Psyllid ID: psy8090

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Local Sequence Feature Prediction

Residue Number Marker
--------10--------20--------30--------40--------50--------60--------70--------80--------90-------100-------110-------120-------130-------140-------150-------160-------170-------180-------190-------200-------210-------220-------230-------240--
Protein Sequence
MLKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRDLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLSLADSDDVSSSMPELTT
Secondary Structure (PSIPRED)
cccccccHHHHHHHHHccccccccccccccHHHHHHHHHHccccccccccccccccHHHHHHHHHHHHHHHHHHHccccEEcccccccccccccccccccEEEEEccccccccccccccccccccccccccccEEEccccccHHHHHHHccccccccccccccccccEEEEEcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccHHHHHHHHHHccHccccccccccHHHHHHHHHHHcccccccHHHHccccHHHHHHHHHHHHHHHHHHcccccEccccccccHHHcccccccccEEEEEcccccccccccccEEEcccHHHEEEEEEEEccccEEccccHHHHccccHHHHcHEEEcccccEEEcccccccccccccccHHHHHccccccccccEEcccccHHHcccHHHHHHHHHHHHccccccccccccccccc
Coil and Loop (DISEMBL)
mlkpskrcsmvhlyfsslpedkvpyvnspgeQYRIRQLLhqlpphdnevrychaLSEDERKELRLFSAQRKREALGRGFVKQLVapmfcencedelqtsdmsvfasragpnscwhpgcftcsVCNELLVDLIYFyrgdklycgrhhaetlkprcsacdeecqtsSQDILYYLTrdserdlpdeyRTERLEHqrdlpesygthrnslnkeqnHSFDNLLKSNLkklsladsddvsssmpeltt
Flexible Loop (DISEMBL)
mlkpskrcsMVHLYFsslpedkvpYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERlehqrdlpesygTHRNSLNKEQNHSFDNLLKSNLKklsladsddvsssmpeltt
Low Complexity Region (SEG)
MLKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRDLPESYGTHRNSLNKEQNHsfdnllksnlkklsladsddvsssMPELTT
Disordered region (IsUnstruct)
*********MVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHAL*******LRLFSA**KREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLT*********************************************************************
Disordered Region (DISOPRED)
MLKPS*RCSMVHLYF*************************QLPPHDNEVRY******************************QLVA*M***N***ELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRDLPESYGTHRNSLNKEQNHSFDNLLKSN***************MP****
Disordered Region (DISEMBL)
********SMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRDLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLS****************
Disordered Region (DISPRO)
MLKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRDLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLS****************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (Phobius)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MLKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRDLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLSLADSDDVSSSMPELTT
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	242	2.2.26 [Sep-21-2011]
A1Z6W3	1299	Protein prickle OS=Drosop	yes	N/A	0.652	0.121	0.708	7e-68
Q292U2	1353	Protein prickle OS=Drosop	yes	N/A	0.652	0.116	0.696	8e-67
Q7QJT4	923	Protein prickle OS=Anophe	yes	N/A	0.652	0.171	0.708	2e-65
Q174I2	916	Protein prickle OS=Aedes	N/A	N/A	0.652	0.172	0.702	9e-65
Q292U5	795	Protein espinas OS=Drosop	no	N/A	0.652	0.198	0.702	4e-63
Q9U1I1	785	Protein espinas OS=Drosop	no	N/A	0.652	0.201	0.702	6e-63
Q90Z06	835	Prickle-like protein 1-A	N/A	N/A	0.652	0.189	0.645	1e-60
Q3U5C7	832	Prickle-like protein 1 OS	yes	N/A	0.652	0.189	0.652	3e-60
Q96MT3	831	Prickle-like protein 1 OS	yes	N/A	0.652	0.190	0.652	4e-60
Q7Z3G6	844	Prickle-like protein 2 OS	no	N/A	0.652	0.187	0.645	7e-60

>sp|A1Z6W3|PRIC1_DROME Protein prickle OS=Drosophila melanogaster GN=pk PE=1 SV=1

 Score =  256 bits (655), Expect = 7e-68,   Method: Compositional matrix adjust.
 Identities = 112/158 (70%), Positives = 134/158 (84%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYFS +P+DKVPYVNSPGEQYR+RQLLHQLPPHDNEVRYCH+L+++ERK
Sbjct: 537 VPPGLRPDQVRLYFSQIPDDKVPYVNSPGEQYRVRQLLHQLPPHDNEVRYCHSLTDEERK 596

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELRLFS QRKR+ALGRG V+QL++   C+ C+D + T D++VFA+R GPN+ WHP CF C
Sbjct: 597 ELRLFSTQRKRDALGRGNVRQLMSARPCDGCDDLISTGDIAVFATRLGPNASWHPACFAC 656

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           SVC ELLVDLIYF+R  ++YCGRHHAETLKPRCSACDE
Sbjct: 657 SVCRELLVDLIYFHRDGRMYCGRHHAETLKPRCSACDE 694

Acts in a planar cell polarity (PCP) complex; polarization along the apical/basal axis of epithelial cells. Correct expression of the alternative isoforms is required for PCP signaling in imaginal disks. PCP signaling in the wing disk requires the receptor fz and the cytoplasmic proteins dsh and pk. These act in a feedback loop leading to activation of the jnk cascade and subsequent polarized arrangement of hairs and bristles. Dgo and pk compete with one another for dsh binding, thereby modulating fz dsh activity and ensuring tight control over fz PCP signaling. Vang, stan and pk function together to regulate the establishment of tissue polarity in the adult eye.
Drosophila melanogaster (taxid: 7227)

>sp|Q292U2|PRIC1_DROPS Protein prickle OS=Drosophila pseudoobscura pseudoobscura GN=pk PE=3 SV=3

 Score =  253 bits (646), Expect = 8e-67,   Method: Compositional matrix adjust.
 Identities = 110/158 (69%), Positives = 134/158 (84%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYFS +P+DKVPYVNSPGEQYR+RQLLHQLPPHDNEVRYCH+L+++ERK
Sbjct: 570 VPPGLRPDQVRLYFSQIPDDKVPYVNSPGEQYRVRQLLHQLPPHDNEVRYCHSLTDEERK 629

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELRLFS QRKR+ALGRG V+QL++   C+ C++ + T D++VFA+R GPN+ WHP CFTC
Sbjct: 630 ELRLFSTQRKRDALGRGNVRQLMSARPCDGCDELISTGDIAVFATRLGPNASWHPACFTC 689

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
            +C ELLVDLIYF+R  ++YCGRHHAETLKPRCSACDE
Sbjct: 690 CICRELLVDLIYFHRDGRMYCGRHHAETLKPRCSACDE 727

Acts in a planar cell polarity (PCP) complex; polarization along the apical/basal axis of epithelial cells. PCP signaling in the wing disk requires the receptor fz and the cytoplasmic proteins dsh and pk. These act in a feedback loop leading to activation of the jnk cascade and subsequent polarized arrangement of hairs and bristles. Dgo and pk compete with one another for dsh binding, thereby modulating fz dsh activity and ensuring tight control over fz PCP signaling. Vang, stan and pk function together to regulate the establishment of tissue polarity in the adult eye.

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

>sp|Q7QJT4|PRIC1_ANOGA Protein prickle OS=Anopheles gambiae GN=pk PE=3 SV=4

 Score =  249 bits (635), Expect = 2e-65,   Method: Compositional matrix adjust.
 Identities = 112/158 (70%), Positives = 131/158 (82%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   VHLYFS++PEDKVPYVNS GE++R+RQLL QLPPHDNEVRYCH+L+++ERK
Sbjct: 297 VPPGLRPDQVHLYFSAIPEDKVPYVNSIGERHRVRQLLQQLPPHDNEVRYCHSLTDEERK 356

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           EL+LFSAQRKREALGRG VKQ+   + CE C +   + DM VFASR  PN+CWHP CF C
Sbjct: 357 ELKLFSAQRKREALGRGTVKQITTTLICERCGECASSGDMMVFASRFEPNTCWHPACFAC 416

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
            VC ELLVDLIYF+R ++LYCGRHHAETLKPRCSACDE
Sbjct: 417 CVCKELLVDLIYFHRENRLYCGRHHAETLKPRCSACDE 454

Acts in a planar cell polarity (PCP) complex; polarization along the apical/basal axis of epithelial cells. PCP signaling in the wing disk requires the receptor fz and the cytoplasmic proteins dsh and pk. These act in a feedback loop leading to activation of the jnk cascade and subsequent polarized arrangement of hairs and bristles. Dgo and pk compete with one another for dsh binding, thereby modulating fz dsh activity and ensuring tight control over fz PCP signaling. Vang, stan and pk function together to regulate the establishment of tissue polarity in the adult eye.

Anopheles gambiae (taxid: 7165)

>sp|Q174I2|PRIC1_AEDAE Protein prickle OS=Aedes aegypti GN=pk PE=3 SV=1

 Score =  246 bits (629), Expect = 9e-65,   Method: Compositional matrix adjust.
 Identities = 111/158 (70%), Positives = 130/158 (82%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   VHLYFS++PEDKVPYVNS GE++R+RQLL QLPPHDNEVRYCH+L+++ERK
Sbjct: 189 VPPGLRPDQVHLYFSAIPEDKVPYVNSIGERHRVRQLLQQLPPHDNEVRYCHSLTDEERK 248

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           EL+LFSAQRKREALGRG VKQL     C+ C + + + DM V+ASR  P +CWHP CF C
Sbjct: 249 ELKLFSAQRKREALGRGTVKQLATNQICDGCGECISSGDMGVYASRFDPGTCWHPACFVC 308

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           SVC ELLVDLIYF+R  +LYCGRHHAETLKPRCSACDE
Sbjct: 309 SVCKELLVDLIYFHREARLYCGRHHAETLKPRCSACDE 346

Acts in a planar cell polarity (PCP) complex; polarization along the apical/basal axis of epithelial cells. PCP signaling in the wing disk requires the receptor fz and the cytoplasmic proteins dsh and pk. These act in a feedback loop leading to activation of the jnk cascade and subsequent polarized arrangement of hairs and bristles. Dgo and pk compete with one another for dsh binding, thereby modulating fz dsh activity and ensuring tight control over fz PCP signaling. Vang, stan and pk function together to regulate the establishment of tissue polarity in the adult eye.

Aedes aegypti (taxid: 7159)

>sp|Q292U5|ESN_DROPS Protein espinas OS=Drosophila pseudoobscura pseudoobscura GN=esn PE=3 SV=1

 Score =  241 bits (614), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 111/158 (70%), Positives = 124/158 (78%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYFS LP+DKVPYVNSPGE+YR++QLLHQLPP DNEVRYCH+LS++ERK
Sbjct: 157 VPPGLRPDQVRLYFSQLPDDKVPYVNSPGEKYRVKQLLHQLPPQDNEVRYCHSLSDEERK 216

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELR+FSAQRKREALGRG V+ L     C+ CE+ L   D+ VFA R G   CWHPGCF C
Sbjct: 217 ELRIFSAQRKREALGRGAVRLLSDERPCKGCEESLSGGDIVVFAQRLGAQLCWHPGCFVC 276

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           SVC ELLVDLIYF R   LYCGRHHAET KPRCSACDE
Sbjct: 277 SVCKELLVDLIYFQRDGNLYCGRHHAETQKPRCSACDE 314

Drosophila pseudoobscura pseudoobscura (taxid: 46245)

>sp|Q9U1I1|ESN_DROME Protein espinas OS=Drosophila melanogaster GN=esn PE=2 SV=1

 Score =  240 bits (613), Expect = 6e-63,   Method: Compositional matrix adjust.
 Identities = 111/158 (70%), Positives = 124/158 (78%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYFS LP+DKVPYVNSPGE+YR++QLLHQLPP DNEVRYCH+LS++ERK
Sbjct: 157 VPPGLRPDQVRLYFSQLPDDKVPYVNSPGEKYRVKQLLHQLPPQDNEVRYCHSLSDEERK 216

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELR+FSAQRKREALGRG V+ L     C+ CE+ L   D+ VFA R G   CWHPGCF C
Sbjct: 217 ELRIFSAQRKREALGRGAVRLLSDERPCKGCEEPLSGGDIVVFAQRLGAQLCWHPGCFVC 276

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           SVC ELLVDLIYF R   LYCGRHHAET KPRCSACDE
Sbjct: 277 SVCKELLVDLIYFQRDGNLYCGRHHAETQKPRCSACDE 314

Drosophila melanogaster (taxid: 7227)

>sp|Q90Z06|PRI1A_XENLA Prickle-like protein 1-A OS=Xenopus laevis GN=prickle1-a PE=1 SV=1

 Score =  233 bits (593), Expect = 1e-60,   Method: Compositional matrix adjust.
 Identities = 104/161 (64%), Positives = 128/161 (79%), Gaps = 3/161 (1%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYF+ LPE+K+PYVNS GE+YRI+QLL+QLPPHDNEVRYC +LSE+E+K
Sbjct: 36  VPPGLRLEQVQLYFACLPEEKIPYVNSVGEKYRIKQLLYQLPPHDNEVRYCQSLSEEEKK 95

Query: 62  ELRLFSAQRKREALGRGFVKQL---VAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGC 118
           EL++FSAQRK+EALGRG +K L   V    CE C +++   ++++F SRAGP  CWHP C
Sbjct: 96  ELQMFSAQRKKEALGRGNIKMLSRAVMHATCEKCGEKINGGEVAIFVSRAGPGVCWHPSC 155

Query: 119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           F CS CNELLVDLIYFY+  K++CGRHHAE LKPRCSACDE
Sbjct: 156 FVCSTCNELLVDLIYFYQDGKIHCGRHHAELLKPRCSACDE 196

Acts in a planar cell polarity (PCP) complex; polarization along the apical/basal axis of epithelial cells. Regulates the polarized assembly of fibronectrin on the surface of the mesoderm during gastrulation. Essential for gastrulation cell movements, cooperating with dvl2/dsh to activate jnk. Acts together with tes to control axial elongation.

Xenopus laevis (taxid: 8355)

>sp|Q3U5C7|PRIC1_MOUSE Prickle-like protein 1 OS=Mus musculus GN=Prickle1 PE=1 SV=1

 Score =  231 bits (590), Expect = 3e-60,   Method: Compositional matrix adjust.
 Identities = 105/161 (65%), Positives = 128/161 (79%), Gaps = 3/161 (1%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   + LYF+ LPE+KVPYVNSPGE++RI+QLL+QLPPHDNEVRYC +LSE+E+K
Sbjct: 36  VPPGLRPEQIQLYFACLPEEKVPYVNSPGEKHRIKQLLYQLPPHDNEVRYCQSLSEEEKK 95

Query: 62  ELRLFSAQRKREALGRGFVKQL---VAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGC 118
           EL++FSAQRK+EALGRG +K L   V    CE C  ++   +++VFASRAGP  CWHP C
Sbjct: 96  ELQVFSAQRKKEALGRGTIKLLSRAVMHAVCEQCGLQMNGGEVAVFASRAGPGVCWHPSC 155

Query: 119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           F C  CNELLVDLIYFY+  K++CGRHHAE LKPRCSACDE
Sbjct: 156 FVCFTCNELLVDLIYFYQDGKIHCGRHHAELLKPRCSACDE 196

Involved in the planar cell polarity pathway that controls convergent extension during gastrulation and neural tube closure (By similarity). Convergent extension is a complex morphogenetic process during which cells elongate, move mediolaterally, and intercalate between neighboring cells, leading to convergence toward the mediolateral axis and extension along the anteroposterior axis. Necessary for nuclear localization of REST. May serve as nuclear receptor.

Mus musculus (taxid: 10090)

>sp|Q96MT3|PRIC1_HUMAN Prickle-like protein 1 OS=Homo sapiens GN=PRICKLE1 PE=1 SV=2

 Score =  231 bits (588), Expect = 4e-60,   Method: Compositional matrix adjust.
 Identities = 105/161 (65%), Positives = 128/161 (79%), Gaps = 3/161 (1%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   + LYF+ LPE+KVPYVNSPGE++RI+QLL+QLPPHDNEVRYC +LSE+E+K
Sbjct: 36  VPPGLRPEQIQLYFACLPEEKVPYVNSPGEKHRIKQLLYQLPPHDNEVRYCQSLSEEEKK 95

Query: 62  ELRLFSAQRKREALGRGFVKQL---VAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGC 118
           EL++FSAQRK+EALGRG +K L   V    CE C  ++   +++VFASRAGP  CWHP C
Sbjct: 96  ELQVFSAQRKKEALGRGTIKLLSRAVMHAVCEQCGLKINGGEVAVFASRAGPGVCWHPSC 155

Query: 119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           F C  CNELLVDLIYFY+  K++CGRHHAE LKPRCSACDE
Sbjct: 156 FVCFTCNELLVDLIYFYQDGKIHCGRHHAELLKPRCSACDE 196

Involved in the planar cell polarity pathway that controls convergent extension during gastrulation and neural tube closure. Convergent extension is a complex morphogenetic process during which cells elongate, move mediolaterally, and intercalate between neighboring cells, leading to convergence toward the mediolateral axis and extension along the anteroposterior axis. Necessary for nuclear localization of REST. May serve as nuclear receptor.

Homo sapiens (taxid: 9606)

>sp|Q7Z3G6|PRIC2_HUMAN Prickle-like protein 2 OS=Homo sapiens GN=PRICKLE2 PE=1 SV=2

 Score =  230 bits (587), Expect = 7e-60,   Method: Compositional matrix adjust.
 Identities = 104/161 (64%), Positives = 126/161 (78%), Gaps = 3/161 (1%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  +   VH Y+S LPE+KVPYVNSPGE+ RI+QLLHQLPPHDNEVRYC++L E+E++
Sbjct: 40  VPPGLKPEQVHQYYSCLPEEKVPYVNSPGEKLRIKQLLHQLPPHDNEVRYCNSLDEEEKR 99

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPM---FCENCEDELQTSDMSVFASRAGPNSCWHPGC 118
           EL+LFS+QRKRE LGRG V+     M    CE C  ++   D++VFASRAG   CWHP C
Sbjct: 100 ELKLFSSQRKRENLGRGNVRPFPVTMTGAICEQCGGQINGGDIAVFASRAGHGVCWHPPC 159

Query: 119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           F C+VCNELLVDLIYFY+  K+YCGRHHAE LKPRC+ACDE
Sbjct: 160 FVCTVCNELLVDLIYFYQDGKIYCGRHHAECLKPRCAACDE 200

Homo sapiens (taxid: 9606)

Close Homologs in the Non-Redundant Database Detected by BLAST

Original result of BLAST against Nonredundant Database

GI	Length	Definition	Q cover	H cover	Identity	E-value
Query	242
270010437	657	hypothetical protein TcasGA2_TC009830 [T	0.652	0.240	0.778	4e-70
242007675	672	LIM domain only protein, putative [Pedic	0.615	0.221	0.805	9e-69
195474329	1308	GE19116 [Drosophila yakuba] gi|194175545	0.652	0.120	0.708	3e-66
328927106	1346	MIP30239p [Drosophila melanogaster]	0.652	0.117	0.708	3e-66
12655372	1299	prickle sple isoform [Drosophila melanog	0.652	0.121	0.708	4e-66
194863868	1326	GG23268 [Drosophila erecta] gi|190662521	0.652	0.119	0.708	4e-66
24586188	1299	prickle, isoform C [Drosophila melanogas	0.652	0.121	0.708	4e-66
195027702	1361	GH21524 [Drosophila grimshawi] gi|193902	0.652	0.116	0.702	5e-66
195402801	1421	GJ15157 [Drosophila virilis] gi|19414085	0.652	0.111	0.702	6e-66
24586174	963	prickle, isoform A [Drosophila melanogas	0.652	0.164	0.708	1e-65

>gi|270010437|gb|EFA06885.1| hypothetical protein TcasGA2_TC009830 [Tribolium castaneum]

 Score =  270 bits (689), Expect = 4e-70,   Method: Compositional matrix adjust.
 Identities = 123/158 (77%), Positives = 138/158 (87%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   VHLYFS+LPEDKVPYVNS GE+YR+RQLL QLPPHDNEVRYCHALS++ERK
Sbjct: 66  VPPGLRPDQVHLYFSALPEDKVPYVNSVGERYRVRQLLQQLPPHDNEVRYCHALSDEERK 125

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELRLFSAQRKREALGRG V+QL APM C+ CE+ L T D+ VFASRAGPN+CWHP CFTC
Sbjct: 126 ELRLFSAQRKREALGRGAVRQLPAPMQCDACEEMLATGDICVFASRAGPNTCWHPACFTC 185

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           +VC ELLVDLIYFY+  +LYCGRHHAET+KPRCSACDE
Sbjct: 186 TVCRELLVDLIYFYKEGRLYCGRHHAETIKPRCSACDE 223

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242007675|ref|XP_002424655.1| LIM domain only protein, putative [Pediculus humanus corporis] gi|212508129|gb|EEB11917.1| LIM domain only protein, putative [Pediculus humanus corporis]

 Score =  265 bits (678), Expect = 9e-69,   Method: Compositional matrix adjust.
 Identities = 120/149 (80%), Positives = 133/149 (89%)

Query: 11  VHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQR 70
           VHLYFS+LPEDKVPYVNS GE+YR+RQLL QLPPHDNEVRYCH LSE+ERKELRLFSAQR
Sbjct: 3   VHLYFSALPEDKVPYVNSIGERYRVRQLLQQLPPHDNEVRYCHGLSEEERKELRLFSAQR 62

Query: 71  KREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVD 130
           KREALGRG  +QL + M C+ C +EL + DMSVFASRAGPN+CWHPGCF+C +C ELLVD
Sbjct: 63  KREALGRGSARQLTSNMPCDTCGEELSSGDMSVFASRAGPNTCWHPGCFSCHICKELLVD 122

Query: 131 LIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           LIYFY+  KLYCGRHHAETLKPRCSACDE
Sbjct: 123 LIYFYKEGKLYCGRHHAETLKPRCSACDE 151

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195474329|ref|XP_002089444.1| GE19116 [Drosophila yakuba] gi|194175545|gb|EDW89156.1| GE19116 [Drosophila yakuba]

 Score =  257 bits (657), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 112/158 (70%), Positives = 134/158 (84%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYFS +P+DKVPYVNSPGEQYR+RQLLHQLPPHDNEVRYCH+L+++ERK
Sbjct: 540 VPPGLRPDQVRLYFSQIPDDKVPYVNSPGEQYRVRQLLHQLPPHDNEVRYCHSLTDEERK 599

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELRLFS QRKR+ALGRG V+QL++   C+ C+D + T D++VFA+R GPN+ WHP CF C
Sbjct: 600 ELRLFSTQRKRDALGRGNVRQLMSARPCDGCDDLISTGDIAVFATRLGPNASWHPACFAC 659

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           SVC ELLVDLIYF+R  ++YCGRHHAETLKPRCSACDE
Sbjct: 660 SVCRELLVDLIYFHRDGRMYCGRHHAETLKPRCSACDE 697

Source: Drosophila yakuba

Species: Drosophila yakuba

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328927106|gb|AEB66928.1| MIP30239p [Drosophila melanogaster]

 Score =  257 bits (657), Expect = 3e-66,   Method: Compositional matrix adjust.
 Identities = 112/158 (70%), Positives = 134/158 (84%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYFS +P+DKVPYVNSPGEQYR+RQLLHQLPPHDNEVRYCH+L+++ERK
Sbjct: 584 VPPGLRPDQVRLYFSQIPDDKVPYVNSPGEQYRVRQLLHQLPPHDNEVRYCHSLTDEERK 643

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELRLFS QRKR+ALGRG V+QL++   C+ C+D + T D++VFA+R GPN+ WHP CF C
Sbjct: 644 ELRLFSTQRKRDALGRGNVRQLMSARPCDGCDDLISTGDIAVFATRLGPNASWHPACFAC 703

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           SVC ELLVDLIYF+R  ++YCGRHHAETLKPRCSACDE
Sbjct: 704 SVCRELLVDLIYFHRDGRMYCGRHHAETLKPRCSACDE 741

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|12655372|emb|CAB57345.3| prickle sple isoform [Drosophila melanogaster]

 Score =  257 bits (656), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 112/158 (70%), Positives = 134/158 (84%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYFS +P+DKVPYVNSPGEQYR+RQLLHQLPPHDNEVRYCH+L+++ERK
Sbjct: 537 VPPGLRPDQVRLYFSQIPDDKVPYVNSPGEQYRVRQLLHQLPPHDNEVRYCHSLTDEERK 596

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELRLFS QRKR+ALGRG V+QL++   C+ C+D + T D++VFA+R GPN+ WHP CF C
Sbjct: 597 ELRLFSTQRKRDALGRGNVRQLMSARPCDGCDDLISTGDIAVFATRLGPNASWHPACFAC 656

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           SVC ELLVDLIYF+R  ++YCGRHHAETLKPRCSACDE
Sbjct: 657 SVCRELLVDLIYFHRDGRMYCGRHHAETLKPRCSACDE 694

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|194863868|ref|XP_001970654.1| GG23268 [Drosophila erecta] gi|190662521|gb|EDV59713.1| GG23268 [Drosophila erecta]

 Score =  257 bits (656), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 112/158 (70%), Positives = 134/158 (84%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYFS +P+DKVPYVNSPGEQYR+RQLLHQLPPHDNEVRYCH+L+++ERK
Sbjct: 560 VPPGLRPDQVRLYFSQIPDDKVPYVNSPGEQYRVRQLLHQLPPHDNEVRYCHSLTDEERK 619

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELRLFS QRKR+ALGRG V+QL++   C+ C+D + T D++VFA+R GPN+ WHP CF C
Sbjct: 620 ELRLFSTQRKRDALGRGNVRQLMSARPCDGCDDLISTGDIAVFATRLGPNASWHPACFAC 679

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           SVC ELLVDLIYF+R  ++YCGRHHAETLKPRCSACDE
Sbjct: 680 SVCRELLVDLIYFHRDGRMYCGRHHAETLKPRCSACDE 717

Source: Drosophila erecta

Species: Drosophila erecta

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24586188|ref|NP_724538.1| prickle, isoform C [Drosophila melanogaster] gi|148887002|sp|A1Z6W3.1|PRIC1_DROME RecName: Full=Protein prickle; AltName: Full=Protein spiny legs gi|21627804|gb|AAF59281.2| prickle, isoform C [Drosophila melanogaster]

 Score =  256 bits (655), Expect = 4e-66,   Method: Compositional matrix adjust.
 Identities = 112/158 (70%), Positives = 134/158 (84%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYFS +P+DKVPYVNSPGEQYR+RQLLHQLPPHDNEVRYCH+L+++ERK
Sbjct: 537 VPPGLRPDQVRLYFSQIPDDKVPYVNSPGEQYRVRQLLHQLPPHDNEVRYCHSLTDEERK 596

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELRLFS QRKR+ALGRG V+QL++   C+ C+D + T D++VFA+R GPN+ WHP CF C
Sbjct: 597 ELRLFSTQRKRDALGRGNVRQLMSARPCDGCDDLISTGDIAVFATRLGPNASWHPACFAC 656

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           SVC ELLVDLIYF+R  ++YCGRHHAETLKPRCSACDE
Sbjct: 657 SVCRELLVDLIYFHRDGRMYCGRHHAETLKPRCSACDE 694

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195027702|ref|XP_001986721.1| GH21524 [Drosophila grimshawi] gi|193902721|gb|EDW01588.1| GH21524 [Drosophila grimshawi]

 Score =  256 bits (655), Expect = 5e-66,   Method: Compositional matrix adjust.
 Identities = 111/158 (70%), Positives = 135/158 (85%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYFS +P+DKVPYVNSPGEQYR+RQLLHQLPPHDNEVRYCH+L+++ERK
Sbjct: 573 VPPGLRPDQVRLYFSQIPDDKVPYVNSPGEQYRVRQLLHQLPPHDNEVRYCHSLTDEERK 632

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELRLFS QRKR+ALGRG V+QL++   C+ C++ + T D++VFA+R GPN+ WHPGCFTC
Sbjct: 633 ELRLFSTQRKRDALGRGNVRQLMSARPCDGCDELISTGDIAVFATRLGPNASWHPGCFTC 692

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
            +C ELLVDLIYF+R  ++YCGRHHAETLKPRCSACDE
Sbjct: 693 CICRELLVDLIYFHRDGRMYCGRHHAETLKPRCSACDE 730

Source: Drosophila grimshawi

Species: Drosophila grimshawi

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|195402801|ref|XP_002059993.1| GJ15157 [Drosophila virilis] gi|194140859|gb|EDW57330.1| GJ15157 [Drosophila virilis]

 Score =  256 bits (654), Expect = 6e-66,   Method: Compositional matrix adjust.
 Identities = 111/158 (70%), Positives = 135/158 (85%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYFS +P+DKVPYVNSPGEQYR+RQLLHQLPPHDNEVRYCH+L+++ERK
Sbjct: 621 VPPGLRPDQVRLYFSQIPDDKVPYVNSPGEQYRVRQLLHQLPPHDNEVRYCHSLTDEERK 680

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELRLFS QRKR+ALGRG V+QL++   C+ C++ + T D++VFA+R GPN+ WHPGCFTC
Sbjct: 681 ELRLFSTQRKRDALGRGNVRQLMSARPCDGCDELISTGDIAVFATRLGPNASWHPGCFTC 740

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
            +C ELLVDLIYF+R  ++YCGRHHAETLKPRCSACDE
Sbjct: 741 CICRELLVDLIYFHRDGRMYCGRHHAETLKPRCSACDE 778

Source: Drosophila virilis

Species: Drosophila virilis

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|24586174|ref|NP_724534.1| prickle, isoform A [Drosophila melanogaster] gi|21627798|gb|AAM68908.1| prickle, isoform A [Drosophila melanogaster]

 Score =  255 bits (652), Expect = 1e-65,   Method: Compositional matrix adjust.
 Identities = 112/158 (70%), Positives = 134/158 (84%)

Query: 2   LKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERK 61
           + P  R   V LYFS +P+DKVPYVNSPGEQYR+RQLLHQLPPHDNEVRYCH+L+++ERK
Sbjct: 201 VPPGLRPDQVRLYFSQIPDDKVPYVNSPGEQYRVRQLLHQLPPHDNEVRYCHSLTDEERK 260

Query: 62  ELRLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTC 121
           ELRLFS QRKR+ALGRG V+QL++   C+ C+D + T D++VFA+R GPN+ WHP CF C
Sbjct: 261 ELRLFSTQRKRDALGRGNVRQLMSARPCDGCDDLISTGDIAVFATRLGPNASWHPACFAC 320

Query: 122 SVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           SVC ELLVDLIYF+R  ++YCGRHHAETLKPRCSACDE
Sbjct: 321 SVCRELLVDLIYFHRDGRMYCGRHHAETLKPRCSACDE 358

Source: Drosophila melanogaster

Species: Drosophila melanogaster

Genus: Drosophila

Family: Drosophilidae

Order: Diptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

---

Prediction of Gene Ontology (GO) Terms

Close Homologs with Gene Ontology terms Detected by BLAST

Original result of BLAST against Gene Ontology (AMIGO)

ID	Length	Definition	Q cover	H cover	Identity	E-value
Query	242
FB|FBgn0003090	1299	pk "prickle" [Drosophila melan	0.644	0.120	0.717	7.4e-63
UNIPROTKB|Q7QJT4	923	pk "Protein prickle" [Anophele	0.644	0.169	0.717	2.4e-62
UNIPROTKB|Q292U2	1353	pk "Protein prickle" [Drosophi	0.644	0.115	0.705	2.9e-62
UNIPROTKB|Q292U5	795	esn "Protein espinas" [Drosoph	0.644	0.196	0.711	3.7e-62
FB|FBgn0263934	785	esn "espinas" [Drosophila mela	0.644	0.198	0.711	4.8e-62
UNIPROTKB|Q174I2	916	pk "Protein prickle" [Aedes ae	0.644	0.170	0.711	1.1e-61
UNIPROTKB|F1N8U0	836	PRICKLE2 "Uncharacterized prot	0.644	0.186	0.666	1.2e-59
UNIPROTKB|Q90Z06	835	prickle1-a "Prickle-like prote	0.644	0.186	0.654	6.6e-58
UNIPROTKB|F1P3B6	832	PRICKLE1 "Uncharacterized prot	0.644	0.187	0.660	1.7e-57
MGI|MGI:1916034	832	Prickle1 "prickle homolog 1 (D	0.644	0.187	0.660	2.2e-57

FB|FBgn0003090 pk "prickle" [Drosophila melanogaster (taxid:7227)]

 Score = 652 (234.6 bits), Expect = 7.4e-63, P = 7.4e-63
 Identities = 112/156 (71%), Positives = 133/156 (85%)

Query:     4 PSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKEL 63
             P  R   V LYFS +P+DKVPYVNSPGEQYR+RQLLHQLPPHDNEVRYCH+L+++ERKEL
Sbjct:   539 PGLRPDQVRLYFSQIPDDKVPYVNSPGEQYRVRQLLHQLPPHDNEVRYCHSLTDEERKEL 598

Query:    64 RLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSV 123
             RLFS QRKR+ALGRG V+QL++   C+ C+D + T D++VFA+R GPN+ WHP CF CSV
Sbjct:   599 RLFSTQRKRDALGRGNVRQLMSARPCDGCDDLISTGDIAVFATRLGPNASWHPACFACSV 658

Query:   124 CNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
             C ELLVDLIYF+R  ++YCGRHHAETLKPRCSACDE
Sbjct:   659 CRELLVDLIYFHRDGRMYCGRHHAETLKPRCSACDE 694

GO:0042067 "establishment of ommatidial planar polarity" evidence=IMP

GO:0007163 "establishment or maintenance of cell polarity" evidence=IMP;NAS

GO:0008104 "protein localization" evidence=TAS

GO:0045185 "maintenance of protein location" evidence=TAS

GO:0016020 "membrane" evidence=NAS

GO:0045184 "establishment of protein localization" evidence=TAS

GO:0005737 "cytoplasm" evidence=TAS

GO:0001736 "establishment of planar polarity" evidence=TAS

GO:0001737 "establishment of imaginal disc-derived wing hair orientation" evidence=IMP;TAS

GO:0005515 "protein binding" evidence=IPI

GO:0008270 "zinc ion binding" evidence=IEA

GO:0001738 "morphogenesis of a polarized epithelium" evidence=IMP

UNIPROTKB|Q7QJT4 pk "Protein prickle" [Anopheles gambiae (taxid:7165)]

 Score = 639 (230.0 bits), Expect = 2.4e-62, P = 2.4e-62
 Identities = 112/156 (71%), Positives = 130/156 (83%)

Query:     4 PSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKEL 63
             P  R   VHLYFS++PEDKVPYVNS GE++R+RQLL QLPPHDNEVRYCH+L+++ERKEL
Sbjct:   299 PGLRPDQVHLYFSAIPEDKVPYVNSIGERHRVRQLLQQLPPHDNEVRYCHSLTDEERKEL 358

Query:    64 RLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSV 123
             +LFSAQRKREALGRG VKQ+   + CE C +   + DM VFASR  PN+CWHP CF C V
Sbjct:   359 KLFSAQRKREALGRGTVKQITTTLICERCGECASSGDMMVFASRFEPNTCWHPACFACCV 418

Query:   124 CNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
             C ELLVDLIYF+R ++LYCGRHHAETLKPRCSACDE
Sbjct:   419 CKELLVDLIYFHRENRLYCGRHHAETLKPRCSACDE 454

