||+.+|.. |+
T Consensus         1 FvCA~CekPF~G~-rhyE~~g~ayCe~Hy~qLfg   33 (35)
T d1u5sb2           1 FVCAKCEKPFLGH-RHYERKGLAYCETHYNQLFG   33 (35)
T ss_dssp             CBCTTTCCBCSSS-CCEEETTEEECHHHHHHHCS
T ss_pred             CcccccCCccCCc-hhhhhcCchHHHHHHHHHhc
Confidence            7899999998776 78999999999999999 87

>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=98.00  E-value=3e-06  Score=37.52  Aligned_cols=31  Identities=16%  Similarity=0.547  Sum_probs=28.0

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      .|..|..+++.. .|..+++..||-.||++ |+
T Consensus         1 ~C~~C~qPIGtk-sfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           1 ICHRCQQPIGTK-SFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CCSSSCCCCCSS-SEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCccccc-ccccCCCCceEeecchhhcC
Confidence            378899999988 89999999999999998 75

>d2d8ya2 g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.00  E-value=2.3e-06  Score=40.79  Aligned_cols=32  Identities=34%  Similarity=0.748  Sum_probs=28.5

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh-hCC
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQ   77 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~   77 (107)
                      +|..|++.|... .+...+|++||++||.. |..
T Consensus         1 rC~~C~~~Ls~~-~yas~~G~lYCkpHf~qLF~~   33 (42)
T d2d8ya2           1 RCSYCNNKLSLG-TYASLHGRIYCKPHFNQLFKS   33 (42)
T ss_dssp             BCTTTCCBCCTT-TCCCSSSCCCCHHHHHHHSCC
T ss_pred             CcCcCCCCccCC-cchhhCCEeccHHHHHHHHHh
Confidence            588999999877 78999999999999998 873

>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=97.99  E-value=1.3e-06  Score=36.91  Aligned_cols=26  Identities=23%  Similarity=0.622  Sum_probs=22.6

Q ss_pred             cccccccccCceE-EeecCcccccccc
Q psy4350          19 CGGCGQPIIDRFY-LLAVDRQWHLGCL   44 (107)
Q Consensus        19 C~~C~~~i~~~~~-~~~~~~~~H~~Cf   44 (107)
                      |..|.+.|.++.. +...|++||..||
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            7789999987654 7999999999997

>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=97.97  E-value=1.4e-06  Score=38.41  Aligned_cols=27  Identities=37%  Similarity=0.849  Sum_probs=24.1

Q ss_pred             CCCccccccccccCceEEeecCcccccc
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLG   42 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~   42 (107)
                      +.+.|+.|+++|.+. .+.++++.||++
T Consensus         4 g~p~C~~C~~PI~~~-~vtAlgk~WHpE   30 (31)
T d1u5sb1           4 GVPICGACRRPIEGR-VVNAMGKQWHVE   30 (31)
T ss_dssp             CCCEETTTTEECCSC-EECCTTSBEETT
T ss_pred             CCcchhhcCCchhhh-HhhhhccccCCC
Confidence            567899999999997 599999999985

>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=97.94  E-value=3.7e-06  Score=36.62  Aligned_cols=29  Identities=17%  Similarity=0.437  Sum_probs=26.4

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR   74 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~   74 (107)
                      .|..|++.|.++ +|...++++||-+||..
T Consensus         1 vC~~C~K~Lag~-rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKLAGQ-RFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBCTTS-CEEECSSCEEEHHHHHH
T ss_pred             CcccccchhcCc-eeEEecceEEEeeeecc
Confidence            488999999998 89999999999999975

>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=97.94  E-value=1.6e-06  Score=37.99  Aligned_cols=30  Identities=27%  Similarity=0.645  Sum_probs=26.2

Q ss_pred             ccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          46 CAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        46 C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      |..|++.|.+. ....+++++||+.||-+ ||
T Consensus         2 C~~C~K~LdSt-Tva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNLDST-TVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEECSS-CCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhccCcc-eeeeecceEEehhhccccCC
Confidence            67889999776 78899999999999988 75

>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=97.93  E-value=4.7e-06  Score=36.81  Aligned_cols=31  Identities=29%  Similarity=0.656  Sum_probs=27.8

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      .|..|..+++.+ .|..+++..||-.||++ |+
T Consensus         1 ~C~~C~qPIGtk-SFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           1 LCSGCEQPLGSR-SFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             BCTTTCCBTTTS-CEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCccccc-ccccCCCcEEEEeccccccC
Confidence            378899999988 89999999999999998 75

>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=97.93  E-value=2.4e-06  Score=37.91  Aligned_cols=28  Identities=32%  Similarity=0.691  Sum_probs=24.4

