Psyllid ID: psy10849

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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-------250-------260-------
Protein Sequence
STSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTMNSKRAKNILTPNQRRQFKSSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFCSSDISLDESTNLDEGGSDSLSLDLGPPSNHDTMLSSLGQINPIDKQRC
Secondary Structure (PSIPRED)
ccccccccccHHHHHHHcccccccccccccccccEEEccccEEEcccccccccccccccccEEEEEccEEEEcccHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHccccccccccccccccccccccccHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccEEEHHHHHHHHcccHHHccccccHHHHHHHHHccEEEEHHHHHHHHHcccccccEEEEEcccEEEcccHHHHHHHcccccccccccccccccccccccccccccEEEcHHHHHHHHHHHHccccccHHHcccccHHHHEEHHHHHHHHHHHHHHHHHcccHHcccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
stshnshvschprgfrlygvkcarcgdrllphEMVMRAQshvyhlpcfvcviccqplqkgeQFILRSGQLFCRQDFEKEMYLmqqsspsddmmldencrprdgrrgpkrprtiLTSAQRRQFkssfevspkpcrkvstmnskrakniltpnqrrqfkssfeissmpcrkvgvhgHYLSLGmslqdssdsifasstkplnpnhpyspddsyamhsndsfcssdisldestnldeggsdslsldlgppsnhdtmlsslgqinpidkqrc
Flexible Loop (DISEMBL)
stshnshvschprgfrlygvKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLMQqsspsddmmldencrprdgrrgpkrprtiltsaqrrqfkssfevspkpcrkvstmnskrakniltpnqrrqfkSSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFCSSDISLDESTNLDEGGSDSLSLDLGPPSNHDTmlsslgqinpidkqrc
Low Complexity Region (SEG)
STSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLMQQSSPSDDMMLDENCrprdgrrgpkrprTILTSAQRRQFKSSFEVSPKPCRKVSTMNSKRAKNILTPNQRRQFKSSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFCSSDISLDESTNldeggsdslsldlgPPSNHDTMLSSLGQINPIDKQRC
Disordered region (IsUnstruct)
*********CHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY************************************************************************************PCRKVGVHGHYLSLG***************************************************************************************
Disordered Region (DISOPRED)
**SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK**********************************************************************TPN********************************************************************************************************************
Disordered Region (DISEMBL)
**********HPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTMNSKRAKNILTPNQRRQFKSSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFCSSDISLDE**********SLSLDLGPPSNHDTMLSSLGQINPIDKQRC
Disordered Region (DISPRO)
*****SHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLM************************KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTMNSKRAKNILTPNQRRQFKSSF*****************************************H****D*SYA*H*N**F*SSD*********************************************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
STSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTMNSKRAKNILTPNQRRQFKSSFEISSMPCRKVGVHGHYLSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFCSSDISLDESTNLDEGGSDSLSLDLGPPSNHDTMLSSLGQINPIDKQRC
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	267	2.2.26 [Sep-21-2011]
Q04650	382	LIM homeobox transcriptio	N/A	N/A	0.531	0.371	0.457	3e-30
Q9JKU8	382	LIM homeobox transcriptio	yes	N/A	0.531	0.371	0.457	3e-30
Q8TE12	382	LIM homeobox transcriptio	yes	N/A	0.531	0.371	0.451	4e-30
O88609	372	LIM homeobox transcriptio	no	N/A	0.531	0.381	0.419	5e-28
O60663	379	LIM homeobox transcriptio	no	N/A	0.531	0.374	0.419	6e-28
Q60564	369	LIM homeobox transcriptio	N/A	N/A	0.531	0.384	0.425	2e-27
Q8UVR3	400	LIM homeobox transcriptio	N/A	N/A	0.531	0.355	0.427	9e-27
P53413	377	LIM/homeobox protein LMX-	no	N/A	0.531	0.376	0.421	4e-26
Q25132	692	LIM/homeobox protein Lhx3	N/A	N/A	0.419	0.161	0.353	7e-17
Q969G2	390	LIM/homeobox protein Lhx4	no	N/A	0.434	0.297	0.340	1e-16

>sp|Q04650|LMX1A_MESAU LIM homeobox transcription factor 1-alpha OS=Mesocricetus auratus GN=LMX1A PE=2 SV=1

 Score =  132 bits (331), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 75/164 (45%), Positives = 97/164 (59%), Gaps = 22/164 (13%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           +L+ VKC  C + + P+E VMRAQ  VYHL CF C +C + LQKG++F+L+ GQL C+ D
Sbjct: 88  KLFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGD 147

Query: 76  FEKEMYLMQQSSP--SDDMMLDEN---CR---------PRDGR--RGPKRPRTILTSAQR 119
           +EKE  L+   SP  SD    D+    C+           DG+  + PKRPRTILT+ QR
Sbjct: 148 YEKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGTSEDGKDHKRPKRPRTILTTQQR 207

Query: 120 RQFKSSFEVSPKPCRKV------STMNSKRAKNILTPNQRRQFK 157
           R FK+SFEVS KPCRKV       T  S R   +   NQR + K
Sbjct: 208 RAFKASFEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMK 251

Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae.
Mesocricetus auratus (taxid: 10036)

>sp|Q9JKU8|LMX1A_MOUSE LIM homeobox transcription factor 1-alpha OS=Mus musculus GN=Lmx1a PE=2 SV=1

 Score =  132 bits (331), Expect = 3e-30,   Method: Compositional matrix adjust.
 Identities = 75/164 (45%), Positives = 97/164 (59%), Gaps = 22/164 (13%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           +L+ VKC  C + + P+E VMRAQ  VYHL CF C +C + LQKG++F+L+ GQL C+ D
Sbjct: 88  KLFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGD 147

Query: 76  FEKEMYLMQQSSP--SDDMMLDEN---CR---------PRDGR--RGPKRPRTILTSAQR 119
           +EKE  L+   SP  SD    D+    C+           DG+  + PKRPRTILT+ QR
Sbjct: 148 YEKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGASEDGKDHKRPKRPRTILTTQQR 207

Query: 120 RQFKSSFEVSPKPCRKV------STMNSKRAKNILTPNQRRQFK 157
           R FK+SFEVS KPCRKV       T  S R   +   NQR + K
Sbjct: 208 RAFKASFEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMK 251

Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae.