GO:0001736 "establishment of planar polarity" evidence=ISS

GO:0005886 "plasma membrane" evidence=ISS

GO:0007164 "establishment of tissue polarity" evidence=ISS

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

UNIPROTKB|Q292U2 pk "Protein prickle" [Drosophila pseudoobscura pseudoobscura (taxid:46245)]

 Score = 647 (232.8 bits), Expect = 2.9e-62, P = 2.9e-62
 Identities = 110/156 (70%), Positives = 133/156 (85%)

Query:     4 PSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKEL 63
             P  R   V LYFS +P+DKVPYVNSPGEQYR+RQLLHQLPPHDNEVRYCH+L+++ERKEL
Sbjct:   572 PGLRPDQVRLYFSQIPDDKVPYVNSPGEQYRVRQLLHQLPPHDNEVRYCHSLTDEERKEL 631

Query:    64 RLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSV 123
             RLFS QRKR+ALGRG V+QL++   C+ C++ + T D++VFA+R GPN+ WHP CFTC +
Sbjct:   632 RLFSTQRKRDALGRGNVRQLMSARPCDGCDELISTGDIAVFATRLGPNASWHPACFTCCI 691

Query:   124 CNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
             C ELLVDLIYF+R  ++YCGRHHAETLKPRCSACDE
Sbjct:   692 CRELLVDLIYFHRDGRMYCGRHHAETLKPRCSACDE 727

GO:0001736 "establishment of planar polarity" evidence=ISS

GO:0005886 "plasma membrane" evidence=ISS

GO:0007164 "establishment of tissue polarity" evidence=ISS

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

UNIPROTKB|Q292U5 esn "Protein espinas" [Drosophila pseudoobscura pseudoobscura (taxid:46245)]

 Score = 617 (222.3 bits), Expect = 3.7e-62, Sum P(2) = 3.7e-62
 Identities = 111/156 (71%), Positives = 123/156 (78%)

Query:     4 PSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKEL 63
             P  R   V LYFS LP+DKVPYVNSPGE+YR++QLLHQLPP DNEVRYCH+LS++ERKEL
Sbjct:   159 PGLRPDQVRLYFSQLPDDKVPYVNSPGEKYRVKQLLHQLPPQDNEVRYCHSLSDEERKEL 218

Query:    64 RLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSV 123
             R+FSAQRKREALGRG V+ L     C+ CE+ L   D+ VFA R G   CWHPGCF CSV
Sbjct:   219 RIFSAQRKREALGRGAVRLLSDERPCKGCEESLSGGDIVVFAQRLGAQLCWHPGCFVCSV 278

Query:   124 CNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
             C ELLVDLIYF R   LYCGRHHAET KPRCSACDE
Sbjct:   279 CKELLVDLIYFQRDGNLYCGRHHAETQKPRCSACDE 314

GO:0003674 "molecular_function" evidence=ND

GO:0005575 "cellular_component" evidence=ND

GO:0008150 "biological_process" evidence=ND

FB|FBgn0263934 esn "espinas" [Drosophila melanogaster (taxid:7227)]

 Score = 616 (221.9 bits), Expect = 4.8e-62, Sum P(2) = 4.8e-62
 Identities = 111/156 (71%), Positives = 123/156 (78%)

Query:     4 PSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKEL 63
             P  R   V LYFS LP+DKVPYVNSPGE+YR++QLLHQLPP DNEVRYCH+LS++ERKEL
Sbjct:   159 PGLRPDQVRLYFSQLPDDKVPYVNSPGEKYRVKQLLHQLPPQDNEVRYCHSLSDEERKEL 218

Query:    64 RLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSV 123
             R+FSAQRKREALGRG V+ L     C+ CE+ L   D+ VFA R G   CWHPGCF CSV
Sbjct:   219 RIFSAQRKREALGRGAVRLLSDERPCKGCEEPLSGGDIVVFAQRLGAQLCWHPGCFVCSV 278

Query:   124 CNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
             C ELLVDLIYF R   LYCGRHHAET KPRCSACDE
Sbjct:   279 CKELLVDLIYFQRDGNLYCGRHHAETQKPRCSACDE 314

GO:0005575 "cellular_component" evidence=ND

GO:0008270 "zinc ion binding" evidence=IEA

GO:0070593 "dendrite self-avoidance" evidence=IMP

UNIPROTKB|Q174I2 pk "Protein prickle" [Aedes aegypti (taxid:7159)]

 Score = 633 (227.9 bits), Expect = 1.1e-61, P = 1.1e-61
 Identities = 111/156 (71%), Positives = 129/156 (82%)

Query:     4 PSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKEL 63
             P  R   VHLYFS++PEDKVPYVNS GE++R+RQLL QLPPHDNEVRYCH+L+++ERKEL
Sbjct:   191 PGLRPDQVHLYFSAIPEDKVPYVNSIGERHRVRQLLQQLPPHDNEVRYCHSLTDEERKEL 250

Query:    64 RLFSAQRKREALGRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSV 123
             +LFSAQRKREALGRG VKQL     C+ C + + + DM V+ASR  P +CWHP CF CSV
Sbjct:   251 KLFSAQRKREALGRGTVKQLATNQICDGCGECISSGDMGVYASRFDPGTCWHPACFVCSV 310

Query:   124 CNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
             C ELLVDLIYF+R  +LYCGRHHAETLKPRCSACDE
Sbjct:   311 CKELLVDLIYFHREARLYCGRHHAETLKPRCSACDE 346

GO:0001736 "establishment of planar polarity" evidence=ISS

GO:0005886 "plasma membrane" evidence=ISS

GO:0007164 "establishment of tissue polarity" evidence=ISS

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

UNIPROTKB|F1N8U0 PRICKLE2 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 589 (212.4 bits), Expect = 1.2e-59, Sum P(2) = 1.2e-59
 Identities = 106/159 (66%), Positives = 124/159 (77%)

Query:     4 PSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKEL 63
             P  +   VH Y+S LPEDKVPYVNSPGE+ RI+QLLHQLPPHDNEVRYC++L E+E++EL
Sbjct:    42 PGLKPEQVHQYYSCLPEDKVPYVNSPGEKSRIKQLLHQLPPHDNEVRYCNSLDEEEKREL 101

Query:    64 RLFSAQRKREALGRGFVKQLVAPM---FCENCEDELQTSDMSVFASRAGPNSCWHPGCFT 120
             +LFS QRKRE LGRG V+     M    CE C  ++   D++VFASRAG   CWHP CF 
Sbjct:   102 KLFSNQRKRENLGRGNVRPFPVTMTGAICEQCGGQINGGDIAVFASRAGHGVCWHPPCFI 161

Query:   121 CSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
             CSVCNELLVDLIYFY+  K+YCGRHHAE LKPRC+ACDE
Sbjct:   162 CSVCNELLVDLIYFYQDGKIYCGRHHAECLKPRCAACDE 200

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005737 "cytoplasm" evidence=IEA

GO:0016327 "apicolateral plasma membrane" evidence=IEA

GO:0016328 "lateral plasma membrane" evidence=IEA

GO:0031175 "neuron projection development" evidence=IEA

GO:0045197 "establishment or maintenance of epithelial cell apical/basal polarity" evidence=IEA

UNIPROTKB|Q90Z06 prickle1-a "Prickle-like protein 1-A" [Xenopus laevis (taxid:8355)]

 Score = 595 (214.5 bits), Expect = 6.6e-58, P = 6.6e-58
 Identities = 104/159 (65%), Positives = 127/159 (79%)

Query:     4 PSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKEL 63
             P  R   V LYF+ LPE+K+PYVNS GE+YRI+QLL+QLPPHDNEVRYC +LSE+E+KEL
Sbjct:    38 PGLRLEQVQLYFACLPEEKIPYVNSVGEKYRIKQLLYQLPPHDNEVRYCQSLSEEEKKEL 97

Query:    64 RLFSAQRKREALGRGFVKQL---VAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFT 120
             ++FSAQRK+EALGRG +K L   V    CE C +++   ++++F SRAGP  CWHP CF 
Sbjct:    98 QMFSAQRKKEALGRGNIKMLSRAVMHATCEKCGEKINGGEVAIFVSRAGPGVCWHPSCFV 157

Query:   121 CSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
             CS CNELLVDLIYFY+  K++CGRHHAE LKPRCSACDE
Sbjct:   158 CSTCNELLVDLIYFYQDGKIHCGRHHAELLKPRCSACDE 196

GO:0001736 "establishment of planar polarity" evidence=IMP

GO:0005515 "protein binding" evidence=IPI

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

GO:0060027 "convergent extension involved in gastrulation" evidence=IMP

UNIPROTKB|F1P3B6 PRICKLE1 "Uncharacterized protein" [Gallus gallus (taxid:9031)]

 Score = 591 (213.1 bits), Expect = 1.7e-57, P = 1.7e-57
 Identities = 105/159 (66%), Positives = 127/159 (79%)

Query:     4 PSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKEL 63
             P  R   V LYF+ LPE+KVPYVNSPGE++RI+QLL+QLPPHDNEVRYC +LSE+E+KEL
Sbjct:    38 PGLRPEQVQLYFACLPEEKVPYVNSPGEKHRIKQLLYQLPPHDNEVRYCQSLSEEEKKEL 97

Query:    64 RLFSAQRKREALGRGFVKQL---VAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFT 120
             ++FS+QRK+EALGRG +K L   V    CE C  ++   +++VFASRAGP  CWHP CF 
Sbjct:    98 QMFSSQRKKEALGRGTIKLLSRAVMHAVCEQCGTKINGGEVAVFASRAGPGVCWHPSCFV 157

Query:   121 CSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
             C  CNELLVDLIYFY+  K++CGRHHAE LKPRCSACDE
Sbjct:   158 CFTCNELLVDLIYFYQDGKIHCGRHHAELLKPRCSACDE 196

GO:0008270 "zinc ion binding" evidence=IEA

GO:0001843 "neural tube closure" evidence=IEA

GO:0005829 "cytosol" evidence=IEA

GO:0031398 "positive regulation of protein ubiquitination" evidence=IEA

GO:0031965 "nuclear membrane" evidence=IEA

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=IEA

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

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=IEA

GO:2000691 "negative regulation of cardiac muscle cell myoblast differentiation" evidence=IEA

MGI|MGI:1916034 Prickle1 "prickle homolog 1 (Drosophila)" [Mus musculus (taxid:10090)]

 Score = 590 (212.7 bits), Expect = 2.2e-57, P = 2.2e-57
 Identities = 105/159 (66%), Positives = 127/159 (79%)

Query:     4 PSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKEL 63
             P  R   + LYF+ LPE+KVPYVNSPGE++RI+QLL+QLPPHDNEVRYC +LSE+E+KEL
Sbjct:    38 PGLRPEQIQLYFACLPEEKVPYVNSPGEKHRIKQLLYQLPPHDNEVRYCQSLSEEEKKEL 97

Query:    64 RLFSAQRKREALGRGFVKQL---VAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFT 120
             ++FSAQRK+EALGRG +K L   V    CE C  ++   +++VFASRAGP  CWHP CF 
Sbjct:    98 QVFSAQRKKEALGRGTIKLLSRAVMHAVCEQCGLQMNGGEVAVFASRAGPGVCWHPSCFV 157

Query:   121 CSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
             C  CNELLVDLIYFY+  K++CGRHHAE LKPRCSACDE
Sbjct:   158 CFTCNELLVDLIYFYQDGKIHCGRHHAELLKPRCSACDE 196

GO:0001843 "neural tube closure" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=IEA

GO:0005829 "cytosol" evidence=ISO

GO:0006606 "protein import into nucleus" evidence=ISO

GO:0008134 "transcription factor binding" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

GO:0016020 "membrane" evidence=IEA

GO:0031398 "positive regulation of protein ubiquitination" evidence=ISO

GO:0031965 "nuclear membrane" evidence=ISO

GO:0032436 "positive regulation of proteasomal ubiquitin-dependent protein catabolic process" evidence=ISO

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

GO:0046872 "metal ion binding" evidence=IEA

GO:0090090 "negative regulation of canonical Wnt receptor signaling pathway" evidence=ISO

GO:2000691 "negative regulation of cardiac muscle cell myoblast differentiation" evidence=ISO

---

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)
A1Z6W3	PRIC1_DROME	No assigned EC number	0.7088	0.6528	0.1216	yes	N/A
Q28FG2	PRIC1_XENTR	No assigned EC number	0.6459	0.6528	0.1896	yes	N/A
Q71QF9	PRIC1_RAT	No assigned EC number	0.6459	0.6528	0.1901	yes	N/A
Q292U2	PRIC1_DROPS	No assigned EC number	0.6962	0.6528	0.1167	yes	N/A
Q7QJT4	PRIC1_ANOGA	No assigned EC number	0.7088	0.6528	0.1711	yes	N/A
Q96MT3	PRIC1_HUMAN	No assigned EC number	0.6521	0.6528	0.1901	yes	N/A
Q3U5C7	PRIC1_MOUSE	No assigned EC number	0.6521	0.6528	0.1899	yes	N/A

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	242
cd09827	97	cd09827, PET_Prickle, The PET domain of Prickle	2e-45
pfam06297	106	pfam06297, PET, PET Domain	1e-40
cd09415	59	cd09415, LIM1_Prickle, The first LIM domain of Pri	6e-36
cd09027	82	cd09027, PET, PET ((Prickle Espinas Testin) domain	4e-33
cd09340	58	cd09340, LIM1_Testin_like, The first LIM domain of	1e-31
cd09841	59	cd09841, LIM1_Prickle_3, The first LIM domain of P	4e-28
cd09484	59	cd09484, LIM1_Prickle_2, The first LIM domain of P	3e-27
cd09483	59	cd09483, LIM1_Prickle_1, The first LIM domain of P	6e-27
cd09413	58	cd09413, LIM1_Testin, The first LIM domain of Test	3e-21
cd09829	88	cd09829, PET_testin, The PET domain of Testin	1e-19
cd09414	58	cd09414, LIM1_LIMPETin, The first LIM domain of pr	1e-17
cd09830	83	cd09830, PET_LIMPETin_LIM-9, The PET domain of pro	8e-16
cd09828	116	cd09828, PET_OEBT, The PET domain of overexpressed	9e-14
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	8e-10
pfam00412	58	pfam00412, LIM, LIM domain	2e-08
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	6e-08
cd09360	52	cd09360, LIM_ALP_like, The LIM domain of ALP (acti	2e-05
cd09459	55	cd09459, LIM3_ENH, The third LIM domain of the Eni	4e-05
cd09421	59	cd09421, LIM3_LIMPETin, The third LIM domain of pr	5e-05
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	9e-05
cd09332	52	cd09332, LIM2_PINCH, The second LIM domain of prot	1e-04
cd09363	54	cd09363, LIM3_Enigma_like, The third LIM domain of	2e-04
cd09371	53	cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b	0.003
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	0.004

>gnl|CDD|193602 cd09827, PET_Prickle, The PET domain of Prickle

 Score =  146 bits (371), Expect = 2e-45
 Identities = 61/74 (82%), Positives = 69/74 (93%)

Query: 10 MVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQ 69
           VH YFS LPEDKVPYVNSPGE+YRI+QLLHQLPPHDNEVRYC++LSE+E++ELRLFSAQ
Sbjct: 23 QVHAYFSCLPEDKVPYVNSPGEKYRIKQLLHQLPPHDNEVRYCNSLSEEEKRELRLFSAQ 82

Query: 70 RKREALGRGFVKQL 83
          RKREALGRG V+ L
Sbjct: 83 RKREALGRGIVRPL 96

The PET domain of Prickle: Prickle contains an N-terminal PET domain and three C-terminal LIM domains. Prickle has been implicated in regulation of cell movement in the planar cell polarity (PCP) pathway which requires the conserved Frizzled/Dishevelled (Dsh); Prickle interacts with Dishevelled, thereby modulating the activity of Frizzled/Dishevelled and the PCP signaling. Two forms of Prickle have been identified, namely Prickle 1 and Prickle 2. These are differentially expressed; Prickle 1 is found in fetal heart and hematological malignancies, while Prickle 2 is expressed in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. The PET domain is a protein-protein interaction domain, usually found in conjunction with the LIM domain, which is also involved in protein-protein interactions. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 97

>gnl|CDD|191489 pfam06297, PET, PET Domain

 Score =  134 bits (340), Expect = 1e-40
 Identities = 48/75 (64%), Positives = 54/75 (72%)

Query: 9   SMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSA 68
            +VH Y   LPE+KVP V S GE+YR RQLLHQLPPHD + RYCH LSE+E KEL  F  
Sbjct: 31  ELVHRYMELLPEEKVPVVGSEGEKYRRRQLLHQLPPHDQDPRYCHGLSEEEVKELEDFVK 90

Query: 69  QRKREALGRGFVKQL 83
           QRK EALG G+VK  
Sbjct: 91  QRKEEALGVGYVKLP 105

This domain is suggested to be involved in protein-protein interactions. The family is found in conjunction with pfam00412. Length = 106

>gnl|CDD|188799 cd09415, LIM1_Prickle, The first LIM domain of Prickle

 Score =  121 bits (305), Expect = 6e-36
 Identities = 39/59 (66%), Positives = 47/59 (79%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHA 147
           CE C +++   D++VFASRAGP +CWHP CF CS C ELLVDLIYFY+  K+YCGRHHA
Sbjct: 1   CEQCGEQISGGDIAVFASRAGPGACWHPACFVCSTCKELLVDLIYFYQDGKVYCGRHHA 59

The first LIM domain of Prickle: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. 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 = 59

>gnl|CDD|193601 cd09027, PET, PET ((Prickle Espinas Testin) domain is involved in protein-protein interactions

 Score =  114 bits (288), Expect = 4e-33
 Identities = 41/75 (54%), Positives = 51/75 (68%)

Query: 4  PSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKEL 63
          P    S++  YF  LP++KVP + S G +YR RQLL+QLP HD + RYC ALSE+ER E 
Sbjct: 8  PGLNASLIEQYFECLPKEKVPRLGSEGAKYRRRQLLYQLPAHDLDPRYCDALSEEERAEF 67

Query: 64 RLFSAQRKREALGRG 78
            F A RK+EALG G
Sbjct: 68 EDFVAARKQEALGVG 82

PET domain is involved in protein-protein interactions and is usually found in conjunction with LIM domain, which is also a protein-protein interaction domain. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. The PET domain has been found at the N-terminal of four known groups of proteins: prickle, testin, LIMPETin/LIM-9 and overexpressed breast tumor protein (OEBT). Prickle has been implicated in regulation of cell movement through its association with the Dishevelled (Dsh) protein in the planar cell polarity (PCP) pathway. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell contact areas, and at focal adhesion plaques. It interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin, and is involved in cell motility and adhesion events. Knockout mice experiments reveal tumor repressor function of Testin. LIMPETin/LIM-9 contains an N-terminal PET domain and 6 LIM domains at the C-terminal. In Schistosoma mansoni, where LIMPETin was first identified, it is down regulated in sexually mature adult females compared to sexually immature adult females and adult males. Its differential expression indicates that it is a transcription regulator. In C. elegans, LIM-9 may play a role in regulating the assembly and maintenance of the muscle A-band by forming a protein complex with SCPL-1 and UNC-89 and other proteins. OEBT displays a PET domain with two LIM domains, and is predicted to be localized in the nucleus with a possible role in cancer differentiation. Length = 82

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

 Score =  109 bits (276), Expect = 1e-31
 Identities = 35/58 (60%), Positives = 45/58 (77%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 146
           CE C++ +   +++VFA RAG ++CWHPGCF C  CNELLVDLIYFY   K+YCGRH+
Sbjct: 1   CEKCKEPINPGEVAVFAERAGEDACWHPGCFVCETCNELLVDLIYFYHDGKIYCGRHY 58

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|188872 cd09841, LIM1_Prickle_3, The first LIM domain of Prickle 3

 Score =  101 bits (252), Expect = 4e-28
 Identities = 36/59 (61%), Positives = 45/59 (76%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHA 147
           C+ C  ++   D++VFASRAG  +CWHP CF C+ C ELLVDLIYFY+  K+YCGRHHA
Sbjct: 1   CQQCGRQICGGDIAVFASRAGLGACWHPQCFQCASCQELLVDLIYFYQDGKIYCGRHHA 59

The first LIM domain of Prickle 3/LIM domain only 6 (LM06): Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. 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 = 59

>gnl|CDD|188868 cd09484, LIM1_Prickle_2, The first LIM domain of Prickle 2

 Score = 98.9 bits (246), Expect = 3e-27
 Identities = 40/59 (67%), Positives = 46/59 (77%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHA 147
           CE C  ++   D++VFASRAG   CWHP CF CSVCNELLVDLIYFY+  K+YCGRHHA
Sbjct: 1   CEQCGGQINGGDIAVFASRAGHGVCWHPQCFVCSVCNELLVDLIYFYQDGKIYCGRHHA 59

The first LIM domain of Prickle 2: Prickle contains three C-terminal LIM domains and a N-terminal PET domain. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. 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 = 59

>gnl|CDD|188867 cd09483, LIM1_Prickle_1, The first LIM domain of Prickle 1

 Score = 98.1 bits (244), Expect = 6e-27
 Identities = 37/59 (62%), Positives = 45/59 (76%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHA 147
           CE C  ++   +++VFASRAGP  CWHP CF C  CNELLVDLIYFY+  K++CGRHHA
Sbjct: 1   CEQCGIKINGGEVAVFASRAGPGVCWHPSCFVCFTCNELLVDLIYFYQDGKIHCGRHHA 59

The first LIM domain of Prickle 1. Prickle contains three C-terminal LIM domains and a N-terminal PET domain Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). PCP establishment requires the conserved Frizzled/Dishevelled PCP pathway. Prickle interacts with Dishevelled, thereby modulating Frizzled/Dishevelled activity and PCP signaling. Four forms of prickles have been identified: prickle 1-4. The best characterized is prickle 1 and prickle 2 which are differentially expressed. While prickle 1 is expressed in fetal heart and hematological malignancies, prickle 2 is found in mainly expressed in fetal brain, adult cartilage, pancreatic islet, and some types of timorous cells. In addition, Prickle 1 regulates cell movements during gastrulation and neuronal migration through interaction with the noncanonical Wnt11/Wnt5 pathway in zebrafish. Mutations in prickle 1 have been linked to progressive myoclonus epilepsy. 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 = 59

>gnl|CDD|188797 cd09413, LIM1_Testin, The first LIM domain of Testin

 Score = 83.3 bits (206), Expect = 3e-21
 Identities = 31/58 (53%), Positives = 41/58 (70%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 146
           C  C+  ++  D +V+A RAG +  WHP CF CS C ELLVD+IYF++  KLYCGRH+
Sbjct: 1   CYCCKQPMKEGDPAVYAERAGYDKLWHPACFVCSTCGELLVDMIYFWKNGKLYCGRHY 58

The first LIM domain of Testin: Testin contains three C-terminal LIM domains and a PET protein-protein interaction domain at the N-terminal. 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. Knockout mice experiments reveal that tumor repressor function of Testin. 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 = 58

>gnl|CDD|193604 cd09829, PET_testin, The PET domain of Testin

 Score = 80.0 bits (198), Expect = 1e-19
 Identities = 32/70 (45%), Positives = 41/70 (58%)

Query: 14 YFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQRKRE 73
          Y   LP++K P   S G QYR +QL  QLP HD +   CH LSE+E K++  F  + K E
Sbjct: 18 YMELLPKEKQPIAGSEGAQYRKKQLQKQLPLHDQDPSLCHELSENEVKQMEQFVKKYKEE 77

Query: 74 ALGRGFVKQL 83
          ALG G V + 
Sbjct: 78 ALGVGKVIEP 87

The PET domain of Testin: Testin contains a PET domain at the N-terminus and three C-terminal LIM domains. 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 is involved in cell motility and adhesion events. Knockout mice experiments reveal a tumor repressor function of Testin. The PET domain is a protein-protein interaction domain and is usually found in conjunction with LIM domain, which is also involved in protein-protein interactions. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 88

>gnl|CDD|188798 cd09414, LIM1_LIMPETin, The first LIM domain of protein LIMPETin

 Score = 74.0 bits (182), Expect = 1e-17
 Identities = 26/58 (44%), Positives = 36/58 (62%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 146
           C  C + L+  +++V A + G +  WHP CF CS C ELLVDL Y    D++YC RH+
Sbjct: 1   CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58

The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. 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 = 58

>gnl|CDD|193605 cd09830, PET_LIMPETin_LIM-9, The PET domain of protein LIMPETin and LIM-9

 Score = 69.7 bits (171), Expect = 8e-16
 Identities = 32/68 (47%), Positives = 41/68 (60%)

Query: 11 VHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQR 70
          +  Y SSLP +KVP + SPGE+YR +QL+ QLP  D  + YC  L EDE++    F   R
Sbjct: 15 IDDYMSSLPNEKVPKLGSPGERYREKQLILQLPKQDLSLAYCKHLEEDEKRSFEDFVNAR 74

Query: 71 KREALGRG 78
             ALG G
Sbjct: 75 NEIALGIG 82

The PET domain of protein LIMPETin and LIM-9: Members of this family contain an N-terminal PETdomain and five to six LIM domains at the C-terminus. Four of the six LIM domains are highly homologous to the four-and-half LIM (FHL) domain family while the other two show sequence similarity to LIM domains of the Testin family. Thus, proteins of this family may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Thus, proteins of this family may be the recombinant product of genes coding Testin and FHL proteins. SmLIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult males. Its differential expression indicates that it is a transcription regulator. In C. elegans, LIM-9 binds to UNC-97 and UNC-96, components of sarcomeric muscle M-lines. LIM-9 also forms a complex with SCPL-1 and UNC-89, whose function is to organize sarcomeric A-bands, especially the M-line of muscle. Thus, it might play a role in regulating the assembly and maintenance of muscle A-band. The PET domain is a protein-protein interaction domain and is usually found in conjunction with LIM domain, which is also involved in protein-protein interactions. The PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 83

>gnl|CDD|193603 cd09828, PET_OEBT, The PET domain of overexpressed breast tumor protein (OEBT)

 Score = 65.3 bits (159), Expect = 9e-14
 Identities = 28/48 (58%), Positives = 38/48 (79%)

Query: 34  RIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQRKREALGRGFVK 81
            +R LL QLPP D++ RYC AL+E+ER +LRLF A+RK+EALG+G  +
Sbjct: 66  GLRTLLQQLPPQDSDERYCLALAEEERAQLRLFCARRKQEALGQGVAR 113

The PET domain of overexpressed breast tumor protein (OEBT): OEBT contains an N-terminal PET domain and two C-terminal LIM domains, and is predicted to be localized in the nucleus. The expression pattern of OEBT in malignant tissues indicates a possible role of OEBT in cancer differentiation. The PET domain is a protein-protein interaction domain and is usually found in conjunction with LIM domain, which is also involved in protein-protein interactions. PET containing proteins serve as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 116

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

 Score = 52.8 bits (127), Expect = 8e-10
 Identities = 16/57 (28%), Positives = 24/57 (42%), Gaps = 4/57 (7%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 145
           C  C   +  ++  + A        WHP CF C+ C + L    +F +  KLYC   
Sbjct: 2   CAGCGKPIYGTERVLRA----LGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 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|215907 pfam00412, LIM, LIM domain

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 17/58 (29%), Positives = 23/58 (39%), Gaps = 4/58 (6%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 146
           C  C   +          R      WHP CF C+VC + L    +F +  KLYC   +
Sbjct: 1   CAGCGKPIY----DRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDY 54

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

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

 Score = 47.7 bits (114), Expect = 6e-08
 Identities = 13/36 (36%), Positives = 19/36 (52%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 146
              WHP CF CSVC + L    ++ +  K YC + +
Sbjct: 18  GKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 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|188746 cd09360, LIM_ALP_like, The LIM domain of ALP (actinin-associated LIM protein) family

 Score = 40.8 bits (96), Expect = 2e-05
 Identities = 14/31 (45%), Positives = 18/31 (58%)

Query: 115 HPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 145
           HP CF C+ C   L +  YF+  D+LYC  H
Sbjct: 21  HPECFVCADCGLNLKNKGYFFIEDELYCETH 51

This family represents the LIM domain of ALP (actinin-associated LIM protein) family. Four proteins: ALP, CLP36, RIL, and Mystique have been classified into the ALP subfamily of LIM domain proteins. Each member of the subfamily contains an N-terminal PDZ domain and a C-terminal LIM domain. Functionally, these proteins bind to alpha-actinin through their PDZ domains and bind or other signaling molecules through their LIM domains. ALP proteins have been implicated in cardiac and skeletal muscle structure, function and disease, platelet, and epithelial cell motility. 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|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog (ENH) family

 Score = 39.9 bits (93), Expect = 4e-05
 Identities = 20/57 (35%), Positives = 26/57 (45%), Gaps = 4/57 (7%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 145
           C  CE  ++  D  + A        WH  CF CSVC E L    +F + DK  C +H
Sbjct: 1   CHGCEFPIEAGDRFLEAL----GHTWHDTCFVCSVCCESLEGQTFFSKKDKPLCKKH 53

The third LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188805 cd09421, LIM3_LIMPETin, The third LIM domain of protein LIMPETin

 Score = 39.9 bits (93), Expect = 5e-05
 Identities = 14/31 (45%), Positives = 18/31 (58%)

Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGR 144
           WH  CF CS C   LVD  +  + D++YCG 
Sbjct: 26  WHEACFLCSKCKISLVDKPFGSKADRIYCGN 56

The third LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. 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 = 59

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

 Score = 39.1 bits (91), Expect = 9e-05
 Identities = 20/58 (34%), Positives = 27/58 (46%), Gaps = 6/58 (10%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 146
           C  C   +Q S              WH  CF CSVC +LL +  Y+ +  KLYC +H+
Sbjct: 1   CTGCGGRIQDSFHYRVV-----QEAWHNSCFQCSVCQDLLTNW-YYEKDGKLYCHKHY 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|188718 cd09332, LIM2_PINCH, The second LIM domain of protein PINCH

 Score = 38.5 bits (90), Expect = 1e-04
 Identities = 11/21 (52%), Positives = 15/21 (71%)

Query: 111 NSCWHPGCFTCSVCNELLVDL 131
           N+ WHP CF C +CN+ L D+
Sbjct: 17  NNNWHPDCFRCEICNKELADI 37

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

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

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 16/57 (28%), Positives = 25/57 (43%), Gaps = 4/57 (7%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRH 145
           C  C+  ++  D  + A        WH  CF C+VC+  L    ++ + DK  C  H
Sbjct: 1   CHGCDFPIEAGDRFLEAL----GHTWHDTCFVCAVCHVNLEGQTFYSKKDKPLCKNH 53

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|188757 cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b

 Score = 34.7 bits (80), Expect = 0.003
 Identities = 15/31 (48%), Positives = 16/31 (51%), Gaps = 1/31 (3%)

Query: 112 SCWHPGCFTCSVCNELLVDLIYFYRGDKLYC 142
             WH  C  CSVC + L    YF R  KLYC
Sbjct: 19  RSWHEECLQCSVCQQPLTTSCYF-RDRKLYC 48

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

 Score = 34.4 bits (79), Expect = 0.004
 Identities = 16/36 (44%), Positives = 22/36 (61%), Gaps = 1/36 (2%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 146
           N  WH  CF CSVC++ L +  YF +  KLYC + +
Sbjct: 18  NQDWHCDCFRCSVCSDSLSNW-YFEKDGKLYCRKDY 52

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	242
PF06297	106	PET: PET Domain; InterPro: IPR010442 The PET domai	100.0
KOG1701|consensus	468		99.91
KOG1701|consensus	468		99.79
KOG2272|consensus	332		99.65
KOG4577|consensus	383		99.6
KOG2272|consensus	332		99.55
KOG1703|consensus	479		99.55
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.5
KOG1703|consensus	479		99.49
KOG1044|consensus	670		99.28
KOG1044|consensus	670		99.11
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.55
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	98.48
KOG1700|consensus	200		98.15
KOG4577|consensus	383		97.71
KOG1700|consensus	200		97.66
KOG1702|consensus	264		97.21
KOG0490|consensus	235		96.07
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	95.3
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	88.47
PRK14890	59	putative Zn-ribbon RNA-binding protein; Provisiona	83.57

>PF06297 PET: PET Domain; InterPro: IPR010442 The PET domain is a ~110 amino acid motif in the N-terminal part of LIM domain proteins

Probab=100.00  E-value=1.3e-33  Score=213.84  Aligned_cols=84  Identities=60%  Similarity=0.924  Sum_probs=82.2

Q ss_pred             CCCCCCChHHHHHHHhcCCCCCCCCcCChhHHHHHHHHhhhCCCCCCCchhcccCCHHHHHHHHHHHHHhhhhccCCCcc
Q psy8090           1 MLKPSKRCSMVHLYFSSLPEDKVPYVNSPGEQYRIRQLLHQLPPHDNEVRYCHALSEDERKELRLFSAQRKREALGRGFV   80 (242)
Q Consensus         1 w~p~~~~~~~~~~y~~~lp~~~~p~~~s~g~~~r~~ql~~qlP~~d~~~~~c~~l~e~e~~~~~~f~~~~~~~~~g~g~v   80 (242)
                      ||||||++++|++||++||++++|++||+||+||++||++|||+||.|++||++|+++|+++|++|+++|+++++|+|.|
T Consensus        23 WvPpgl~~~~v~~Ym~~LP~~~vP~~gS~Ge~~R~~QL~~QLP~hD~d~~~C~~Lse~E~k~l~~F~~~rk~~alG~G~V  102 (106)
T PF06297_consen   23 WVPPGLSPELVEQYMSCLPEEKVPVVGSPGEKYRRRQLLYQLPPHDLDPRYCHSLSEEEKKELEDFVKQRKEEALGVGTV  102 (106)
T ss_pred             ecCCCCChHHHHHHHHhCCCcCCCCCCCHHHHHHHHHHHHcCCcccCCHHHHhhCCHHHHHHHHHHHHHHHHHcCCeeEE
Confidence            99999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             cccc
Q psy8090          81 KQLV   84 (242)
Q Consensus        81 ~~~~   84 (242)
                      +.+|
T Consensus       103 ~~~~  106 (106)
T PF06297_consen  103 KELP  106 (106)
T ss_pred             EeCC
Confidence            8754

The domain was described in Drosophila proteins involved in cell differentiation and is named after Prickle, Espinas and Testin. PET domain proteins contain about three zinc-binding LIM domains (see PDOC00382 from INTERPRO, IPR001781 from INTERPRO) and are found among metazoans. The PET domain has been suggested to play a role in protein-protein interactions with proteins involved in planar polarity signalling or organisation of the cytoskeleton []. Some proteins known to contain a PET domain: Mammalian testin protein (Q9UGI8 from SWISSPROT), which may function as a tumour suppressor. Mammalian LIM domain only protein 6 (LMO6/Prickle3, O43900 from SWISSPROT). Fruit fly prickle (A1Z6W3 from SWISSPROT) and espinas (Q9U1I1 from SWISSPROT) proteins encoded by the tissue polarity gene prickle (pk), involved in the control of orientation of bristles and hairs. Mammalian prickle-like proteins 1 (Q96MT3 from SWISSPROT) and 2 (Q7Z3G6 from SWISSPROT). ; GO: 0008270 zinc ion binding

>KOG1701|consensus

Probab=99.91  E-value=3.4e-26  Score=206.53  Aligned_cols=128  Identities=16%  Similarity=0.292  Sum_probs=116.3