Q ss_pred             CccccccccccCceEE-eecCcccccccc
Q psy4350          17 SSCGGCGQPIIDRFYL-LAVDRQWHLGCL   44 (107)
Q Consensus        17 ~~C~~C~~~i~~~~~~-~~~~~~~H~~Cf   44 (107)
                      ..|++|++.|.+.+++ .+.++.||..||
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            3599999999877764 899999999998

>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=97.85  E-value=7e-06  Score=35.82  Aligned_cols=29  Identities=17%  Similarity=0.604  Sum_probs=26.2

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR   74 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~   74 (107)
                      .|..|+..|+++ .|+-.+.+.||+.||..
T Consensus         1 vC~tC~~kLRGq-pFYAvekkayCE~CYi~   29 (32)
T d1x61a2           1 VCSTCRAQLRGQ-HFYAVERRAYCEGCYVA   29 (32)
T ss_dssp             BCSSSCCBCTTS-CEEESSSCEEEHHHHHH
T ss_pred             CeeEeCceecCC-cceEeeccccccceeee
Confidence            478899999998 89999999999999975

>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=97.83  E-value=3e-06  Score=35.68  Aligned_cols=26  Identities=27%  Similarity=0.749  Sum_probs=22.3

Q ss_pred             cccccccccCceE-EeecCcccccccc
Q psy4350          19 CGGCGQPIIDRFY-LLAVDRQWHLGCL   44 (107)
Q Consensus        19 C~~C~~~i~~~~~-~~~~~~~~H~~Cf   44 (107)
                      |..|.+.|.++.. +...|+.||..||
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            6789999987654 7889999999997

>d1x4la1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 2, FHL2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.82  E-value=3.9e-06  Score=36.15  Aligned_cols=26  Identities=42%  Similarity=1.041  Sum_probs=21.6

Q ss_pred             ccccccccc---CceEEeecCcccccccc
Q psy4350          19 CGGCGQPII---DRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        19 C~~C~~~i~---~~~~~~~~~~~~H~~Cf   44 (107)
                      |..|.++|.   ....+++.++.||..||
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            788999996   33348999999999997

>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=97.82  E-value=1.1e-06  Score=42.29  Aligned_cols=24  Identities=8%  Similarity=0.069  Sum_probs=23.3

Q ss_pred             CCCCCCCCCCcchhhhhhhccccCCC
Q psy4350          78 ARYPDLPIPKTLVSFLYDKQGAASEP  103 (107)
Q Consensus        78 ~~C~~~~C~~~i~~~~~~~~g~~~~p  103 (107)
                      |.|+.  |+++|.|..+++.|+.|||
T Consensus        19 P~C~~--C~~pI~g~~vtAlgk~WHP   42 (45)
T d2dara2          19 PMCAH--CNQVIRGPFLVALGKSWHP   42 (45)
T ss_dssp             CBBSS--SCCBCCSCEEEETTEEECT
T ss_pred             eeccc--cCCcccCceeeecCCccCc
Confidence            78999  9999999999999999999

>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=97.76  E-value=1.5e-05  Score=35.58  Aligned_cols=33  Identities=27%  Similarity=0.564  Sum_probs=28.4

Q ss_pred             CCCCCCCccccccccccCceEEeecCcccccccc
Q psy4350          11 PCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        11 ~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      ......+.|.+|+..|.... +.++++.+|++||
T Consensus         3 g~~qklp~CdkCg~GIVG~~-VK~rDk~rHPeCf   35 (35)
T d1x62a2           3 GNAQKLPMCDKCGTGIVGVF-VKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCCCCCCSSSCCCCCSSC-EECSSCEECTTTT
T ss_pred             CccccCccccccCCCcEeEE-EEeccccCCCCCC
Confidence            34556789999999999884 8999999999997

>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=97.74  E-value=8.4e-06  Score=36.17  Aligned_cols=32  Identities=16%  Similarity=0.320  Sum_probs=27.8

Q ss_pred             CCCCCccccccccccCceEEeecCcccccccc
Q psy4350          13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      -.+..+|..|.+.++-++-+...|++||..||
T Consensus         4 ~ggg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           4 WGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCCCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             cCCCceeccccceEeeeeeeeecCcccccccC
Confidence            34667899999999877779999999999997

>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=97.70  E-value=2.9e-05  Score=36.84  Aligned_cols=35  Identities=23%  Similarity=0.513  Sum_probs=30.1

Q ss_pred             CCCCCCCCCccccccccccCceEEeecCcccccccc
Q psy4350           9 SSPCPEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus         9 ~~~~~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      ..+.....+.|.+|+..|.... +.++++.+|++||
T Consensus        11 ~~~~~QkLP~CdkCg~GIVG~~-VK~rDK~rHPeCf   45 (45)
T d1x64a1          11 GAGSAQRMPLCDKCGSGIVGAV-VKARDKYRHPECF   45 (45)
T ss_dssp             CCSCCCSCCBCTTTCCBCCSCC-EESSSCEECTTTC
T ss_pred             CCCccccCccccccCCCcEEEE-EEeccccCCCCCC
Confidence            3455667889999999999885 8999999999997