Mus musculus (taxid: 10090)

>sp|Q8TE12|LMX1A_HUMAN LIM homeobox transcription factor 1-alpha OS=Homo sapiens GN=LMX1A PE=2 SV=1

 Score =  131 bits (330), Expect = 4e-30,   Method: Compositional matrix adjust.
 Identities = 74/164 (45%), Positives = 95/164 (57%), Gaps = 22/164 (13%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           +L+ VKC  C + + P+E VMRAQ  VYHL CF C +C + LQKG++F+L+ GQL C+ D
Sbjct: 88  KLFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGD 147

Query: 76  FEKEMYLMQQSSP--SDDMMLDEN---CRPRDG-----------RRGPKRPRTILTSAQR 119
           +EKE  L+   SP  SD    D+    C+   G            + PKRPRTILT+ QR
Sbjct: 148 YEKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGTAEEGKDHKRPKRPRTILTTQQR 207

Query: 120 RQFKSSFEVSPKPCRKV------STMNSKRAKNILTPNQRRQFK 157
           R FK+SFEVS KPCRKV       T  S R   +   NQR + K
Sbjct: 208 RAFKASFEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMK 251

Acts as a transcriptional activator by binding to an A/T-rich sequence, the FLAT element, in the insulin gene promoter. Required for development of the roof plate and, in turn, for specification of dorsal cell fates in the CNS and developing vertebrae.

Homo sapiens (taxid: 9606)

>sp|O88609|LMX1B_MOUSE LIM homeobox transcription factor 1-beta OS=Mus musculus GN=Lmx1b PE=2 SV=2

 Score =  124 bits (312), Expect = 5e-28,   Method: Compositional matrix adjust.
 Identities = 70/167 (41%), Positives = 95/167 (56%), Gaps = 25/167 (14%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           +L+  KC+ C +++ P E VMRA   VYHL CF C +C + L+KG++F+L+ GQL C+ D
Sbjct: 86  QLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCERQLRKGDEFVLKEGQLLCKGD 145

Query: 76  FEKEMYLMQQSSPSDDMML-----DENCRPRDGR--------------RGPKRPRTILTS 116
           +EKE  L+   SP +   +     D + +P  G+              R PKRPRTILT+
Sbjct: 146 YEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTT 205

Query: 117 AQRRQFKSSFEVSPKPCRKV------STMNSKRAKNILTPNQRRQFK 157
            QRR FK+SFEVS KPCRKV       T  S R   +   NQR + K
Sbjct: 206 QQRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMK 252

Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels.

Mus musculus (taxid: 10090)

>sp|O60663|LMX1B_HUMAN LIM homeobox transcription factor 1-beta OS=Homo sapiens GN=LMX1B PE=1 SV=2

 Score =  124 bits (312), Expect = 6e-28,   Method: Compositional matrix adjust.
 Identities = 70/167 (41%), Positives = 95/167 (56%), Gaps = 25/167 (14%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           +L+  KC+ C +++ P E VMRA   VYHL CF C +C + L+KG++F+L+ GQL C+ D
Sbjct: 86  QLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCERQLRKGDEFVLKEGQLLCKGD 145

Query: 76  FEKEMYLMQQSSPSDDMML-----DENCRPRDGR--------------RGPKRPRTILTS 116
           +EKE  L+   SP +   +     D + +P  G+              R PKRPRTILT+
Sbjct: 146 YEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGSGDDGKDPRRPKRPRTILTT 205

Query: 117 AQRRQFKSSFEVSPKPCRKV------STMNSKRAKNILTPNQRRQFK 157
            QRR FK+SFEVS KPCRKV       T  S R   +   NQR + K
Sbjct: 206 QQRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMK 252

Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels.

Homo sapiens (taxid: 9606)

>sp|Q60564|LMX1B_MESAU LIM homeobox transcription factor 1-beta (Fragment) OS=Mesocricetus auratus GN=LMX1B PE=2 SV=1

 Score =  122 bits (307), Expect = 2e-27,   Method: Compositional matrix adjust.
 Identities = 71/167 (42%), Positives = 96/167 (57%), Gaps = 25/167 (14%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           +L+  KC+ C +++ P E VMRA   VYHL CF C +C + L+KG++F+L+ GQL C+ D
Sbjct: 76  QLFAAKCSGCMEKIAPTEFVMRALECVYHLGCFCCCVCERQLRKGDEFVLKEGQLLCKGD 135

Query: 76  FEKEMYLMQQSSPSDDMML-----DENCRPR------------DGR--RGPKRPRTILTS 116
           +EKE  L+   SP +   +     D + +P             DG+  R PKRPRTILT+
Sbjct: 136 YEKEKDLLSSVSPDESDSVKSEDEDGDMKPAKGQGSQSKGGGDDGKDPRRPKRPRTILTT 195

Query: 117 AQRRQFKSSFEVSPKPCRKV------STMNSKRAKNILTPNQRRQFK 157
            QRR FK+SFEVS KPCRKV       T  S R   +   NQR + K
Sbjct: 196 QQRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMK 242

Essential for the specification of dorsal limb fate at both the zeugopodal and autopodal levels. Mediates physical interaction and transcriptional synergy with E47/PAN-1.

Mesocricetus auratus (taxid: 10036)

>sp|Q8UVR3|LMX1B_XENLA LIM homeobox transcription factor 1-beta.1 OS=Xenopus laevis GN=lmx1b.1 PE=2 SV=1

 Score =  120 bits (302), Expect = 9e-27,   Method: Compositional matrix adjust.
 Identities = 71/166 (42%), Positives = 95/166 (57%), Gaps = 24/166 (14%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           +L+  KC+ C +++ P E VMRA   VYHL CF C +C + L+KG++F+L+ GQL C+ D
Sbjct: 109 QLFAAKCSGCMEKIAPTEFVMRALECVYHLSCFCCCVCERQLRKGDEFVLKEGQLLCKSD 168

Query: 76  FEKEMYLMQQSSPSDDMML-----DENCRPRDGR-------------RGPKRPRTILTSA 117
           +EKE  L+   SP D   +     + + +P  GR             R PKRPRTILT+ 
Sbjct: 169 YEKEKDLLSSGSPDDSDSVKSDDEEGDVKPGKGRVNQGKGSDDGKDPRRPKRPRTILTTQ 228

Query: 118 QRRQFKSSFEVSPKPCRKV------STMNSKRAKNILTPNQRRQFK 157
           QRR FK+SFEVS KPCRKV       T  S R   +   NQR + K
Sbjct: 229 QRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKIK 274

Required for early specification of the kidney glomus, lying upstream of wt1 in the pathway controlling glomus differentiation. The balance in levels and expression patterns of binding partners such as lhx1/lim-1 influences differentiation into glomus or tubule derivatives. Involved in specification of serotonergic neurons.