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCcc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQD  167 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~~  167 (242)
                      +|.+|+|.|.+...++.    ||++.||..||+|.+|++.|.+..||..|+++||+.||.+. ..||..|+++|++.+  
T Consensus       276 iC~~C~K~V~g~~~ac~----Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~t-lekC~~Cg~~I~d~i--  348 (468)
T KOG1701|consen  276 ICAFCHKTVSGQGLAVE----AMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDT-LEKCNKCGEPIMDRI--  348 (468)
T ss_pred             hhhhcCCcccCcchHHH----HhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHH-HHHHhhhhhHHHHHH--
Confidence            69999999999999987    89999999999999999999999999999999999999965 489999999999755  


Q ss_pred             eeeeeecCCCCCCCCCCCcccCCCccC--CCCCCCCCCccc-CCCCCCCHHHHhhhhcccccCCCCCCCC
Q psy8090         168 ILYYLTRDSERDLPDEYRTERLEHQRD--LPESYGTHRNSL-NKEQNHSFDNLLKSNLKKLSLADSDDVS  234 (242)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g~~~f~~-~d~~~yC~~cy~~~~a~kc~~~~~~~~~  234 (242)
                                  +.|+++.+|..||.+  +.+.+++..|++ .++++||++||+++||+||++|...++-
T Consensus       349 ------------LrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P  406 (468)
T KOG1701|consen  349 ------------LRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILP  406 (468)
T ss_pred             ------------HHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccC
Confidence                        578999999999943  457889998885 6999999999999999999999887653

>KOG1701|consensus

Probab=99.79  E-value=4e-20  Score=167.39  Aligned_cols=129  Identities=22%  Similarity=0.392  Sum_probs=104.4

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCcccee-eCCeeccHhhhhcccCCCcccCCCcccCCC
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFY-RGDKLYCGRHHAETLKPRCSACDEECQTSS  165 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~-~dg~~yC~~~y~~~~~prC~~C~~~I~~~~  165 (242)
                      .+|..|++.|.+  +++.    |+|+.||+.||+|.+|++.|.+..|.+ .++++||..||+++|+|||+.|+++|++.+
T Consensus       335 ekC~~Cg~~I~d--~iLr----A~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~  408 (468)
T KOG1701|consen  335 EKCNKCGEPIMD--RILR----ALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRD  408 (468)
T ss_pred             HHHhhhhhHHHH--HHHH----hcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCC
Confidence            359999999986  6665    899999999999999999999888876 689999999999999999999999999876


Q ss_pred             cc--eeeeeecCCCCCCCCCCCcccCCCccCCC-CCCCCCCcccCCCCCCCHHHHhhhhcccc
Q psy8090         166 QD--ILYYLTRDSERDLPDEYRTERLEHQRDLP-ESYGTHRNSLNKEQNHSFDNLLKSNLKKL  225 (242)
Q Consensus       166 ~~--~~~~~~~~~~~~~~~~~~~~h~~~f~~~~-~~~g~~~f~~~d~~~yC~~cy~~~~a~kc  225 (242)
                      ..  ..++|..|+.+++. ||++..+.  ..++ +..|..+|.+ |++.+|..|..+.....+
T Consensus       409 G~~etvRvvamdr~fHv~-CY~CEDCg--~~LS~e~e~qgCyPl-d~HllCk~Ch~~Rl~~~~  467 (468)
T KOG1701|consen  409 GKDETVRVVAMDRDFHVN-CYKCEDCG--LLLSSEEEGQGCYPL-DGHLLCKTCHLKRLQAGS  467 (468)
T ss_pred             CCcceEEEEEcccccccc-ceehhhcC--ccccccCCCCcceec-cCceeechhhhhhhcccC
Confidence            43  34555566666655 88776544  3443 6677788877 889999999998866554

>KOG2272|consensus

Probab=99.65  E-value=4.4e-18  Score=145.01  Aligned_cols=116  Identities=20%  Similarity=0.365  Sum_probs=103.8

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQ  166 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~  166 (242)
                      +.|.+|.....+.+.++.    ..+..||..||+|+.|-+++.+.+||..+|+.||+.+|..+|+|-|..|++.|.++. 
T Consensus        13 ~~C~RC~~gF~~~e~~vn----s~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrV-   87 (332)
T KOG2272|consen   13 MVCERCRDGFEPAEKIVN----SNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRV-   87 (332)
T ss_pred             HHHHHHhccCCchhhhhc----cCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHH-
Confidence            479999999999988886    678999999999999999999999999999999999999999999999999999753 


Q ss_pred             ceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCCCCCcccCCCCCCCHHHHhhh
Q psy8090         167 DILYYLTRDSERDLPDEYRTERLEHQRD--LPESYGTHRNSLNKEQNHSFDNLLKS  220 (242)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g~~~f~~~d~~~yC~~cy~~~  220 (242)
                                   +.+++..||+.||++  +.+.+...-|+-+.|+.+|.+|-.+.
T Consensus        88 -------------ikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~  130 (332)
T KOG2272|consen   88 -------------IKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKE  130 (332)
T ss_pred             -------------HHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhh
Confidence                         466889999999943  34577888899999999999998884

>KOG4577|consensus

Probab=99.60  E-value=4e-17  Score=141.40  Aligned_cols=126  Identities=19%  Similarity=0.374  Sum_probs=100.7

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCcc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQD  167 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~~  167 (242)
                      +|++|.+.|.+.. +..    .+++.||..|++|+.|...|.+ .+|.++|.+||+.+|.++|+.+|++|++.|.+..+ 
T Consensus        35 ~CagC~q~IlDrF-ilK----vl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqV-  107 (383)
T KOG4577|consen   35 ICAGCDQHILDRF-ILK----VLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQV-  107 (383)
T ss_pred             cccchHHHHHHHH-HHH----HHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHH-
Confidence            7999999998753 333    6899999999999999999977 89999999999999999999999999999988652 


Q ss_pred             eeeeeecCCCCCCCCCCCcccCCCc----cCCCCCCCCCCcccCCCCCCCHHHHhhhhcccccCCCCC
Q psy8090         168 ILYYLTRDSERDLPDEYRTERLEHQ----RDLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLSLADSD  231 (242)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~~h~~~f----~~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~~~~~~  231 (242)
                          |.       .|..-.+|..||    |...-..|...|...|.+.+|.++|+..-++.|..++++
T Consensus       108 ----VR-------kAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd  164 (383)
T KOG4577|consen  108 ----VR-------KAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGD  164 (383)
T ss_pred             ----HH-------HhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccc
Confidence                11       334566788888    333234455555567899999999999888888655554

>KOG2272|consensus

Probab=99.55  E-value=5.4e-16  Score=132.34  Aligned_cols=111  Identities=13%  Similarity=0.239  Sum_probs=94.3

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCcc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQD  167 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~~  167 (242)
                      +|..|.++|..  .++.    ++|+.||.++|+|+.|.+|+-+-..|++.|..||+.||.++|+..|..|+..|.++.  
T Consensus       197 iCgaC~rpIee--rvi~----amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~v--  268 (332)
T KOG2272|consen  197 ICGACRRPIEE--RVIF----AMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRVIGGDV--  268 (332)
T ss_pred             ccccccCchHH--HHHH----HhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhhhhheecCCccCccH--
Confidence            68999999984  5565    899999999999999999999999999999999999999999999999999998653  


Q ss_pred             eeeeeecCCCCCCCCCCCcccCCCccCC---CCCCCCCCcccCCCCCCCHHHHh
Q psy8090         168 ILYYLTRDSERDLPDEYRTERLEHQRDL---PESYGTHRNSLNKEQNHSFDNLL  218 (242)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~~h~~~f~~~---~~~~g~~~f~~~d~~~yC~~cy~  218 (242)
                                  +.+.++.|-.+||.+.   .+-.-...|.+-|..|+|..||.
T Consensus       269 ------------v~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~  310 (332)
T KOG2272|consen  269 ------------VSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYD  310 (332)
T ss_pred             ------------HHHhhhhhccccccccccccccccccceeeeccchHHHHHHh
Confidence                        4668899999999321   12222346788899999999997

>KOG1703|consensus

Probab=99.55  E-value=3.7e-15  Score=141.43  Aligned_cols=125  Identities=17%  Similarity=0.238  Sum_probs=109.5

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQ  166 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~  166 (242)
                      ..|..|++.|.....++     ++++.||+.+|.|..|...+....|...+|++||..||.+.++|+|.+|.++|.+.. 
T Consensus       304 p~c~~c~~~i~~~~~i~-----~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~~-  377 (479)
T KOG1703|consen  304 PLCLSCNQKIRSVKVIV-----ALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEEG-  377 (479)
T ss_pred             ccccccccCcccceeEe-----eccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHhH-
Confidence            47999999998843333     789999999999999999999888889999999999999999999999999999754 


Q ss_pred             ceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCCCCCcccCCCCCCCHHHHhhhhcccccCCCC
Q psy8090         167 DILYYLTRDSERDLPDEYRTERLEHQRD--LPESYGTHRNSLNKEQNHSFDNLLKSNLKKLSLADS  230 (242)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~~~~~  230 (242)
                                   +.+.++.||.+||.+  +...+....|...++.+||..||+++|.++|..+.-
T Consensus       378 -------------v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~  430 (479)
T KOG1703|consen  378 -------------VCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKK  430 (479)
T ss_pred             -------------hhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccc
Confidence                         345689999999932  367888999999999999999999999989876643

>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=99.50  E-value=1.5e-14  Score=98.32  Aligned_cols=58  Identities=26%  Similarity=0.695  Sum_probs=53.0

Q ss_pred             cccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhccc
Q psy8090          89 CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL  150 (242)
Q Consensus        89 C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~  150 (242)
                      |.+|+++|.+++.++.    +.++.||++||+|..|+++|.+..|+..||++||..||.++|
T Consensus         1 C~~C~~~I~~~~~~~~----~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIK----AMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEEE----ETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEEE----eCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence            8899999998877654    679999999999999999999888999999999999999875

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 ....

>KOG1703|consensus

Probab=99.49  E-value=6.4e-15  Score=139.81  Aligned_cols=114  Identities=17%  Similarity=0.360  Sum_probs=97.9

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCC
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSS  165 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~  165 (242)
                      ...|.+|+++|.+.  .|.    +++..||++||+|..|+++|....||..||.+||+.||.+++.++|..|+.+|+.+.
T Consensus       363 ~p~C~~C~~~i~~~--~v~----a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~  436 (479)
T KOG1703|consen  363 RPNCKRCLLPILEE--GVC----ALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGS  436 (479)
T ss_pred             CccccccCCchHHh--Hhh----hccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhccccchhccchhHhhh
Confidence            34799999999874  344    679999999999999999999999999999999999999999999999999988654


Q ss_pred             cceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCCCCCcccCCCCCCCHHHH
Q psy8090         166 QDILYYLTRDSERDLPDEYRTERLEHQRD--LPESYGTHRNSLNKEQNHSFDNL  217 (242)
Q Consensus       166 ~~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g~~~f~~~d~~~yC~~cy  217 (242)
                      .            .+.+.+..||..||.+  +...+.++.|..+.++|+|..|+
T Consensus       437 ~------------~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~  478 (479)
T KOG1703|consen  437 R------------QIEADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF  478 (479)
T ss_pred             h------------HhhccCccccccceehhhhhccccCCceeecCCccccccCC
Confidence            3            2456889999999932  34577888899999999998775

>KOG1044|consensus

Probab=99.28  E-value=8.3e-13  Score=123.87  Aligned_cols=87  Identities=21%  Similarity=0.532  Sum_probs=77.2

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQ  166 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~  166 (242)
                      ..|++|++.|..+..++     |+++.||..||+|..|...|.+ .|..+||.+||++||.+.|+-+|..|.+.|.++. 
T Consensus       134 s~cagc~~~lk~gq~ll-----ald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisgkv-  206 (670)
T KOG1044|consen  134 STCAGCGEELKNGQALL-----ALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKV-  206 (670)
T ss_pred             ccccchhhhhhccceee-----eeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhhhh-
Confidence            46999999999887766     8999999999999999999965 8999999999999999999999999999999753 


Q ss_pred             ceeeeeecCCCCCCCCCCCcccCCCcc
Q psy8090         167 DILYYLTRDSERDLPDEYRTERLEHQR  193 (242)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~h~~~f~  193 (242)
                                   +.|-++.+|+.|-+
T Consensus       207 -------------Lqag~kh~HPtCAR  220 (670)
T KOG1044|consen  207 -------------LQAGDKHFHPTCAR  220 (670)
T ss_pred             -------------hhccCcccCcchhh
Confidence                         45567788888873

>KOG1044|consensus

Probab=99.11  E-value=2.6e-11  Score=113.96  Aligned_cols=112  Identities=13%  Similarity=0.153  Sum_probs=85.2

Q ss_pred             CCCCcccCCcccccccCCCCCCc-cceeeCCeeccHhhhhc-------c-cCCCcccCCCcccCCCcceeeeeecCCCCC
Q psy8090         109 GPNSCWHPGCFTCSVCNELLVDL-IYFYRGDKLYCGRHHAE-------T-LKPRCSACDEECQTSSQDILYYLTRDSERD  179 (242)
Q Consensus       109 ~~~~~wH~~CF~C~~C~~~L~~~-~~~~~dg~~yC~~~y~~-------~-~~prC~~C~~~I~~~~~~~~~~~~~~~~~~  179 (242)
                      ++|+.||+.||.|++|..++... ....-.....|..|-.-       . ....|++|++.|..+..             
T Consensus        82 a~gktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~-------------  148 (670)
T KOG1044|consen   82 TLGKTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQA-------------  148 (670)
T ss_pred             cccceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccce-------------
Confidence            78999999999999999998533 33334445677777642       1 22579999999987652             


Q ss_pred             CCCCCCcccCCCc-cCCCCCCCCCCcccCCCCCCCHHHHhhhhcccccCCCCCCC
Q psy8090         180 LPDEYRTERLEHQ-RDLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLSLADSDDV  233 (242)
Q Consensus       180 ~~~~~~~~h~~~f-~~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~~~~~~~~  233 (242)
                      +.|.++.||..|| |......-...|..+|+.|||..||..+|.-||..|...+.
T Consensus       149 llald~qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~fgvkc~~c~~fis  203 (670)
T KOG1044|consen  149 LLALDKQWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAKFGVKCEECEKFIS  203 (670)
T ss_pred             eeeeccceeeeeeehhhhcccccceeeccCCCcchhhhhhhhcCeehHHhhhhhh
Confidence            4568899999999 43222344556899999999999999999999988876554

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

Probab=98.55  E-value=3.8e-08  Score=60.71  Aligned_cols=38  Identities=29%  Similarity=0.823  Sum_probs=32.4

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCC
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV  129 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~  129 (242)
                      +|.+|+++|.+++..+.    +.+..||+.||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~----~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLR----ALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEE----eCCccccccCCCCcccCCcCc
Confidence            48999999998744554    679999999999999999985

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

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

Probab=98.48  E-value=8.5e-08  Score=64.73  Aligned_cols=56  Identities=11%  Similarity=-0.009  Sum_probs=44.5

Q ss_pred             cccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhh
Q psy8090         154 CSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSN  221 (242)
Q Consensus       154 C~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~  221 (242)
                      |++|+++|.+....+            .+.++.||.+||.  .+..++....|...++++||..||.++|
T Consensus         1 C~~C~~~I~~~~~~~------------~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVI------------KAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEE------------EETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEE------------EeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence            789999999765311            2378899999993  2446777777999999999999999876

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

>KOG1700|consensus

Probab=98.15  E-value=5.9e-07  Score=76.22  Aligned_cols=62  Identities=21%  Similarity=0.442  Sum_probs=52.6

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCC
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPR  153 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~pr  153 (242)
                      ..|..|++.+...+.+.     ..+..||..||.|..|.+.|....+..+++.+||..+|...++|+
T Consensus         8 ~kc~~c~k~vy~~e~~~-----~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~   69 (200)
T KOG1700|consen    8 DKCNACGKTVYFVEKVQ-----KDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPK   69 (200)
T ss_pred             chhhhccCcchHHHHHh-----ccCcchhhhHHhccccccccccccccccccccccccchHhhhCcc
Confidence            36999999998766543     568899999999999999999889999999999999776666543

>KOG4577|consensus

Probab=97.71  E-value=8.9e-06  Score=71.39  Aligned_cols=64  Identities=19%  Similarity=0.593  Sum_probs=51.5

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCC-Cccce-eeCCeeccHhhhhcccCCCc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV-DLIYF-YRGDKLYCGRHHAETLKPRC  154 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~-~~~~~-~~dg~~yC~~~y~~~~~prC  154 (242)
                      .+|..|...|.+..++    |-|.+..||..||.|..|++.|. +..|| ..|+++.|+++|.+.-..-|
T Consensus        93 TKCsaC~~GIpPtqVV----RkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~  158 (383)
T KOG4577|consen   93 TKCSACQEGIPPTQVV----RKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHC  158 (383)
T ss_pred             CcchhhcCCCChHHHH----HHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccc
Confidence            3699999999986544    34889999999999999999995 44555 57899999999986544444

>KOG1700|consensus

Probab=97.66  E-value=1.5e-05  Score=67.65  Aligned_cols=59  Identities=25%  Similarity=0.559  Sum_probs=52.7

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL  150 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~  150 (242)
                      ..|..|.+.+++.+.+.     +.+..||..||+|+.|+..|....|...+|.+||..++.+.+
T Consensus       109 ~~c~~c~k~vy~~Ek~~-----~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~  167 (200)
T KOG1700|consen  109 EKCARCQKTVYPLEKVT-----GNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF  167 (200)
T ss_pred             cccccccceeeehHHHh-----hhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence            46999999999887765     678999999999999999999999999999999988877655

>KOG1702|consensus

Probab=97.21  E-value=3.3e-05  Score=64.94  Aligned_cols=59  Identities=25%  Similarity=0.494  Sum_probs=51.0

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccC
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLK  151 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~  151 (242)
                      .|..|++.+.+-+.+-     -+++.||..||.|..|+..|....|--.|.++||..||-...+
T Consensus         6 n~~~cgk~vYPvE~v~-----cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a   64 (264)
T KOG1702|consen    6 NREDCGKTVYPVEEVK-----CLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA   64 (264)
T ss_pred             hhhhhccccccHHHHh-----hHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence            5889999998866543     4689999999999999999988888888999999999987664

>KOG0490|consensus

Probab=96.07  E-value=0.001  Score=56.71  Aligned_cols=112  Identities=16%  Similarity=0.275  Sum_probs=75.5

Q ss_pred             cCCCceecCccccccccCCCCCcccCCcccccccCCCCC-CccceeeCCeeccHhhhhc--ccCCCcccCCCcccCCCcc
Q psy8090          91 NCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV-DLIYFYRGDKLYCGRHHAE--TLKPRCSACDEECQTSSQD  167 (242)
Q Consensus        91 ~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~-~~~~~~~dg~~yC~~~y~~--~~~prC~~C~~~I~~~~~~  167 (242)
                      +|+..|.+.... .    ..+..||..|..|..|...|. ....|..+|.+||..+|..  .+..+|..|...|...+..
T Consensus         1 ~~~~~~~~~~~l-~----~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~l   75 (235)
T KOG0490|consen    1 GCGRQILDRYLL-R----VLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDEL   75 (235)
T ss_pred             CCCccccchHHh-h----cccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhccccccCCCCCcCHHHHH
Confidence            366677664332 2    448899999999999999996 3455555999999999998  7889999999998654421


Q ss_pred             eeeeeecCCCCCCCCCCCcccCCCcc---CCCCCCCCCCcccCCC-CCCCHHHHhhh
Q psy8090         168 ILYYLTRDSERDLPDEYRTERLEHQR---DLPESYGTHRNSLNKE-QNHSFDNLLKS  220 (242)
Q Consensus       168 ~~~~~~~~~~~~~~~~~~~~h~~~f~---~~~~~~g~~~f~~~d~-~~yC~~cy~~~  220 (242)
                      +..            ..+. |.-||.   +....+.+..+.+.+. +++|-..+...
T Consensus        76 er~------------f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~  119 (235)
T KOG0490|consen   76 ERA------------FEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE  119 (235)
T ss_pred             HHh------------hcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence            111            1223 666662   1222344555555555 88998877544

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

Probab=95.30  E-value=0.014  Score=35.16  Aligned_cols=30  Identities=13%  Similarity=0.193  Sum_probs=22.0

Q ss_pred             CcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCccC
Q psy8090         153 RCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRD  194 (242)
Q Consensus       153 rC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~  194 (242)
                      +|.+|+++|.++..    +        +.+.++.||.+||.+
T Consensus         1 ~C~~C~~~i~~~~~----~--------~~~~~~~~H~~Cf~C   30 (39)
T smart00132        1 KCAGCGKPIRGGEL----V--------LRALGKVWHPECFKC   30 (39)
T ss_pred             CccccCCcccCCcE----E--------EEeCCccccccCCCC
Confidence            68999999987532    1        233678999999943

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.

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

Probab=88.47  E-value=0.76  Score=34.11  Aligned_cols=31  Identities=26%  Similarity=0.422  Sum_probs=23.5

Q ss_pred             cccccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          85 APMFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        85 ~~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      ....|..|+++|.....+++    ..|..+|..|+
T Consensus        77 ~~~~C~vC~k~l~~~~f~~~----p~~~v~H~~C~  107 (109)
T PF10367_consen   77 ESTKCSVCGKPLGNSVFVVF----PCGHVVHYSCI  107 (109)
T ss_pred             CCCCccCcCCcCCCceEEEe----CCCeEEecccc
Confidence            34579999999988666554    56777898886

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

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

Probab=83.57  E-value=1.2  Score=30.28  Aligned_cols=48  Identities=23%  Similarity=0.610  Sum_probs=30.0

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCC
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACD  158 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~  158 (242)
                      .+|..|+..|.+.+..+.              |.|-.|++.+..          -|.+|-.....-+|..|+
T Consensus         8 ~~CtSCg~~i~~~~~~~~--------------F~CPnCG~~~I~----------RC~~CRk~~~~Y~CP~CG   55 (59)
T PRK14890          8 PKCTSCGIEIAPREKAVK--------------FLCPNCGEVIIY----------RCEKCRKQSNPYTCPKCG   55 (59)
T ss_pred             ccccCCCCcccCCCccCE--------------eeCCCCCCeeEe----------echhHHhcCCceECCCCC
Confidence            369999999987664442              888888876321          155554444344555554

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

No homologous structure with e-value below 0.005

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	242
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	5e-17
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	6e-15
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	3e-13
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	3e-11
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	4e-10
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	4e-10
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	1e-09
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-10
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	6e-10
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	6e-10
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	7e-10
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	9e-10
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	1e-09
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	2e-09
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	4e-09
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	2e-09
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	3e-04
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	2e-09
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	3e-09
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-05
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	3e-09
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	4e-09
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	5e-06
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	9e-09
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	1e-08
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	1e-08
2cuq_A	80	Four and A half LIM domains 3; structural genomics	2e-08
2cuq_A	80	Four and A half LIM domains 3; structural genomics	1e-04
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	3e-08
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	5e-07
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	4e-08
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	5e-08
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	9e-08
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	2e-07
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	2e-07
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	3e-07
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	2e-07
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	2e-07
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	4e-07
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	5e-07
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	8e-07
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	2e-06
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	2e-06
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	2e-06
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	1e-05
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	1e-05
2cor_A	79	Pinch protein; LIM domain, particularly interestin	3e-05
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-04
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	9e-04

>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 = 73.2 bits (180), Expect = 5e-17
 Identities = 16/71 (22%), Positives = 26/71 (36%), Gaps = 4/71 (5%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE 148
           C  C   +      V       N  WH  CF C+ C   L +  +  + +K+ C +    
Sbjct: 8   CVECRKPIGADSKEVHYK----NRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTR 63

Query: 149 TLKPRCSACDE 159
              P+C  C +
Sbjct: 64  EDSPKCKGCFK 74

>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 = 66.7 bits (163), Expect = 6e-15
 Identities = 13/46 (28%), Positives = 22/46 (47%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA 156
           +   HP C+ C+ C   L    +F+  D++YC +H  E +    S 
Sbjct: 34  DRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSSG 79

>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 = 62.5 bits (152), Expect = 3e-13
 Identities = 15/46 (32%), Positives = 19/46 (41%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA 156
           +   HP CF C+ CN  L    YF+   +LYC  H         S 
Sbjct: 44  DKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSSG 89

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

 Score = 57.0 bits (138), Expect = 3e-11
 Identities = 10/46 (21%), Positives = 18/46 (39%)

Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           +H  CF C VC + L          ++YC   + +   P+     +
Sbjct: 30  FHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGYGYGQ 75

>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 = 53.5 bits (129), Expect = 4e-10
 Identities = 11/45 (24%), Positives = 18/45 (40%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCS 155
           +  WH  CF C  C++ L    +    D+ YC   +   +    S
Sbjct: 24  DQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSS 68

>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 = 56.6 bits (136), Expect = 4e-10
 Identities = 16/60 (26%), Positives = 23/60 (38%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQDILY 170
            S +H  CF C VC + L        GD++YC   + +   P+         T S D   
Sbjct: 27  GSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGTLSTDKGE 86

>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 = 55.0 bits (132), Expect = 1e-09
 Identities = 11/49 (22%), Positives = 20/49 (40%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
              WH  CF C+ C + L       +  ++YC   +A+   P+     +
Sbjct: 135 GKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQ 183

>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 = 53.6 bits (129), Expect = 4e-10
 Identities = 11/68 (16%), Positives = 25/68 (36%), Gaps = 4/68 (5%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE 148
           C+ C+  +      +        S WH  CF C  C + +    +  + ++ +C   + +
Sbjct: 8   CQECKKTIMPGTRKMEYK----GSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEK 63

Query: 149 TLKPRCSA 156
                 S+
Sbjct: 64  QHASGPSS 71

>2dar_A PDZ and LIM domain protein 5; enigma homolog protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 90

 Score = 53.6 bits (129), Expect = 6e-10
 Identities = 10/46 (21%), Positives = 17/46 (36%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA 156
              WHP  F C+ C   +  + +      LYC   + +      S+
Sbjct: 44  GKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPSS 89

>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 = 53.2 bits (128), Expect = 6e-10
 Identities = 16/69 (23%), Positives = 27/69 (39%), Gaps = 5/69 (7%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE 148
           C  C +++      V A     +  +H GCF CS C   L    ++    + YC   +  
Sbjct: 8   CGGCGEDVVGDGAGVVAL----DRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVA 63

Query: 149 TLKPRCSAC 157
           TL+    + 
Sbjct: 64  TLE-SGPSS 71

>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 = 52.7 bits (127), Expect = 7e-10
 Identities = 12/46 (26%), Positives = 17/46 (36%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA 156
              WH  CF C+ C + L    +  R D  YC     +      S+
Sbjct: 24  EQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPSS 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 = 52.9 bits (127), Expect = 9e-10
 Identities = 11/43 (25%), Positives = 17/43 (39%)

Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA 156
           +H GCF C  C   L D  +  +  +L C   +        S+
Sbjct: 39  FHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGPSS 81

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

 Score = 52.4 bits (126), Expect = 1e-09
 Identities = 13/68 (19%), Positives = 20/68 (29%), Gaps = 4/68 (5%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE 148
           C  C + +      +          WH  CF CS C + L    +       YC   +  
Sbjct: 8   CSACGETVMPGSRKLEYG----GQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYEN 63

Query: 149 TLKPRCSA 156
                 S+
Sbjct: 64  KFASGPSS 71

>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 = 54.5 bits (131), Expect = 2e-09
 Identities = 15/49 (30%), Positives = 23/49 (46%), Gaps = 1/49 (2%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           +  WH  C  CS C+  L +   F RG+ +YC     +    +C+AC  
Sbjct: 26  DRHWHSKCLKCSDCHVPLAE-RCFSRGESVYCKDDFFKRFGTKCAACQL 73

>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 = 53.3 bits (128), Expect = 4e-09
 Identities = 14/78 (17%), Positives = 24/78 (30%), Gaps = 6/78 (7%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV--DLIYFYRGDKLYCGRHH 146
           C  C+  +  + +   A     +  +H  CF C VC   L   D  Y     +L C   +
Sbjct: 68  CAACQLGIPPTQVVRRAQ----DFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY 123

Query: 147 AETLKPRCSACDEECQTS 164
               +            +
Sbjct: 124 ETAKQGGSGGSGGSGGGT 141

>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 = 52.0 bits (125), Expect = 2e-09
 Identities = 14/46 (30%), Positives = 22/46 (47%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA 156
            + WH  CFTCS C +++    +F +G+  YC   H        S+
Sbjct: 36  GTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPSS 81

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

 Score = 37.7 bits (88), Expect = 3e-04
 Identities = 5/23 (21%), Positives = 8/23 (34%)

Query: 137 GDKLYCGRHHAETLKPRCSACDE 159
           G     G+       P+C  C +
Sbjct: 1   GSSGSSGKCTTREDSPKCKGCFK 23

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

 Score = 51.7 bits (124), Expect = 2e-09
 Identities = 14/46 (30%), Positives = 20/46 (43%), Gaps = 2/46 (4%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL--KPRC 154
           N+ WHP CF C +C E+L D+ +     +  C   H       P  
Sbjct: 24  NNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGPSS 69

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

 Score = 52.8 bits (127), Expect = 3e-09
 Identities = 13/46 (28%), Positives = 17/46 (36%)

Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
           WH   F C  C+ +L   IY    DK  C   + +     C  C  
Sbjct: 26  WHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHN 71

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

 Score = 42.8 bits (101), Expect = 1e-05
 Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 6/62 (9%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPG--CFTCSVCNELLVDLIYFYRGDKLYCGRHH 146
           C+ C + +      V  +    N  WH    CF CS C++ L+   +      ++C    
Sbjct: 66  CQGCHNAIDPEVQRVTYN----NFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVEC 121

Query: 147 AE 148
            +
Sbjct: 122 KK 123

>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 = 51.6 bits (124), Expect = 3e-09
 Identities = 11/46 (23%), Positives = 18/46 (39%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA 156
           ++ WHP CF C  C        +F    + +C  H+        S+
Sbjct: 34  DTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGPSS 79

>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 = 53.4 bits (128), Expect = 4e-09
 Identities = 15/50 (30%), Positives = 23/50 (46%), Gaps = 1/50 (2%)

Query: 110 PNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDE 159
            +  WH  C  CS C+  L +   F RG+ +YC     +    +C+AC  
Sbjct: 79  LDRHWHSKCLKCSDCHVPLAE-RCFSRGESVYCKDDFFKRFGTKCAACQL 127

>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 = 44.5 bits (105), Expect = 5e-06
 Identities = 15/60 (25%), Positives = 23/60 (38%), Gaps = 6/60 (10%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV--DLIYFYRGDKLYCGRHH 146
           C  C+  +  + +     RA  +  +H  CF C VC   L   D  Y     +L C   +
Sbjct: 122 CAACQLGIPPTQVVR---RAQ-DFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY 177

>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 = 9e-09
 Identities = 14/66 (21%), Positives = 22/66 (33%), Gaps = 2/66 (3%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE 148
           C  C + +     + + S       WH  CF C  C+  LV   +    D + C     +
Sbjct: 8   CAGCTNPISGLGGTKYISFEE--RQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKD 65

Query: 149 TLKPRC 154
              P  
Sbjct: 66  ISGPSS 71

>1x6a_A LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 50.2 bits (120), Expect = 1e-08
 Identities = 17/70 (24%), Positives = 24/70 (34%), Gaps = 8/70 (11%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV--DLIYFYRGDKLYCGRHH 146
           C  C   +    M            +HP CF C  C  ++   D     +   LYCG+ H
Sbjct: 18  CHGCSLLMTGPFMVAG------EFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCH 71

Query: 147 AETLKPRCSA 156
            E +    S 
Sbjct: 72  NEVVSGPSSG 81

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

 Score = 49.7 bits (119), Expect = 1e-08
 Identities = 12/47 (25%), Positives = 20/47 (42%), Gaps = 1/47 (2%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFY-RGDKLYCGRHHAETLKPRCSA 156
              +HPGCFTC VC+  L  + +      +++C            S+
Sbjct: 34  GKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGPSS 80

>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 = 49.3 bits (118), Expect = 2e-08
 Identities = 11/43 (25%), Positives = 15/43 (34%)

Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA 156
           WH  C  C+ C   L    +  R +  YC     E      S+
Sbjct: 37  WHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPSS 79

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

 Score = 38.9 bits (91), Expect = 1e-04
 Identities = 6/23 (26%), Positives = 9/23 (39%)

Query: 137 GDKLYCGRHHAETLKPRCSACDE 159
           G     G  +     PRC+ C +
Sbjct: 1   GSSGSSGPCYENKFAPRCARCSK 23

>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 = 51.2 bits (122), Expect = 3e-08
 Identities = 18/74 (24%), Positives = 25/74 (33%), Gaps = 5/74 (6%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFY-RGDKLYCGRHHA 147
           C  C   +  S++     RA   + +H  CFTCS C   LV    F+     L+C     
Sbjct: 72  CSACGQSIPASEL---VMRAQ-GNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRP 127

Query: 148 ETLKPRCSACDEEC 161
             L           
Sbjct: 128 TALINGHLNSGGSG 141

>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 = 47.7 bits (113), Expect = 5e-07
 Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 4/55 (7%)

Query: 111 NSCWHPGCFTCSVCNELLVDLI--YFYRGDKLYCGRHHAET--LKPRCSACDEEC 161
           +S WH  C  CS C   L D+    + +   + C   +         CSAC +  
Sbjct: 25  DSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSI 79

>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 = 48.7 bits (116), Expect = 4e-08
 Identities = 13/45 (28%), Positives = 20/45 (44%)

Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACD 158
           +H  CF CS CN  L    Y     ++YC  H  +  K + +  +
Sbjct: 38  FHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDE 82

>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 = 48.2 bits (115), Expect = 5e-08
 Identities = 11/46 (23%), Positives = 17/46 (36%), Gaps = 1/46 (2%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA 156
           +  WH  CF C  C+ +L    Y  +    YC   +        S+
Sbjct: 35  DKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPSS 79

>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 = 47.4 bits (113), Expect = 9e-08
 Identities = 12/64 (18%), Positives = 25/64 (39%), Gaps = 4/64 (6%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE 148
           CE C+     ++  V ++       +H  CF C+ C +   + +++    + YC      
Sbjct: 14  CERCKGGFAPAEKIVNSN----GELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQM 69

Query: 149 TLKP 152
              P
Sbjct: 70  LFAP 73

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

 Score = 46.1 bits (110), Expect = 2e-07
 Identities = 9/38 (23%), Positives = 16/38 (42%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE 148
              WH   F C+ C +  +   ++ R    YC  H+ +
Sbjct: 24  GKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQ 61

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

 Score = 47.8 bits (114), Expect = 2e-07
 Identities = 12/74 (16%), Positives = 29/74 (39%), Gaps = 5/74 (6%)

Query: 79  FVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFY-RG 137
           +++       C +C+  ++  +M++   R   +  +H  CF C+ C +       +    
Sbjct: 59  YLRLFGQDGLCASCDKRIRAYEMTM---RVK-DKVYHLECFKCAACQKHFCVGDRYLLIN 114

Query: 138 DKLYCGRHHAETLK 151
             + C +   E  K
Sbjct: 115 SDIVCEQDIYEWTK 128

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

 Score = 47.0 bits (112), Expect = 3e-07
 Identities = 12/54 (22%), Positives = 24/54 (44%), Gaps = 4/54 (7%)