>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=97.66  E-value=1.4e-05  Score=35.37  Aligned_cols=31  Identities=16%  Similarity=0.552  Sum_probs=26.7

Q ss_pred             cccccCCCCCCCCceeccCCeeccH-HHHhh-hC
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCK-QDFFR-YS   76 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~-~~y~~-~~   76 (107)
                      +|..|++.|... ...++++++||. +||.. ||
T Consensus         1 kCekC~ktL~~G-~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTPG-GHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCTT-SCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCCC-CccccCCCcCcCcchHHhhcC
Confidence            588899999887 789999999997 59987 65

>d1x68a1 g.39.1.3 (A:8-36) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.65  E-value=1.4e-05  Score=34.28  Aligned_cols=26  Identities=35%  Similarity=0.880  Sum_probs=21.4

Q ss_pred             ccccccccc---CceEEeecCcccccccc
Q psy4350          19 CGGCGQPII---DRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        19 C~~C~~~i~---~~~~~~~~~~~~H~~Cf   44 (107)
                      |..|.++|.   ....+++.++.||.+||
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            778999985   33348999999999997

>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=97.64  E-value=1.3e-05  Score=33.73  Aligned_cols=27  Identities=26%  Similarity=0.688  Sum_probs=24.5

Q ss_pred             ccccccccccCceEEeecCcccccccc
Q psy4350          18 SCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        18 ~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      +|+.|.+.++.++-+...|++||..||
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            689999999987779999999999987

>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=97.64  E-value=2.2e-05  Score=35.07  Aligned_cols=31  Identities=29%  Similarity=0.660  Sum_probs=26.1

Q ss_pred             cccccCCCCCCCCce-eccCCeeccHHHHhh-hC
Q psy4350          45 QCAHCHVPLHSELSC-FSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~-~~~~~~~~C~~~y~~-~~   76 (107)
                      +|..|++.|.+. .| ...++++||-.||++ |+
T Consensus         1 tCvvC~~~LDGv-PFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           1 TCVVCHRGLDGI-PFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             BCSSSCCBCTTS-CEECCTTCCCEEHHHHHHHTT
T ss_pred             CeeEcCcccCCC-cEEEcCCCCEeehhhhhhhcC
Confidence            478899999887 55 567889999999998 75

>d2cuqa2 g.39.1.3 (A:8-42) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains 3, FHL3
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.48  E-value=4.4e-06  Score=37.78  Aligned_cols=31  Identities=13%  Similarity=0.036  Sum_probs=26.8

Q ss_pred             HHHhh-hCCCCCCCCCCCCcchhhhhhhccccCCC
Q psy4350          70 QDFFR-YSQARYPDLPIPKTLVSFLYDKQGAASEP  103 (107)
Q Consensus        70 ~~y~~-~~~~~C~~~~C~~~i~~~~~~~~g~~~~p  103 (107)
                      +||++ |+ ++|..  |+++|+...++..++.+|-
T Consensus         1 PCyE~kfa-~~C~~--Ckk~It~GGvtY~dqpWHk   32 (35)
T d2cuqa2           1 PCYENKFA-PRCAR--CSKTLTQGGVTYRDQPWHR   32 (35)
T ss_dssp             CCCCCCSS-CCCTT--TCCCCCSCCEESSSSEECT
T ss_pred             CchHHHHH-HHHhh--cCCccccCceeecCCcchh
Confidence            37888 99 79999  9999998888888888873

>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=97.43  E-value=3.9e-05  Score=32.06  Aligned_cols=26  Identities=35%  Similarity=0.691  Sum_probs=20.9

Q ss_pred             ccccccccc-CceEEeecCcccccccc
Q psy4350          19 CGGCGQPII-DRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        19 C~~C~~~i~-~~~~~~~~~~~~H~~Cf   44 (107)
                      |..|.++|. +..-+...++.||..||
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            678999995 44337889999999997

>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=97.02  E-value=0.0001  Score=31.94  Aligned_cols=25  Identities=8%  Similarity=0.058  Sum_probs=23.2

Q ss_pred             CCCCCCCCCCcchhhhhhhccccCCCC
Q psy4350          78 ARYPDLPIPKTLVSFLYDKQGAASEPL  104 (107)
Q Consensus        78 ~~C~~~~C~~~i~~~~~~~~g~~~~p~  104 (107)
                      ..|..  |.+.|+|.++.+.++-|||.
T Consensus         6 sgC~~--C~~~ItGkVLEAG~khYHP~   30 (32)
T d1wiga1           6 SGCDS--CEKYITGRVLEAGEKHYHPS   30 (32)
T ss_dssp             CSCSS--SCCCCSSCCBCCSSCCBCTT
T ss_pred             chhhh--hhhhhhhhhhhccccccCCC
Confidence            47999  99999999999999999995