Xenopus laevis (taxid: 8355)

>sp|P53413|LMX1B_CHICK LIM/homeobox protein LMX-1.2 OS=Gallus gallus GN=LMX1B PE=2 SV=1

 Score =  118 bits (295), Expect = 4e-26,   Method: Compositional matrix adjust.
 Identities = 70/166 (42%), Positives = 94/166 (56%), Gaps = 24/166 (14%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           +L+  KC+ C +++ P E VMRA   VYHL CF C +C + L+KG++F+L+ GQL C+ D
Sbjct: 86  QLFAAKCSGCMEKIAPTEFVMRALECVYHLSCFCCCVCERQLRKGDEFVLKEGQLLCKSD 145

Query: 76  FEKEMYLMQQSSPSDDMMLDE-----NCRPRDGR-------------RGPKRPRTILTSA 117
           +EKE  L+   SP D   +       + +P  G+             R PKRPRTILT+ 
Sbjct: 146 YEKEKDLLSSVSPDDSDSVKSDDEDGDVKPTKGQVTQGKGSDDGKDPRRPKRPRTILTTQ 205

Query: 118 QRRQFKSSFEVSPKPCRKV------STMNSKRAKNILTPNQRRQFK 157
           QRR FK+SFEVS KPCRKV       T  S R   +   NQR + K
Sbjct: 206 QRRAFKASFEVSSKPCRKVRETLAAETGLSVRVVQVWFQNQRAKMK 251

Specifies dorsal cell fate during limb development.

Gallus gallus (taxid: 9031)

>sp|Q25132|LHX3_HALRO LIM/homeobox protein Lhx3 OS=Halocynthia roretzi GN=LHX3 PE=2 SV=2

 Score = 87.8 bits (216), Expect = 7e-17,   Method: Compositional matrix adjust.
 Identities = 46/130 (35%), Positives = 66/130 (50%), Gaps = 18/130 (13%)

Query: 8   VSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQF-ILR 66
           V C    F+ +G KC  CG  + P E++ RAQ +VYHL  F C +C + +  G+QF +L 
Sbjct: 327 VFCKDDFFKRFGTKCTACGHGIPPTEVIRRAQDNVYHLEGFCCFLCHEKMGTGDQFYLLE 386

Query: 67  SGQLFCRQDFEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSF 126
             +L C++D+E+                    R  D   G KRPRT +T+ Q    KS++
Sbjct: 387 DNRLVCKKDYEQ-----------------AKSRDADIENGVKRPRTTITAKQLETLKSAY 429

Query: 127 EVSPKPCRKV 136
             SPKP R V
Sbjct: 430 NQSPKPARHV 439

May be involved in the determination of cell lineage of endoderm and notochord cells before gastrulation, and in specification of a distinct group of cells in neural tissue after gastrulation.

Halocynthia roretzi (taxid: 7729)

>sp|Q969G2|LHX4_HUMAN LIM/homeobox protein Lhx4 OS=Homo sapiens GN=LHX4 PE=1 SV=2

 Score = 87.4 bits (215), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 46/135 (34%), Positives = 71/135 (52%), Gaps = 19/135 (14%)

Query: 3   SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
           S    V C    F+ +G KC  C   + P ++V +AQ  VYHL CF C+IC + L  G++
Sbjct: 70  SRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDE 129

Query: 63  F-ILRSGQLFCRQDFEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQ 121
           F ++  G+L C++D+E        ++  +D          D   G KRPRT +T+ Q   
Sbjct: 130 FYLMEDGRLVCKEDYE--------TAKQND----------DSEAGAKRPRTTITAKQLET 171

Query: 122 FKSSFEVSPKPCRKV 136
            K++++ SPKP R V
Sbjct: 172 LKNAYKNSPKPARHV 186

May play a critical role in the development of respiratory control mechanisms and in the normal growth and maturation of the lung.

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	267
91077954	472	PREDICTED: similar to CG32105 CG32105-PB	0.966	0.546	0.587	3e-82
270002859	388	LIM homeobox transcription factor 1, bet	0.966	0.664	0.587	1e-81
357612982	327	hypothetical protein KGM_10626 [Danaus p	0.940	0.767	0.526	5e-72
242007294	389	Homeobox protein ceh-14, putative [Pedic	0.827	0.568	0.539	2e-64
328715997	407	PREDICTED: LIM homeobox transcription fa	0.850	0.557	0.539	4e-63
307204532	402	LIM homeobox transcription factor 1 beta	0.831	0.552	0.506	2e-55
350402518	402	PREDICTED: LIM homeobox transcription fa	0.771	0.512	0.521	5e-54
340711972	402	PREDICTED: LIM homeobox transcription fa	0.771	0.512	0.521	7e-54
383861320	402	PREDICTED: LIM homeobox transcription fa	0.771	0.512	0.517	2e-53
307189897	402	LIM homeobox transcription factor 1 beta	0.831	0.552	0.5	3e-53

>gi|91077954|ref|XP_967240.1| PREDICTED: similar to CG32105 CG32105-PB [Tribolium castaneum]

 Score =  310 bits (795), Expect = 3e-82,   Method: Compositional matrix adjust.
 Identities = 174/296 (58%), Positives = 202/296 (68%), Gaps = 38/296 (12%)

Query: 3   SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
           + N+ + C     R++GVKC+RCGDRLLPHEMVMRAQ HV+HLPCFVCV+CCQPLQKGEQ
Sbjct: 168 TRNTKLYCKADYDRIFGVKCSRCGDRLLPHEMVMRAQQHVFHLPCFVCVVCCQPLQKGEQ 227

Query: 63  FILRSGQLFCRQDFEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQF 122
           F+LR+GQLFCRQDFEKEMYLMQQ+S  DD MLDEN RPRDGRRGPKRPRTILTSAQRRQF
Sbjct: 228 FVLRAGQLFCRQDFEKEMYLMQQASSGDDDMLDENSRPRDGRRGPKRPRTILTSAQRRQF 287