Query: 110 PNSCWHPGCFTCSVCNELLVDLI--YFYRGDKLYCGRHHAETL--KPRCSACDE 159
            +  WH  C +C +C   L ++    +Y+  +  C R +         C++CD+
Sbjct: 21  IDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDK 74

>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 = 47.4 bits (112), Expect = 2e-07
 Identities = 15/86 (17%), Positives = 27/86 (31%), Gaps = 5/86 (5%)

Query: 110 PNSCWHPGCFTCSVCNELLVDL--IYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQD 167
            +  WH  C +C +C   L ++    +Y+  +  C R +                    +
Sbjct: 22  IDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGSGGDVMVVGE 81

Query: 168 ILYYLTRDSERDLPDEYRTERLEHQR 193
                    E    DE    RLE+ +
Sbjct: 82  P---TLMGGEFGDEDERLITRLENTQ 104

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

 Score = 45.4 bits (108), Expect = 4e-07
 Identities = 10/48 (20%), Positives = 14/48 (29%), Gaps = 1/48 (2%)

Query: 111 NSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL-KPRCSAC 157
              WH  C  C  C + L    +     K YC       +  P+    
Sbjct: 20  GKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGR 67

>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 = 45.6 bits (108), Expect = 5e-07
 Identities = 11/60 (18%), Positives = 22/60 (36%), Gaps = 1/60 (1%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE 148
           C  C++ +                 WH  CF C  C+  L +  + +  +++YC     +
Sbjct: 18  CAGCKNPITGFGKGSSVVAYE-GQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

>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 = 44.7 bits (106), Expect = 8e-07
 Identities = 11/44 (25%), Positives = 17/44 (38%), Gaps = 1/44 (2%)

Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL-KPRCSA 156
           WH  C  C  C++ L    +     K +C +    TL     S+
Sbjct: 32  WHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGPSS 75

>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 = 45.0 bits (106), Expect = 2e-06
 Identities = 10/51 (19%), Positives = 17/51 (33%), Gaps = 2/51 (3%)

Query: 110 PNSCWHPGCFTCSVCNELLVDL--IYFYRGDKLYCGRHHAETLKPRCSACD 158
            +S WH  C  CS C   L D+    + +   + C   +        +   
Sbjct: 24  MDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGS 74

>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B Length = 72

 Score = 43.2 bits (102), Expect = 2e-06
 Identities = 11/60 (18%), Positives = 24/60 (40%), Gaps = 4/60 (6%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE 148
           CE C+     ++  V ++       +H  CF C+ C +   + +++    + YC      
Sbjct: 14  CERCKGGFAPAEKIVNSN----GELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQM 69

>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 = 43.3 bits (102), Expect = 2e-06
 Identities = 9/29 (31%), Positives = 15/29 (51%)

Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYC 142
           WH  CF C  C+  LV   +  +  +++C
Sbjct: 31  WHSECFNCGKCSVSLVGKGFLTQNKEIFC 59

>1v6g_A Actin binding LIM protein 2; LIM domain, zinc binding domain, ablim2, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 81

 Score = 41.3 bits (97), Expect = 1e-05
 Identities = 12/59 (20%), Positives = 21/59 (35%), Gaps = 7/59 (11%)

Query: 89  CENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFY-RGDKLYCGRHH 146
           C +C+  ++   +S           +HP CF C+VC             G +  C +  
Sbjct: 18  CFSCDQFIEGEVVSAL------GKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCS 70

>2l4z_A DNA endonuclease RBBP8, LIM domain transcription LMO4; protein-protein interaction, LIM-interaction DOM LMO4, RBBP8/CTIP, LIM-only protein; HET: DNA; NMR {Homo sapiens} Length = 123

 Score = 42.4 bits (99), Expect = 1e-05
 Identities = 10/40 (25%), Positives = 15/40 (37%), Gaps = 2/40 (5%)

Query: 111 NSCWHPGCFTCSVCNELLVD--LIYFYRGDKLYCGRHHAE 148
           +S WH  C  CS C   L D     + +   + C   +  
Sbjct: 81  DSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIR 120

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

 Score = 40.5 bits (95), Expect = 3e-05
 Identities = 11/43 (25%), Positives = 17/43 (39%), Gaps = 1/43 (2%)

Query: 114 WHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA 156
           +HP  F C+ C + L          +LYC   H +      S+
Sbjct: 37  YHPDHFNCANCGKEL-TADARELKGELYCLPCHDKMGVSGPSS 78

>1vt4_I APAF-1 related killer DARK; drosophila apoptosome, apoptosis, programmed cell death; HET: DTP; 6.90A {Drosophila melanogaster} PDB: 3iz8_A* Length = 1221

 Score = 39.8 bits (92), Expect = 5e-04
 Identities = 48/307 (15%), Positives = 84/307 (27%), Gaps = 111/307 (36%)

Query: 4   PSKRCSMVHLYFSSLPEDKVPY----VNSPGEQYRIRQLLHQLPPHDNEVRY-------- 51
           PS    M       L  D   +    V+      ++RQ L +L P  N +          
Sbjct: 105 PSMMTRMYIEQRDRLYNDNQVFAKYNVSRLQPYLKLRQALLELRPAKNVLIDGVLGSGKT 164

Query: 52  CHALS--EDERKELRL--------FSAQRKREALGRGFVKQL------VAPMFCENCE-- 93
             AL      + + ++               E +    ++ L      + P +    +  
Sbjct: 165 WVALDVCLSYKVQCKMDFKIFWLNLKNCNSPETV----LEMLQKLLYQIDPNWTSRSDHS 220

Query: 94  -------DELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHH 146
                    +Q     +  S+   N               LLV L        +     +
Sbjct: 221 SNIKLRIHSIQAELRRLLKSKPYENC--------------LLV-L------LNVQ----N 255

Query: 147 AETLKPRCSACDEECQTSSQDILYYLTRDSE--RDLPDEYRTE-RLEHQR---------- 193
           A+       A +  C+     +L   TR  +    L     T   L+H            
Sbjct: 256 AKAWN----AFNLSCKI----LL--TTRFKQVTDFLSAATTTHISLDHHSMTLTPDEVKS 305

Query: 194 -----------DLP-ESYGTHRNSLN------KEQNHSFDNLLKSNLKKLSLADSDDVSS 235
                      DLP E   T+   L+      ++   ++DN    N  KL+      + S
Sbjct: 306 LLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTI----IES 361

Query: 236 SMPELTT 242
           S+  L  
Sbjct: 362 SLNVLEP 368

>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 = 36.0 bits (83), Expect = 9e-04
 Identities = 10/36 (27%), Positives = 16/36 (44%), Gaps = 2/36 (5%)

Query: 111 NSCWH--PGCFTCSVCNELLVDLIYFYRGDKLYCGR 144
           N  WH    CF CS C++ L+   +      ++C  
Sbjct: 23  NFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSV 58

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	242
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.91
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.91
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.91
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.89
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.88
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.88
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.85
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.85
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.78
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.68
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.66
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.65
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.65
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.65
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.64
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.64
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.64
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.61
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.61
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.6
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.6
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.6
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.6
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.59
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.59
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.58
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.58
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.57
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.56
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.56
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.56
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.55
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.55
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.54
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.54
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.53
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.53
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.53
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.53
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.53
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.51
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.5
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.47
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.46
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.43
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.43
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.43
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.41
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.4
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.38
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.25
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.24
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.22
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.22
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.21
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.19
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.19
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.13
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.13
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.1
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.1
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.08
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.05
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.04
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.03
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.02
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.02
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.01
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.0
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	98.98
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	98.97
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	98.96
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	98.96
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	98.95
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	98.95
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	98.94
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	98.93
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	98.91
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	98.85
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	98.85
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	98.84
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	98.77
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	98.77
2co8_A	82	NEDD9 interacting protein with calponin homology a	98.59
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	97.59
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	95.42

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

Probab=99.91  E-value=2.6e-25  Score=185.70  Aligned_cols=128  Identities=16%  Similarity=0.245  Sum_probs=108.3

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCC------------
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPR------------  153 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~pr------------  153 (242)
                      ..+|.+|+++|..++.+.     ++++.||++||+|..|+++|.+..|+.+||++||+.||.++|+|+            
T Consensus         7 ~~~C~~C~~~I~~~~~v~-----a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~c~~c~~~~g~~~   81 (192)
T 1b8t_A            7 GKKCGVCQKAVYFAEEVQ-----CEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGTLS   81 (192)
T ss_dssp             CEECTTTCCEECSSCCEE-----ETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCCCC
T ss_pred             CCcCccCCCeecceeEEE-----eCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCccccccccccccEe
Confidence            347999999998776543     689999999999999999999989999999999999999999987            


Q ss_pred             ------------------------------------cccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CC
Q psy8090         154 ------------------------------------CSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DL  195 (242)
Q Consensus       154 ------------------------------------C~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~  195 (242)
                                                          |++|+++|.++..             +.+.++.||.+||.  .+
T Consensus        82 ~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~C~~C~~~I~~~~~-------------v~a~~~~~H~~CF~C~~C  148 (192)
T 1b8t_A           82 TDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAEK-------------VIGAGKSWHKSCFRCAKC  148 (192)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECTTTSCEECSSSC-------------EEETTEEECTTTCBCTTT
T ss_pred             cCCCcccccccccccccCCCCcCccccccccCCCCcCCCCCCEecCcEE-------------EecCCCccchhcCCcccc
Confidence                                                5667777765431             23478999999993  24


Q ss_pred             CCCCCCCCcccCCCCCCCHHHHhhhhcccccCCCCC
Q psy8090         196 PESYGTHRNSLNKEQNHSFDNLLKSNLKKLSLADSD  231 (242)
Q Consensus       196 ~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~~~~~~  231 (242)
                      ..++.+..|..+++++||..||.++|++||..++..
T Consensus       149 ~~~L~~~~~~~~~g~~yC~~cy~~~f~~kc~~C~~~  184 (192)
T 1b8t_A          149 GKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQG  184 (192)
T ss_dssp             CCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCC
T ss_pred             CCCCCCCcccccCCEEeCHHHHHHhcCCcCCCCCCc
Confidence            567777789999999999999999999999988765

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

Probab=99.91  E-value=8.4e-26  Score=177.28  Aligned_cols=121  Identities=15%  Similarity=0.337  Sum_probs=102.1

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCC--CccceeeCCeeccHhhhhcccCC--CcccCCCccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV--DLIYFYRGDKLYCGRHHAETLKP--RCSACDEECQ  162 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~--~~~~~~~dg~~yC~~~y~~~~~p--rC~~C~~~I~  162 (242)
                      .+|.+|+++|.+.+ ++.    ++++.||++||+|..|+++|.  +..|+.+||++||+.||.++|++  +|.+|+++|.
T Consensus         3 ~~C~~C~~~I~~~~-~~~----a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~   77 (131)
T 2xjy_A            3 LTCGGCQQNIGDRY-FLK----AIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIR   77 (131)
T ss_dssp             CBBTTTCCBCCSSE-EEE----ETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEEC
T ss_pred             ccCcCCCCEeCCcE-EEE----ECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccC
Confidence            47999999999754 344    789999999999999999995  47899999999999999999999  9999999998


Q ss_pred             CCCcceeeeeecCCCCCCCCCCCcccCCCccC--CCCCC-CCCCcccCCCCCCCHHHHhhhhccc
Q psy8090         163 TSSQDILYYLTRDSERDLPDEYRTERLEHQRD--LPESY-GTHRNSLNKEQNHSFDNLLKSNLKK  224 (242)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~-g~~~f~~~d~~~yC~~cy~~~~a~k  224 (242)
                      +.+..+            .+.++.||.+||.+  +..++ .+..|...++++||..||.++|+++
T Consensus        78 ~~e~~~------------~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~~~  130 (131)
T 2xjy_A           78 AYEMTM------------RVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKIN  130 (131)
T ss_dssp             TTSEEE------------EETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHHHHHH
T ss_pred             ccceeE------------eeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHHhhcc
Confidence            754222            33789999999942  34566 3667888999999999999999865

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

Probab=99.91  E-value=2e-25  Score=174.04  Aligned_cols=119  Identities=16%  Similarity=0.225  Sum_probs=102.5

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQ  166 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~  166 (242)
                      .+|.+|+++|..++.+ .    ++++.||++||+|..|+++|.+..|+.+||++||..||.++|+++|++|+++|.+++.
T Consensus         4 ~~C~~C~~~I~~~~~~-~----a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~   78 (126)
T 2xqn_T            4 PRCAGCDELIFSNEYT-Q----AENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEVQ   78 (126)
T ss_dssp             CBBTTTSSBCCSSCEE-E----ETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCTTTCSBCCTTSC
T ss_pred             CCCccCCCEeCCceEE-e----eCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCcccCCcCCcCce
Confidence            3799999999976643 3    7899999999999999999998899999999999999999999999999999997553


Q ss_pred             ceeeeeecCCCCCCCCCCCccc--CCCccC--CCCCCCCCCcccCCCCCCCHHHHhhhhc
Q psy8090         167 DILYYLTRDSERDLPDEYRTER--LEHQRD--LPESYGTHRNSLNKEQNHSFDNLLKSNL  222 (242)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~h--~~~f~~--~~~~~g~~~f~~~d~~~yC~~cy~~~~a  222 (242)
                      .|            .+.++.||  .+||.+  +..++.+..|.+.++++||..+|.+.|+
T Consensus        79 ~~------------~a~~~~~H~~~~CF~C~~C~~~l~~~~f~~~~~~~yC~~~~~~~f~  126 (126)
T 2xqn_T           79 RV------------TYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRMS  126 (126)
T ss_dssp             EE------------EETTEEEESSTTTSBCTTTCCBCTTSEEEEETTEEESSHHHHHSCC
T ss_pred             EE------------ECCCCEeeCCCCCcCcCCCCCccCCCeeEeECCEEcchHHhhhhcC
Confidence            22            33679999  999932  4567888899999999999988887763

>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=99.89  E-value=1.8e-24  Score=180.07  Aligned_cols=126  Identities=15%  Similarity=0.258  Sum_probs=100.7

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCC--ccceeeCCeeccHhhhhcccCC--CcccCCCccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVD--LIYFYRGDKLYCGRHHAETLKP--RCSACDEECQ  162 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~--~~~~~~dg~~yC~~~y~~~~~p--rC~~C~~~I~  162 (242)
                      .+|.+|+++|.+.. ++.    ++++.||++||+|..|+++|.+  ..||.+||++||+.||.++|++  +|.+|+++|.
T Consensus         6 ~~C~~C~~~I~~~~-~~~----a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~   80 (188)
T 1rut_X            6 KRCAGCGGKIADRF-LLY----AMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIP   80 (188)
T ss_dssp             CBBTTTCCBCCCSE-EEE----ETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEEC
T ss_pred             CcCccCCCEeCCce-eEE----ecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCccc
Confidence            47999999999754 343    6899999999999999999975  6899999999999999999999  7999999998


Q ss_pred             CCCcceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCC-CCCcccCCCCCCCHHHHhhhhcccccCCC
Q psy8090         163 TSSQDILYYLTRDSERDLPDEYRTERLEHQRD--LPESYG-THRNSLNKEQNHSFDNLLKSNLKKLSLAD  229 (242)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g-~~~f~~~d~~~yC~~cy~~~~a~kc~~~~  229 (242)
                      +.+..    +        .+.++.||.+||.+  +...+. +..|...++++||..||.++++++|...+
T Consensus        81 ~~e~~----i--------~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~~~~~~~g  138 (188)
T 1rut_X           81 ASELV----M--------RAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHLNSG  138 (188)
T ss_dssp             TTSEE----E--------EETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC-------
T ss_pred             cCcEE----E--------EcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhcccccccC
Confidence            75422    2        33678999999943  345664 56788999999999999999999986443

>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=99.88  E-value=1.7e-23  Score=171.31  Aligned_cols=121  Identities=15%  Similarity=0.314  Sum_probs=98.5

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQ  166 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~  166 (242)
                      .+|.+|+++|.+.++ +.    ++++.||++||+|..|+++|.+.. |.+||++||+.||.++|+++|.+|+++|.+.+.
T Consensus         7 ~~C~~C~~~I~~~~~-~~----a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~~~C~~C~~~I~~~~~   80 (169)
T 2rgt_A            7 PMCAGCDQHILDRFI-LK----ALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQV   80 (169)
T ss_dssp             CBBSSSSSBCCSSSC-EE----CSSCEECTTTSBCTTTCCBCCSCC-EESSSCEECHHHHHHHHSCBCTTTCCBCCTTSE
T ss_pred             CccccCCCccCCcEE-EE----ECCcEEccccCccCCCCCcCCCCC-cccCCeeeecccccccccccccccccccCCCcE
Confidence            479999999997543 43    789999999999999999998755 689999999999999999999999999987652


Q ss_pred             ceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCC-CCCc-ccCCCCCCCHHHHhhhhcccc
Q psy8090         167 DILYYLTRDSERDLPDEYRTERLEHQRD--LPESYG-THRN-SLNKEQNHSFDNLLKSNLKKL  225 (242)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g-~~~f-~~~d~~~yC~~cy~~~~a~kc  225 (242)
                      .+            .+.++.||.+||.+  +...+. +..| ...++++||..||.+.++..+
T Consensus        81 v~------------~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~~~~~  131 (169)
T 2rgt_A           81 VR------------RAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGGS  131 (169)
T ss_dssp             EE------------EETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHHHCC-
T ss_pred             EE------------EcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHhhccC
Confidence            11            34678999999932  345564 4444 567999999999999887643

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

Probab=99.88  E-value=4.3e-23  Score=170.85  Aligned_cols=117  Identities=15%  Similarity=0.332  Sum_probs=95.4

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCC
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSS  165 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~  165 (242)
                      ..+|.+|+++|.+.+. +.    ++++.||+.||+|..|+++|.+.. |.+||++||..||.++|+++|.+|+++|.+.+
T Consensus        60 ~~~C~~C~~~I~~~~~-~~----a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~~kC~~C~~~I~~~~  133 (182)
T 2jtn_A           60 IPMCAGCDQHILDRFI-LK----ALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQ  133 (182)
T ss_dssp             CCBCBTSSSBCCCSEE-EE----ETTEEECSSTTSCTTTCCCCSSCC-EEETTEEECHHHHHHTTSCCCTTTCCCCCSSC
T ss_pred             CCcCccCCCCccCcee-EE----ecCCeEccccCccCCCCCccCCCc-eeECCEeeecCccccccccccccCCCccCCCc
Confidence            4589999999997543 33    689999999999999999998755 68999999999999999999999999998754


Q ss_pred             cceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCC-CCCc-ccCCCCCCCHHHHhhh
Q psy8090         166 QDILYYLTRDSERDLPDEYRTERLEHQRD--LPESYG-THRN-SLNKEQNHSFDNLLKS  220 (242)
Q Consensus       166 ~~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g-~~~f-~~~d~~~yC~~cy~~~  220 (242)
                      ..            +.+.++.||.+||.+  +..++. +..| ...++++||..||.+.
T Consensus       134 ~v------------~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~~  180 (182)
T 2jtn_A          134 VV------------RRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETA  180 (182)
T ss_dssp             CC------------CEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHHH
T ss_pred             eE------------EecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHHh
Confidence            21            234778999999932  345565 3444 5679999999999874

>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=99.85  E-value=2.2e-22  Score=156.43  Aligned_cols=108  Identities=11%  Similarity=0.192  Sum_probs=90.9

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCC--CccceeeCCeeccHhhhhcccCC--CcccCCCccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV--DLIYFYRGDKLYCGRHHAETLKP--RCSACDEECQ  162 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~--~~~~~~~dg~~yC~~~y~~~~~p--rC~~C~~~I~  162 (242)
                      .+|.+|+++|.+.+. +.    ++++.||++||+|..|+++|.  +..||.+||++||..||.++|++  +|++|+++|.
T Consensus         6 ~~C~~C~~~I~~~~~-~~----a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~   80 (122)
T 1m3v_A            6 KRCAGCGGKIADRFL-LY----AMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGS   80 (122)
T ss_dssp             CCBSSSSSCCCSSCC-EE----ETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSC
T ss_pred             CCCcccCCEeCCcEE-EE----ECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcC
Confidence            379999999998754 33    689999999999999999997  46899999999999999999999  9999999999


Q ss_pred             CCCcceeeeeecCCCCCCCCCCCcccCCCccCCCCCCCCCCcccCCCCCCCHHHHhhhhccc
Q psy8090         163 TSSQDILYYLTRDSERDLPDEYRTERLEHQRDLPESYGTHRNSLNKEQNHSFDNLLKSNLKK  224 (242)
Q Consensus       163 ~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~k  224 (242)
                      ++.      +        .+.++           ..+.++.|+.+++++||..||.+.++.+
T Consensus        81 ~~~------~--------~~~g~-----------~~l~g~~f~~~~~~~yC~~~~~~~~~~~  117 (122)
T 1m3v_A           81 GGD------V--------MVVGE-----------PTLMGGEFGDEDERLITRLENTQFDAAN  117 (122)
T ss_dssp             CEE------S--------SSSSS-----------SSCCSCTTCCTTCCCCEECTTTTTTCCS
T ss_pred             chh------e--------EEcCC-----------cCCCCCccEecCCEeEccCcchhchhhc
Confidence            743      1        11222           1467889999999999999999886554

>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=99.85  E-value=8.6e-22  Score=147.61  Aligned_cols=92  Identities=18%  Similarity=0.448  Sum_probs=79.9

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCCc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSSQ  166 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~~  166 (242)
                      .+|.+|+++|..+..++.    ++++.||++||+|..|+++|.+..|+.+||++||..||.++|+++|.+|+++|.+++.
T Consensus         6 ~~C~~C~~~I~~~~~~~~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~   81 (101)
T 2cup_A            6 SGCVECRKPIGADSKEVH----YKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQ   81 (101)
T ss_dssp             CBCSSSCCBCCSSSCEEE----ETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCSSSCCBCCSSSC
T ss_pred             CcCcccCCcccCCceEEE----ECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccccCCCccccCCe
Confidence            479999999986444454    6899999999999999999998889999999999999999999999999999997653


Q ss_pred             ceeeeeecCCCCCCCCCCCcccCCCccC
Q psy8090         167 DILYYLTRDSERDLPDEYRTERLEHQRD  194 (242)
Q Consensus       167 ~~~~~~~~~~~~~~~~~~~~~h~~~f~~  194 (242)
                      .            +.+.++.||.+||.+
T Consensus        82 ~------------~~a~~~~~H~~CF~C   97 (101)
T 2cup_A           82 N------------VEYKGTVWHKDCFSG   97 (101)
T ss_dssp             E------------EESSSCEEETTTCCC
T ss_pred             E------------EEeCCcchHHhCCCC
Confidence            2            234789999999954

>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=99.78  E-value=1.6e-19  Score=138.63  Aligned_cols=104  Identities=12%  Similarity=0.216  Sum_probs=83.5

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCC--ccceeeCCeeccHhhhhcccCCCcccCCCcccCC
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVD--LIYFYRGDKLYCGRHHAETLKPRCSACDEECQTS  164 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~--~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~  164 (242)
                      .+|.+|+++|.+.+. +.    ++++.||++||+|..|+++|.+  ..||.+||++||+.||.++|+|+|..|..    +
T Consensus         4 ~~C~~C~~~I~~~~~-~~----a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c~~----~   74 (114)
T 1j2o_A            4 LTCGGCQQNIGDRYF-LK----AIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGSG----G   74 (114)
T ss_dssp             BCBSSSCSCBCSSEE-EE----CSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSCBS----C
T ss_pred             CCCcCCCCeeCCcEE-EE----ECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcCCC----C
Confidence            479999999997543 44    7899999999999999999975  68999999999999999999999998862    1


Q ss_pred             CcceeeeeecCCCCCCCCCCCcccCCCccCCCCCCCCCCcccCCCCCCCHHHHhhhhccc
Q psy8090         165 SQDILYYLTRDSERDLPDEYRTERLEHQRDLPESYGTHRNSLNKEQNHSFDNLLKSNLKK  224 (242)
Q Consensus       165 ~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~k  224 (242)
                      .     ++        . +.           ...+.++.|+.+++++||..||.+..+..
T Consensus        75 ~-----~~--------~-~~-----------~~~~~g~~f~~~~~~~~C~~~~~~~~~~~  109 (114)
T 1j2o_A           75 D-----VM--------V-VG-----------EPTLMGGEFGDEDERLITRLENTQFDAAN  109 (114)
T ss_dssp             S-----CC--------C-SS-----------CSSTTSSBCCCSSSCCCEEEECTTCCCTT
T ss_pred             c-----ee--------E-cC-----------CccCCCCeeEEcCCEeecchhhhcccccc
Confidence            1     01        0 11           12356778999999999999988765443

>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=99.68  E-value=1.5e-17  Score=118.31  Aligned_cols=70  Identities=19%  Similarity=0.385  Sum_probs=63.6

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccH-hhhhcccCCCcccCCCccc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCG-RHHAETLKPRCSACDEECQ  162 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~-~~y~~~~~prC~~C~~~I~  162 (242)
                      +|.+|+++|..++.+.     ++++.||++||+|..|+++|.+..|+.+||++||. .||.++|+++|++|++.+.
T Consensus         2 ~C~~C~~~I~~~~~v~-----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~~C~~~~~   72 (76)
T 1iml_A            2 KCPKCDKEVYFAERVT-----SLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGGAES   72 (76)
T ss_dssp             BCTTTSSBCCGGGEEE-----ETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSCCCSSS
T ss_pred             cCCCCCCEEECceEEE-----ECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCCCcCCcee
Confidence            6999999999776643     67999999999999999999988999999999999 5999999999999997764

>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=99.66  E-value=2.2e-17  Score=118.81  Aligned_cols=71  Identities=17%  Similarity=0.371  Sum_probs=55.3

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcc
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEEC  161 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I  161 (242)
                      ..+|.+|+++|..++.+ .    +.++.||++||+|..|+++|.+..|+.+|+++||..||.++|+|+|.+|++..
T Consensus         7 ~~~C~~C~~~I~~~~~~-~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~gcg~g~   77 (81)
T 1a7i_A            7 GNKCGACGRTVYHAEEV-Q----CDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGYGYGQGA   77 (81)
T ss_dssp             -CBCSSSCCBCSSTTEE-E----ETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC----------
T ss_pred             CCcCcCcCccccCceeE-E----eCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCcccccCCcc
Confidence            34799999999877654 3    68999999999999999999988899999999999999999999999998764

>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=99.65  E-value=7.3e-17  Score=116.23  Aligned_cols=66  Identities=23%  Similarity=0.632  Sum_probs=59.3

Q ss_pred             cccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090          85 APMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        85 ~~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      ....|.+|+++|..++.+.     ++++.||++||+|..|+++|.+ .||.+||++||+.||.++|+++|++
T Consensus        14 ~~~~C~~C~~~I~~~~~v~-----a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C~~   79 (80)
T 2dj7_A           14 GPSHCAGCKEEIKHGQSLL-----ALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPSS   79 (80)
T ss_dssp             SCSCCTTTCCCCSSSCCEE-----ETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCSTT
T ss_pred             CCCCCcCcCCeeCCCeEEE-----ECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCCCC
Confidence            3457999999998776644     6899999999999999999986 7999999999999999999999975

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

Probab=99.65  E-value=1.1e-16  Score=112.39  Aligned_cols=66  Identities=20%  Similarity=0.395  Sum_probs=60.0

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      .+|.+|+++|.+++.++.    ++++.||++||+|..|+++|.+..|+.++|++||..||.++|+|+|++
T Consensus         6 ~~C~~C~~~I~~~~~~~~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1wyh_A            6 SGCSACGETVMPGSRKLE----YGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGPSS   71 (72)
T ss_dssp             CBCSSSCCBCCSSSCEEC----STTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCCCC
T ss_pred             CCCccCCCccccCccEEE----ECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcCCC
Confidence            379999999998655554    789999999999999999999889999999999999999999999974

>1x4k_A Skeletal muscle LIM-protein 3; LIM domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.65  E-value=8.8e-17  Score=112.88  Aligned_cols=66  Identities=17%  Similarity=0.425  Sum_probs=60.3

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      .+|.+|+++|.+++.++.    ++++.||++||+|..|+++|.+..|+.+||++||..||.++|+|+|+.
T Consensus         6 ~~C~~C~~~I~~~~~~~~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1x4k_A            6 SGCQECKKTIMPGTRKME----YKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGPSS   71 (72)
T ss_dssp             CCBSSSCCCCCSSSCEEE----ETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCCCC
T ss_pred             CCCccCCCcccCCceEEE----ECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCCCC
Confidence            379999999998765565    689999999999999999999889999999999999999999999974

>1x68_A FHL5 protein; four-and-A-half LIM protein 5, zinc finger domain, AN actin- interacting protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3

Probab=99.64  E-value=7.3e-17  Score=114.79  Aligned_cols=68  Identities=18%  Similarity=0.446  Sum_probs=61.0

Q ss_pred             cccccCCCceec--CccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCC
Q psy8090          87 MFCENCEDELQT--SDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACD  158 (242)
Q Consensus        87 ~~C~~C~~~I~~--~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~  158 (242)
                      .+|.+|+++|.+  +..++.    ++++.||++||+|..|+++|.+..|+.+||++||..||.++|+++|+.+.
T Consensus         6 ~~C~~C~~~I~~~g~~~~~~----a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C~~~s   75 (76)
T 1x68_A            6 SGCVACSKPISGLTGAKFIC----FQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISGPSS   75 (76)
T ss_dssp             CCCTTTCCCCCTTTTCCEEE----ETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSSSSSC
T ss_pred             CCCccCCCcccCCCCceeEE----ECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcCCCCC
Confidence            379999999996  334454    78999999999999999999998999999999999999999999999874

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

Probab=99.64  E-value=1.2e-16  Score=113.65  Aligned_cols=66  Identities=18%  Similarity=0.499  Sum_probs=58.6

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcc
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCS  155 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~  155 (242)
                      ...|.+|+++|.+++.++.    +.++.||++||+|..|+++|.+..|+.+||++||+.||.++|+|+|+
T Consensus        11 ~~~C~~C~~~I~~~~~~~~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C~   76 (77)
T 1g47_A           11 SATCERCKGGFAPAEKIVN----SNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCWI   76 (77)
T ss_dssp             CCBCSSSCCBCCSTTTCEE----ETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC--
T ss_pred             CCCchhcCCccCCCceEEE----eCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcccC
Confidence            3479999999997666665    67999999999999999999988999999999999999999999996

>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=99.64  E-value=1.4e-16  Score=113.16  Aligned_cols=66  Identities=18%  Similarity=0.339  Sum_probs=59.8

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccH-hhhhcccCCCccc
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCG-RHHAETLKPRCSA  156 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~-~~y~~~~~prC~~  156 (242)
                      ..+|.+|+++|..++.+.     ++++.||++||+|..|+++|.+..|+.+|+++||. .||.++|+|+|.+
T Consensus         9 ~~~C~~C~~~I~~~~~v~-----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~kc~g   75 (76)
T 2cu8_A            9 ASKCPKCDKTVYFAEKVS-----SLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGPSS   75 (76)
T ss_dssp             CCBCTTTCCBCCTTTEEE-----ETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSSCSC
T ss_pred             CCCCcCCCCEeECCeEEE-----ECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccccCC
Confidence            347999999999777643     68999999999999999999988999999999999 7999999999974

>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=99.61  E-value=4e-16  Score=112.38  Aligned_cols=65  Identities=22%  Similarity=0.543  Sum_probs=59.6

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      +|.+|+++|.+++.++.    ++++.||++||+|..|+++|.+..|+.+++++||..||.++|+++|++
T Consensus        17 ~C~~C~~~I~~~~~~~~----a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C~~   81 (82)
T 2ehe_A           17 TCAECQQLIGHDSRELF----YEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGPSS   81 (82)
T ss_dssp             BCTTTCCBCCSSCCBCC----CSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGGGSSCC
T ss_pred             cCccCCCccccCcEEEE----eCCccccccCCeecCCCCccCCCccEeeCCEEECHHHHhhhcCCCCCC
Confidence            79999999996556564    789999999999999999999989999999999999999999999974

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

Probab=99.61  E-value=4e-16  Score=109.01  Aligned_cols=64  Identities=25%  Similarity=0.492  Sum_probs=58.0

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      .+|.+|+++|.+. . +.    ++++.||++||+|..|+++|.+..|+.+|+++||..||.++|+|+|++
T Consensus         6 ~~C~~C~~~I~~~-~-~~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~~   69 (70)
T 2d8z_A            6 SGCVQCKKPITTG-G-VT----YREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPSS   69 (70)
T ss_dssp             CBCSSSCCBCCSS-E-EE----SSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCTT
T ss_pred             CCCcccCCeeccc-e-EE----ECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccCC
Confidence            3799999999863 3 43    789999999999999999999889999999999999999999999974

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

Probab=99.60  E-value=5.6e-16  Score=108.89  Aligned_cols=64  Identities=20%  Similarity=0.482  Sum_probs=57.7

Q ss_pred             cccccCCCceec--CccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCc
Q psy8090          87 MFCENCEDELQT--SDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRC  154 (242)
Q Consensus        87 ~~C~~C~~~I~~--~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC  154 (242)
                      .+|.+|+++|.+  ++.++.    ++++.||++||+|..|+++|.+..|+.+||++||..||.++|+|++
T Consensus         6 ~~C~~C~~~I~~~~~~~~~~----a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p~~   71 (72)
T 1x4l_A            6 SGCAGCTNPISGLGGTKYIS----FEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPSS   71 (72)
T ss_dssp             CSBTTTTBCCCCSSSCSCEE----CSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCSSC
T ss_pred             CCCcCCCccccCCCCcceEE----ECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCCCC
Confidence            479999999996  445554    7899999999999999999999899999999999999999999986

>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=99.60  E-value=3.5e-16  Score=112.11  Aligned_cols=78  Identities=12%  Similarity=0.091  Sum_probs=67.2

Q ss_pred             CCeeccHhhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCH
Q psy8090         137 GDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSF  214 (242)
Q Consensus       137 dg~~yC~~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~  214 (242)
                      +|++||+.||.++++++|++|+++|.+..              +.+.++.||.+||.  .+..++.+..|...++++||.
T Consensus         1 gg~~yC~~cy~~~~~~~C~~C~~~I~~~~--------------v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~   66 (80)
T 2cuq_A            1 GSSGSSGPCYENKFAPRCARCSKTLTQGG--------------VTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCV   66 (80)
T ss_dssp             CCCCSCCCCCCCCSSCCCTTTCCCCCSCC--------------EESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEH
T ss_pred             CCcEEcHHHHccccCCcCCCCCCEecCcE--------------EEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECH
Confidence            58999999999999999999999998631              24478999999993  245677788899999999999


Q ss_pred             HHHhhhhcccccCC
Q psy8090         215 DNLLKSNLKKLSLA  228 (242)
Q Consensus       215 ~cy~~~~a~kc~~~  228 (242)
                      .||.++|+++|+++
T Consensus        67 ~cy~~~f~~~c~s~   80 (80)
T 2cuq_A           67 ACFGELFASGPSSG   80 (80)
T ss_dssp             HHHHHHTTCSTTCC
T ss_pred             HHHHHHcCCCCCCC
Confidence            99999999999864

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

Probab=99.60  E-value=3.9e-16  Score=108.79  Aligned_cols=64  Identities=20%  Similarity=0.478  Sum_probs=57.9