>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=96.93  E-value=0.00055  Score=29.30  Aligned_cols=31  Identities=19%  Similarity=0.577  Sum_probs=26.4

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh-hC
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      +|+.|...++.. .|+.+...+||-.|+.. |+
T Consensus         1 tcs~ckq~igsg-sffpkg~d~ycvtche~kfa   32 (32)
T d1x63a2           1 TCSNCKQVIGTG-SFFPKGEDFYCVTCHETKFA   32 (32)
T ss_dssp             CCSSSCCCCTTS-CEEEETTEEEEHHHHHHHTS
T ss_pred             Ccchhhhhcccc-cccCCCCcEEEEEeeccccC
Confidence            478899888887 78999999999999886 64

>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=96.91  E-value=0.00023  Score=31.52  Aligned_cols=32  Identities=28%  Similarity=0.866  Sum_probs=25.3

Q ss_pred             cccccCCCCCC-CCceeccCCeeccHHHHhh-hC
Q psy4350          45 QCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR-YS   76 (107)
Q Consensus        45 ~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~~-~~   76 (107)
                      +|+-|...|.+ ....+.+.+.++|+.+|.+ ||
T Consensus         1 KCscC~~~LgeiG~s~ytk~~mILCk~DY~rlFG   34 (34)
T d1rutx2           1 KCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG   34 (34)
T ss_dssp             BCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHS
T ss_pred             CCcchhcChhhccchheecCCEEEEchhHHHhcC
Confidence            46777777753 2268999999999999999 86

>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=96.81  E-value=0.00049  Score=29.71  Aligned_cols=27  Identities=30%  Similarity=0.787  Sum_probs=23.3

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHH
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDF   72 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y   72 (107)
                      .|+.|+..|.+. .++..++++||+.+-
T Consensus         1 vC~dCg~NLKqr-G~Ffv~~~lyCE~HA   27 (31)
T d1x64a2           1 VCADCNLNLKQK-GYFFVEGELYCETHA   27 (31)
T ss_dssp             CCSSSCCCTTTS-CCEEETTEEECHHHH
T ss_pred             CccccccChhhc-ceEEeccEEeehhhh
Confidence            488999999887 788889999999874

>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=96.74  E-value=0.00043  Score=32.35  Aligned_cols=28  Identities=25%  Similarity=0.495  Sum_probs=23.7

Q ss_pred             CCCccccccccccCceEEeecCccccccc
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGC   43 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~C   43 (107)
                      ...+|..|.+.|... ++.+.++.||+.|
T Consensus        14 fG~~C~~C~~~ItG~-V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          14 YGTRCFSCDQFIEGE-VVSALGKTYHPDC   41 (41)
T ss_dssp             CCCBCTTTCCBCCSC-CEEETTEEECTTT
T ss_pred             hCcccccccCEeeee-eeEecCcccCCCC
Confidence            356799999999654 6899999999987

>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=96.69  E-value=0.00014  Score=32.33  Aligned_cols=30  Identities=7%  Similarity=0.098  Sum_probs=24.2

Q ss_pred             HHhh-hCCCCCCCCCCCCcchhhhhhhccccCCC
Q psy4350          71 DFFR-YSQARYPDLPIPKTLVSFLYDKQGAASEP  103 (107)
Q Consensus        71 ~y~~-~~~~~C~~~~C~~~i~~~~~~~~g~~~~p  103 (107)
                      +|+. |+ ..|..  |...|+|-+.-+....|||
T Consensus         2 dYw~kfg-e~C~~--C~~~itGpvMvAG~~K~HP   32 (34)
T d1x6aa1           2 DYWGKFG-EFCHG--CSLLMTGPFMVAGEFKYHP   32 (34)
T ss_dssp             CSSCCSS-CBCTT--TCCBCCSCCBCCTTCCBCT
T ss_pred             cHHHHHH-HHhhh--hHhhcccceeeecccccCC
Confidence            5777 99 59999  9999997666666666998

>d1wiga1 g.39.1.3 (A:1-32) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=96.67  E-value=0.00055  Score=29.56  Aligned_cols=29  Identities=31%  Similarity=0.654  Sum_probs=24.2

Q ss_pred             CCCCccccccccccCceEEeecCccccccc
Q psy4350          14 EEKSSCGGCGQPIIDRFYLLAVDRQWHLGC   43 (107)
Q Consensus        14 ~~~~~C~~C~~~i~~~~~~~~~~~~~H~~C   43 (107)
                      ++..-|..|.+.|... ++.+-++.||+.|
T Consensus         3 sgssgC~~C~~~ItGk-VLEAG~khYHP~C   31 (32)
T d1wiga1           3 SGSSGCDSCEKYITGR-VLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCCSCSSSCCCCSSC-CBCCSSCCBCTTT
T ss_pred             Cccchhhhhhhhhhhh-hhhccccccCCCC
Confidence            4556699999999887 5789999999987