Query: 123 KSSFEVSPKPCRKV------STMNSKRAKNILTPNQRR-----QFKSSFEISSMPCRKVG 171
           K+SFEVSPKPCRKV       T  S R   +   NQR      Q K+  +    P  K  
Sbjct: 288 KASFEVSPKPCRKVREALAKETGLSVRVVQVWFQNQRAKMKKIQRKAKQDDGKSPGDKDK 347

Query: 172 V---------------HGHYLSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSND 216
                           HGH++ +G    + SDS F SS++PLNPN PYSPDD+Y  HS +
Sbjct: 348 GDKDDKIIKQESPSSDHGHFMGMG----NLSDSHFPSSSQPLNPNIPYSPDDAYPAHSGE 403

Query: 217 SFCSSDISLDESTN---LDEGGSDSLSL-DLGPPSN----HDTMLSSLGQINPIDK 264
           SFCSSDISLD+STN   LDE  SD+LSL +L   S+    HD +  S    NPIDK
Sbjct: 404 SFCSSDISLDDSTNFDHLDEATSDTLSLQNLELQSSHSHQHDNVPPSGSIANPIDK 459

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|270002859|gb|EEZ99306.1| LIM homeobox transcription factor 1, beta [Tribolium castaneum]

 Score =  308 bits (790), Expect = 1e-81,   Method: Compositional matrix adjust.
 Identities = 174/296 (58%), Positives = 202/296 (68%), Gaps = 38/296 (12%)

Query: 3   SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
           + N+ + C     R++GVKC+RCGDRLLPHEMVMRAQ HV+HLPCFVCV+CCQPLQKGEQ
Sbjct: 84  TRNTKLYCKADYDRIFGVKCSRCGDRLLPHEMVMRAQQHVFHLPCFVCVVCCQPLQKGEQ 143

Query: 63  FILRSGQLFCRQDFEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQF 122
           F+LR+GQLFCRQDFEKEMYLMQQ+S  DD MLDEN RPRDGRRGPKRPRTILTSAQRRQF
Sbjct: 144 FVLRAGQLFCRQDFEKEMYLMQQASSGDDDMLDENSRPRDGRRGPKRPRTILTSAQRRQF 203

Query: 123 KSSFEVSPKPCRKV------STMNSKRAKNILTPNQRR-----QFKSSFEISSMPCRKVG 171
           K+SFEVSPKPCRKV       T  S R   +   NQR      Q K+  +    P  K  
Sbjct: 204 KASFEVSPKPCRKVREALAKETGLSVRVVQVWFQNQRAKMKKIQRKAKQDDGKSPGDKDK 263

Query: 172 V---------------HGHYLSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSND 216
                           HGH++ +G    + SDS F SS++PLNPN PYSPDD+Y  HS +
Sbjct: 264 GDKDDKIIKQESPSSDHGHFMGMG----NLSDSHFPSSSQPLNPNIPYSPDDAYPAHSGE 319

Query: 217 SFCSSDISLDESTN---LDEGGSDSLSL-DLGPPSN----HDTMLSSLGQINPIDK 264
           SFCSSDISLD+STN   LDE  SD+LSL +L   S+    HD +  S    NPIDK
Sbjct: 320 SFCSSDISLDDSTNFDHLDEATSDTLSLQNLELQSSHSHQHDNVPPSGSIANPIDK 375

Source: Tribolium castaneum

Species: Tribolium castaneum

Genus: Tribolium

Family: Tenebrionidae

Order: Coleoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|357612982|gb|EHJ68260.1| hypothetical protein KGM_10626 [Danaus plexippus]

 Score =  276 bits (707), Expect = 5e-72,   Method: Compositional matrix adjust.
 Identities = 157/298 (52%), Positives = 193/298 (64%), Gaps = 47/298 (15%)

Query: 3   SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
           + N+ + C P   RL+GVKC RCGDRLLP EMVMRAQ +V+H+ CFVCV+CCQPLQKGEQ
Sbjct: 28  TRNAKLYCKPDYDRLFGVKCTRCGDRLLPQEMVMRAQQYVFHIQCFVCVMCCQPLQKGEQ 87

Query: 63  FILRSGQLFCRQDFEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQF 122
           +++R+GQ+FCRQDFEKEMYLMQ +   DDM++D++ RPRDGRRGPKRPRTILTSAQRRQF
Sbjct: 88  YVIRAGQIFCRQDFEKEMYLMQHAE--DDMIIDDSERPRDGRRGPKRPRTILTSAQRRQF 145

Query: 123 KSSFEVSPKPCRKV------STMNSKRAKNILTPNQRRQFKSSFEISSMPCRKVGV---- 172
           K+SFEVSPKPCRKV       T  S R   +   NQR + K     +     K       
Sbjct: 146 KASFEVSPKPCRKVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKAKQEGDKNNDKDKD 205

Query: 173 --------------HGHYLSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSF 218
                         HG+YL L        D+ +++S++PLNPN PYSPDD Y  HS DSF
Sbjct: 206 KDEKSIKQESPSSEHGNYLGL--------DNSYSASSQPLNPNLPYSPDD-YPAHSGDSF 256

Query: 219 CSSDISLDEST--NLDEGGSDSLSLD---------LGPPSNHDTM-LSSLGQINPIDK 264
           CSSDISLD S    LDEG SD++SL           G  S+H+ + L +   +NPIDK
Sbjct: 257 CSSDISLDGSNFDQLDEGTSDTMSLQNLEVPHLPHHGNHSSHEPLNLGTGAVVNPIDK 314

Source: Danaus plexippus

Species: Danaus plexippus

Genus: Danaus

Family: Nymphalidae

Order: Lepidoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|242007294|ref|XP_002424476.1| Homeobox protein ceh-14, putative [Pediculus humanus corporis] gi|212507894|gb|EEB11738.1| Homeobox protein ceh-14, putative [Pediculus humanus corporis]

 Score =  251 bits (641), Expect = 2e-64,   Method: Compositional matrix adjust.
 Identities = 138/256 (53%), Positives = 171/256 (66%), Gaps = 35/256 (13%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           R++GVKC+RCGDR+LPHE+VMRAQ  V+HL CF C+ C Q LQKGEQF+L++GQLFCR D
Sbjct: 82  RIFGVKCSRCGDRILPHELVMRAQHLVFHLQCFCCIACGQHLQKGEQFVLKAGQLFCRPD 141