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      .+|.+|+++|.+ +. +.    ++++.||++||+|..|+++|.+..|+.+|+++||..||.++|+++|++
T Consensus         6 ~~C~~C~~~I~~-~~-~~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~g   69 (69)
T 2cur_A            6 SGCVKCNKAITS-GG-IT----YQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSSG   69 (69)
T ss_dssp             CCCSSSCCCCCT-TC-EE----ETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSCCC
T ss_pred             CCCcccCCEeCc-ce-EE----ECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCCCC
Confidence            379999999986 33 33    679999999999999999999889999999999999999999999975

>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=99.60  E-value=7.9e-16  Score=113.15  Aligned_cols=68  Identities=24%  Similarity=0.485  Sum_probs=61.2

Q ss_pred             cccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccC
Q psy8090          85 APMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSAC  157 (242)
Q Consensus        85 ~~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C  157 (242)
                      ....|.+|+++|.+++.+ .    ++++.||++||+|..|+++|.+..|+.+|+++||..||.++|+++|..+
T Consensus        14 ~~~~C~~C~~~I~~~~~v-~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~   81 (91)
T 2d8y_A           14 ARETCVECQKTVYPMERL-L----ANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYD   81 (91)
T ss_dssp             SSCBCTTTCCBCCTTSEE-E----CSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCC
T ss_pred             CCCcCccCCCccCCceeE-E----ECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCcc
Confidence            345899999999987764 3    7899999999999999999998889999999999999999999999843

>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=99.59  E-value=1.1e-15  Score=109.90  Aligned_cols=66  Identities=27%  Similarity=0.635  Sum_probs=60.3

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      .+|.+|+++|..++.++.    ++++.||++||+|..|+++|.+..|+.+++++||..||.++|+|+|..
T Consensus        16 ~~C~~C~~~I~~~~~~~~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~~   81 (82)
T 1x63_A           16 PKCKGCFKAIVAGDQNVE----YKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPSS   81 (82)
T ss_dssp             CBCSSSCCBCCSSSCEEE----CSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCSC
T ss_pred             CcCccCCcccccCceEEE----ECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCCC
Confidence            379999999998776665    789999999999999999999889999999999999999999999863

>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=99.59  E-value=7.3e-16  Score=113.12  Aligned_cols=64  Identities=19%  Similarity=0.516  Sum_probs=57.6

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      .+|.+|+++|.+ +. +.    ++++.||++||+|..|+++|.+..|+.++|++||..||.++|+|+|+.
T Consensus        26 ~~C~~C~~~I~~-~~-v~----a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c~s   89 (90)
T 2dar_A           26 PMCAHCNQVIRG-PF-LV----ALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPSS   89 (90)
T ss_dssp             CBBSSSCCBCCS-CE-EE----ETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCCCC
T ss_pred             CCCccCCCEecc-eE-EE----ECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCCCC
Confidence            479999999964 33 43    689999999999999999999889999999999999999999999974

>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=99.58  E-value=8.6e-16  Score=106.12  Aligned_cols=61  Identities=20%  Similarity=0.487  Sum_probs=55.2

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCC
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPR  153 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~pr  153 (242)
                      ..|.+|+++|. ++. +.    ++++.||++||+|..|+++|.+..|+.+||++||..||.++|+|+
T Consensus         6 ~~C~~C~~~I~-~~~-~~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~k   66 (66)
T 1nyp_A            6 PICGACRRPIE-GRV-VN----AMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGDV   66 (66)
T ss_dssp             CEETTTTEECC-SCE-EC----CTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSCC
T ss_pred             CCCcccCCEec-ceE-EE----ECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHhCCC
Confidence            37999999999 444 43    789999999999999999999989999999999999999999875

>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=99.58  E-value=3.5e-16  Score=112.69  Aligned_cols=80  Identities=16%  Similarity=0.082  Sum_probs=68.6

Q ss_pred             CCeeccHhhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCH
Q psy8090         137 GDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSF  214 (242)
Q Consensus       137 dg~~yC~~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~  214 (242)
                      +|++||+.||.++|+++|++|+++|.+.+.            .+.+.++.||.+||.  .+..++.+..|...++++||.
T Consensus         1 ~g~~yC~~~y~~~~~~~C~~C~~~I~~~~~------------~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~   68 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFANTCAECQQLIGHDSR------------ELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCN   68 (82)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSSCC------------BCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEET
T ss_pred             CCceechhHhCcccCCcCccCCCccccCcE------------EEEeCCccccccCCeecCCCCccCCCccEeeCCEEECH
Confidence            689999999999999999999999985332            145578999999993  245678888899999999999


Q ss_pred             HHHhhhhcccccCC
Q psy8090         215 DNLLKSNLKKLSLA  228 (242)
Q Consensus       215 ~cy~~~~a~kc~~~  228 (242)
                      .||.++|++||+.+
T Consensus        69 ~c~~~~~~~~C~~~   82 (82)
T 2ehe_A           69 DCYCSAFSSGPSSG   82 (82)
T ss_dssp             TTSSCCGGGSSCCC
T ss_pred             HHHhhhcCCCCCCC
Confidence            99999999999864

>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=99.57  E-value=2.3e-15  Score=110.25  Aligned_cols=65  Identities=28%  Similarity=0.578  Sum_probs=58.2

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      ..+|.+|++.|.+ + ++.    ++++.||++||+|..|++.|.+..||.+|+++||+.||.++|+|+|.+
T Consensus        25 ~~~C~~C~~~I~~-~-~~~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~~g   89 (89)
T 1x64_A           25 MPLCDKCGSGIVG-A-VVK----ARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSSG   89 (89)
T ss_dssp             CCBCTTTCCBCCS-C-CEE----SSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCCCC
T ss_pred             CCCcccCCCEecc-c-EEE----ECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCCC
Confidence            3479999999996 3 344    789999999999999999999889999999999999999999999863

>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=99.56  E-value=1.1e-15  Score=109.50  Aligned_cols=78  Identities=14%  Similarity=0.074  Sum_probs=66.6

Q ss_pred             CCeeccHhhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCH
Q psy8090         137 GDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSF  214 (242)
Q Consensus       137 dg~~yC~~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~  214 (242)
                      +|++||++||.++++++|++|+++|.+..              +.+.++.||.+||.  .+..++.+..|...++++||.
T Consensus         1 gg~~yC~~~y~~~~~~~C~~C~~~I~~~~--------------v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~   66 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFSPKCGGCNRPVLENY--------------LSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCE   66 (80)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSSC--------------EEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECH
T ss_pred             CCCccchhHHhhhcCCccccCCCeeccee--------------EEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECH
Confidence            47899999999999999999999998621              23478999999993  245677777899999999999


Q ss_pred             HHHhhhhcccccCC
Q psy8090         215 DNLLKSNLKKLSLA  228 (242)
Q Consensus       215 ~cy~~~~a~kc~~~  228 (242)
                      .||.++|+++|+.+
T Consensus        67 ~~y~~~f~~~C~~~   80 (80)
T 1x3h_A           67 LHYHHRRGSGPSSG   80 (80)
T ss_dssp             HHHHHHHSSSCCCC
T ss_pred             HHHHHHcCCCCCCC
Confidence            99999999999864

>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=99.56  E-value=1.8e-15  Score=106.15  Aligned_cols=66  Identities=23%  Similarity=0.530  Sum_probs=57.8

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccC
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSAC  157 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C  157 (242)
                      .+|.+|+++|.+++.++.    ++++.||++||+|..|+++|.+..|+.+|+++||..||.++| .+|..+
T Consensus         6 ~~C~~C~~~I~~~~~~~~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~-~~~~~~   71 (72)
T 1x61_A            6 SGCGGCGEDVVGDGAGVV----ALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATL-ESGPSS   71 (72)
T ss_dssp             CCCSSSCSCCCSSSCCEE----CSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHH-HTCSSC
T ss_pred             CCCccCCCccCCCceEEE----ECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHH-ccCCCC
Confidence            479999999998655555    789999999999999999999888999999999999999888 456554

>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=99.56  E-value=1.8e-15  Score=108.37  Aligned_cols=64  Identities=20%  Similarity=0.502  Sum_probs=58.0

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      ..|.+|+++|.+ +. +.    ++++.||+.||+|..|+++|.+..|+.+|+++||..||.++|+++|++
T Consensus        16 ~~C~~C~~~I~~-~~-v~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C~~   79 (80)
T 1x3h_A           16 PKCGGCNRPVLE-NY-LS----AMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGPSS   79 (80)
T ss_dssp             CBCTTTCCBCCS-SC-EE----ETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHHHSSSCCC
T ss_pred             CccccCCCeecc-ee-EE----ECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHHcCCCCCC
Confidence            379999999997 33 33    689999999999999999999889999999999999999999999975

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

Probab=99.55  E-value=1.5e-15  Score=108.83  Aligned_cols=65  Identities=25%  Similarity=0.537  Sum_probs=58.1

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      ..+|.+|+++|.+.  ++.    ++++.||++||+|..|+++|.+..|+.+|+++||..||.++|+|++.+
T Consensus        15 ~~~C~~C~~~I~~~--~~~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g~g   79 (79)
T 1x62_A           15 LPMCDKCGTGIVGV--FVK----LRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSSG   79 (79)
T ss_dssp             CCCCSSSCCCCCSS--CEE----CSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCCCC
T ss_pred             CCccccCCCCccCc--EEE----ECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCCC
Confidence            45899999999973  344    789999999999999999999888999999999999999999999753

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

Probab=99.55  E-value=5.6e-15  Score=105.92  Aligned_cols=62  Identities=23%  Similarity=0.397  Sum_probs=54.8

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCS  155 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~  155 (242)
                      .+|.+|+++|.+ +. +.    ++++.||++||+|..|+++|.+. +|.+||++||..||.++|+|+++
T Consensus        16 ~~C~~C~~~I~~-~~-v~----a~~~~~H~~CF~C~~C~~~L~~~-~f~~~g~~yC~~cy~~~f~p~~s   77 (79)
T 2cor_A           16 YICQKCHAIIDE-QP-LI----FKNDPYHPDHFNCANCGKELTAD-ARELKGELYCLPCHDKMGVSGPS   77 (79)
T ss_dssp             CBCTTTCCBCCS-CC-CC----CSSSCCCTTTSBCSSSCCBCCTT-CEEETTEEECHHHHHTTSCCSSC
T ss_pred             CCCccCCCEecc-eE-EE----ECcceeCCCCCEeCCCCCccCCC-CEeECCEEeCHHHHHHhCCCCCC
Confidence            479999999994 44 43    78999999999999999999876 67999999999999999999875

>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=99.54  E-value=3.5e-15  Score=106.82  Aligned_cols=64  Identities=23%  Similarity=0.478  Sum_probs=58.0

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      .+|.+|+++|.+. . +.    ++++.||++||+|..|+++|.+..|+.+|+++||..||.++|+|+|+.
T Consensus        16 ~~C~~C~~~I~~~-~-v~----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~s   79 (80)
T 2cuq_A           16 PRCARCSKTLTQG-G-VT----YRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPSS   79 (80)
T ss_dssp             CCCTTTCCCCCSC-C-EE----SSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCSTTC
T ss_pred             CcCCCCCCEecCc-E-EE----ECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCCCCC
Confidence            3799999999874 3 43    789999999999999999999889999999999999999999999974

>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=99.54  E-value=2.7e-15  Score=107.78  Aligned_cols=77  Identities=8%  Similarity=0.017  Sum_probs=64.6

Q ss_pred             CCeeccHhhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccC-CCCCCC
Q psy8090         137 GDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLN-KEQNHS  213 (242)
Q Consensus       137 dg~~yC~~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~-d~~~yC  213 (242)
                      ||++||+.||. +++++|++|+++|.+.      +        +.+.++.||.+||.  .+..++.+..|... ++++||
T Consensus         2 ~g~~yC~~~y~-~~~~~C~~C~~~I~~~------~--------~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC   66 (81)
T 2dlo_A            2 SSGSSGEGCYV-ATLEKCATCSQPILDR------I--------LRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHC   66 (81)
T ss_dssp             CCCCCCCCCCC-SSCCBCTTTCCBCCSC------C--------EEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEE
T ss_pred             cCCEECHHHhh-cCCCccccCCCeecce------e--------EEECCccccHHhcCcccCCCccCCCeeEECCCCEEEC
Confidence            78999999999 7999999999999842      1        23478999999993  24567888888876 789999


Q ss_pred             HHHHhhhhcccccCC
Q psy8090         214 FDNLLKSNLKKLSLA  228 (242)
Q Consensus       214 ~~cy~~~~a~kc~~~  228 (242)
                      ..||.++|++||+.+
T Consensus        67 ~~cy~~~f~~~C~~~   81 (81)
T 2dlo_A           67 IEDFHRKFASGPSSG   81 (81)
T ss_dssp             HHHHHHHTTSSSCCC
T ss_pred             HHHHHHHhcCcCCCC
Confidence            999999999999864

>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=99.53  E-value=3e-15  Score=107.69  Aligned_cols=80  Identities=13%  Similarity=0.044  Sum_probs=67.6

Q ss_pred             CCeeccHhhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCH
Q psy8090         137 GDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSF  214 (242)
Q Consensus       137 dg~~yC~~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~  214 (242)
                      ++.+||+.||.++++++|.+|+++|.+++.    +        +.+.++.||.+||.  .+..++.+..|..+++++||.
T Consensus         1 ~~~~yC~~cy~~~~~~~C~~C~~~I~~~~~----~--------~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~   68 (82)
T 1x63_A            1 GSSGSSGKCTTREDSPKCKGCFKAIVAGDQ----N--------VEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCV   68 (82)
T ss_dssp             CCSCCCCCCCSCCCSCBCSSSCCBCCSSSC----E--------EECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEH
T ss_pred             CCCcCchhHHccccCCcCccCCcccccCce----E--------EEECccccccccCchhhCCCccCCCccEeeCCEEECH
Confidence            468999999999999999999999987553    2        23478999999993  345678888899999999999


Q ss_pred             HHHhhhhcccccCC
Q psy8090         215 DNLLKSNLKKLSLA  228 (242)
Q Consensus       215 ~cy~~~~a~kc~~~  228 (242)
                      .||.++|++|++.+
T Consensus        69 ~cy~~~f~~~~~~g   82 (82)
T 1x63_A           69 TCHETKFASGPSSG   82 (82)
T ss_dssp             HHHHHHTSCCCSCC
T ss_pred             HHHHHHhCCCCCCC
Confidence            99999999998753

>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=99.53  E-value=3.8e-15  Score=107.03  Aligned_cols=64  Identities=22%  Similarity=0.503  Sum_probs=56.4

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceee-CCeeccHhhhhcccCCCccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYR-GDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~-dg~~yC~~~y~~~~~prC~~  156 (242)
                      .+|.+|+++|.+ . ++.    ++++.||++||+|..|+++|.+..|+.. ||++||..||.++|+|+|++
T Consensus        16 ~~C~~C~~~I~~-~-~~~----a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~~~C~~   80 (81)
T 2dlo_A           16 EKCATCSQPILD-R-ILR----AMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGPSS   80 (81)
T ss_dssp             CBCTTTCCBCCS-C-CEE----ETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTTSSSCC
T ss_pred             CccccCCCeecc-e-eEE----ECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhcCcCCC
Confidence            479999999985 3 444    6899999999999999999998777766 79999999999999999975

>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=99.53  E-value=6.1e-15  Score=102.98  Aligned_cols=63  Identities=25%  Similarity=0.626  Sum_probs=56.0

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCS  155 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~  155 (242)
                      .+|.+|+++|.+ +. +.    ++++.||++||+|..|+++|.+..|+.+||++||..||.++|+++..
T Consensus         6 ~~C~~C~~~I~~-~~-~~----a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~   68 (70)
T 2d8x_A            6 SGCHQCGEFIIG-RV-IK----AMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGPS   68 (70)
T ss_dssp             SBCSSSCCBCCS-CC-EE----ETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCCSC
T ss_pred             CcCccCCCEecc-eE-EE----ECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCCCC
Confidence            379999999985 33 43    68999999999999999999988899999999999999999998764

>3f6q_B LIM and senescent cell antigen-like-containing domain protein 1; ILK, integrin-linked kinase, pinch, ankyrin repeat, ANK, IPP; 1.60A {Homo sapiens} PDB: 2kbx_B 3ixe_B

Probab=99.53  E-value=4.1e-15  Score=103.93  Aligned_cols=62  Identities=18%  Similarity=0.517  Sum_probs=56.0

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccC
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLK  151 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~  151 (242)
                      ..+|.+|+++|.+++.++.    +.++.||++||+|..|+++|.+..|+.+||++||+.||.++|+
T Consensus        11 ~~~C~~C~~~i~~~e~~~~----~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B           11 SATCERCKGGFAPAEKIVN----SNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             TCBCTTTCCBCCTTCEEEE----ETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHTC
T ss_pred             CccchhcCccccCCceEEE----eCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhhC
Confidence            3479999999998877665    6799999999999999999988899999999999999998875

>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=99.53  E-value=5.3e-15  Score=123.06  Aligned_cols=72  Identities=19%  Similarity=0.533  Sum_probs=65.5

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCccc
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQ  162 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~  162 (242)
                      ..+|.+|+++|.+++.+.     ++++.||++||+|..|+++|.+..|+.+||++||..||.++|+++|.+|+++|-
T Consensus       115 ~~~C~~C~~~I~~~~~v~-----a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~kc~~C~~~~g  186 (192)
T 1b8t_A          115 SDGCPRCGQAVYAAEKVI-----GAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQGAG  186 (192)
T ss_dssp             CEECTTTSCEECSSSCEE-----ETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCCCC
T ss_pred             CCcCCCCCCEecCcEEEe-----cCCCccchhcCCccccCCCCCCCcccccCCEEeCHHHHHHhcCCcCCCCCCccc
Confidence            347999999999876654     679999999999999999998888999999999999999999999999999863

>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=99.51  E-value=7.8e-15  Score=105.92  Aligned_cols=66  Identities=24%  Similarity=0.413  Sum_probs=57.1

Q ss_pred             cccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccce--eeCCeeccHhhhhcccCCCcc
Q psy8090          85 APMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYF--YRGDKLYCGRHHAETLKPRCS  155 (242)
Q Consensus        85 ~~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~--~~dg~~yC~~~y~~~~~prC~  155 (242)
                      ....|.+|+++|..++.++     ++++.||++||+|..|+++|.+..|+  .+||++||+.||.++|++.++
T Consensus        14 ~~~~C~~C~~~I~~~e~v~-----a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~   81 (82)
T 2co8_A           14 AGDLCALCGEHLYVLERLC-----VNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSGPSS   81 (82)
T ss_dssp             SSCBCSSSCCBCCTTTBCC-----BTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCCCCC
T ss_pred             CCCCCcccCCCcccceEEE-----ECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcCCCC
Confidence            3457999999998877654     67999999999999999999988887  479999999999999886554

>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=99.47  E-value=2.8e-14  Score=102.37  Aligned_cols=76  Identities=8%  Similarity=-0.116  Sum_probs=63.1

Q ss_pred             CCeeccHhhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCC-CCCcc-cCCCCCC
Q psy8090         137 GDKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRD--LPESYG-THRNS-LNKEQNH  212 (242)
Q Consensus       137 dg~~yC~~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g-~~~f~-~~d~~~y  212 (242)
                      .+.+||++||.++|+++|++|+++|.+..              +.+.++.||.+||.+  +..+++ +..|. ..++++|
T Consensus         1 g~~~yC~~~y~~~~~~~C~~C~~~I~~~~--------------~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~   66 (81)
T 1x6a_A            1 GSSGSSGKDYWGKFGEFCHGCSLLMTGPF--------------MVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLY   66 (81)
T ss_dssp             CCCCCCCCCSSCCSSCBCTTTCCBCCSCC--------------BCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEE
T ss_pred             CCCccchhHHhhhcCCcCccCCCCcCceE--------------EEECCceeccccCCccCCCCccCCCCcEEEeeCCEEE
Confidence            36899999999999999999999998321              355789999999932  445675 46777 5899999


Q ss_pred             CHHHHhhhhccccc
Q psy8090         213 SFDNLLKSNLKKLS  226 (242)
Q Consensus       213 C~~cy~~~~a~kc~  226 (242)
                      |..||.++|++++|
T Consensus        67 C~~c~~~~~~~~~s   80 (81)
T 1x6a_A           67 CGKCHNEVVSGPSS   80 (81)
T ss_dssp             EHHHHHHHHCTTSC
T ss_pred             CHHHHHHHhcCCCC
Confidence            99999999999876

>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=99.46  E-value=5.7e-14  Score=99.14  Aligned_cols=60  Identities=15%  Similarity=0.445  Sum_probs=52.8

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcccccccCCCCC-CccceeeCCeeccHhhhhcccCC
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV-DLIYFYRGDKLYCGRHHAETLKP  152 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~-~~~~~~~dg~~yC~~~y~~~~~p  152 (242)
                      ..|.+|+++|.+ + ++.    ++++.||++||+|..|+++|. +..|+.+++++||..||.++++.
T Consensus         6 ~~C~~C~~~I~~-~-~v~----a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~   66 (73)
T 1wig_A            6 SGCDSCEKYITG-R-VLE----AGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTE   66 (73)
T ss_dssp             CSCSSSCCCCSS-C-CBC----CSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSS
T ss_pred             CCcccCCCEecC-e-eEE----eCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhcc
Confidence            379999999987 3 343    789999999999999999998 77899999999999999987764

>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=99.43  E-value=3.6e-14  Score=110.28  Aligned_cols=61  Identities=18%  Similarity=0.505  Sum_probs=53.4

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcccccccCCCCC--CccceeeCCeeccHhhhhcccC
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV--DLIYFYRGDKLYCGRHHAETLK  151 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~--~~~~~~~dg~~yC~~~y~~~~~  151 (242)
                      ...|.+|+++|.+... +.    ++++.||+.||+|..|+++|.  +..||.+||++||+.||.++|+
T Consensus        61 ~~~C~~C~~~I~~~~~-v~----a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           61 WKRCAGCGGKIADRFL-LY----AMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             CSBBSSSSSBCCSSSE-EE----ETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             CCcCcCCCCCcCCcEE-EE----eCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            3479999999997643 33    689999999999999999997  4689999999999999999885

>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=99.43  E-value=8.9e-14  Score=99.72  Aligned_cols=63  Identities=29%  Similarity=0.690  Sum_probs=54.4

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCC-ccce-eeCCeeccHhhhhcccCCCccc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVD-LIYF-YRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~-~~~~-~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      +|.+|+++|. ++. +.    ++++.||++||+|..|+++|.+ ..|+ .+++++||..||.++|++.|++
T Consensus        17 ~C~~C~~~I~-~~~-~~----a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~~sg   81 (81)
T 1x6a_A           17 FCHGCSLLMT-GPF-MV----AGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSGPSSG   81 (81)
T ss_dssp             BCTTTCCBCC-SCC-BC----CTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCTTSCC
T ss_pred             cCccCCCCcC-ceE-EE----ECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcCCCCC
Confidence            7999999999 333 43    7899999999999999999974 5566 4899999999999999998874

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

Probab=99.43  E-value=7.7e-14  Score=96.17  Aligned_cols=59  Identities=22%  Similarity=0.602  Sum_probs=51.7

Q ss_pred             cccccCCCceecCccccccccCCCCCccc--CCcccccccCCCCCCccceeeCCeecc-Hhhhhcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWH--PGCFTCSVCNELLVDLIYFYRGDKLYC-GRHHAET  149 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH--~~CF~C~~C~~~L~~~~~~~~dg~~yC-~~~y~~~  149 (242)
                      ..|.+|+++|.+++..+.    ++++.||  ++||+|..|+++|.+..|+.+||++|| ..||.++
T Consensus         3 ~~C~~C~~~I~~~~~~v~----a~~~~wH~~~~CF~C~~C~~~L~~~~f~~~~g~~yC~~~C~~k~   64 (65)
T 2iyb_E            3 VVCQGCHNAIDPEVQRVT----YNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             EECTTTSSEECTTSCEEE----ETTEEEETTTTTSBCTTTCCBCTTSCCEEETTEEESSHHHHHTT
T ss_pred             CCCcCCCCeeccCceEEE----ECCCccCCCCCCEECCCCCCcCCCCceEEECCEEecCHHHhhhh
Confidence            379999999997534454    7899999  999999999999999899999999999 8888754

>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=99.41  E-value=9.4e-14  Score=98.57  Aligned_cols=58  Identities=21%  Similarity=0.598  Sum_probs=51.3

Q ss_pred             cccccCCCceec---CccccccccCCCCCcccCCcccccccCCCCCCccceeeCCeeccHhhhhc
Q psy8090          87 MFCENCEDELQT---SDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAE  148 (242)
Q Consensus        87 ~~C~~C~~~I~~---~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~  148 (242)
                      .+|.+|+++|.+   ...++.    ++++.||+.||+|..|+++|.+..|+.++|++||..||.+
T Consensus        16 ~~C~~C~~~I~~~g~~~~~~~----a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A           16 KKCAGCKNPITGFGKGSSVVA----YEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CCCSSSCCCCCCCSSCCCEEE----ETTEEEETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHH
T ss_pred             ccCcccCCcccCCCCCceeEE----ECcceeCcccCEehhcCCCCCCCccEeECCEEEChHHhcc
Confidence            379999999996   334454    6899999999999999999998899999999999999975

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

Probab=99.40  E-value=1.6e-13  Score=113.07  Aligned_cols=118  Identities=14%  Similarity=0.075  Sum_probs=93.7

Q ss_pred             cCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceee------CCeeccHhhhh---cccCCCcccCCCcc
Q psy8090          91 NCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYR------GDKLYCGRHHA---ETLKPRCSACDEEC  161 (242)
Q Consensus        91 ~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~------dg~~yC~~~y~---~~~~prC~~C~~~I  161 (242)
                      +|.+.+..++.+|.++|.+.            .|.+.|+++.++..      ++..||++++.   ....++|.+|+++|
T Consensus         3 ~~~~~~~~ge~~~~~~~~g~------------~~~~l~~~l~~~~~~~~ng~~~~~~~~~~~~~~~~~~~~~C~~C~~~I   70 (182)
T 2jtn_A            3 QVPDVMVVGEPTLMGGEFGD------------EDERLITRLENTQFDAANGIDDEGGSGGHMGSGGTPEIPMCAGCDQHI   70 (182)
T ss_dssp             CCCSCEECCCCCCCCCCCCT------------TTSCCCEEEECSCTTSSSCSSSSCSSSSSCCCCCCCSCCBCBTSSSBC
T ss_pred             cccccccCCCcccccccccc------------hhHHHHHhhhccccccccCcccccccccccccCCCCCCCcCccCCCCc
Confidence            46778888999998766442            28888888888865      46789999987   55679999999999


Q ss_pred             cCCCcceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCCCCCcccCCCCCCCHHHHhhhhcccccCCCCCCCC
Q psy8090         162 QTSSQDILYYLTRDSERDLPDEYRTERLEHQRD--LPESYGTHRNSLNKEQNHSFDNLLKSNLKKLSLADSDDVS  234 (242)
Q Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~~~~~~~~~  234 (242)
                      ....     +        +.+.++.||.+||.+  +..++++..| .+++++||..||.++|+++|+.+...+..
T Consensus        71 ~~~~-----~--------~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~~kC~~C~~~I~~  131 (182)
T 2jtn_A           71 LDRF-----I--------LKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTKCAACQLGIPP  131 (182)
T ss_dssp             CCSE-----E--------EEETTEEECSSTTSCTTTCCCCSSCCE-EETTEEECHHHHHHTTSCCCTTTCCCCCS
T ss_pred             cCce-----e--------EEecCCeEccccCccCCCCCccCCCce-eECCEeeecCccccccccccccCCCccCC
Confidence            8642     1        234789999999942  4567877776 68999999999999999999999886654

>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=99.38  E-value=2e-13  Score=96.81  Aligned_cols=71  Identities=15%  Similarity=0.120  Sum_probs=59.0

Q ss_pred             CCeeccHhhhhcccCCCcccCCCcccC---CCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCC
Q psy8090         137 GDKLYCGRHHAETLKPRCSACDEECQT---SSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQN  211 (242)
Q Consensus       137 dg~~yC~~~y~~~~~prC~~C~~~I~~---~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~  211 (242)
                      ++++||+.||.++++++|++|+++|.+   ...    +        +.+.++.||.+||.  .+..++.+..|...++++
T Consensus         1 g~~~yC~~cy~~~~~~~C~~C~~~I~~~g~~~~----~--------~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~   68 (77)
T 2egq_A            1 GSSGSSGDCYKNFVAKKCAGCKNPITGFGKGSS----V--------VAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQV   68 (77)
T ss_dssp             CCSSCCTTCCCSCCCCCCSSSCCCCCCCSSCCC----E--------EEETTEEEETTTCBCSSSCCBCTTSCCCEETTEE
T ss_pred             CCCeEchhHhchhhCccCcccCCcccCCCCCce----e--------EEECcceeCcccCEehhcCCCCCCCccEeECCEE
Confidence            478999999999999999999999996   221    2        23478999999993  245678888899999999


Q ss_pred             CCHHHHhh
Q psy8090         212 HSFDNLLK  219 (242)
Q Consensus       212 yC~~cy~~  219 (242)
                      ||..||.+
T Consensus        69 yC~~cy~~   76 (77)
T 2egq_A           69 YCPDCAKK   76 (77)
T ss_dssp             CCHHHHHH
T ss_pred             EChHHhcc
Confidence            99999976

>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=99.25  E-value=3.7e-12  Score=88.97  Aligned_cols=69  Identities=12%  Similarity=0.072  Sum_probs=56.9

Q ss_pred             cccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhcccc
Q psy8090         148 ETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKL  225 (242)
Q Consensus       148 ~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc  225 (242)
                      ++|+++|++|+++|.+.+..            +.+.++.||.+||.  .+..++.+..|..+++++||..||.++|+++|
T Consensus         2 ~~~~~~C~~C~~~I~~~~~~------------~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C   69 (72)
T 1x4k_A            2 SSGSSGCQECKKTIMPGTRK------------MEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGP   69 (72)
T ss_dssp             CSCCCCBSSSCCCCCSSSCE------------EEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCC
T ss_pred             CccCCCCccCCCcccCCceE------------EEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCC
Confidence            46889999999999975422            23378899999993  24567888889999999999999999999999


Q ss_pred             cCC
Q psy8090         226 SLA  228 (242)
Q Consensus       226 ~~~  228 (242)
                      +.+
T Consensus        70 ~~~   72 (72)
T 1x4k_A           70 SSG   72 (72)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>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=99.24  E-value=5.2e-12  Score=87.83  Aligned_cols=67  Identities=9%  Similarity=0.042  Sum_probs=55.5

Q ss_pred             cccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhcccc
Q psy8090         148 ETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKL  225 (242)
Q Consensus       148 ~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc  225 (242)
                      ++++++|.+|+++|.+..              +.+.++.||.+||.  .+..++.+..|..+++++||..||.++|++||
T Consensus         2 ~~~~~~C~~C~~~I~~~~--------------~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c   67 (70)
T 2d8z_A            2 SSGSSGCVQCKKPITTGG--------------VTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGP   67 (70)
T ss_dssp             CCCCCBCSSSCCBCCSSE--------------EESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCC
T ss_pred             CCCCCCCcccCCeeccce--------------EEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhcccc
Confidence            467899999999997531              23478999999993  24567888889999999999999999999999


Q ss_pred             cCC
Q psy8090         226 SLA  228 (242)
Q Consensus       226 ~~~  228 (242)
                      +.+
T Consensus        68 ~~~   70 (70)
T 2d8z_A           68 SSG   70 (70)
T ss_dssp             TTC
T ss_pred             CCC
Confidence            864

>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=99.22  E-value=3.9e-12  Score=93.02  Aligned_cols=73  Identities=12%  Similarity=-0.018  Sum_probs=58.5

Q ss_pred             cHhhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhh
Q psy8090         142 CGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLK  219 (242)
Q Consensus       142 C~~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~  219 (242)
                      +...+...+.++|.+|+++|.+.      ++        .+.++.||.+||.  .+...+.+..|..+++++||..||.+
T Consensus        16 ~~~~~~~~~~~~C~~C~~~I~~~------~v--------~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~   81 (90)
T 2dar_A           16 AEHIPAGKRTPMCAHCNQVIRGP------FL--------VALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEK   81 (90)
T ss_dssp             CEEECTTTCCCBBSSSCCBCCSC------EE--------EETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHH
T ss_pred             cccCCCCCCCCCCccCCCEecce------EE--------EECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHH
Confidence            33445677889999999999632      22        3478999999993  24567888889999999999999999


Q ss_pred             hhcccccCC
Q psy8090         220 SNLKKLSLA  228 (242)
Q Consensus       220 ~~a~kc~~~  228 (242)
                      +|++||+.+
T Consensus        82 ~f~~~c~s~   90 (90)
T 2dar_A           82 FFASGPSSG   90 (90)
T ss_dssp             HTSCCCCCC
T ss_pred             HcCCCCCCC
Confidence            999999864

>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=99.22  E-value=6e-12  Score=87.91  Aligned_cols=69  Identities=16%  Similarity=0.057  Sum_probs=56.9

Q ss_pred             cccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhcccc
Q psy8090         148 ETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKL  225 (242)
Q Consensus       148 ~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc  225 (242)
                      ++++++|.+|+++|.+.+.    +        +.+.++.||.+||.  .+..++.+..|...++++||..||.++|++||
T Consensus         2 ~~~~~~C~~C~~~I~~~~~----~--------~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C   69 (72)
T 1wyh_A            2 SSGSSGCSACGETVMPGSR----K--------LEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGP   69 (72)
T ss_dssp             CCCCCBCSSSCCBCCSSSC----E--------ECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCC
T ss_pred             CccCCCCccCCCccccCcc----E--------EEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcC
Confidence            4678999999999996432    1        34578999999993  24567888889999999999999999999999


Q ss_pred             cCC
Q psy8090         226 SLA  228 (242)
Q Consensus       226 ~~~  228 (242)
                      +.+
T Consensus        70 ~~~   72 (72)
T 1wyh_A           70 SSG   72 (72)
T ss_dssp             CCC
T ss_pred             CCC
Confidence            864

>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=99.21  E-value=4e-12  Score=105.25  Aligned_cols=68  Identities=24%  Similarity=0.553  Sum_probs=54.7

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCC-CccceeeCCeeccHhhhhcccCCCcccCCC
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV-DLIYFYRGDKLYCGRHHAETLKPRCSACDE  159 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~-~~~~~~~dg~~yC~~~y~~~~~prC~~C~~  159 (242)
                      +|.+|+++|.+.+.++.    +.++.||+.||+|..|+++|. +..|+..++++||..||.++++++|...+.
T Consensus        71 ~C~~C~~~I~~~e~~i~----a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~~~~~~~g~  139 (188)
T 1rut_X           71 ACSACGQSIPASELVMR----AQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHLNSGG  139 (188)
T ss_dssp             ECTTTCCEECTTSEEEE----ETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC--------
T ss_pred             ccccCCCccccCcEEEE----cCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhcccccccCC
Confidence            69999999998776665    679999999999999999995 567999999999999999999999987765

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

Probab=99.19  E-value=2.7e-12  Score=99.93  Aligned_cols=61  Identities=21%  Similarity=0.573  Sum_probs=54.4