>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=96.65  E-value=0.00063  Score=29.56  Aligned_cols=28  Identities=21%  Similarity=0.542  Sum_probs=23.6

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHH
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDF   72 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y   72 (107)
                      .|+.|...|..+.+|...+|.+||+.+-
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            4888999887766899999999998774

>d2d8xa2 g.39.1.3 (A:8-32) 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=96.61  E-value=0.00014  Score=29.94  Aligned_cols=23  Identities=4%  Similarity=0.031  Sum_probs=21.1

Q ss_pred             CCCCCCCCcchhhhhhhccccCCCC
Q psy4350          80 YPDLPIPKTLVSFLYDKQGAASEPL  104 (107)
Q Consensus        80 C~~~~C~~~i~~~~~~~~g~~~~p~  104 (107)
                      |+.  |++.|.|.+++++...+||-
T Consensus         1 c~k--cgefiigrvikamn~~whp~   23 (26)
T d2d8xa2           1 CHQ--CGEFIIGRVIKAMNNSWHPE   23 (26)
T ss_dssp             CSS--SCCBCCSCCEEETTEEECTT
T ss_pred             CCc--cccchhHHHHHHHhccCCcc
Confidence            677  99999999999999999994

>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=96.55  E-value=0.00082  Score=29.92  Aligned_cols=31  Identities=19%  Similarity=0.267  Sum_probs=26.1

Q ss_pred             CCCCCccccccccccCceEEeecCcccccccc
Q psy4350          13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf   44 (107)
                      ..+.-+|.+|...|.+.. +.+.+..||+..|
T Consensus         5 glGk~vC~KCh~iIdd~p-L~Fr~d~YHp~HF   35 (35)
T d2cora2           5 GLGKYICQKCHAIIDEQP-LIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCCBCTTTCCBCCSCC-CCCSSSCCCTTTS
T ss_pred             chhhHHHHHHHhhhhcCc-ceecCCCCCCCCC
Confidence            457788999999998865 8999999998765

>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=96.37  E-value=0.00038  Score=30.88  Aligned_cols=25  Identities=8%  Similarity=0.074  Sum_probs=23.3

Q ss_pred             CCCCCCCCCCcchhhhhhhccccCCCC
Q psy4350          78 ARYPDLPIPKTLVSFLYDKQGAASEPL  104 (107)
Q Consensus        78 ~~C~~~~C~~~i~~~~~~~~g~~~~p~  104 (107)
                      |.|..  |+..|.|.++++..+.+||-
T Consensus         9 p~Cdk--Cg~GIVG~~VK~rDk~rHPe   33 (35)
T d1x62a2           9 PMCDK--CGTGIVGVFVKLRDRHRHPE   33 (35)
T ss_dssp             CCCSS--SCCCCCSSCEECSSCEECTT
T ss_pred             ccccc--cCCCcEeEEEEeccccCCCC
Confidence            68999  99999999999999999993

>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=96.13  E-value=0.00052  Score=32.37  Aligned_cols=24  Identities=8%  Similarity=0.080  Sum_probs=23.0

Q ss_pred             CCCCCCCCCCcchhhhhhhccccCCC
Q psy4350          78 ARYPDLPIPKTLVSFLYDKQGAASEP  103 (107)
Q Consensus        78 ~~C~~~~C~~~i~~~~~~~~g~~~~p  103 (107)
                      |.|..  |+..|.|.++.+.++.+||
T Consensus        19 P~Cdk--Cg~GIVG~~VK~rDK~rHP   42 (45)
T d1x64a1          19 PLCDK--CGSGIVGAVVKARDKYRHP   42 (45)
T ss_dssp             CBCTT--TCCBCCSCCEESSSCEECT
T ss_pred             ccccc--cCCCcEEEEEEeccccCCC
Confidence            68999  9999999999999999999

>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=96.07  E-value=0.0036  Score=27.52  Aligned_cols=31  Identities=19%  Similarity=0.501  Sum_probs=24.5

Q ss_pred             ccccccCCCCCCCCcee-ccCCeeccHHHHhh
Q psy4350          44 LQCAHCHVPLHSELSCF-SRHGNIYCKQDFFR   74 (107)
Q Consensus        44 f~C~~C~~~l~~~~~~~-~~~~~~~C~~~y~~   74 (107)
                      |.|..|+.-+++.+.+. ..-.++||..||.+
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy~~   32 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCHNE   32 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecchhc
Confidence            67889999998776664 45568999999975

>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=95.97  E-value=0.0034  Score=26.83  Aligned_cols=28  Identities=25%  Similarity=0.587  Sum_probs=22.8