Query: 76  FEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRK 135
           FEKE+YL+  S   +D+ LD+  R RDGRRGPKRPRTILTSAQRRQFK+SFEVSPKPCRK
Sbjct: 142 FEKEIYLL-HSPTGEDLDLDDGIRHRDGRRGPKRPRTILTSAQRRQFKASFEVSPKPCRK 200

Query: 136 V------STMNSKRAKNILTPNQRRQFK--------------------SSFEISSMPCRK 169
           V       T  S R   +   NQR + K                     S ++ S    +
Sbjct: 201 VREALAKETGLSVRVVQVWFQNQRAKVKKIQRKAKQEQDKGLDKDKDEKSIKVESPDSDQ 260

Query: 170 VGVHGHYLSL-GMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFCSSDISLDES 228
           V    HYL L G++ QD+  +  +S+   +NP  P+SP+D+Y  +SNDSFCSSDISLD S
Sbjct: 261 V----HYLGLSGLNYQDNDTTTASSAQSSVNPIIPFSPEDNYHTNSNDSFCSSDISLDGS 316

Query: 229 T---NLDEGGSDSLSL 241
           T    LDEGGSDSLS+
Sbjct: 317 TQFEGLDEGGSDSLSV 332

Source: Pediculus humanus corporis

Species: Pediculus humanus

Genus: Pediculus

Family: Pediculidae

Order: Phthiraptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|328715997|ref|XP_001946565.2| PREDICTED: LIM homeobox transcription factor 1-beta-like [Acyrthosiphon pisum]

 Score =  247 bits (631), Expect = 4e-63,   Method: Compositional matrix adjust.
 Identities = 144/267 (53%), Positives = 174/267 (65%), Gaps = 40/267 (14%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQ-SHVYHLPCFVCVICCQPLQKGEQFILRSG--QLFC 72
           RL+GVKC RCG+ L   E+VMRA  SHVYH+ CF CV C QPLQKG+Q+++++G  QLFC
Sbjct: 86  RLFGVKCGRCGEPLGARELVMRAGPSHVYHVGCFACVACMQPLQKGQQYVVKAGGGQLFC 145

Query: 73  RQDFEKEMYLMQQS----SPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEV 128
           R DFEKE++LMQQ+     P D + LDENCRPRDGRRGPKRPRTILTS QRRQFK+SFEV
Sbjct: 146 RTDFEKEIFLMQQTVGSPQPDDSLTLDENCRPRDGRRGPKRPRTILTSVQRRQFKASFEV 205

Query: 129 SPKPCRKV------STMNSKRAKNILTPNQRRQFK-----------------------SS 159
           SPKPCRKV       T  S R   +   NQR + K                       + 
Sbjct: 206 SPKPCRKVREALAKDTGLSVRVVQVWFQNQRAKMKKIQRKSKQDDKNTNNNNANNTDKNE 265

Query: 160 FEISSMPCRKVGVHGHYLSLG-MSLQDSSDSIFASSTKPLNPNHPYSPDDSYAM-HSNDS 217
            E ++     V    HYLSL  +S+ DSSDS + +S +PLNPN PYSP+ +Y   HS DS
Sbjct: 266 TEHATNTTSSVCSGDHYLSLSTLSMHDSSDSNYQNS-QPLNPNIPYSPEGTYTGDHSVDS 324

Query: 218 FCSSDISLDESTN-LDEGGSDSLSLDL 243
           FCSSD+SLD ST   DE GSD++SLDL
Sbjct: 325 FCSSDVSLDGSTTAADEIGSDTMSLDL 351

Source: Acyrthosiphon pisum

Species: Acyrthosiphon pisum

Genus: Acyrthosiphon

Family: Aphididae

Order: Hemiptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307204532|gb|EFN83212.1| LIM homeobox transcription factor 1 beta [Harpegnathos saltator]

 Score =  221 bits (564), Expect = 2e-55,   Method: Compositional matrix adjust.
 Identities = 125/247 (50%), Positives = 160/247 (64%), Gaps = 25/247 (10%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           +++GVKCARC +++   ++VMR  S V+H+ CF+C +C QPL +G  FILR GQ  CR+D
Sbjct: 112 KIFGVKCARCMEKISCSDLVMRVASLVFHVECFMCCMCGQPLPRGAHFILRQGQPICRRD 171

Query: 76  FEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRK 135
           FE E+YL   +SP DD +LDEN RPRDGRRGPKRPRTILTSAQRRQFK+SFEVSPKPCRK
Sbjct: 172 FEHELYL---NSPQDDDLLDEN-RPRDGRRGPKRPRTILTSAQRRQFKASFEVSPKPCRK 227

Query: 136 V------STMNSKRAKNILTPNQR-------RQFKSSFEISSMPCRKVGV------HGHY 176
           V       T  S R   +   NQR       R+ K+       P  +         H HY
Sbjct: 228 VREALAKDTGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGSDKEPKEERRTESPHSDHSHY 287

Query: 177 LSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFCSSDISLDES-TNLDEGG 235
           L+  ++++D   S F S+T+PLNPN+PYSPDD+Y  HS +SFCSSD+SLD +    D G 
Sbjct: 288 LN-ALNMRDGESSSFPSATQPLNPNNPYSPDDAYPGHSGESFCSSDLSLDGTEAGFDIGE 346

Query: 236 SDSLSLD 242
           +D    D
Sbjct: 347 NDGGGAD 353

Source: Harpegnathos saltator

Species: Harpegnathos saltator

Genus: Harpegnathos

Family: Formicidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|350402518|ref|XP_003486514.1| PREDICTED: LIM homeobox transcription factor 1-beta-like [Bombus impatiens]

 Score =  217 bits (552), Expect = 5e-54,   Method: Compositional matrix adjust.
 Identities = 120/230 (52%), Positives = 151/230 (65%), Gaps = 24/230 (10%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           R++GVKCARC +++   + V+RA   V+H+ CF C +C QPL  G Q+ LR GQ  CR+D
Sbjct: 111 RIFGVKCARCMEKISCSDFVLRAPGLVFHVECFACCMCGQPLLPGTQYFLRQGQPICRRD 170