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcccccccCCCC-CCccceeeCCeeccHhhhhcccCC
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELL-VDLIYFYRGDKLYCGRHHAETLKP  152 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L-~~~~~~~~dg~~yC~~~y~~~~~p  152 (242)
                      .|.+|+++|.+.+.++.    +.++.||++||+|..|+++| .+..|+..||++||..||.+++++
T Consensus        68 ~C~~C~~~I~~~e~~~~----a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~~  129 (131)
T 2xjy_A           68 LCASCDKRIRAYEMTMR----VKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKI  129 (131)
T ss_dssp             ECTTTCCEECTTSEEEE----ETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHHHHH
T ss_pred             ChhhcCCccCccceeEe----eCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHHhhc
Confidence            79999999998776665    68999999999999999999 477799999999999999988764

>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=99.19  E-value=9.5e-12  Score=89.06  Aligned_cols=58  Identities=19%  Similarity=0.404  Sum_probs=48.6

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCCCccceeeCC-eeccHhhhhcccC
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLVDLIYFYRGD-KLYCGRHHAETLK  151 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~~~~~~~~dg-~~yC~~~y~~~~~  151 (242)
                      +|.+|+++|.+ + ++.    ++++.||++||+|..|+++|.+..+|..++ .+||..||.+.+.
T Consensus        17 ~C~~C~~~I~~-~-~v~----a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~   75 (81)
T 1v6g_A           17 RCFSCDQFIEG-E-VVS----ALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSV   75 (81)
T ss_dssp             BCTTTCCBCCS-C-CEE----ETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSS
T ss_pred             cCccccCEecc-c-eEE----ECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCC
Confidence            79999999994 3 344    789999999999999999998777777666 5799999986654

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

Probab=99.13  E-value=2.3e-11  Score=94.06  Aligned_cols=60  Identities=22%  Similarity=0.620  Sum_probs=53.6

Q ss_pred             cccccCCCceecCccccccccCCCCCccc--CCcccccccCCCCCCccceeeCCeeccHhhhhccc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWH--PGCFTCSVCNELLVDLIYFYRGDKLYCGRHHAETL  150 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH--~~CF~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~  150 (242)
                      ..|.+|+++|.+++.++.    +.++.||  ++||+|..|+++|.+..|+.+||++||..||.++|
T Consensus        64 ~~C~~C~~~I~~~~~~~~----a~~~~~H~~~~CF~C~~C~~~l~~~~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           64 VVCQGCHNAIDPEVQRVT----YNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             CBCTTTCSBCCTTSCEEE----ETTEEEESSTTTSBCTTTCCBCTTSEEEEETTEEESSHHHHHSC
T ss_pred             ccCcccCCcCCcCceEEE----CCCCEeeCCCCCcCcCCCCCccCCCeeEeECCEEcchHHhhhhc
Confidence            379999999998666665    7899999  99999999999999889999999999998888765

>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=99.13  E-value=2.3e-11  Score=84.33  Aligned_cols=64  Identities=9%  Similarity=0.064  Sum_probs=53.2

Q ss_pred             ccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhccccc
Q psy8090         149 TLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLS  226 (242)
Q Consensus       149 ~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~  226 (242)
                      +++++|.+|+++|.+..              +.+.++.||.+||.  .+..++.+..|...++++||..||.++|++||+
T Consensus         3 ~~~~~C~~C~~~I~~~~--------------~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~   68 (69)
T 2cur_A            3 SGSSGCVKCNKAITSGG--------------ITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSS   68 (69)
T ss_dssp             CCCCCCSSSCCCCCTTC--------------EEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSCC
T ss_pred             CCcCCCcccCCEeCcce--------------EEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCCC
Confidence            56799999999997531              23367999999993  245678788899999999999999999999996

>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=99.10  E-value=2.3e-11  Score=87.02  Aligned_cols=73  Identities=10%  Similarity=-0.005  Sum_probs=54.7

Q ss_pred             CeeccHhhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCCCCCcccCCCC-CCCH
Q psy8090         138 DKLYCGRHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRD--LPESYGTHRNSLNKEQ-NHSF  214 (242)
Q Consensus       138 g~~yC~~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g~~~f~~~d~~-~yC~  214 (242)
                      +.+||++||.++|+++|++|+++|.+.  .            +.+.++.||.+||.+  +..++....|...+++ +||.
T Consensus         2 ~~~yC~~dy~~~~~~~C~~C~~~I~~~--~------------v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~   67 (81)
T 1v6g_A            2 SSGSSGLDYQRLYGTRCFSCDQFIEGE--V------------VSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQ   67 (81)
T ss_dssp             CCCCCCSCGGGSCCCBCTTTCCBCCSC--C------------EEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEH
T ss_pred             CCCcchHHHHhHhCCcCccccCEeccc--e------------EEECCceeCccCCccccCCCCCCCCCEEEeCCCCEECh
Confidence            568999999999999999999999842  1            234789999999932  3456665544444554 6999


Q ss_pred             HHHhhhhccc
Q psy8090         215 DNLLKSNLKK  224 (242)
Q Consensus       215 ~cy~~~~a~k  224 (242)
                      .||.+.+...
T Consensus        68 ~C~~~~~~~~   77 (81)
T 1v6g_A           68 KCSLPVSVSG   77 (81)
T ss_dssp             HHHSCCSSCC
T ss_pred             hhhcccCCCC
Confidence            9998765543

>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=99.10  E-value=2e-11  Score=86.42  Aligned_cols=69  Identities=7%  Similarity=-0.045  Sum_probs=56.6

Q ss_pred             cccCCCcccCCCcccC--CCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhcc
Q psy8090         148 ETLKPRCSACDEECQT--SSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLK  223 (242)
Q Consensus       148 ~~~~prC~~C~~~I~~--~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~  223 (242)
                      ++|+++|++|+++|.+  ...    +        +.+.++.||.+||.  .+..++.+..|...++++||..||.++|++
T Consensus         2 ~~~~~~C~~C~~~I~~~g~~~----~--------~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~   69 (76)
T 1x68_A            2 SSGSSGCVACSKPISGLTGAK----F--------ICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTD   69 (76)
T ss_dssp             TTCCCCCTTTCCCCCTTTTCC----E--------EEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCC
T ss_pred             CccCCCCccCCCcccCCCCce----e--------EEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCC
Confidence            4688999999999986  221    1        23478999999993  245678888899999999999999999999


Q ss_pred             cccCC
Q psy8090         224 KLSLA  228 (242)
Q Consensus       224 kc~~~  228 (242)
                      +|+.+
T Consensus        70 ~C~~~   74 (76)
T 1x68_A           70 ISGPS   74 (76)
T ss_dssp             SSSSS
T ss_pred             cCCCC
Confidence            99865

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

Probab=99.08  E-value=5.4e-11  Score=84.05  Aligned_cols=67  Identities=4%  Similarity=-0.087  Sum_probs=52.3

Q ss_pred             ccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhccccc
Q psy8090         149 TLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLS  226 (242)
Q Consensus       149 ~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~  226 (242)
                      .++++|.+|+++|.+.+..            +.+.++.||.+||.  .+..++.+..|...++++||..||.++|+++|+
T Consensus         9 ~~~~~C~~C~~~I~~~~~~------------~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C~   76 (77)
T 1g47_A            9 LASATCERCKGGFAPAEKI------------VNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCWI   76 (77)
T ss_dssp             CCCCBCSSSCCBCCSTTTC------------EEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC--
T ss_pred             CCCCCchhcCCccCCCceE------------EEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcccC
Confidence            4579999999999865421            23478899999993  245677777899999999999999999999997


Q ss_pred             C
Q psy8090         227 L  227 (242)
Q Consensus       227 ~  227 (242)
                      +
T Consensus        77 ~   77 (77)
T 1g47_A           77 L   77 (77)
T ss_dssp             -
T ss_pred             C
Confidence            4

>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=99.05  E-value=1.6e-10  Score=80.66  Aligned_cols=65  Identities=11%  Similarity=0.017  Sum_probs=53.1

Q ss_pred             ccCCCcccCCCcccC--CCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhccc
Q psy8090         149 TLKPRCSACDEECQT--SSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKK  224 (242)
Q Consensus       149 ~~~prC~~C~~~I~~--~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~k  224 (242)
                      .++++|.+|+++|.+  ...    +        +.+.++.||.+||.  .+..++.+..|..+++++||..||.+.|+++
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~----~--------~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p~   70 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTK----Y--------ISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPS   70 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCS----C--------EECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCSS
T ss_pred             CCCCCCcCCCccccCCCCcc----e--------EEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCCC
Confidence            567999999999986  221    1        34478999999993  2456788889999999999999999999988


Q ss_pred             c
Q psy8090         225 L  225 (242)
Q Consensus       225 c  225 (242)
                      +
T Consensus        71 ~   71 (72)
T 1x4l_A           71 S   71 (72)
T ss_dssp             C
T ss_pred             C
Confidence            5

>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=99.04  E-value=1.5e-10  Score=82.62  Aligned_cols=65  Identities=12%  Similarity=-0.000  Sum_probs=52.3

Q ss_pred             ccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhccccc
Q psy8090         149 TLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLS  226 (242)
Q Consensus       149 ~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~  226 (242)
                      .+.++|.+|+++|.+..              +.+.++.||.+||.  .+..++.+..| .+++++||..||.++|+++++
T Consensus        13 ~~~~~C~~C~~~I~~~~--------------v~a~~~~~H~~CF~C~~C~~~L~~~~f-~~~g~~yC~~cy~~~f~p~~s   77 (79)
T 2cor_A           13 LGKYICQKCHAIIDEQP--------------LIFKNDPYHPDHFNCANCGKELTADAR-ELKGELYCLPCHDKMGVSGPS   77 (79)
T ss_dssp             CCCCBCTTTCCBCCSCC--------------CCCSSSCCCTTTSBCSSSCCBCCTTCE-EETTEEECHHHHHTTSCCSSC
T ss_pred             cCCCCCccCCCEecceE--------------EEECcceeCCCCCEeCCCCCccCCCCE-eECCEEeCHHHHHHhCCCCCC
Confidence            45799999999998321              35578999999994  24567777766 889999999999999999887


Q ss_pred             CC
Q psy8090         227 LA  228 (242)
Q Consensus       227 ~~  228 (242)
                      .+
T Consensus        78 s~   79 (79)
T 2cor_A           78 SG   79 (79)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

>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=99.03  E-value=6.2e-11  Score=83.73  Aligned_cols=68  Identities=6%  Similarity=0.022  Sum_probs=55.3

Q ss_pred             cccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCH-HHHhhhhccc
Q psy8090         148 ETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSF-DNLLKSNLKK  224 (242)
Q Consensus       148 ~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~-~cy~~~~a~k  224 (242)
                      ..++++|.+|+++|.+++.     +        .+.++.||.+||.  .+..++.+..|..+++++||. .||.++|++|
T Consensus         6 ~~~~~~C~~C~~~I~~~~~-----v--------~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~k   72 (76)
T 2cu8_A            6 SGMASKCPKCDKTVYFAEK-----V--------SSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSG   72 (76)
T ss_dssp             CCCCCBCTTTCCBCCTTTE-----E--------EETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSS
T ss_pred             CCCCCCCcCCCCEeECCeE-----E--------EECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccc
Confidence            3567999999999996541     2        3367999999993  345678888899999999999 7999999999


Q ss_pred             ccCC
Q psy8090         225 LSLA  228 (242)
Q Consensus       225 c~~~  228 (242)
                      |+.+
T Consensus        73 c~g~   76 (76)
T 2cu8_A           73 PSSG   76 (76)
T ss_dssp             CSCC
T ss_pred             cCCC
Confidence            9753

>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=99.02  E-value=8.1e-11  Score=80.83  Aligned_cols=63  Identities=14%  Similarity=0.073  Sum_probs=51.8

Q ss_pred             cccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhccc
Q psy8090         148 ETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKK  224 (242)
Q Consensus       148 ~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~k  224 (242)
                      ++++++|++|+++|.+ .     +        +.+.++.||.+||.  .+..++.+..|...++++||..||.++|++|
T Consensus         2 ~~~~~~C~~C~~~I~~-~-----~--------~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~k   66 (66)
T 1nyp_A            2 SMGVPICGACRRPIEG-R-----V--------VNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGDV   66 (66)
T ss_dssp             CCCCCEETTTTEECCS-C-----E--------ECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSCC
T ss_pred             CcCCCCCcccCCEecc-e-----E--------EEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHhCCC
Confidence            4678999999999983 2     2        24578999999994  2456788888999999999999999999986

>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=99.02  E-value=8.2e-11  Score=84.28  Aligned_cols=64  Identities=9%  Similarity=-0.009  Sum_probs=51.5

Q ss_pred             CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhcccccCC
Q psy8090         151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLSLA  228 (242)
Q Consensus       151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~~~  228 (242)
                      .++|.+|+++|..+.     +        +.+.++.||.+||.  .+..++.+ .|..+|+++||..||.++|++||+.+
T Consensus        15 ~~~C~~C~~~I~~~~-----~--------v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C~~~   80 (80)
T 2dj7_A           15 PSHCAGCKEEIKHGQ-----S--------LLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPSSG   80 (80)
T ss_dssp             CSCCTTTCCCCSSSC-----C--------EEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCSTTC
T ss_pred             CCCCcCcCCeeCCCe-----E--------EEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCCCCC
Confidence            579999999998654     1        23478999999993  24456665 58899999999999999999999863

>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=99.01  E-value=2.6e-10  Score=84.65  Aligned_cols=74  Identities=9%  Similarity=-0.024  Sum_probs=60.5

Q ss_pred             ccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhccccc
Q psy8090         149 TLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLS  226 (242)
Q Consensus       149 ~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~  226 (242)
                      .++++|.+|+++|.++..    +        +.+.++.||.+||.  .+..++.+..|..+++++||..||.++|++||+
T Consensus         3 ~~~~~C~~C~~~I~~~~~----~--------~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~   70 (101)
T 2cup_A            3 SGSSGCVECRKPIGADSK----E--------VHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCK   70 (101)
T ss_dssp             SCCCBCSSSCCBCCSSSC----E--------EEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCS
T ss_pred             CCCCcCcccCCcccCCce----E--------EEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccc
Confidence            567999999999985332    1        23478999999993  245678888899999999999999999999999


Q ss_pred             CCCCCCCC
Q psy8090         227 LADSDDVS  234 (242)
Q Consensus       227 ~~~~~~~~  234 (242)
                      .+...+..
T Consensus        71 ~C~~~I~~   78 (101)
T 2cup_A           71 GCFKAIVA   78 (101)
T ss_dssp             SSCCBCCS
T ss_pred             cCCCcccc
Confidence            99877763

>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=98.98  E-value=3.1e-10  Score=79.73  Aligned_cols=63  Identities=6%  Similarity=0.021  Sum_probs=51.8

Q ss_pred             cccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCC-CCCcccCCCCCCCHHHHhhhhccc
Q psy8090         148 ETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYG-THRNSLNKEQNHSFDNLLKSNLKK  224 (242)
Q Consensus       148 ~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g-~~~f~~~d~~~yC~~cy~~~~a~k  224 (242)
                      .+|+++|++|+++|.+..              +.+.++.||.+||.  .+..++. +..|..+++++||..||.+.++.+
T Consensus         2 s~~~~~C~~C~~~I~~~~--------------v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~~   67 (73)
T 1wig_A            2 SSGSSGCDSCEKYITGRV--------------LEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTED   67 (73)
T ss_dssp             CCSCCSCSSSCCCCSSCC--------------BCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSSS
T ss_pred             CcCcCCcccCCCEecCee--------------EEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhccc
Confidence            368899999999998621              35678999999993  2456777 778999999999999999998875

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

Probab=98.97  E-value=1.2e-10  Score=82.33  Aligned_cols=67  Identities=9%  Similarity=0.010  Sum_probs=55.0

Q ss_pred             CCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCH-HHHhhhhcccccCC
Q psy8090         152 PRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSF-DNLLKSNLKKLSLA  228 (242)
Q Consensus       152 prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~-~cy~~~~a~kc~~~  228 (242)
                      |+|.+|+++|.++.     ++        .+.++.||.+||.  .+..++.+..|...++++||. .||.++|++||+.+
T Consensus         1 p~C~~C~~~I~~~~-----~v--------~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~~C   67 (76)
T 1iml_A            1 PKCPKCDKEVYFAE-----RV--------TSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGR   67 (76)
T ss_dssp             CBCTTTSSBCCGGG-----EE--------EETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSC
T ss_pred             CcCCCCCCEEECce-----EE--------EECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCCCc
Confidence            68999999998654     12        3368999999993  245678887899999999999 69999999999998


Q ss_pred             CCC
Q psy8090         229 DSD  231 (242)
Q Consensus       229 ~~~  231 (242)
                      +..
T Consensus        68 ~~~   70 (76)
T 1iml_A           68 GGA   70 (76)
T ss_dssp             CCS
T ss_pred             CCc
Confidence            754

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

Probab=98.96  E-value=5.8e-10  Score=81.51  Aligned_cols=67  Identities=7%  Similarity=0.003  Sum_probs=54.4

Q ss_pred             ccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCCCCCcccCCCCCCCHHHHhhhhccccc
Q psy8090         149 TLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRD--LPESYGTHRNSLNKEQNHSFDNLLKSNLKKLS  226 (242)
Q Consensus       149 ~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~  226 (242)
                      ...++|.+|+++|.+.+.             +.+.++.||.+||.+  +..++....|...++++||..||.++|++||+
T Consensus        13 ~~~~~C~~C~~~I~~~~~-------------v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~   79 (91)
T 2d8y_A           13 PARETCVECQKTVYPMER-------------LLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGN   79 (91)
T ss_dssp             SSSCBCTTTCCBCCTTSE-------------EECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSC
T ss_pred             CCCCcCccCCCccCCcee-------------EEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcC
Confidence            346899999999986541             234789999999932  45677777799999999999999999999997


Q ss_pred             CC
Q psy8090         227 LA  228 (242)
Q Consensus       227 ~~  228 (242)
                      -.
T Consensus        80 ~~   81 (91)
T 2d8y_A           80 YD   81 (91)
T ss_dssp             CC
T ss_pred             cc
Confidence            43

>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=98.96  E-value=6.6e-10  Score=77.44  Aligned_cols=66  Identities=6%  Similarity=-0.063  Sum_probs=52.0

Q ss_pred             ccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhccccc
Q psy8090         149 TLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLS  226 (242)
Q Consensus       149 ~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~  226 (242)
                      .++++|.+|+++|.+.+.    +        +.+.++.||.+||.  .+..++.+..|...++++||..||.++|+ +|+
T Consensus         3 ~~~~~C~~C~~~I~~~~~----~--------~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~~-~~~   69 (72)
T 1x61_A            3 SGSSGCGGCGEDVVGDGA----G--------VVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLE-SGP   69 (72)
T ss_dssp             SCCCCCSSSCSCCCSSSC----C--------EECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHHH-TCS
T ss_pred             CCCCCCccCCCccCCCce----E--------EEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHHc-cCC
Confidence            568999999999986432    1        24478999999993  34567888889999999999999999985 444


Q ss_pred             C
Q psy8090         227 L  227 (242)
Q Consensus       227 ~  227 (242)
                      .
T Consensus        70 ~   70 (72)
T 1x61_A           70 S   70 (72)
T ss_dssp             S
T ss_pred             C
Confidence            3

>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1; LIM-interaction-domain (LID), metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=98.95  E-value=7.7e-10  Score=84.30  Aligned_cols=68  Identities=9%  Similarity=0.041  Sum_probs=54.3

Q ss_pred             CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCCC--CCcccCCCCCCCHHHHhhhhccccc
Q psy8090         151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRD--LPESYGT--HRNSLNKEQNHSFDNLLKSNLKKLS  226 (242)
Q Consensus       151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g~--~~f~~~d~~~yC~~cy~~~~a~kc~  226 (242)
                      .++|++|+++|.++.     +        +.+.++.||.+||.+  +..+++.  ..|..+++++||..||.++|++||.
T Consensus         3 ~~~C~~C~~~I~~~~-----~--------~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~   69 (114)
T 1j2o_A            3 LLTCGGCQQNIGDRY-----F--------LKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGH   69 (114)
T ss_dssp             CBCBSSSCSCBCSSE-----E--------EECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCS
T ss_pred             CCCCcCCCCeeCCcE-----E--------EEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccC
Confidence            479999999998642     2        345789999999942  4457763  6799999999999999999999988


Q ss_pred             CCCCC
Q psy8090         227 LADSD  231 (242)
Q Consensus       227 ~~~~~  231 (242)
                      -+...
T Consensus        70 ~c~~~   74 (114)
T 1j2o_A           70 MGSGG   74 (114)
T ss_dssp             SCBSC
T ss_pred             cCCCC
Confidence            76543

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3

Probab=98.95  E-value=1.4e-10  Score=89.51  Aligned_cols=73  Identities=7%  Similarity=-0.057  Sum_probs=59.6

Q ss_pred             ccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCC--CCCcccCCCCCCCHHHHhhhhcc-
Q psy8090         149 TLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRD--LPESYG--THRNSLNKEQNHSFDNLLKSNLK-  223 (242)
Q Consensus       149 ~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g--~~~f~~~d~~~yC~~cy~~~~a~-  223 (242)
                      ++.++|++|+++|.+..     +        +.+.++.||.+||.+  +..+++  +..|..+++++||..||.++|++ 
T Consensus         3 ~~~~~C~~C~~~I~~~~-----~--------~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~   69 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADRF-----L--------LYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNS   69 (122)
T ss_dssp             SCCCCBSSSSSCCCSSC-----C--------EEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCC
T ss_pred             CCCCCCcccCCEeCCcE-----E--------EEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCC
Confidence            56799999999998653     1        234789999999932  456776  46789999999999999999999 


Q ss_pred             -cccCCCCCCCC
Q psy8090         224 -KLSLADSDDVS  234 (242)
Q Consensus       224 -kc~~~~~~~~~  234 (242)
                       +|+.+...+.+
T Consensus        70 ~~C~~C~~~I~~   81 (122)
T 1m3v_A           70 GAGGSGGHMGSG   81 (122)
T ss_dssp             CSSSCSSCCSCC
T ss_pred             CccccCCCCcCc
Confidence             99999877664

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

Probab=98.94  E-value=3.5e-10  Score=78.48  Aligned_cols=65  Identities=12%  Similarity=-0.036  Sum_probs=52.7

Q ss_pred             ccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhccccc
Q psy8090         149 TLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLS  226 (242)
Q Consensus       149 ~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~  226 (242)
                      .+.++|.+|+++|.+.      +        +.+.++.||.+||.  .+..++.+..|..+++++||..||.++|+++.+
T Consensus         3 ~~~~~C~~C~~~I~~~------~--------~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~   68 (70)
T 2d8x_A            3 SGSSGCHQCGEFIIGR------V--------IKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGPS   68 (70)
T ss_dssp             CCSSBCSSSCCBCCSC------C--------EEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCCSC
T ss_pred             CCCCcCccCCCEecce------E--------EEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCCCC
Confidence            3568999999999842      1        23478999999993  245678888899999999999999999999875


Q ss_pred             C
Q psy8090         227 L  227 (242)
Q Consensus       227 ~  227 (242)
                      .
T Consensus        69 s   69 (70)
T 2d8x_A           69 S   69 (70)
T ss_dssp             C
T ss_pred             C
Confidence            4

>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=98.93  E-value=2.8e-10  Score=92.53  Aligned_cols=63  Identities=17%  Similarity=0.460  Sum_probs=53.2

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcccccccCCCCC-Ccccee-eCCeeccHhhhhcccCCCc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCFTCSVCNELLV-DLIYFY-RGDKLYCGRHHAETLKPRC  154 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF~C~~C~~~L~-~~~~~~-~dg~~yC~~~y~~~~~prC  154 (242)
                      .|.+|+++|.+++.++.    +.++.||+.||+|..|+++|. +..||. .||++||..||.+.+...+
T Consensus        67 ~C~~C~~~I~~~~~v~~----a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~~~~~  131 (169)
T 2rgt_A           67 KCAACQLGIPPTQVVRR----AQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGGS  131 (169)
T ss_dssp             BCTTTCCBCCTTSEEEE----ETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHHHCC-
T ss_pred             cccccccccCCCcEEEE----cCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHhhccC
Confidence            79999999998776654    689999999999999999997 445654 6899999999998876544

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

Probab=98.91  E-value=2.1e-10  Score=81.97  Aligned_cols=67  Identities=9%  Similarity=-0.051  Sum_probs=48.4

Q ss_pred             cCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhcccccC
Q psy8090         150 LKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLSL  227 (242)
Q Consensus       150 ~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~~  227 (242)
                      ..++|.+|+++|.+++.             +.+.++.||.+||.  .+..++.+..|..+++++||..||.++|++||.-
T Consensus         6 ~~~~C~~C~~~I~~~~~-------------~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~g   72 (81)
T 1a7i_A            6 GGNKCGACGRTVYHAEE-------------VQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGYG   72 (81)
T ss_dssp             --CBCSSSCCBCSSTTE-------------EEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC-----
T ss_pred             CCCcCcCcCccccCcee-------------EEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCcccc
Confidence            46899999999986541             23377999999993  2456788888999999999999999999999986


Q ss_pred             CC
Q psy8090         228 AD  229 (242)
Q Consensus       228 ~~  229 (242)
                      ++
T Consensus        73 cg   74 (81)
T 1a7i_A           73 YG   74 (81)
T ss_dssp             --
T ss_pred             cC
Confidence            53

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

Probab=98.85  E-value=1.4e-09  Score=79.13  Aligned_cols=63  Identities=10%  Similarity=-0.008  Sum_probs=51.4

Q ss_pred             cCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhccccc
Q psy8090         150 LKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLS  226 (242)
Q Consensus       150 ~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~  226 (242)
                      ..++|.+|++.|.+.      +        +.+.++.||.+||.  .+...+.+..|...++++||..||.++|++|+.
T Consensus        24 ~~~~C~~C~~~I~~~------~--------~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~~   88 (89)
T 1x64_A           24 RMPLCDKCGSGIVGA------V--------VKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSS   88 (89)
T ss_dssp             SCCBCTTTCCBCCSC------C--------EESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCCC
T ss_pred             cCCCcccCCCEeccc------E--------EEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            458999999999852      1        23477999999993  345677777888999999999999999999975

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

Probab=98.85  E-value=7.8e-10  Score=78.69  Aligned_cols=63  Identities=13%  Similarity=0.062  Sum_probs=50.9

Q ss_pred             cCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhccccc
Q psy8090         150 LKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNLKKLS  226 (242)
Q Consensus       150 ~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a~kc~  226 (242)
                      ..++|.+|+++|.+.      +        +.+.++.||.+||.  .+...+.+..|...++++||..||.++|++|.+
T Consensus        14 ~~~~C~~C~~~I~~~------~--------~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g~   78 (79)
T 1x62_A           14 KLPMCDKCGTGIVGV------F--------VKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSS   78 (79)
T ss_dssp             CCCCCSSSCCCCCSS------C--------EECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCCC
T ss_pred             CCCccccCCCCccCc------E--------EEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            358999999999852      1        24478999999993  244567777789999999999999999999864

>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=98.84  E-value=1.2e-09  Score=75.77  Aligned_cols=65  Identities=3%  Similarity=-0.055  Sum_probs=51.3

Q ss_pred             hhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcccCCCCCCCHHHHhhhhc
Q psy8090         146 HAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNSLNKEQNHSFDNLLKSNL  222 (242)
Q Consensus       146 y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~~~d~~~yC~~cy~~~~a  222 (242)
                      |...+.++|++|+++|.+.+.    +        +.+.++.||.+||.  .+..++....|...++++||..||.++||
T Consensus         6 y~~~~~~~C~~C~~~i~~~e~----~--------~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B            6 FQGSASATCERCKGGFAPAEK----I--------VNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             CCCCTTCBCTTTCCBCCTTCE----E--------EEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHTC
T ss_pred             ccCcCCccchhcCccccCCce----E--------EEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhhC
Confidence            344678999999999997652    1        13367899999994  24567777788899999999999999886

>2l4z_A DNA endonuclease RBBP8, LIM domain transcription LMO4; protein-protein interaction, LIM-interaction DOM LMO4, RBBP8/CTIP, LIM-only protein; HET: DNA; NMR {Homo sapiens}

Probab=98.77  E-value=3.5e-09  Score=81.94  Aligned_cols=62  Identities=8%  Similarity=-0.025  Sum_probs=49.1

Q ss_pred             cccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCccC--CCCCCC--CCCcccCCCCCCCHHHHhhhhc
Q psy8090         148 ETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQRD--LPESYG--THRNSLNKEQNHSFDNLLKSNL  222 (242)
Q Consensus       148 ~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~~--~~~~~g--~~~f~~~d~~~yC~~cy~~~~a  222 (242)
                      ..++++|.+|+++|.+..     +        +.+.++.||.+||.+  +..+++  +..|..+++++||..||.++|+
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 GLSWKRCAGCGGKIADRF-----L--------LYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             CSSCSBBSSSSSBCCSSS-----E--------EEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             CccCCcCcCCCCCcCCcE-----E--------EEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            356789999999998642     1        244789999999943  456775  4679999999999999999885

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

Probab=98.77  E-value=2.4e-09  Score=73.36  Aligned_cols=59  Identities=7%  Similarity=-0.046  Sum_probs=47.0

Q ss_pred             cCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCccc--CCCcc--CCCCCCCCCCcccCCCCCCC-HHHHhhh
Q psy8090         150 LKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTER--LEHQR--DLPESYGTHRNSLNKEQNHS-FDNLLKS  220 (242)
Q Consensus       150 ~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h--~~~f~--~~~~~~g~~~f~~~d~~~yC-~~cy~~~  220 (242)
                      |+++|.+|+++|.+++..            +.+.++.||  .+||.  .+..++.+..|..+++++|| .+||.+.
T Consensus         1 fa~~C~~C~~~I~~~~~~------------v~a~~~~wH~~~~CF~C~~C~~~L~~~~f~~~~g~~yC~~~C~~k~   64 (65)
T 2iyb_E            1 HAVVCQGCHNAIDPEVQR------------VTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             -CEECTTTSSEECTTSCE------------EEETTEEEETTTTTSBCTTTCCBCTTSCCEEETTEEESSHHHHHTT
T ss_pred             CcCCCcCCCCeeccCceE------------EEECCCccCCCCCCEECCCCCCcCCCCceEEECCEEecCHHHhhhh
Confidence            578999999999975322            234789999  99994  34568888899999999999 9999764

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

Probab=98.59  E-value=2.4e-08  Score=71.50  Aligned_cols=61  Identities=10%  Similarity=0.009  Sum_probs=48.0

Q ss_pred             CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCcc--CCCCCCCCCCcc--cCCCCCCCHHHHhhhhccc
Q psy8090         151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQR--DLPESYGTHRNS--LNKEQNHSFDNLLKSNLKK  224 (242)
Q Consensus       151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f~--~~~~~~g~~~f~--~~d~~~yC~~cy~~~~a~k  224 (242)
                      .++|.+|+++|...+.             +.+.++.||.+||.  .+..++....|.  .+|+++||..||.++|+.-
T Consensus        15 ~~~C~~C~~~I~~~e~-------------v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~   79 (82)
T 2co8_A           15 GDLCALCGEHLYVLER-------------LCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSGP   79 (82)
T ss_dssp             SCBCSSSCCBCCTTTB-------------CCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCCC
T ss_pred             CCCCcccCCCcccceE-------------EEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcCC
Confidence            4799999999976542             34578999999993  245677887777  5799999999999987753

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

Probab=97.59  E-value=2.5e-05  Score=45.51  Aligned_cols=28  Identities=21%  Similarity=0.600  Sum_probs=24.8

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      ..|..|++.|+..+.+.     +.|+.||..||
T Consensus         4 ~~C~~C~k~Vy~~Ek~~-----~~g~~~Hk~CF   31 (31)
T 1zfo_A            4 PNCARCGKIVYPTEKVN-----CLDKFWHKACF   31 (31)
T ss_dssp             CBCSSSCSBCCGGGCCC-----SSSSCCCGGGC
T ss_pred             CcCCccCCEEecceeEE-----ECCeEecccCC
Confidence            37999999999988765     67999999998

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

Probab=95.42  E-value=0.0075  Score=34.75  Aligned_cols=29  Identities=10%  Similarity=0.178  Sum_probs=22.8

Q ss_pred             CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      .++|..|++.+-+.+.             +.+.++.||..||
T Consensus         3 ~~~C~~C~k~Vy~~Ek-------------~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            3 NPNCARCGKIVYPTEK-------------VNCLDKFWHKACF   31 (31)
T ss_dssp             CCBCSSSCSBCCGGGC-------------CCSSSSCCCGGGC
T ss_pred             CCcCCccCCEEeccee-------------EEECCeEecccCC
Confidence            5799999999976542             3447899999987

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

Original result of RPS-BLAST against SCOP70(version1.75) database

No hit with e-value below 0.005

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	242
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.93
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.79
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.68
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.57
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.49
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.32
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.27
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.18
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.17
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.14
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.12
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.08
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.07
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.05
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.03
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	97.99
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	97.96
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.92
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.92
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.9
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.89
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	97.89
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.87
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	97.82
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.82
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.79
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.76
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.69
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.68
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	97.67
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.65
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.65
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.64
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.59
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.59
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	97.57
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.52
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.51
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.5
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.47
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.45
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.39
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.39
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.37
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.36
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.35
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.31
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.29
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.26
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.25
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.25
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	97.22
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.22
d2co8a2	36	Nedd9 interacting protein with calponin homology,	97.17
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	97.15
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.09
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.09
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.08
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.07
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.04
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.04
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.04
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	96.92
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.9
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.84
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	96.73
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	96.71
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	96.59
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	96.31
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	96.09
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.0
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	95.8
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	95.8
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	95.72
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	95.7
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.62
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	95.37
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.35
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.11
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	94.63
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	94.61
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	94.39
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	94.32
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	94.31
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	94.09
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	93.54
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	93.41
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	93.37
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	93.37
d2co8a2	36	Nedd9 interacting protein with calponin homology,	93.3
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	93.05
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	93.05
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	92.99
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	92.92
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	92.44
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	91.72
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	91.41
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	90.83
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	90.59
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	90.42
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	90.0
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	89.72
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	89.03
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	88.97
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	88.78
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	87.45
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	87.24
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	86.16
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	85.99
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	81.32

>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=98.93  E-value=2e-10  Score=67.75  Aligned_cols=34  Identities=18%  Similarity=0.561  Sum_probs=33.0

Q ss_pred             ccccccCCCCCCccceeeCCeeccHhhhhcccCC
Q psy8090         119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKP  152 (242)
Q Consensus       119 F~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~p  152 (242)
                      |+|+.|+++|.+..||++||++||+.||.++|+|
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhcCC
Confidence            8999999999999999999999999999999987

>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=98.79  E-value=4.1e-10  Score=66.47  Aligned_cols=35  Identities=14%  Similarity=0.285  Sum_probs=30.3

Q ss_pred             hhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         144 RHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       144 ~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      +||.++|+|+|++|+++|++..              +.|.++.||++||
T Consensus         1 ~DY~~~fapkC~~C~~~I~g~~--------------v~Al~~~wHpeCF   35 (35)
T d1x3ha1           1 KDFLAMFSPKCGGCNRPVLENY--------------LSAMDTVWHPECF   35 (35)
T ss_dssp             CCCCCCCSCBCTTTCCBCCSSC--------------EEETTEEECTTTC
T ss_pred             CcHHHHhChhhhhcCCcccchh--------------eeecCCccCcccC
Confidence            4789999999999999998642              4568999999998