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR   74 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~   74 (107)
                      .|..|++.|...  .....+++||.+|+.+
T Consensus         1 nC~~Cgkeltad--ArEl~geLyCLpChdK   28 (31)
T d2cora1           1 NCANCGKELTAD--ARELKGELYCLPCHDK   28 (31)
T ss_dssp             BCSSSCCBCCTT--CEEETTEEECHHHHHT
T ss_pred             Cccccccccchh--HHHhcCCEEEEecccc
Confidence            377899988763  5678899999999876

>d1x62a1 g.39.1.3 (A:43-73) PDZ and LIM domain protein 1 Elfin {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 1 Elfin
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.77  E-value=0.00062  Score=29.42  Aligned_cols=28  Identities=25%  Similarity=0.591  Sum_probs=22.8

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHh
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFF   73 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   73 (107)
                      .|+.|+..|.+. .++..++++||+.+-.
T Consensus         1 vC~dCg~NLKqr-G~Ffve~~lyCE~HAr   28 (31)
T d1x62a1           1 VCTDCGTNLKQK-GHFFVEDQIYCEKHAR   28 (31)
T ss_dssp             SCSSSCCCHHHH-CCEESSSCEECHHHHH
T ss_pred             CccccccChhhc-ceEEeccEEehhhhhh
Confidence            488999998776 6778889999998753

>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=95.30  E-value=0.00058  Score=31.32  Aligned_cols=29  Identities=17%  Similarity=0.054  Sum_probs=22.6

Q ss_pred             HHhh-hCCCCCCCCCCCCcchh--hhhhhccccCC
Q psy4350          71 DFFR-YSQARYPDLPIPKTLVS--FLYDKQGAASE  102 (107)
Q Consensus        71 ~y~~-~~~~~C~~~~C~~~i~~--~~~~~~g~~~~  102 (107)
                      ||.+ |+ ++|..  |.++|..  ..+.+.|+.+|
T Consensus         2 Cy~~~~a-~~C~~--C~k~I~~G~k~veykg~~WH   33 (37)
T d1x63a1           2 CTTREDS-PKCKG--CFKAIVAGDQNVEYKGTVWH   33 (37)
T ss_dssp             CCSCCCS-CBCSS--SCCBCCSSSCEEECSSCEEE
T ss_pred             ccccccC-ccccc--CCCccCCCCeEeEeCCccch
Confidence            6778 88 69999  9999963  55666677776

>d1x61a1 g.39.1.3 (A:8-34) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Thyroid receptor interacting protein 6, TRIP6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.29  E-value=0.0047  Score=25.11  Aligned_cols=26  Identities=46%  Similarity=1.211  Sum_probs=20.4

Q ss_pred             ccccccccc-CceEEeecCcccccccc
Q psy4350          19 CGGCGQPII-DRFYLLAVDRQWHLGCL   44 (107)
Q Consensus        19 C~~C~~~i~-~~~~~~~~~~~~H~~Cf   44 (107)
                      |..|++-+. +..-+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            678988764 44447889999999887

>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=94.91  E-value=0.014  Score=25.10  Aligned_cols=29  Identities=21%  Similarity=0.427  Sum_probs=25.3

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHhh
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFFR   74 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~   74 (107)
                      +|..|...|.+. .|....|+.+|.+|..+
T Consensus         1 rC~~C~~~LAD~-GFvKnagR~LCrpch~r   29 (32)
T d2d8xa1           1 RCDLCQEVLADI-GFVKNAGRHLCRPCHNR   29 (32)
T ss_dssp             BCSSSCCBCSSS-CCEEETTEEECHHHHHH
T ss_pred             CchHHHhHHHHh-hhhhcccccccchhhhh
Confidence            478899999988 88889999999999865

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 5, FHL-5
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.82  E-value=0.007  Score=26.14  Aligned_cols=25  Identities=24%  Similarity=0.764  Sum_probs=20.1

Q ss_pred             ccccCCCCCCCCceeccCCeeccHHH
Q psy4350          46 CAHCHVPLHSELSCFSRHGNIYCKQD   71 (107)
Q Consensus        46 C~~C~~~l~~~~~~~~~~~~~~C~~~   71 (107)
                      |..|+.+|.++ .|.-.+..++|..|
T Consensus         2 cgkcsvslvg~-gfltq~~~i~c~~c   26 (34)
T d1x68a2           2 CGKCSVSLVGK-GFLTQNKEIFCQKC   26 (34)
T ss_dssp             CTTTCCBCSSS-CEEEETTEEEETTT
T ss_pred             CccceEEEEee-eeeeccCcEEehhc
Confidence            67888899887 78888889999544

>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=94.72  E-value=0.011  Score=26.04  Aligned_cols=29  Identities=14%  Similarity=0.318  Sum_probs=22.6