Query: 76  FEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRK 135
           +E E+YL   +SP DD +LDEN RPRDGRRGPKRPRTILTSAQRRQFK++FEVSPKPCRK
Sbjct: 171 YEHELYL---NSPQDDDLLDEN-RPRDGRRGPKRPRTILTSAQRRQFKAAFEVSPKPCRK 226

Query: 136 V------STMNSKRAKNILTPNQR-------RQFKSSFEISSMPCRKVGV------HGHY 176
           V       T  S R   +   NQR       R+ K+       P  +         H HY
Sbjct: 227 VREALAKETGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGSDKEPKEERRTESPHSDHSHY 286

Query: 177 LSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFCSSDISLD 226
           L+  M+++D   S F SST+PLNPN+PYSPDD+Y  HS +SFCSSD+SLD
Sbjct: 287 LN-AMNMRDGESSSFPSSTQPLNPNNPYSPDDAYPGHSGESFCSSDLSLD 335

Source: Bombus impatiens

Species: Bombus impatiens

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|340711972|ref|XP_003394539.1| PREDICTED: LIM homeobox transcription factor 1-beta-like [Bombus terrestris]

 Score =  216 bits (551), Expect = 7e-54,   Method: Compositional matrix adjust.
 Identities = 120/230 (52%), Positives = 151/230 (65%), Gaps = 24/230 (10%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           R++GVKCARC +++   + V+RA   V+H+ CF C +C QPL  G Q+ LR GQ  CR+D
Sbjct: 111 RIFGVKCARCMEKISCSDFVLRAPGLVFHVECFACCMCGQPLLPGTQYFLRQGQPICRRD 170

Query: 76  FEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRK 135
           +E E+YL   +SP DD +LDEN RPRDGRRGPKRPRTILTSAQRRQFK++FEVSPKPCRK
Sbjct: 171 YEHELYL---NSPQDDDLLDEN-RPRDGRRGPKRPRTILTSAQRRQFKAAFEVSPKPCRK 226

Query: 136 V------STMNSKRAKNILTPNQR-------RQFKSSFEISSMPCRKVGV------HGHY 176
           V       T  S R   +   NQR       R+ K+       P  +         H HY
Sbjct: 227 VREALAKETGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGSDKEPKEERRTESPHSDHSHY 286

Query: 177 LSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFCSSDISLD 226
           L+  M+++D   S F SST+PLNPN+PYSPDD+Y  HS +SFCSSD+SLD
Sbjct: 287 LN-AMNMRDGESSSFPSSTQPLNPNNPYSPDDAYPGHSGESFCSSDLSLD 335

Source: Bombus terrestris

Species: Bombus terrestris

Genus: Bombus

Family: Apidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|383861320|ref|XP_003706134.1| PREDICTED: LIM homeobox transcription factor 1-beta-like [Megachile rotundata]

 Score =  215 bits (547), Expect = 2e-53,   Method: Compositional matrix adjust.
 Identities = 119/230 (51%), Positives = 150/230 (65%), Gaps = 24/230 (10%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           R++GVKCARC +++   + V+R    V+H+ CF C +C QPL  G Q+ LR GQ  CR+D
Sbjct: 111 RIFGVKCARCMEKISCSDFVLRTPGLVFHVECFACCMCGQPLPPGTQYFLRQGQPICRRD 170

Query: 76  FEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRK 135
           +E E+YL   +SP DD +LDEN RPRDGRRGPKRPRTILTSAQRRQFK+SFEVSPKPCRK
Sbjct: 171 YEHELYL---NSPQDDDLLDEN-RPRDGRRGPKRPRTILTSAQRRQFKASFEVSPKPCRK 226

Query: 136 V------STMNSKRAKNILTPNQR-------RQFKSSFEISSMPCRKVGV------HGHY 176
           V       T  S R   +   NQR       R+ K+       P  +         H HY
Sbjct: 227 VREALAKDTGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGSDKEPKEERRTESPHSDHSHY 286

Query: 177 LSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFCSSDISLD 226
           L+  M+++D   S F S+T+PLNPN+PYSPDD+Y  HS +SFCSSD+SLD
Sbjct: 287 LN-AMNMRDGESSSFPSATQPLNPNNPYSPDDAYPGHSGESFCSSDLSLD 335

Source: Megachile rotundata

Species: Megachile rotundata

Genus: Megachile

Family: Megachilidae

Order: Hymenoptera

Class: Insecta

Phylum: Arthropoda

Superkingdom: Eukaryota

>gi|307189897|gb|EFN74141.1| LIM homeobox transcription factor 1 beta [Camponotus floridanus]

 Score =  214 bits (545), Expect = 3e-53,   Method: Compositional matrix adjust.
 Identities = 124/248 (50%), Positives = 159/248 (64%), Gaps = 26/248 (10%)

Query: 16  RLYGVKCARCGDRLLPHEMVMRAQSH-VYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQ 74
           R++GVKCARC +++   ++VMR  S  V+H+ CF C +C QPL +G  +ILR GQ  CR+
Sbjct: 111 RIFGVKCARCMEKISCSDLVMRPVSGLVFHVECFACCMCGQPLPRGAHYILRQGQPICRR 170

Query: 75  DFEKEMYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCR 134
           DFE E++L   +SP DD +LDEN RPRDGRRGPKRPRTILTSAQRRQFK+SFEVSPKPCR
Sbjct: 171 DFEHELFL---NSPQDDDLLDEN-RPRDGRRGPKRPRTILTSAQRRQFKASFEVSPKPCR 226

Query: 135 KV------STMNSKRAKNILTPNQR-------RQFKSSFEISSMPCRKVGV------HGH 175
           KV       T  S R   +   NQR       R+ K+       P  +         H H
Sbjct: 227 KVREALAKDTGLSVRVVQVWFQNQRAKMKKLQRKAKTEPGSDKEPKEERRTESPHSDHSH 286

Query: 176 YLSLGMSLQDSSDSIFASSTKPLNPNHPYSPDDSYAMHSNDSFCSSDISLDES-TNLDEG 234
           YL+  ++++D   S F S+T+PLNPN+PYSPDD+Y  HS +SFCSSD+SLD +    D G
Sbjct: 287 YLN-ALNMRDGESSSFPSATQPLNPNNPYSPDDAYPGHSGESFCSSDLSLDGTDGGFDIG 345