>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=98.68  E-value=3e-09  Score=63.05  Aligned_cols=37  Identities=14%  Similarity=0.277  Sum_probs=33.5

Q ss_pred             hhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         144 RHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       144 ~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      .||.+.|+++|.+|+++|.++++.++|            .++.||.+||
T Consensus         1 kCy~~~~a~~C~~C~k~I~~G~k~vey------------kg~~WHe~CF   37 (37)
T d1x63a1           1 KCTTREDSPKCKGCFKAIVAGDQNVEY------------KGTVWHKDCF   37 (37)
T ss_dssp             CCCSCCCSCBCSSSCCBCCSSSCEEEC------------SSCEEETTTC
T ss_pred             CccccccCcccccCCCccCCCCeEeEe------------CCccchhccC
Confidence            478999999999999999999987666            8899999998

>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=98.57  E-value=8.7e-09  Score=59.40  Aligned_cols=35  Identities=14%  Similarity=0.268  Sum_probs=30.8

Q ss_pred             hhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         144 RHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       144 ~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      .||.++|+++|..|+++|+.|+              +...+..||.+||
T Consensus         1 PCyE~kfa~~C~~Ckk~It~GG--------------vtY~dqpWHkeCF   35 (35)
T d2cuqa2           1 PCYENKFAPRCARCSKTLTQGG--------------VTYRDQPWHRECL   35 (35)
T ss_dssp             CCCCCCSSCCCTTTCCCCCSCC--------------EESSSSEECTTTC
T ss_pred             CchHHHHHHHHhhcCCccccCc--------------eeecCCcchhhhC
Confidence            3799999999999999999886              3447899999998

>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=98.49  E-value=4.5e-08  Score=61.34  Aligned_cols=41  Identities=17%  Similarity=0.400  Sum_probs=37.8

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCc
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEE  160 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~  160 (242)
                      +|..|++.|.....+.+|+++||+.||.++|+|+..+.+..
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~g~G~g   41 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQG   41 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCccCcccC
Confidence            68999999998899999999999999999999999988753

>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=98.32  E-value=1e-07  Score=54.20  Aligned_cols=31  Identities=16%  Similarity=0.350  Sum_probs=28.8

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhccc
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAETL  150 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~  150 (242)
                      +|.+|.+++.+..||+.||++||+.||.++-
T Consensus         1 VC~~C~~PF~~~~Fy~~~g~PyCe~HyH~~~   31 (32)
T d1x3ha2           1 VCGDCFTSFSTGSFFELDGRPFCELHYHHRR   31 (32)
T ss_dssp             BCSSSCCBSCSSCCEESSSCEECHHHHHHHH
T ss_pred             CcCccCCcCCCCCeEeECCccchHHhhhhhc
Confidence            6999999999999999999999999998753

>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=98.27  E-value=1.5e-07  Score=53.25  Aligned_cols=27  Identities=4%  Similarity=0.004  Sum_probs=25.0

Q ss_pred             CCCCCCCCcccCCCCCCCHHHHhhhhc
Q psy8090         196 PESYGTHRNSLNKEQNHSFDNLLKSNL  222 (242)
Q Consensus       196 ~~~~g~~~f~~~d~~~yC~~cy~~~~a  222 (242)
                      .++++|++|+.+|++|||.+||..+||
T Consensus         6 ~~~L~GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           6 RKQLSGQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             CCBCTTSCCEESSSSEECHHHHHHHTC
T ss_pred             CccccCceeeecCCCeehHHhhHhhcC
Confidence            358999999999999999999999987

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

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

Probab=98.18  E-value=5.1e-07  Score=51.12  Aligned_cols=34  Identities=21%  Similarity=0.509  Sum_probs=32.1

Q ss_pred             ccccccCCCCCCccceeeCCeeccHhhhhcccCC
Q psy8090         119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKP  152 (242)
Q Consensus       119 F~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~p  152 (242)
                      |+|+.|.+++.+...|++.|..||+.||.++|+.
T Consensus         1 FvCA~CekPF~G~rhyE~~g~ayCe~Hy~qLfg~   34 (35)
T d1u5sb2           1 FVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGD   34 (35)
T ss_dssp             CBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSC
T ss_pred             CcccccCCccCCchhhhhcCchHHHHHHHHHhcc
Confidence            8999999999999999999999999999999863

>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=98.17  E-value=4e-07  Score=51.46  Aligned_cols=32  Identities=22%  Similarity=0.465  Sum_probs=29.9

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhcccC
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAETLK  151 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~  151 (242)
                      +|..|+++|.++.|..+|+++||-.||.++|+
T Consensus         1 ~C~~C~~~L~GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQLSGQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBCTTSCCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCccccCceeeecCCCeehHHhhHhhcC
Confidence            58999999999999999999999999998875

>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=98.14  E-value=5.6e-07  Score=50.14  Aligned_cols=31  Identities=19%  Similarity=0.526  Sum_probs=28.1

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhcccC
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAETLK  151 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~  151 (242)
                      +|..|+..|.+ .|..+||.+||++||+..|+
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            58999999966 89999999999999998875

>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=98.12  E-value=5.1e-07  Score=54.63  Aligned_cols=34  Identities=29%  Similarity=0.566  Sum_probs=31.9

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhcccCCC
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPR  153 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~pr  153 (242)
                      +|..|+..|.-..|...+|.+||+.||.++|+++
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~k   34 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK   34 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhh
Confidence            6999999999889999999999999999999875

>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=98.08  E-value=4.1e-07  Score=53.23  Aligned_cols=27  Identities=26%  Similarity=0.770  Sum_probs=22.9

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      .+|.+|+++|.+.  +|.    |+++.||++||
T Consensus         9 pkC~~C~~~I~g~--~v~----Al~~~wHpeCF   35 (35)
T d1x3ha1           9 PKCGGCNRPVLEN--YLS----AMDTVWHPECF   35 (35)
T ss_dssp             CBCTTTCCBCCSS--CEE----ETTEEECTTTC
T ss_pred             hhhhhcCCcccch--hee----ecCCccCcccC
Confidence            3799999999873  444    89999999998

>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=98.07  E-value=8e-07  Score=49.60  Aligned_cols=32  Identities=22%  Similarity=0.473  Sum_probs=30.0

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhcccC
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAETLK  151 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~  151 (242)
                      +|..|+++|.+..|..+|.++||..||.++|+
T Consensus         1 vCt~Ck~~LaGqrFTSrde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1           1 VCTGCQTPLAGQQFTSRDEDPYCVACFGELFA   32 (32)
T ss_dssp             BCSSSCCBCTTCCEEECSSSEEEHHHHHHHTT
T ss_pred             CccccCccccCCccccCCCCccHHHHhHhhcC
Confidence            58999999999999999999999999998874

>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=98.05  E-value=9.2e-07  Score=48.37  Aligned_cols=30  Identities=23%  Similarity=0.532  Sum_probs=28.1

Q ss_pred             ccccccCCCCCCccceeeCCeeccHhhhhc
Q psy8090         119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAE  148 (242)
Q Consensus       119 F~C~~C~~~L~~~~~~~~dg~~yC~~~y~~  148 (242)
                      |+|..|++.|.......+||.+||+.||++
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeeeec
Confidence            899999999998888999999999999985

>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=98.03  E-value=6.6e-07  Score=49.95  Aligned_cols=27  Identities=4%  Similarity=-0.106  Sum_probs=25.0

Q ss_pred             CCCCCCCCcccCCCCCCCHHHHhhhhc
Q psy8090         196 PESYGTHRNSLNKEQNHSFDNLLKSNL  222 (242)
Q Consensus       196 ~~~~g~~~f~~~d~~~yC~~cy~~~~a  222 (242)
                      ++++.|++|+.+|++|||++||-++||
T Consensus         6 k~~LaGqrFTSrde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1           6 QTPLAGQQFTSRDEDPYCVACFGELFA   32 (32)
T ss_dssp             CCBCTTCCEEECSSSEEEHHHHHHHTT
T ss_pred             CccccCCccccCCCCccHHHHhHhhcC
Confidence            458999999999999999999999986

>d1imla2 g.39.1.3 (A:29-76) Cysteine-rich (intestinal) protein, CRP, CRIP {Rat (Rattus rattus) [TaxId: 10117]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=97.99  E-value=1.4e-06  Score=53.75  Aligned_cols=36  Identities=19%  Similarity=0.293  Sum_probs=32.7

Q ss_pred             cccccCCCCCCccceeeCCeecc-HhhhhcccCCCcc
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYC-GRHHAETLKPRCS  155 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC-~~~y~~~~~prC~  155 (242)
                      +|..|++.|......++|+++|| ..||..+|+|+=.
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FGPkG~   37 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGF   37 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCS
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccCCCcc
Confidence            58999999999899999999999 6799999999743

>d1x63a1 g.39.1.3 (A:8-44) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.96  E-value=1.4e-06  Score=51.26  Aligned_cols=29  Identities=28%  Similarity=0.660  Sum_probs=26.6

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      ..|.+|+++|.+++..|.    +.++.||..||
T Consensus         9 ~~C~~C~k~I~~G~k~ve----ykg~~WHe~CF   37 (37)
T d1x63a1           9 PKCKGCFKAIVAGDQNVE----YKGTVWHKDCF   37 (37)
T ss_dssp             CBCSSSCCBCCSSSCEEE----CSSCEEETTTC
T ss_pred             cccccCCCccCCCCeEeE----eCCccchhccC
Confidence            479999999999988886    89999999998

>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=97.92  E-value=2.2e-06  Score=45.75  Aligned_cols=27  Identities=11%  Similarity=0.276  Sum_probs=25.1

Q ss_pred             cccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         154 CSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       154 C~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      |..|++.|+++.++|+|            .+..||..||
T Consensus         1 C~~C~ktiMPGsrKme~------------kG~~WHEtCF   27 (27)
T d1x4ka2           1 CQECKKTIMPGTRKMEY------------KGSSWHETCF   27 (27)
T ss_dssp             BSSSCCCCCSSSCEEEE------------TTEEEETTTT
T ss_pred             CccccccccCCceeecc------------cCCccccccC
Confidence            88999999999999998            7899999998

>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=97.92  E-value=1.2e-06  Score=53.44  Aligned_cols=27  Identities=22%  Similarity=0.655  Sum_probs=23.1

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      ..|..|+++|.+  .++.    |+|+.|||+||
T Consensus        19 P~C~~C~~pI~g--~~vt----Algk~WHPEhF   45 (45)
T d2dara2          19 PMCAHCNQVIRG--PFLV----ALGKSWHPEEF   45 (45)
T ss_dssp             CBBSSSCCBCCS--CEEE----ETTEEECTTTC
T ss_pred             eeccccCCcccC--ceee----ecCCccCcCCC
Confidence            479999999987  3454    89999999998

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

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

Probab=97.90  E-value=2.7e-06  Score=56.03  Aligned_cols=37  Identities=24%  Similarity=0.522  Sum_probs=33.8

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhcccCCCccc
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSA  156 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~  156 (242)
                      .|..|++.|.......+++++||+.||.++|+|+=.+
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG~G   37 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKG   37 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCccc
Confidence            4899999999989999999999999999999998554

>d1wyha2 g.39.1.3 (A:8-34) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.89  E-value=2.7e-06  Score=45.27  Aligned_cols=27  Identities=30%  Similarity=0.395  Sum_probs=24.7

Q ss_pred             cccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         154 CSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       154 C~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      |.+|++.|+++.++|+|            .+..||..||
T Consensus         1 C~~C~ktiMPGsrKmey------------~G~sWHE~CF   27 (27)
T d1wyha2           1 CSACGETVMPGSRKLEY------------GGQTWHEHCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEECS------------TTCCEETTTC
T ss_pred             CccccceecCCcccccc------------cCcccccccC
Confidence            88999999999988877            7899999998

>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=97.89  E-value=1.4e-06  Score=48.63  Aligned_cols=29  Identities=21%  Similarity=0.314  Sum_probs=24.6

Q ss_pred             ccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCC
Q psy8090         149 TLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEH  191 (242)
Q Consensus       149 ~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~  191 (242)
                      .+.|+|++|.++|.+..              +.|.++.||.+|
T Consensus         3 mg~p~C~~C~~PI~~~~--------------vtAlgk~WHpEH   31 (31)
T d1u5sb1           3 MGVPICGACRRPIEGRV--------------VNAMGKQWHVEH   31 (31)
T ss_dssp             CCCCEETTTTEECCSCE--------------ECCTTSBEETTT
T ss_pred             cCCcchhhcCCchhhhH--------------hhhhccccCCCC
Confidence            56799999999999753              467999999987

>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=97.87  E-value=1.5e-06  Score=53.00  Aligned_cols=28  Identities=18%  Similarity=0.274  Sum_probs=23.7

Q ss_pred             CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      .|+|++|+++|.+..              +.|.++.||++||
T Consensus        18 ~P~C~~C~~pI~g~~--------------vtAlgk~WHPEhF   45 (45)
T d2dara2          18 TPMCAHCNQVIRGPF--------------LVALGKSWHPEEF   45 (45)
T ss_dssp             CCBBSSSCCBCCSCE--------------EEETTEEECTTTC
T ss_pred             CeeccccCCcccCce--------------eeecCCccCcCCC
Confidence            589999999998642              3569999999998

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.82  E-value=2e-06  Score=48.19  Aligned_cols=26  Identities=19%  Similarity=0.138  Sum_probs=24.5

Q ss_pred             CCCCCCCcccCCCCCCCHHHHhhhhc
Q psy8090         197 ESYGTHRNSLNKEQNHSFDNLLKSNL  222 (242)
Q Consensus       197 ~~~g~~~f~~~d~~~yC~~cy~~~~a  222 (242)
                      .++|++.|+.+|++.||+.||+++||
T Consensus         7 qPIGtksfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           7 QPIGTKSFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CCCCSSSEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccccccCCCCceEeecchhhcC
Confidence            48999999999999999999999997

>d2dara1 g.39.1.3 (A:53-84) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.79  E-value=5.4e-06  Score=46.31  Aligned_cols=32  Identities=16%  Similarity=0.421  Sum_probs=29.1

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhcccC
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAETLK  151 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~  151 (242)
                      .|+.|+.+|.+..|.+..|++||+.||.+.|+
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHHTS
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHhcC
Confidence            38999999999999999999999999997664

>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=97.76  E-value=2.1e-06  Score=49.43  Aligned_cols=34  Identities=9%  Similarity=0.072  Sum_probs=27.8

Q ss_pred             hhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         144 RHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       144 ~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      .||.. ...+|+.|+++|++..              +.|.|+.+|+.||
T Consensus         2 ~Cy~~-tlEkC~~C~~~I~dri--------------LrA~Gk~yHP~CF   35 (35)
T d2dloa1           2 GCYVA-TLEKCATCSQPILDRI--------------LRAMGKAYHPGCF   35 (35)
T ss_dssp             CCCCS-SCCBCTTTCCBCCSCC--------------EEETTEEECTTTC
T ss_pred             hhHHH-HHHHHHHhchHHHHHH--------------HHHhCCCCCCCCC
Confidence            45654 3589999999999865              5779999999998

>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=97.69  E-value=1.2e-05  Score=44.25  Aligned_cols=29  Identities=34%  Similarity=0.702  Sum_probs=26.7

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhc
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAE  148 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~  148 (242)
                      +|+.|+..|....||+.++++||+.|..+
T Consensus         1 vC~dCg~NLKqrG~Ffv~~~lyCE~HAr~   29 (31)
T d1x64a2           1 VCADCNLNLKQKGYFFVEGELYCETHARA   29 (31)
T ss_dssp             CCSSSCCCTTTSCCEEETTEEECHHHHHH
T ss_pred             CccccccChhhcceEEeccEEeehhhhhc
Confidence            59999999999999999999999998754

>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=97.68  E-value=4.1e-06  Score=46.81  Aligned_cols=27  Identities=7%  Similarity=-0.015  Sum_probs=24.8

Q ss_pred             CCCCCCCCcccCCCCCCCHHHHhhhhc
Q psy8090         196 PESYGTHRNSLNKEQNHSFDNLLKSNL  222 (242)
Q Consensus       196 ~~~~g~~~f~~~d~~~yC~~cy~~~~a  222 (242)
                      ..++|.+.|+.++++.||+.||+++||
T Consensus         6 ~qPIGtkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           6 EQPLGSRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             CCBTTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             cCcccccccccCCCcEEEEeccccccC
Confidence            348999999999999999999999987

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

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

Probab=97.67  E-value=7.6e-06  Score=46.74  Aligned_cols=28  Identities=25%  Similarity=0.814  Sum_probs=25.0

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      ..|.+|++.|..+...+     ++++.||.+||
T Consensus         9 ~~CagCg~eik~gQaL~-----ALdkqWH~~CF   36 (36)
T d2dj7a2           9 SHCAGCKEEIKHGQSLL-----ALDKQWHVSCF   36 (36)
T ss_dssp             SCCTTTCCCCSSSCCEE-----ETTEEECTTTC
T ss_pred             ccccccchhhhCCceee-----eeecceeeeeC
Confidence            36999999999987766     89999999998

>d1x4ka1 g.39.1.3 (A:35-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.65  E-value=1.5e-05  Score=44.57  Aligned_cols=32  Identities=9%  Similarity=0.316  Sum_probs=29.7

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhcccC
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAETLK  151 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~  151 (242)
                      .|..|.+++..+.|..+|+..||..||.++|+
T Consensus         1 ~C~~C~qPIGtksfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           1 ICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CCSSSCCCCCSSSEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCcccccccccCCCCceEeecchhhcC
Confidence            48999999999999999999999999999875

>d2cu8a2 g.39.1.3 (A:38-70) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.65  E-value=1.3e-05  Score=44.83  Aligned_cols=32  Identities=19%  Similarity=0.249  Sum_probs=28.9

Q ss_pred             cccccCCCCCCccceeeCCeeccH-hhhhcccC
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCG-RHHAETLK  151 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~-~~y~~~~~  151 (242)
                      +|..|++.|......++||++||. .||..+|+
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCCCCccccCCCcCcCcchHHhhcC
Confidence            589999999999999999999996 59998875

>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=97.64  E-value=1.3e-05  Score=45.27  Aligned_cols=34  Identities=24%  Similarity=0.542  Sum_probs=28.3

Q ss_pred             CCcccccccccccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          77 RGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        77 ~g~v~~~~~~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      +|.++.+|   .|.+|+..|.+  .+|.    +.++.+||+||
T Consensus         2 vg~~qklp---~CdkCg~GIVG--~~VK----~rDk~rHPeCf   35 (35)
T d1x62a2           2 IGNAQKLP---MCDKCGTGIVG--VFVK----LRDRHRHPECY   35 (35)
T ss_dssp             CCCCCCCC---CCSSSCCCCCS--SCEE----CSSCEECTTTT
T ss_pred             CCccccCc---cccccCCCcEe--EEEE----eccccCCCCCC
Confidence            46677777   79999999998  4565    77999999998

>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=97.59  E-value=1.3e-05  Score=42.58  Aligned_cols=27  Identities=22%  Similarity=0.668  Sum_probs=24.0

Q ss_pred             cccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          89 CENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        89 C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      |..|.+.|.++..-+.    ..|+.||..||
T Consensus         1 C~~C~ktiMPGsrKme----y~G~sWHE~CF   27 (27)
T d1wyha2           1 CSACGETVMPGSRKLE----YGGQTWHEHCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEEC----STTCCEETTTC
T ss_pred             CccccceecCCccccc----ccCcccccccC
Confidence            7899999999987775    78999999998

>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=97.59  E-value=7.9e-06  Score=43.52  Aligned_cols=27  Identities=26%  Similarity=0.751  Sum_probs=24.0

Q ss_pred             cccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          89 CENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        89 C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      |..|.+.|.++..-+.    ..|..||..||
T Consensus         1 C~~C~ktiMPGsrKme----~kG~~WHEtCF   27 (27)
T d1x4ka2           1 CQECKKTIMPGTRKME----YKGSSWHETCF   27 (27)
T ss_dssp             BSSSCCCCCSSSCEEE----ETTEEEETTTT
T ss_pred             CccccccccCCceeec----ccCCccccccC
Confidence            7899999999987775    67999999998

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LASP-1
domain: LASP-1
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=97.57  E-value=1.4e-05  Score=43.75  Aligned_cols=28  Identities=21%  Similarity=0.600  Sum_probs=24.6

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      ..|++|++.+++.+.+.     -+++.||..||
T Consensus         3 ~~CaRC~k~VYp~Ekl~-----ClDk~WHK~CF   30 (30)
T d1zfoa_           3 PNCARCGKIVYPTEKVN-----CLDKFWHKACF   30 (30)
T ss_dssp             CBCSSSCSBCCGGGCCC-----SSSSCCCGGGC
T ss_pred             CcccccCCccccHHHhh-----hhHHHHhhccC
Confidence            36999999999988765     57999999998

>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=97.52  E-value=1.3e-05  Score=46.01  Aligned_cols=27  Identities=26%  Similarity=0.704  Sum_probs=23.5

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      .+|..|+++|.+  .++.    |+|+.|||.||
T Consensus         9 EkC~~C~~~I~d--riLr----A~Gk~yHP~CF   35 (35)
T d2dloa1           9 EKCATCSQPILD--RILR----AMGKAYHPGCF   35 (35)
T ss_dssp             CBCTTTCCBCCS--CCEE----ETTEEECTTTC
T ss_pred             HHHHHhchHHHH--HHHH----HhCCCCCCCCC
Confidence            379999999987  5665    79999999998

>d2d8za1 g.39.1.3 (A:8-32) 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=97.51  E-value=1.4e-05  Score=42.17  Aligned_cols=25  Identities=16%  Similarity=0.235  Sum_probs=21.3

Q ss_pred             cccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         154 CSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       154 C~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      |..|+++|+.++              +...+++||.+||
T Consensus         1 C~~C~K~ItsGG--------------vtY~~~PWH~eCF   25 (26)
T d2d8za1           1 CVQCKKPITTGG--------------VTYREQPWHKECF   25 (26)
T ss_dssp             CSSSCCBCCSSE--------------EESSSSEEETTTS
T ss_pred             CcccCcceecCc--------------eeecCCcchhhhc
Confidence            789999999876              3447899999998

>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=97.50  E-value=3e-05  Score=43.21  Aligned_cols=32  Identities=19%  Similarity=0.322  Sum_probs=29.6

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhcccC
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAETLK  151 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~  151 (242)
                      .|..|.+++....|..+++..||..||.++|+
T Consensus         1 ~C~~C~qPIGtkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           1 LCSGCEQPLGSRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             BCTTTCCBTTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCcccccccccCCCcEEEEeccccccC
Confidence            48899999999999999999999999998875

>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=97.47  E-value=3e-05  Score=46.60  Aligned_cols=35  Identities=26%  Similarity=0.676  Sum_probs=29.4

Q ss_pred             CCCcccccccccccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          76 GRGFVKQLVAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        76 g~g~v~~~~~~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      ..|..+.+|   .|.+|+..|.+  .+|.    +.++.+||+||
T Consensus        11 ~~~~~QkLP---~CdkCg~GIVG--~~VK----~rDK~rHPeCf   45 (45)
T d1x64a1          11 GAGSAQRMP---LCDKCGSGIVG--AVVK----ARDKYRHPECF   45 (45)
T ss_dssp             CCSCCCSCC---BCTTTCCBCCS--CCEE----SSSCEECTTTC
T ss_pred             CCCccccCc---cccccCCCcEE--EEEE----eccccCCCCCC
Confidence            466777777   89999999998  4565    77999999998

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.45  E-value=1.7e-05  Score=43.89  Aligned_cols=28  Identities=18%  Similarity=0.516  Sum_probs=24.6

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      ..|.+|+++++..|.+.     ++|+.||..|+
T Consensus         3 ~~CprC~K~VYfaEk~~-----~lgk~WHk~Cl   30 (30)
T d2cu8a1           3 SKCPKCDKTVYFAEKVS-----SLGKDWHKFCL   30 (30)
T ss_dssp             CBCTTTCCBCCTTTEEE-----ETTEEEETTTC
T ss_pred             CcCCCCCCceeeHHhhc-----cCCcccccccC
Confidence            47999999999998875     68999999885

>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=97.39  E-value=1.4e-05  Score=44.12  Aligned_cols=29  Identities=31%  Similarity=0.701  Sum_probs=26.6

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhc
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAE  148 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~  148 (242)
                      +|+.|+..|....||+.++++||+.|..+
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr~   29 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHARE   29 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhhh
Confidence            59999999999999999999999999764

>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=97.39  E-value=3.9e-05  Score=42.14  Aligned_cols=29  Identities=21%  Similarity=0.449  Sum_probs=27.1

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhc
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAE  148 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~  148 (242)
                      +|..|.+.|.+..|..+++++||..||..
T Consensus         1 vC~~C~K~Lag~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKLAGQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBCTTSCEEECSSCEEEHHHHHH
T ss_pred             CcccccchhcCceeEEecceEEEeeeecc
Confidence            58999999999999999999999999974

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.37  E-value=4e-05  Score=44.35  Aligned_cols=31  Identities=19%  Similarity=0.490  Sum_probs=26.9

Q ss_pred             ccccccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          84 VAPMFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        84 ~~~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      |....|..|++.++..|.+.     +.|+.||..||
T Consensus         5 p~~~kC~~C~K~VY~~E~~~-----a~g~~~Hk~CF   35 (35)
T d2d8ya1           5 PARETCVECQKTVYPMERLL-----ANQQVFHISCF   35 (35)
T ss_dssp             SSSCBCTTTCCBCCTTSEEE-----CSSSEEETTTC
T ss_pred             CCCcccccCCCEEeeeeeEe-----cCCeehhhccC
Confidence            44558999999999988865     78999999998

>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=97.36  E-value=3.8e-05  Score=42.29  Aligned_cols=30  Identities=23%  Similarity=0.503  Sum_probs=27.5

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhcc
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAET  149 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~  149 (242)
                      +|.+|+..|.++.||..+.+.||+.||...
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi~t   30 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYVAT   30 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceeeee
Confidence            589999999999999999999999999753

>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=97.35  E-value=2e-05  Score=44.12  Aligned_cols=28  Identities=21%  Similarity=0.667  Sum_probs=26.0

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      .|.+|++.|.+.++++.    +.+..||..||
T Consensus         4 ~Ca~C~~~I~~~e~VmR----A~~~VyHl~CF   31 (31)
T d1rutx3           4 ACSACGQSIPASELVMR----AQGNVYHLKCF   31 (31)
T ss_dssp             ECTTTCCEECTTSEEEE----ETTEEECGGGC
T ss_pred             ccccccCcCChhHhhee----cccceeeeccC
Confidence            69999999999999886    78999999998

>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=97.31  E-value=4.7e-05  Score=42.01  Aligned_cols=31  Identities=19%  Similarity=0.406  Sum_probs=28.3

Q ss_pred             ccccCCCCCCccceeeCCeeccHhhhhcccC
Q psy8090         121 CSVCNELLVDLIYFYRGDKLYCGRHHAETLK  151 (242)
Q Consensus       121 C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~  151 (242)
                      |..|++.|....-..+++.+||+.||.++|+
T Consensus         2 C~~C~K~LdStTva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEECSSCCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhccCcceeeeecceEEehhhccccCC
Confidence            7889999998889999999999999998774

>d2cura1 g.39.1.3 (A:33-63) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.29  E-value=3.6e-05  Score=42.30  Aligned_cols=25  Identities=12%  Similarity=0.073  Sum_probs=22.5

Q ss_pred             CCCCCCCCCcccCCCCCCCHHHHhh
Q psy8090         195 LPESYGTHRNSLNKEQNHSFDNLLK  219 (242)
Q Consensus       195 ~~~~~g~~~f~~~d~~~yC~~cy~~  219 (242)
                      +++++++++|+..+++.||++||.+
T Consensus         5 C~K~Lag~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           5 CSKKLAGQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             TCCBCTTSCEEECSSCEEEHHHHHH
T ss_pred             ccchhcCceeEEecceEEEeeeecc
Confidence            3568999999999999999999975

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.26  E-value=6e-05  Score=40.43  Aligned_cols=27  Identities=26%  Similarity=0.781  Sum_probs=24.0

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGC  118 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~C  118 (242)
                      .+|.+|++.++..+.++     +-|+.||..|
T Consensus         2 d~CpRC~~~VyaAEkvi-----GaG~~WHk~C   28 (28)
T d1ibia1           2 EKCSRCGDSVYAAEKVI-----GAGKPWHKNC   28 (28)
T ss_dssp             EECTTTSSEESSSSCEE-----SSSSEECSSC
T ss_pred             CcCcccchhHHHHHHHh-----cCCCccccCC
Confidence            37999999999999987     6799999987

>d2cura2 g.39.1.3 (A:8-32) 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=97.25  E-value=3.5e-05  Score=40.61  Aligned_cols=25  Identities=12%  Similarity=0.294  Sum_probs=20.9

Q ss_pred             cccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         154 CSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       154 C~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      |..|++.|+.+.  +            ...+.+||.+||
T Consensus         1 CvkC~k~ItsGG--v------------tY~~qPWH~eCF   25 (26)
T d2cura2           1 CVKCNKAITSGG--I------------TYQDQPWHADCF   25 (26)
T ss_dssp             CSSSCCCCCTTC--E------------EETTEEECTTTT
T ss_pred             CcccCceEecCc--e------------eecCCcchhhhc
Confidence            789999999876  2            337899999998

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

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

Probab=97.25  E-value=4.7e-05  Score=46.21  Aligned_cols=29  Identities=24%  Similarity=0.762  Sum_probs=25.6

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      ...|..|++.++..|.+.     +.|+.||..||
T Consensus        15 ~~kC~~C~k~VY~~E~~~-----~~g~~~Hk~CF   43 (43)
T d1b8ta3          15 SDGCPRCGQAVYAAEKVI-----GAGKSWHKSCF   43 (43)
T ss_dssp             CEECTTTSCEECSSSCEE-----ETTEEECTTTC
T ss_pred             CCcCccCCCEeeHHHHhh-----cCCCccccCCC
Confidence            347999999999998876     67999999998

>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=97.22  E-value=4.3e-05  Score=42.46  Aligned_cols=25  Identities=20%  Similarity=0.481  Sum_probs=21.5

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGC  118 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~C  118 (242)
                      +|..|+++|.+  .+|.    |+++.||+++
T Consensus         7 ~C~~C~~PI~~--~~vt----Algk~WHpEH   31 (31)
T d1u5sb1           7 ICGACRRPIEG--RVVN----AMGKQWHVEH   31 (31)
T ss_dssp             EETTTTEECCS--CEEC----CTTSBEETTT
T ss_pred             chhhcCCchhh--hHhh----hhccccCCCC
Confidence            79999999987  4565    8999999974

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=97.17  E-value=0.00011  Score=42.61  Aligned_cols=29  Identities=21%  Similarity=0.479  Sum_probs=25.6

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      ...|..|++.+...+.+.     +.|+.||..||
T Consensus         8 ~~~C~~C~K~VY~~Erl~-----a~g~~yHk~CF   36 (36)
T d2co8a2           8 GDLCALCGEHLYVLERLC-----VNGHFFHRSCF   36 (36)
T ss_dssp             SCBCSSSCCBCCTTTBCC-----BTTBCCBTTTC
T ss_pred             CCcccccCCEEeeeeEEE-----ecCcEeccccC
Confidence            457999999999988765     78999999998

>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=97.15  E-value=4.3e-05  Score=44.31  Aligned_cols=28  Identities=0%  Similarity=-0.255  Sum_probs=25.6

Q ss_pred             CCCCCCCCcccCCCCCCCHHHHhhhhcc
Q psy8090         196 PESYGTHRNSLNKEQNHSFDNLLKSNLK  223 (242)
Q Consensus       196 ~~~~g~~~f~~~d~~~yC~~cy~~~~a~  223 (242)
                      .+++++..|.+.||+|||..||+++|||
T Consensus         7 ~~~f~~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           7 FQQFPEGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCCGGGCSEEETTEEECHHHHHHHCCC
T ss_pred             cCCCCCCCeEEECCEecChHhHHhhcCC
Confidence            4578889999999999999999999997

>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=97.09  E-value=9.5e-05  Score=42.15  Aligned_cols=27  Identities=22%  Similarity=0.646  Sum_probs=22.8

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      ..|.+|+++|..|.+.      ..++.||.+||
T Consensus         9 ~~C~~Ckk~It~GGvt------Y~dqpWHkeCF   35 (35)
T d2cuqa2           9 PRCARCSKTLTQGGVT------YRDQPWHRECL   35 (35)
T ss_dssp             CCCTTTCCCCCSCCEE------SSSSEECTTTC
T ss_pred             HHHhhcCCccccCcee------ecCCcchhhhC
Confidence            3799999999987543      57999999998

>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=97.09  E-value=6.9e-05  Score=39.60  Aligned_cols=27  Identities=30%  Similarity=0.778  Sum_probs=22.7

Q ss_pred             cccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          89 CENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        89 C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      |..|.++|..+..-+-    ..++.||..||
T Consensus         1 c~ecrkpigad~ke~h----~knr~wh~~cf   27 (27)
T d2cupa3           1 CVECRKPIGADSKEVH----YKNRFWHDTCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEEE----ETTEEEETTTC
T ss_pred             CccccCCcCcchHHhh----ccccccccccC
Confidence            7889999988766664    67899999998

>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=97.08  E-value=0.00011  Score=41.43  Aligned_cols=32  Identities=19%  Similarity=0.399  Sum_probs=27.8

Q ss_pred             cccccCCCCCCcccee-eCCeeccHhhhhcccC
Q psy8090         120 TCSVCNELLVDLIYFY-RGDKLYCGRHHAETLK  151 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~-~dg~~yC~~~y~~~~~  151 (242)
                      +|..|++.|.+..|.. .++++||-.+|+++|+
T Consensus         1 tCvvC~~~LDGvPFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           1 TCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             BCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             CeeEcCcccCCCcEEEcCCCCEeehhhhhhhcC
Confidence            5889999999888876 5789999999998875

>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=97.07  E-value=0.00012  Score=39.75  Aligned_cols=27  Identities=22%  Similarity=0.677  Sum_probs=21.0

Q ss_pred             cccCCCceec--CccccccccCCCCCcccCCcc
Q psy8090          89 CENCEDELQT--SDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        89 C~~C~~~I~~--~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      |..|.++|.+  +...+.    ..++.||..||
T Consensus         1 C~~C~kPItg~gg~kyis----FE~R~WH~~CF   29 (29)
T d1x4la1           1 CAGCTNPISGLGGTKYIS----FEERQWHNDCF   29 (29)
T ss_dssp             BTTTTBCCCCSSSCSCEE----CSSCEECTTTC
T ss_pred             CCccCCcccccCCceEEE----eecccccccCC
Confidence            8899999965  334443    67999999998

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.04  E-value=9.2e-05  Score=44.00  Aligned_cols=34  Identities=15%  Similarity=0.182  Sum_probs=26.8

Q ss_pred             hhhhcccCCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCC
Q psy8090         144 RHHAETLKPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEH  191 (242)
Q Consensus       144 ~~y~~~~~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~  191 (242)
                      .||+++|+.+|..|++.|+...              +.+-++.+|++|
T Consensus         8 ~DYq~~fG~~C~~C~~~ItG~V--------------~~Ag~~~yHP~C   41 (41)
T d1v6ga1           8 LDYQRLYGTRCFSCDQFIEGEV--------------VSALGKTYHPDC   41 (41)
T ss_dssp             SCGGGSCCCBCTTTCCBCCSCC--------------EEETTEEECTTT
T ss_pred             ccHHHHhCcccccccCEeeeee--------------eEecCcccCCCC
Confidence            5899999999999999997532              234667888876