Q ss_pred             CCCccccccccccCceE-EeecCccccccc
Q psy4350          15 EKSSCGGCGQPIIDRFY-LLAVDRQWHLGC   43 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~-~~~~~~~~H~~C   43 (107)
                      ..-.|.+|+....+.+. +...|..||..|
T Consensus         6 ~~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           6 ASATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHHHccCCCchHHhhcCCCccccccC
Confidence            44569999998876665 678889999876

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Actin-binding LIM protein 2, abLIM2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.53  E-value=0.0058  Score=28.02  Aligned_cols=28  Identities=32%  Similarity=0.573  Sum_probs=20.3

Q ss_pred             ccccccccccCceE-EeecCccccccccc
Q psy4350          18 SCGGCGQPIIDRFY-LLAVDRQWHLGCLQ   45 (107)
Q Consensus        18 ~C~~C~~~i~~~~~-~~~~~~~~H~~Cf~   45 (107)
                      .|.+|+....+++- ...-+..||+.|-.
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            48899998876553 35566789998853

>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=94.50  E-value=0.017  Score=24.59  Aligned_cols=28  Identities=29%  Similarity=0.658  Sum_probs=22.5

Q ss_pred             cccccCCCCCCCCceeccCCeeccHHHHh
Q psy4350          45 QCAHCHVPLHSELSCFSRHGNIYCKQDFF   73 (107)
Q Consensus        45 ~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   73 (107)
                      +|..|-.+|... .|..++++++|..|-.
T Consensus         1 RCaKC~hpLA~E-~F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPLANE-TFVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCTTSS-CCEEETTEEECHHHHT
T ss_pred             CchhhccccccC-cccccCCeEeeccccc
Confidence            477788888877 7888999999987743

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Lim domain kinase 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=94.07  E-value=0.015  Score=25.54  Aligned_cols=28  Identities=21%  Similarity=0.554  Sum_probs=20.5

Q ss_pred             CCCccccccccccCceEEeecCccccccc
Q psy4350          15 EKSSCGGCGQPIIDRFYLLAVDRQWHLGC   43 (107)
Q Consensus        15 ~~~~C~~C~~~i~~~~~~~~~~~~~H~~C   43 (107)
                      ....|..|.+.|... ++.+-...||+.|
T Consensus         7 fge~C~~C~~~itGp-vMvAG~~K~HPEC   34 (34)
T d1x6aa1           7 FGEFCHGCSLLMTGP-FMVAGEFKYHPEC   34 (34)
T ss_dssp             SSCBCTTTCCBCCSC-CBCCTTCCBCTTS
T ss_pred             HHHHhhhhHhhcccc-eeeecccccCCCC
Confidence            456799999988744 3555566799987

>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

Probab=93.89  E-value=0.0097  Score=26.31  Aligned_cols=25  Identities=4%  Similarity=-0.209  Sum_probs=22.2

Q ss_pred             CCCCCCCCCCcchhhhhhhccccCCCC
Q psy4350          78 ARYPDLPIPKTLVSFLYDKQGAASEPL  104 (107)
Q Consensus        78 ~~C~~~~C~~~i~~~~~~~~g~~~~p~  104 (107)
                      ..|..  |...|.+.-++-.|+.|||+
T Consensus         9 ~vC~K--Ch~iIdd~pL~Fr~d~YHp~   33 (35)
T d2cora2           9 YICQK--CHAIIDEQPLIFKNDPYHPD   33 (35)
T ss_dssp             CBCTT--TCCBCCSCCCCCSSSCCCTT
T ss_pred             HHHHH--HHhhhhcCcceecCCCCCCC
Confidence            46888  99999988899999999997

>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=92.58  E-value=0.066  Score=24.06  Aligned_cols=30  Identities=17%  Similarity=0.369  Sum_probs=21.1

Q ss_pred             ccccccCCCCCCCCceeccCCeeccHHHHh
Q psy4350          44 LQCAHCHVPLHSELSCFSRHGNIYCKQDFF   73 (107)
Q Consensus        44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~   73 (107)
                      |+|+.|+.++..+.+......+..|..|-.
T Consensus         1 FvC~vCr~pFP~GDRVTFnGKeC~CQ~Cs~   30 (40)
T d1v6ga2           1 FVCAVCRLPFPPGDRVTFNGKECMCQKCSL   30 (40)
T ss_dssp             SSCSSSCCCCCSSSCEEEETTEEEEHHHHS
T ss_pred             CcccccCCCCCCCCeEEEcCceeehhhcCC
Confidence            678888888765546666666777777754

>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=92.03  E-value=0.094  Score=22.40  Aligned_cols=30  Identities=23%  Similarity=0.642  Sum_probs=21.7