Query: 235 GSDSLSLD 242
            +D    D
Sbjct: 346 ENDGGGAD 353

Source: Camponotus floridanus

Species: Camponotus floridanus

Genus: Camponotus

Family: Formicidae

Order: Hymenoptera

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	267
FB|FBgn0052105	640	CG32105 [Drosophila melanogast	0.573	0.239	0.469	7.3e-40
UNIPROTKB|Q8UVR3	400	lmx1b.1 "LIM homeobox transcri	0.280	0.187	0.466	1e-25
ZFIN|ZDB-GENE-050114-2	375	lmx1bb "LIM homeobox transcrip	0.280	0.2	0.453	5.5e-25
UNIPROTKB|F1S229	295	LMX1A "Uncharacterized protein	0.453	0.410	0.452	2e-24
UNIPROTKB|I3L863	296	LMX1A "Uncharacterized protein	0.453	0.408	0.452	2e-24
UNIPROTKB|F1MC25	382	LMX1A "Uncharacterized protein	0.453	0.316	0.445	2.6e-24
UNIPROTKB|F1PDJ1	382	LMX1A "Uncharacterized protein	0.453	0.316	0.445	2.6e-24
UNIPROTKB|Q8TE12	382	LMX1A "LIM homeobox transcript	0.453	0.316	0.445	2.6e-24
MGI|MGI:1888519	382	Lmx1a "LIM homeobox transcript	0.453	0.316	0.445	2.6e-24
RGD|1304784	382	Lmx1a "LIM homeobox transcript	0.453	0.316	0.445	2.6e-24

FB|FBgn0052105 CG32105 [Drosophila melanogaster (taxid:7227)]

 Score = 319 (117.4 bits), Expect = 7.3e-40, Sum P(2) = 7.3e-40
 Identities = 77/164 (46%), Positives = 94/164 (57%)

Query:     5 NSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRA-QSHVYHLPCFVCVICCQPLQKGEQF 63
             NS + C     RL+GVKC+ C   +LP E+VMR   + V+HLPCFVC  C  PLQKGEQF
Sbjct:   317 NSKLYCKMDYDRLFGVKCSSCCHAILPQELVMRPIPNFVFHLPCFVCYACRLPLQKGEQF 376

Query:    64 ILRSGQLFC-RQDFEKEMYLMQQSSPSDDMM-LDEN--CXXXXXXXXXXXXXTILTSAQR 119
             +LR GQLFC R D EKEM+L   ++     + LDE                 TILTS QR
Sbjct:   377 MLRDGQLFCYRHDLEKEMFLAAAAAQHCGFVGLDEEDLLRPRDGRRGPKRPRTILTSQQR 436

Query:   120 RQFKSSFEVSPKPCRKV------STMNSKRAKNILTPNQRRQFK 157
             +QFK+SF+ SPKPCRKV       T  S R   +   NQR + K
Sbjct:   437 KQFKASFDQSPKPCRKVREALAKDTGLSVRVVQVWFQNQRAKMK 480

GO:0005634 "nucleus" evidence=ISS

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

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|Q8UVR3 lmx1b.1 "LIM homeobox transcription factor 1-beta.1" [Xenopus laevis (taxid:8355)]

 Score = 211 (79.3 bits), Expect = 1.0e-25, Sum P(2) = 1.0e-25
 Identities = 35/75 (46%), Positives = 51/75 (68%)

Query:    16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
             +L+  KC+ C +++ P E VMRA   VYHL CF C +C + L+KG++F+L+ GQL C+ D
Sbjct:   109 QLFAAKCSGCMEKIAPTEFVMRALECVYHLSCFCCCVCERQLRKGDEFVLKEGQLLCKSD 168

Query:    76 FEKEMYLMQQSSPSD 90
             +EKE  L+   SP D
Sbjct:   169 YEKEKDLLSSGSPDD 183

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

GO:0005634 "nucleus" evidence=ISS

GO:0030182 "neuron differentiation" evidence=IMP

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

GO:0072013 "glomus development" evidence=IEP;IMP

ZFIN|ZDB-GENE-050114-2 lmx1bb "LIM homeobox transcription factor 1, beta b" [Danio rerio (taxid:7955)]

 Score = 203 (76.5 bits), Expect = 5.5e-25, Sum P(2) = 5.5e-25
 Identities = 34/75 (45%), Positives = 51/75 (68%)

Query:    16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
             +L+  KC+ C +++ P E VMRA   VYHL CF C +C + L+KG++F+L+ GQL C+ D
Sbjct:    86 QLFATKCSGCLEKIAPTEFVMRALECVYHLNCFCCCVCDRQLRKGDEFVLKDGQLLCKSD 145

Query:    76 FEKEMYLMQQSSPSD 90
             +E+E  L+   SP D
Sbjct:   146 YEREKDLLGSVSPDD 160

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

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

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

GO:0005634 "nucleus" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0003677 "DNA binding" evidence=IEA

GO:0030917 "midbrain-hindbrain boundary development" evidence=IGI

GO:0042472 "inner ear morphogenesis" evidence=IMP

GO:0021592 "fourth ventricle development" evidence=IGI

GO:0060117 "auditory receptor cell development" evidence=IMP

GO:0032474 "otolith morphogenesis" evidence=IMP

GO:0048752 "semicircular canal morphogenesis" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

GO:0002072 "optic cup morphogenesis involved in camera-type eye development" evidence=IGI

GO:0061386 "closure of optic fissure" evidence=IGI

GO:0060041 "retina development in camera-type eye" evidence=IGI

UNIPROTKB|F1S229 LMX1A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 62/137 (45%), Positives = 78/137 (56%)

Query:    16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
             RL+ VKC  C + + P+E VMRAQ  VYHL CF C +C + LQKG++F+L+ GQL C+ D
Sbjct:     1 RLFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGD 60

Query:    76 FEKEMYLMQQSSP--SDDMMLDEN---CXXXXXXXXXXXXX-----------TILTSAQR 119
             +EKE  L+   SP  SD    D+    C                        TILT+ QR
Sbjct:    61 YEKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGAPEDGKDHKRPKRPRTILTTQQR 120

Query:   120 RQFKSSFEVSPKPCRKV 136
             R FK+SFEVS KPCRKV
Sbjct:   121 RAFKASFEVSSKPCRKV 137

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|I3L863 LMX1A "Uncharacterized protein" [Sus scrofa (taxid:9823)]