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.04  E-value=0.00013  Score=40.37  Aligned_cols=26  Identities=19%  Similarity=0.691  Sum_probs=21.7

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGC  118 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~C  118 (242)
                      .|++|+++|.+... +.    ++++.||..|
T Consensus         5 ~CaGC~~~I~DRfl-L~----a~Dr~WH~~C   30 (30)
T d1j2oa1           5 TCGGCQQNIGDRYF-LK----AIDQYWHEDC   30 (30)
T ss_dssp             CBSSSCSCBCSSEE-EE----CSSSEECTTT
T ss_pred             ccCCCCCcchHHHH-HH----HHHHHHhcCC
Confidence            69999999998644 44    7899999987

>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=96.92  E-value=0.00032  Score=38.12  Aligned_cols=32  Identities=28%  Similarity=0.716  Sum_probs=29.0

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhcccC
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAETLK  151 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~  151 (242)
                      +|+.|.+.+....||.+....||..|+..+|+
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtche~kfa   32 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA   32 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcchhhhhcccccccCCCCcEEEEEeeccccC
Confidence            58999999999999999999999999987764

>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=96.90  E-value=9.8e-05  Score=40.95  Aligned_cols=27  Identities=22%  Similarity=0.782  Sum_probs=22.1

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      .|++|+++|.+... +.    +.++.||..|.
T Consensus         4 ~CaGC~~~I~DRfl-L~----v~dr~WH~~CL   30 (30)
T d1rutx1           4 RCAGCGGKIADRFL-LY----AMDSYWHSRCL   30 (30)
T ss_dssp             BBTTTCCBCCCSEE-EE----ETTEEECGGGC
T ss_pred             ccCCCCCccchhhh-hc----cchhhhhhhhC
Confidence            69999999998644 44    68999999884

>d2dloa2 g.39.1.3 (A:43-75) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.84  E-value=0.00026  Score=39.87  Aligned_cols=26  Identities=8%  Similarity=0.097  Sum_probs=21.6

Q ss_pred             CCCCCCCccc-CCCCCCCHHHHhhhhc
Q psy8090         197 ESYGTHRNSL-NKEQNHSFDNLLKSNL  222 (242)
Q Consensus       197 ~~~g~~~f~~-~d~~~yC~~cy~~~~a  222 (242)
                      +++.|..|+. .++++||++||+|+||
T Consensus         7 ~~LDGvPFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           7 RGLDGIPFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             CBCTTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             cccCCCcEEEcCCCCEeehhhhhhhcC
Confidence            3566777775 6899999999999997

>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=96.73  E-value=0.0002  Score=37.38  Aligned_cols=25  Identities=16%  Similarity=0.150  Sum_probs=20.5

Q ss_pred             cccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         154 CSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       154 C~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      |..|++.|.++.              +.+++..||++||
T Consensus         1 c~kcgefiigrv--------------ikamn~~whp~cf   25 (26)
T d2d8xa2           1 CHQCGEFIIGRV--------------IKAMNNSWHPECF   25 (26)
T ss_dssp             CSSSCCBCCSCC--------------EEETTEEECTTTS
T ss_pred             CCccccchhHHH--------------HHHHhccCCcccc
Confidence            788999998753              3558889999998

>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=96.71  E-value=0.00037  Score=37.71  Aligned_cols=29  Identities=17%  Similarity=0.204  Sum_probs=21.1

Q ss_pred             cccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         154 CSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       154 C~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      |++|.+||++-.  ...|        +....|.||.+||
T Consensus         1 C~~C~kPItg~g--g~ky--------isFE~R~WH~~CF   29 (29)
T d1x4la1           1 CAGCTNPISGLG--GTKY--------ISFEERQWHNDCF   29 (29)
T ss_dssp             BTTTTBCCCCSS--SCSC--------EECSSCEECTTTC
T ss_pred             CCccCCcccccC--CceE--------EEeecccccccCC
Confidence            899999998643  1223        3447899999998

>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=96.59  E-value=0.00021  Score=38.65  Aligned_cols=27  Identities=26%  Similarity=0.692  Sum_probs=20.5

Q ss_pred             cccCCCceec--CccccccccCCCCCcccCCcc
Q psy8090          89 CENCEDELQT--SDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        89 C~~C~~~I~~--~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      |..|.++|.+  +...+.    ..++.||.+||
T Consensus         1 C~~C~kPItg~gG~k~is----FedR~WH~~CF   29 (29)
T d1x68a1           1 CVACSKPISGLTGAKFIC----FQDSQWHSECF   29 (29)
T ss_dssp             CTTTCCCCCTTTTCCEEE----ETTEEEEGGGC
T ss_pred             CccccccccccCCceEEE----eehhhcccccC
Confidence            7899999975  333343    67899999998

>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=96.31  E-value=0.00051  Score=38.98  Aligned_cols=28  Identities=18%  Similarity=0.324  Sum_probs=23.1

Q ss_pred             CCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         152 PRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       152 prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      ..|++|++.|..+..             +.|..+.||.+||
T Consensus         9 ~~CagCg~eik~gQa-------------L~ALdkqWH~~CF   36 (36)
T d2dj7a2           9 SHCAGCKEEIKHGQS-------------LLALDKQWHVSCF   36 (36)
T ss_dssp             SCCTTTCCCCSSSCC-------------EEETTEEECTTTC
T ss_pred             ccccccchhhhCCce-------------eeeeecceeeeeC
Confidence            579999999987652             4558899999998

>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=96.09  E-value=0.00057  Score=36.88  Aligned_cols=29  Identities=14%  Similarity=0.095  Sum_probs=20.8

Q ss_pred             cccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         154 CSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       154 C~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      |.+|.+||++-.  ...||        ....|.||.+||
T Consensus         1 C~~C~kPItg~g--G~k~i--------sFedR~WH~~CF   29 (29)
T d1x68a1           1 CVACSKPISGLT--GAKFI--------CFQDSQWHSECF   29 (29)
T ss_dssp             CTTTCCCCCTTT--TCCEE--------EETTEEEEGGGC
T ss_pred             CccccccccccC--CceEE--------EeehhhcccccC
Confidence            889999998643  22333        336799999997

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

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

Probab=96.00  E-value=0.0017  Score=33.58  Aligned_cols=27  Identities=26%  Similarity=0.781  Sum_probs=22.3

Q ss_pred             cccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          89 CENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        89 C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      |.+|++.+.++...+.    ++++.||..||
T Consensus         1 cggcgedvvgdgagvv----aldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVV----ALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEE----CSSSEECTTTC
T ss_pred             CCCcccccccCCcceE----EEeeeEEeccC
Confidence            7899998877655554    88999999998

>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=95.80  E-value=0.0014  Score=35.98  Aligned_cols=27  Identities=15%  Similarity=0.342  Sum_probs=21.0

Q ss_pred             CCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCC
Q psy8090         152 PRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEH  191 (242)
Q Consensus       152 prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~  191 (242)
                      ..|++|+++|.++     |+        +.+..+.||..|
T Consensus         4 ~~CaGC~~~I~DR-----fl--------L~a~Dr~WH~~C   30 (30)
T d1j2oa1           4 LTCGGCQQNIGDR-----YF--------LKAIDQYWHEDC   30 (30)
T ss_dssp             BCBSSSCSCBCSS-----EE--------EECSSSEECTTT
T ss_pred             cccCCCCCcchHH-----HH--------HHHHHHHHhcCC
Confidence            5799999999863     33        456789999876

>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=95.80  E-value=0.0025  Score=33.45  Aligned_cols=27  Identities=19%  Similarity=0.340  Sum_probs=20.9

Q ss_pred             cccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         154 CSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       154 C~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      |..|.+||..+...+.|            .+|-||..||
T Consensus         1 c~ecrkpigad~ke~h~------------knr~wh~~cf   27 (27)
T d2cupa3           1 CVECRKPIGADSKEVHY------------KNRFWHDTCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEEEE------------TTEEEETTTC
T ss_pred             CccccCCcCcchHHhhc------------cccccccccC
Confidence            78899999876543333            7899999997

>d2cupa2 g.39.1.3 (A:35-65) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Four and a half LIM domains protein 1, FHL-1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=95.72  E-value=0.004  Score=33.77  Aligned_cols=28  Identities=18%  Similarity=0.570  Sum_probs=25.5

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhh
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHA  147 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~  147 (242)
                      +|..|-.+|....|..+|++++|..|-.
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHHT
T ss_pred             CchhhccccccCcccccCCeEeeccccc
Confidence            5889999999999999999999999864

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.70  E-value=0.0018  Score=36.38  Aligned_cols=29  Identities=21%  Similarity=0.534  Sum_probs=25.5

Q ss_pred             ccccccCCCceecCccccccccCCCCCcccCCc
Q psy8090          86 PMFCENCEDELQTSDMSVFASRAGPNSCWHPGC  118 (242)
Q Consensus        86 ~~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~C  118 (242)
                      ++.|.+|+....+.+.+|.    ..|..||+.|
T Consensus         7 ~~~C~RC~~gF~p~EkiVN----SnGEl~H~qC   35 (35)
T d1g47a1           7 SATCERCKGGFAPAEKIVN----SNGELYHEQC   35 (35)
T ss_dssp             CCBCSSSCCBCCSTTTCEE----ETTEEECTTT
T ss_pred             HHHHHHHccCCCchHHhhc----CCCccccccC
Confidence            3479999999999999887    6799999987

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=95.62  E-value=0.0037  Score=34.28  Aligned_cols=27  Identities=33%  Similarity=0.743  Sum_probs=22.7

Q ss_pred             cccccCCCCC-CccceeeCCeeccHhhh
Q psy8090         120 TCSVCNELLV-DLIYFYRGDKLYCGRHH  146 (242)
Q Consensus       120 ~C~~C~~~L~-~~~~~~~dg~~yC~~~y  146 (242)
                      .|++|...|+ +..|...+|.+||+.+.
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            5899998886 55788899999999874

>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=95.37  E-value=0.005  Score=34.37  Aligned_cols=20  Identities=10%  Similarity=0.169  Sum_probs=17.5

Q ss_pred             hhhhcccCCCcccCCCcccC
Q psy8090         144 RHHAETLKPRCSACDEECQT  163 (242)
Q Consensus       144 ~~y~~~~~prC~~C~~~I~~  163 (242)
                      .||+.+|+..|.+|.+.|++
T Consensus         1 kdYw~kfge~C~~C~~~itG   20 (34)
T d1x6aa1           1 KDYWGKFGEFCHGCSLLMTG   20 (34)
T ss_dssp             CCSSCCSSCBCTTTCCBCCS
T ss_pred             CcHHHHHHHHhhhhHhhccc
Confidence            37899999999999998874

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=95.35  E-value=0.0031  Score=35.18  Aligned_cols=32  Identities=16%  Similarity=0.368  Sum_probs=27.6

Q ss_pred             cccccCCCCC--CccceeeCCeeccHhhhhcccC
Q psy8090         120 TCSVCNELLV--DLIYFYRGDKLYCGRHHAETLK  151 (242)
Q Consensus       120 ~C~~C~~~L~--~~~~~~~dg~~yC~~~y~~~~~  151 (242)
                      +|+-|+..|.  +...|.+.|.+.|+++|.++|+
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            4788888884  7789999999999999998874

>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=95.11  E-value=0.0019  Score=35.61  Aligned_cols=27  Identities=15%  Similarity=0.246  Sum_probs=20.7

Q ss_pred             CCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCC
Q psy8090         152 PRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEH  191 (242)
Q Consensus       152 prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~  191 (242)
                      ..|++|+++|.++     |+        +.+.++.||..|
T Consensus         3 ~~CaGC~~~I~DR-----fl--------L~v~dr~WH~~C   29 (30)
T d1rutx1           3 KRCAGCGGKIADR-----FL--------LYAMDSYWHSRC   29 (30)
T ss_dssp             CBBTTTCCBCCCS-----EE--------EEETTEEECGGG
T ss_pred             cccCCCCCccchh-----hh--------hccchhhhhhhh
Confidence            4799999999863     22        345789999876

>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=94.63  E-value=0.0054  Score=33.91  Aligned_cols=28  Identities=21%  Similarity=0.280  Sum_probs=21.6

Q ss_pred             CcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         153 RCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       153 rC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      .|++|++.|.+.+..|+            +.+..+|..||
T Consensus         4 ~Ca~C~~~I~~~e~VmR------------A~~~VyHl~CF   31 (31)
T d1rutx3           4 ACSACGQSIPASELVMR------------AQGNVYHLKCF   31 (31)
T ss_dssp             ECTTTCCEECTTSEEEE------------ETTEEECGGGC
T ss_pred             ccccccCcCChhHhhee------------cccceeeeccC
Confidence            59999999999884333            35678888887

>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=94.61  E-value=0.0053  Score=36.17  Aligned_cols=25  Identities=24%  Similarity=0.697  Sum_probs=20.6

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGC  118 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~C  118 (242)
                      .|..|++-|.+ ++ +.    +.++.|||+|
T Consensus        17 ~C~~C~~~ItG-~V-~~----Ag~~~yHP~C   41 (41)
T d1v6ga1          17 RCFSCDQFIEG-EV-VS----ALGKTYHPDC   41 (41)
T ss_dssp             BCTTTCCBCCS-CC-EE----ETTEEECTTT
T ss_pred             ccccccCEeee-ee-eE----ecCcccCCCC
Confidence            79999999975 34 44    6789999998

>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=94.39  E-value=0.007  Score=33.56  Aligned_cols=28  Identities=21%  Similarity=0.510  Sum_probs=23.6

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      ..|..|.+.++..+-+.     -.|+.||..||
T Consensus         8 ~kcg~c~ktvy~aeevq-----c~g~sfhk~cf   35 (35)
T d1b8ta1           8 KKCGVCQKAVYFAEEVQ-----CEGSSFHKSCF   35 (35)
T ss_dssp             EECTTTCCEECSSCCEE-----ETTEEECTTTC
T ss_pred             ceeccccceEeeeeeee-----ecCcccccccC
Confidence            47999999999877655     35899999998

>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=94.32  E-value=0.012  Score=31.83  Aligned_cols=29  Identities=10%  Similarity=0.178  Sum_probs=22.1

Q ss_pred             CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      .|.|+.|++.+-+-+.             +.-..+.||..||
T Consensus         2 n~~CaRC~k~VYp~Ek-------------l~ClDk~WHK~CF   30 (30)
T d1zfoa_           2 NPNCARCGKIVYPTEK-------------VNCLDKFWHKACF   30 (30)
T ss_dssp             CCBCSSSCSBCCGGGC-------------CCSSSSCCCGGGC
T ss_pred             CCcccccCCccccHHH-------------hhhhHHHHhhccC
Confidence            4789999999877542             2335799999987

>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=94.31  E-value=0.0067  Score=31.94  Aligned_cols=27  Identities=19%  Similarity=0.486  Sum_probs=22.7

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      .|+.|.+.++..+-+-     -.|+.||..||
T Consensus         2 kcg~c~ktvy~aeevq-----c~grsfhk~cf   28 (28)
T d1a7ia1           2 KCGACGRTVYHAEEVQ-----CDGRSFHRCCF   28 (28)
T ss_dssp             BCSSSCCBCSSTTEEE-----ETTEEEESSSE
T ss_pred             ccccccceEeeeeeee-----ecCceeccccC
Confidence            6999999998877654     35899999998

>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=94.09  E-value=0.016  Score=35.43  Aligned_cols=26  Identities=8%  Similarity=-0.373  Sum_probs=21.4

Q ss_pred             cccCCCCCCCHHHHhhhhcccccCCC
Q psy8090         204 NSLNKEQNHSFDNLLKSNLKKLSLAD  229 (242)
Q Consensus       204 f~~~d~~~yC~~cy~~~~a~kc~~~~  229 (242)
                      ..+.|+++||..||-++|.+|..--+
T Consensus        14 ~~ehdg~~YCk~CY~k~fGPKG~g~G   39 (49)
T d1b8ta4          14 LADKDGEIYCKGCYAKNFGPKGFGFG   39 (49)
T ss_dssp             EEEETTEEEEHHHHHHHTCCCCCCCC
T ss_pred             ccccCCcccchhhhhhccCCCccCcc
Confidence            34579999999999999999965544

>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=93.54  E-value=0.0096  Score=32.08  Aligned_cols=26  Identities=12%  Similarity=-0.153  Sum_probs=22.3

Q ss_pred             CCCCCCCcccCCCCCCCHHHHhhhhc
Q psy8090         197 ESYGTHRNSLNKEQNHSFDNLLKSNL  222 (242)
Q Consensus       197 ~~~g~~~f~~~d~~~yC~~cy~~~~a  222 (242)
                      .-+|...|..+.+..||+.|.+.+||
T Consensus         7 q~igsgsffpkg~d~ycvtche~kfa   32 (32)
T d1x63a2           7 QVIGTGSFFPKGEDFYCVTCHETKFA   32 (32)
T ss_dssp             CCCTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             hhcccccccCCCCcEEEEEeeccccC
Confidence            35777888889999999999999886

>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=93.41  E-value=0.017  Score=32.89  Aligned_cols=29  Identities=10%  Similarity=0.224  Sum_probs=22.9

Q ss_pred             CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      ..+|..|++.+-+-+    .         +.+.++.||..||
T Consensus         7 ~~kC~~C~K~VY~~E----~---------~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           7 RETCVECQKTVYPME----R---------LLANQQVFHISCF   35 (35)
T ss_dssp             SCBCTTTCCBCCTTS----E---------EECSSSEEETTTC
T ss_pred             CcccccCCCEEeeee----e---------EecCCeehhhccC
Confidence            479999999987644    2         3557899999998

>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=93.37  E-value=0.025  Score=31.44  Aligned_cols=25  Identities=24%  Similarity=0.600  Sum_probs=19.7

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGC  118 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~C  118 (242)
                      .|.+|.+.|.+  .++.    +-+..|||+|
T Consensus        10 ~C~~C~~~itG--pvMv----AG~~K~HPEC   34 (34)
T d1x6aa1          10 FCHGCSLLMTG--PFMV----AGEFKYHPEC   34 (34)
T ss_dssp             BCTTTCCBCCS--CCBC----CTTCCBCTTS
T ss_pred             HhhhhHhhccc--ceee----ecccccCCCC
Confidence            69999998885  3443    6678899998

>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=93.37  E-value=0.02  Score=31.80  Aligned_cols=31  Identities=35%  Similarity=0.820  Sum_probs=23.7

Q ss_pred             ccccccCCCCCCc-ccee-eCCeeccHhhhhcc
Q psy8090         119 FTCSVCNELLVDL-IYFY-RGDKLYCGRHHAET  149 (242)
Q Consensus       119 F~C~~C~~~L~~~-~~~~-~dg~~yC~~~y~~~  149 (242)
                      |.|..|+.-+.+. .|.. ...++||+.||.+.
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy~~~   33 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCHNEV   33 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecchhcc
Confidence            7899999988644 4554 45789999999753

>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=93.30  E-value=0.032  Score=31.84  Aligned_cols=29  Identities=14%  Similarity=0.043  Sum_probs=22.9

Q ss_pred             CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      ..+|..|++.+-+-+.             +.+.++.||..||
T Consensus         8 ~~~C~~C~K~VY~~Er-------------l~a~g~~yHk~CF   36 (36)
T d2co8a2           8 GDLCALCGEHLYVLER-------------LCVNGHFFHRSCF   36 (36)
T ss_dssp             SCBCSSSCCBCCTTTB-------------CCBTTBCCBTTTC
T ss_pred             CCcccccCCEEeeeeE-------------EEecCcEeccccC
Confidence            4789999999876442             4568899999998

>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=93.05  E-value=0.012  Score=34.09  Aligned_cols=28  Identities=25%  Similarity=0.712  Sum_probs=20.6

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      .|.+|++....++-+..    --+..|||.|-
T Consensus         1 ~C~rC~~mF~EGEEMYL----QGs~IWHP~C~   28 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYL----QGSSIWHPACR   28 (41)
T ss_dssp             CCSSSCCCCCSSCCCEE----ETTEEECTTHH
T ss_pred             Ccchhhccccccceeee----cCCceeCCccc
Confidence            38999999887765432    34678999884

>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=93.05  E-value=0.025  Score=30.66  Aligned_cols=25  Identities=24%  Similarity=0.639  Sum_probs=20.8

Q ss_pred             ccccCCCceecCccccccccCCCCCcccCCc
Q psy8090          88 FCENCEDELQTSDMSVFASRAGPNSCWHPGC  118 (242)
Q Consensus        88 ~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~C  118 (242)
                      -|..|.+-|.+  .++.    +-++.|||.|
T Consensus         7 gC~~C~~~ItG--kVLE----AG~khYHP~C   31 (32)
T d1wiga1           7 GCDSCEKYITG--RVLE----AGEKHYHPSC   31 (32)
T ss_dssp             SCSSSCCCCSS--CCBC----CSSCCBCTTT
T ss_pred             hhhhhhhhhhh--hhhh----ccccccCCCC
Confidence            59999999998  4554    6789999988

>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=92.99  E-value=0.041  Score=29.64  Aligned_cols=28  Identities=25%  Similarity=0.413  Sum_probs=22.5

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhc
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAE  148 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~  148 (242)
                      .|+.|++.|.. .--+.+|.+||..|+.+
T Consensus         1 nC~~Cgkelta-dArEl~geLyCLpChdK   28 (31)
T d2cora1           1 NCANCGKELTA-DARELKGELYCLPCHDK   28 (31)
T ss_dssp             BCSSSCCBCCT-TCEEETTEEECHHHHHT
T ss_pred             Cccccccccch-hHHHhcCCEEEEecccc
Confidence            38899999864 44577899999999875

>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=92.92  E-value=0.013  Score=32.07  Aligned_cols=21  Identities=5%  Similarity=-0.222  Sum_probs=18.1

Q ss_pred             CCCcccCCCCCCCHHHHhhhh
Q psy8090         201 THRNSLNKEQNHSFDNLLKSN  221 (242)
Q Consensus       201 ~~~f~~~d~~~yC~~cy~~~~  221 (242)
                      ...|..+|+.|||..||+.+|
T Consensus        10 ~gEYm~kdG~PyCe~DY~~~F   30 (31)
T d2dj7a1          10 TGEYISKDGVPYCESDYHAQF   30 (31)
T ss_dssp             SSCCEEETTEEECTTHHHHHT
T ss_pred             cceeecCCCCcccHHHHHHhc
Confidence            345888999999999999887

>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=92.44  E-value=0.012  Score=35.11  Aligned_cols=29  Identities=7%  Similarity=0.171  Sum_probs=22.2

Q ss_pred             CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      .++|..|++.+-.-++             +.+.++.||..||
T Consensus        15 ~~kC~~C~k~VY~~E~-------------~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          15 SDGCPRCGQAVYAAEK-------------VIGAGKSWHKSCF   43 (43)
T ss_dssp             CEECTTTSCEECSSSC-------------EEETTEEECTTTC
T ss_pred             CCcCccCCCEeeHHHH-------------hhcCCCccccCCC
Confidence            3789999999876542             2347899999998

>d2d8xa1 g.39.1.3 (A:33-64) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=91.72  E-value=0.075  Score=28.81  Aligned_cols=29  Identities=24%  Similarity=0.661  Sum_probs=26.3

Q ss_pred             cccccCCCCCCccceeeCCeeccHhhhhc
Q psy8090         120 TCSVCNELLVDLIYFYRGDKLYCGRHHAE  148 (242)
Q Consensus       120 ~C~~C~~~L~~~~~~~~dg~~yC~~~y~~  148 (242)
                      +|..|...|.+..|.--.|+..|..|+.+
T Consensus         1 rC~~C~~~LAD~GFvKnagR~LCrpch~r   29 (32)
T d2d8xa1           1 RCDLCQEVLADIGFVKNAGRHLCRPCHNR   29 (32)
T ss_dssp             BCSSSCCBCSSSCCEEETTEEECHHHHHH
T ss_pred             CchHHHhHHHHhhhhhcccccccchhhhh
Confidence            58999999999999999999999999864

>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=91.41  E-value=0.03  Score=30.49  Aligned_cols=28  Identities=11%  Similarity=0.216  Sum_probs=21.5

Q ss_pred             CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCC
Q psy8090         151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEH  191 (242)
Q Consensus       151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~  191 (242)
                      .++|..|++++-.-+.             +...++.||..|
T Consensus         2 ~~~CprC~K~VYfaEk-------------~~~lgk~WHk~C   29 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEK-------------VSSLGKDWHKFC   29 (30)
T ss_dssp             CCBCTTTCCBCCTTTE-------------EEETTEEEETTT
T ss_pred             CCcCCCCCCceeeHHh-------------hccCCccccccc
Confidence            5799999999987653             233689999876

>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=90.83  E-value=0.03  Score=36.14  Aligned_cols=26  Identities=8%  Similarity=-0.093  Sum_probs=20.7

Q ss_pred             CCCCCcccCCCCCCCHHHHhhhhccc
Q psy8090         199 YGTHRNSLNKEQNHSFDNLLKSNLKK  224 (242)
Q Consensus       199 ~g~~~f~~~d~~~yC~~cy~~~~a~k  224 (242)
                      +........++++||..||-++|.+|
T Consensus         9 LdS~~~~eh~~e~YCk~CY~k~fGPk   34 (65)
T d1b8ta2           9 LDSTTVAVHGDEIYCKSCYGKKYGPK   34 (65)
T ss_dssp             CCSSSEEEETTEEEEHHHHHHHHSCC
T ss_pred             cCCCccccCCCcccchhhhccccCCC
Confidence            34444566788999999999999877

>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=90.59  E-value=0.093  Score=29.22  Aligned_cols=27  Identities=22%  Similarity=0.577  Sum_probs=21.1

Q ss_pred             cccccCCCceecCccccccccCCCCCcccCCcc
Q psy8090          87 MFCENCEDELQTSDMSVFASRAGPNSCWHPGCF  119 (242)
Q Consensus        87 ~~C~~C~~~I~~~~~~v~~~r~~~~~~wH~~CF  119 (242)
                      .+|.+|...|.... ..     ..+..|||..|
T Consensus         9 ~vC~KCh~iIdd~p-L~-----Fr~d~YHp~HF   35 (35)
T d2cora2           9 YICQKCHAIIDEQP-LI-----FKNDPYHPDHF   35 (35)
T ss_dssp             CBCTTTCCBCCSCC-CC-----CSSSCCCTTTS
T ss_pred             HHHHHHHhhhhcCc-ce-----ecCCCCCCCCC
Confidence            47999999997743 33     46889999887

>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=90.42  E-value=0.076  Score=28.88  Aligned_cols=26  Identities=19%  Similarity=0.599  Sum_probs=23.0

Q ss_pred             ccccCCCCCCccceeeCCeeccHhhh
Q psy8090         121 CSVCNELLVDLIYFYRGDKLYCGRHH  146 (242)
Q Consensus       121 C~~C~~~L~~~~~~~~dg~~yC~~~y  146 (242)
                      |..|+-+|++..|...+..++|..|-
T Consensus         2 cgkcsvslvg~gfltq~~~i~c~~cg   27 (34)
T d1x68a2           2 CGKCSVSLVGKGFLTQNKEIFCQKCG   27 (34)
T ss_dssp             CTTTCCBCSSSCEEEETTEEEETTTT
T ss_pred             CccceEEEEeeeeeeccCcEEehhcC
Confidence            77899999999999999999997764

>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=90.00  E-value=0.083  Score=28.91  Aligned_cols=25  Identities=8%  Similarity=-0.377  Sum_probs=21.6

Q ss_pred             CCCCCCcccCCCCCCCHHHHhhhhc
Q psy8090         198 SYGTHRNSLNKEQNHSFDNLLKSNL  222 (242)
Q Consensus       198 ~~g~~~f~~~d~~~yC~~cy~~~~a  222 (242)
                      ++..--|++..++.||.-||.+-||
T Consensus         8 sL~d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           8 TMAYIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             BCSSSCBEESSSCEECHHHHHHHTS
T ss_pred             cHhhcceeeecCcEeHHHHHHHhcC
Confidence            5667779999999999999998765

>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=89.72  E-value=0.029  Score=33.94  Aligned_cols=23  Identities=4%  Similarity=-0.203  Sum_probs=19.2

Q ss_pred             CCcccCCCCCCC-HHHHhhhhccc
Q psy8090         202 HRNSLNKEQNHS-FDNLLKSNLKK  224 (242)
Q Consensus       202 ~~f~~~d~~~yC-~~cy~~~~a~k  224 (242)
                      ....+.|++||| ..||-++|.||
T Consensus        12 g~~aeHdg~pYC~k~CY~~~FGPk   35 (48)
T d1imla2          12 GGHAEHEGKPYCNHPCYSAMFGPK   35 (48)
T ss_dssp             TTEEEETTEEEETTTHHHHHSSCC
T ss_pred             CChhhcCCcccccccchhhccCCC
Confidence            344567999999 77999999998

>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=89.03  E-value=0.12  Score=28.55  Aligned_cols=24  Identities=8%  Similarity=-0.151  Sum_probs=20.8

Q ss_pred             CCCCCCCcccCCCCCCCHHHHhhh
Q psy8090         197 ESYGTHRNSLNKEQNHSFDNLLKS  220 (242)
Q Consensus       197 ~~~g~~~f~~~d~~~yC~~cy~~~  220 (242)
                      +++.+..|.+-|++|||...|+.+
T Consensus         7 ~PF~~~~Fy~~~g~PyCe~HyH~~   30 (32)
T d1x3ha2           7 TSFSTGSFFELDGRPFCELHYHHR   30 (32)
T ss_dssp             CBSCSSCCEESSSCEECHHHHHHH
T ss_pred             CcCCCCCeEeECCccchHHhhhhh
Confidence            467788899999999999999876

>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=88.97  E-value=0.18  Score=29.55  Aligned_cols=24  Identities=4%  Similarity=-0.249  Sum_probs=21.0

Q ss_pred             CCCcccCCCCCCCHHHHhhhhccc
Q psy8090         201 THRNSLNKEQNHSFDNLLKSNLKK  224 (242)
Q Consensus       201 ~~~f~~~d~~~yC~~cy~~~~a~k  224 (242)
                      ...|...++.+||..+|..+|.+|
T Consensus        11 ~~~yas~~G~lYCkpHf~qLF~~k   34 (42)
T d2d8ya2          11 LGTYASLHGRIYCKPHFNQLFKSK   34 (42)
T ss_dssp             TTTCCCSSSCCCCHHHHHHHSCCC
T ss_pred             CCcchhhCCEeccHHHHHHHHHhh
Confidence            345788899999999999999988

>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=88.78  E-value=0.19  Score=34.46  Aligned_cols=47  Identities=15%  Similarity=0.507  Sum_probs=25.9

Q ss_pred             ccccccCCCCCCccceeeCCeeccHhhhhcccCCCcccCCCcccCCC
Q psy8090         119 FTCSVCNELLVDLIYFYRGDKLYCGRHHAETLKPRCSACDEECQTSS  165 (242)
Q Consensus       119 F~C~~C~~~L~~~~~~~~dg~~yC~~~y~~~~~prC~~C~~~I~~~~  165 (242)
                      +.|..|...+.+-.....=|..||..|..+.+..+|..|...+....
T Consensus        23 l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~~~CP~Cr~~~~~~~   69 (97)
T d1jm7b_          23 LRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQD   69 (97)
T ss_dssp             TSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTTTBCSSSCCBCSCSS
T ss_pred             CCCccCCchhhcCceeCCCCCchhHHHHHHHHhccccccCCcCchhh
Confidence            34444444443322122335556666655555667999988876543

>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=87.45  E-value=0.23  Score=26.72  Aligned_cols=26  Identities=12%  Similarity=0.238  Sum_probs=20.2

Q ss_pred             CCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCC
Q psy8090         152 PRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEH  191 (242)
Q Consensus       152 prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~  191 (242)
                      .-|..|++.|+...              +.+-.+.+|+.|
T Consensus         6 sgC~~C~~~ItGkV--------------LEAG~khYHP~C   31 (32)
T d1wiga1           6 SGCDSCEKYITGRV--------------LEAGEKHYHPSC   31 (32)
T ss_dssp             CSCSSSCCCCSSCC--------------BCCSSCCBCTTT
T ss_pred             chhhhhhhhhhhhh--------------hhccccccCCCC
Confidence            46999999999753              466778888876

>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=87.24  E-value=0.15  Score=28.14  Aligned_cols=28  Identities=18%  Similarity=0.205  Sum_probs=21.3

Q ss_pred             CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      -|.|..|+..|.+-.              +.+..+..|++||
T Consensus         8 lp~CdkCg~GIVG~~--------------VK~rDk~rHPeCf   35 (35)
T d1x62a2           8 LPMCDKCGTGIVGVF--------------VKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCSSSCCCCCSSC--------------EECSSCEECTTTT
T ss_pred             CccccccCCCcEeEE--------------EEeccccCCCCCC
Confidence            489999999998633              3446678899887

>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=86.16  E-value=0.26  Score=26.67  Aligned_cols=29  Identities=24%  Similarity=0.568  Sum_probs=22.7

Q ss_pred             cccccCCCC--CCccceeeCCeeccHhhhhc
Q psy8090         120 TCSVCNELL--VDLIYFYRGDKLYCGRHHAE  148 (242)
Q Consensus       120 ~C~~C~~~L--~~~~~~~~dg~~yC~~~y~~  148 (242)
                      .|.-|+..|  ++...|.+.+.+.|+++|.+
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            456666666  57788899999999999964

>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=85.99  E-value=0.18  Score=29.67  Aligned_cols=28  Identities=14%  Similarity=0.248  Sum_probs=21.9

Q ss_pred             CCCcccCCCcccCCCcceeeeeecCCCCCCCCCCCcccCCCc
Q psy8090         151 KPRCSACDEECQTSSQDILYYLTRDSERDLPDEYRTERLEHQ  192 (242)
Q Consensus       151 ~prC~~C~~~I~~~~~~~~~~~~~~~~~~~~~~~~~~h~~~f  192 (242)
                      -|.|..|+..|.+-.              +.+-++..|++||
T Consensus        18 LP~CdkCg~GIVG~~--------------VK~rDK~rHPeCf   45 (45)
T d1x64a1          18 MPLCDKCGSGIVGAV--------------VKARDKYRHPECF   45 (45)
T ss_dssp             CCBCTTTCCBCCSCC--------------EESSSCEECTTTC
T ss_pred             CccccccCCCcEEEE--------------EEeccccCCCCCC
Confidence            489999999998632              3456788899997

>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=81.32  E-value=0.48  Score=24.80  Aligned_cols=27  Identities=22%  Similarity=0.461  Sum_probs=22.6

Q ss_pred             ccccCCCCCCccceeeCCeeccHhhhh
Q psy8090         121 CSVCNELLVDLIYFYRGDKLYCGRHHA  147 (242)
Q Consensus       121 C~~C~~~L~~~~~~~~dg~~yC~~~y~  147 (242)
                      |..|.-+|++..|....+.+.|..|-.
T Consensus         2 c~kcsvslvgrgflterddilc~dcgk   28 (30)
T d1x4la2           2 CKKCSLSLVGRGFLTERDDILCPDCGK   28 (30)
T ss_dssp             CSSSCCBCTTSCCEECSSSEECHHHHH
T ss_pred             cceeeEEEEeeeccccccceeccccCc
Confidence            778889999999998878888988754