Q ss_pred             cccccCCCCCC-CCceeccCCeeccHHHHhh
Q psy4350          45 QCAHCHVPLHS-ELSCFSRHGNIYCKQDFFR   74 (107)
Q Consensus        45 ~C~~C~~~l~~-~~~~~~~~~~~~C~~~y~~   74 (107)
                      +|.-|...|+. +...+.+.+.++|+.+|.+
T Consensus         2 kC~cC~cRLGEVG~tlytk~nliLCkrDYlR   32 (33)
T d1j2oa2           2 SCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR   32 (33)
T ss_dssp             CCSSSCSCCCCSSSCCCCBTTBCCCHHHHHH
T ss_pred             ccccccccccchhhHHHhhcceeeehhhhhc
Confidence            46666766753 2256788899999999975

>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=91.15  E-value=0.091  Score=21.77  Aligned_cols=26  Identities=19%  Similarity=0.536  Sum_probs=18.8

Q ss_pred             ccccCCCCCCCCceeccCCeeccHHHH
Q psy4350          46 CAHCHVPLHSELSCFSRHGNIYCKQDF   72 (107)
Q Consensus        46 C~~C~~~l~~~~~~~~~~~~~~C~~~y   72 (107)
                      |..|+.+|.+. .|.-.-+.++|.+|-
T Consensus         2 c~kcsvslvgr-gflterddilc~dcg   27 (30)
T d1x4la2           2 CKKCSLSLVGR-GFLTERDDILCPDCG   27 (30)
T ss_dssp             CSSSCCBCTTS-CCEECSSSEECHHHH
T ss_pred             cceeeEEEEee-eccccccceeccccC
Confidence            67788888776 666556678888773

>d2cs3a1 g.44.1.3 (A:8-87) Protein c14orf4 (KIAA1865) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: Variant RING domain
domain: Protein c14orf4 (KIAA1865)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=87.63  E-value=0.16  Score=26.15  Aligned_cols=36  Identities=17%  Similarity=0.384  Sum_probs=28.8

Q ss_pred             CCCCCccccccccccCceEEeecCcccccccccccc
Q psy4350          13 PEEKSSCGGCGQPIIDRFYLLAVDRQWHLGCLQCAH   48 (107)
Q Consensus        13 ~~~~~~C~~C~~~i~~~~~~~~~~~~~H~~Cf~C~~   48 (107)
                      .+.+-.|.-|.+.+.+...+..-...-|+-||.|+.
T Consensus         5 ~~~~l~CtlC~erLEdtHFVQCPsv~~HkFCFpCsr   40 (80)
T d2cs3a1           5 NSGPLCCTICHERLEDTHFVQCPSVPSHKFCFPCSR   40 (80)
T ss_dssp             SCCSCCCSSSCSCCSSTTSEECSSCSSCEECHHHHH
T ss_pred             CCCceeeeeehhhhcCCceEeCCCCcCCceeccccH
Confidence            345578999999998877677777788999998874

>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=83.10  E-value=0.44  Score=25.45  Aligned_cols=43  Identities=19%  Similarity=0.399  Sum_probs=30.3

Q ss_pred             ccccccCCCCCCCCceeccCCeeccHHHHhh-hCCCCCCCCCCCCcch
Q psy4350          44 LQCAHCHVPLHSELSCFSRHGNIYCKQDFFR-YSQARYPDLPIPKTLV   90 (107)
Q Consensus        44 f~C~~C~~~l~~~~~~~~~~~~~~C~~~y~~-~~~~~C~~~~C~~~i~   90 (107)
                      +.|..|...+... .....-|..||..|..+ +. ..|-.  |..++.
T Consensus        23 l~C~IC~~~~~~p-v~~~~CgH~fC~~Ci~~~~~-~~CP~--Cr~~~~   66 (97)
T d1jm7b_          23 LRCSRCTNILREP-VCLGGCEHIFCSNCVSDCIG-TGCPV--CYTPAW   66 (97)
T ss_dssp             TSCSSSCSCCSSC-BCCCSSSCCBCTTTGGGGTT-TBCSS--SCCBCS
T ss_pred             CCCccCCchhhcC-ceeCCCCCchhHHHHHHHHh-ccccc--cCCcCc
Confidence            5778888777553 22335678899999887 76 57888  887764

>d2gvia2 g.39.1.18 (A:169-201) Uncharacterized protein Ta1109 {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: FwdE C-terminal domain-like
domain: Uncharacterized protein Ta1109
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=82.00  E-value=0.24  Score=20.73  Aligned_cols=14  Identities=29%  Similarity=0.636  Sum_probs=10.8

Q ss_pred             eccCCeeccHHHHh
Q psy4350          60 FSRHGNIYCKQDFF   73 (107)
Q Consensus        60 ~~~~~~~~C~~~y~   73 (107)
                      ...++++.|+++|.
T Consensus        19 kllngkpvckpdyy   32 (33)
T d2gvia2          19 KLLNGKPVCKPDYY   32 (33)
T ss_dssp             EEETTEEECHHHHH
T ss_pred             hhhCCCcccCcccC
Confidence            45678889998885