 Score = 279 (103.3 bits), Expect = 2.0e-24, P = 2.0e-24
 Identities = 62/137 (45%), Positives = 78/137 (56%)

Query:    16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
             RL+ VKC  C + + P+E VMRAQ  VYHL CF C +C + LQKG++F+L+ GQL C+ D
Sbjct:     1 RLFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGD 60

Query:    76 FEKEMYLMQQSSP--SDDMMLDEN---CXXXXXXXXXXXXX-----------TILTSAQR 119
             +EKE  L+   SP  SD    D+    C                        TILT+ QR
Sbjct:    61 YEKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGAPEDGKDHKRPKRPRTILTTQQR 120

Query:   120 RQFKSSFEVSPKPCRKV 136
             R FK+SFEVS KPCRKV
Sbjct:   121 RAFKASFEVSSKPCRKV 137

GO:0005634 "nucleus" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0021953 "central nervous system neuron differentiation" evidence=IEA

GO:0021549 "cerebellum development" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0001558 "regulation of cell growth" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|F1MC25 LMX1A "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 61/137 (44%), Positives = 78/137 (56%)

Query:    16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
             +L+ VKC  C + + P+E VMRAQ  VYHL CF C +C + LQKG++F+L+ GQL C+ D
Sbjct:    88 KLFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGD 147

Query:    76 FEKEMYLMQQSSP--SDDMMLDEN---CXXXXXXXXXXXXX-----------TILTSAQR 119
             +EKE  L+   SP  SD    D+    C                        TILT+ QR
Sbjct:   148 YEKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGASEDSKDHKRPKRPRTILTTQQR 207

Query:   120 RQFKSSFEVSPKPCRKV 136
             R FK+SFEVS KPCRKV
Sbjct:   208 RAFKASFEVSSKPCRKV 224

GO:0005634 "nucleus" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0021953 "central nervous system neuron differentiation" evidence=IEA

GO:0021549 "cerebellum development" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0001558 "regulation of cell growth" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|F1PDJ1 LMX1A "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 61/137 (44%), Positives = 78/137 (56%)

Query:    16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
             +L+ VKC  C + + P+E VMRAQ  VYHL CF C +C + LQKG++F+L+ GQL C+ D
Sbjct:    88 KLFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGD 147

Query:    76 FEKEMYLMQQSSP--SDDMMLDEN---CXXXXXXXXXXXXX-----------TILTSAQR 119
             +EKE  L+   SP  SD    D+    C                        TILT+ QR
Sbjct:   148 YEKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGAAEDGKDHKRPKRPRTILTTQQR 207

Query:   120 RQFKSSFEVSPKPCRKV 136
             R FK+SFEVS KPCRKV
Sbjct:   208 RAFKASFEVSSKPCRKV 224

GO:0005634 "nucleus" evidence=IEA

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

GO:0008270 "zinc ion binding" evidence=IEA

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

UNIPROTKB|Q8TE12 LMX1A "LIM homeobox transcription factor 1-alpha" [Homo sapiens (taxid:9606)]

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 61/137 (44%), Positives = 78/137 (56%)

Query:    16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
             +L+ VKC  C + + P+E VMRAQ  VYHL CF C +C + LQKG++F+L+ GQL C+ D
Sbjct:    88 KLFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGD 147

Query:    76 FEKEMYLMQQSSP--SDDMMLDEN---CXXXXXXXXXXXXX-----------TILTSAQR 119
             +EKE  L+   SP  SD    D+    C                        TILT+ QR
Sbjct:   148 YEKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGTAEEGKDHKRPKRPRTILTTQQR 207

Query:   120 RQFKSSFEVSPKPCRKV 136
             R FK+SFEVS KPCRKV
Sbjct:   208 RAFKASFEVSSKPCRKV 224

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

GO:0008270 "zinc ion binding" evidence=IEA

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

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

GO:0001558 "regulation of cell growth" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA

GO:0021542 "dentate gyrus development" evidence=IEA

GO:0021549 "cerebellum development" evidence=IEA

GO:0021953 "central nervous system neuron differentiation" evidence=IEA

GO:0030901 "midbrain development" evidence=IEA

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA

GO:0005634 "nucleus" evidence=IEA

MGI|MGI:1888519 Lmx1a "LIM homeobox transcription factor 1 alpha" [Mus musculus (taxid:10090)]

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 61/137 (44%), Positives = 78/137 (56%)

Query:    16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
             +L+ VKC  C + + P+E VMRAQ  VYHL CF C +C + LQKG++F+L+ GQL C+ D
Sbjct:    88 KLFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGD 147

Query:    76 FEKEMYLMQQSSP--SDDMMLDEN---CXXXXXXXXXXXXX-----------TILTSAQR 119
             +EKE  L+   SP  SD    D+    C                        TILT+ QR
Sbjct:   148 YEKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGASEDGKDHKRPKRPRTILTTQQR 207

Query:   120 RQFKSSFEVSPKPCRKV 136
             R FK+SFEVS KPCRKV
Sbjct:   208 RAFKASFEVSSKPCRKV 224

GO:0001558 "regulation of cell growth" evidence=IMP

GO:0003677 "DNA binding" evidence=IEA

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

GO:0005634 "nucleus" evidence=IEA

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

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

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007411 "axon guidance" evidence=IMP

GO:0007417 "central nervous system development" evidence=IMP

GO:0007420 "brain development" evidence=ISO

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0021542 "dentate gyrus development" evidence=IMP

GO:0021549 "cerebellum development" evidence=IMP

GO:0021766 "hippocampus development" evidence=IMP

GO:0021953 "central nervous system neuron differentiation" evidence=IMP

GO:0030182 "neuron differentiation" evidence=IMP

GO:0030901 "midbrain development" evidence=IMP

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

GO:0045665 "negative regulation of neuron differentiation" evidence=IMP

GO:0046872 "metal ion binding" evidence=IEA

GO:0071542 "dopaminergic neuron differentiation" evidence=IMP

RGD|1304784 Lmx1a "LIM homeobox transcription factor 1 alpha" [Rattus norvegicus (taxid:10116)]

 Score = 278 (102.9 bits), Expect = 2.6e-24, P = 2.6e-24
 Identities = 61/137 (44%), Positives = 78/137 (56%)

Query:    16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
             +L+ VKC  C + + P+E VMRAQ  VYHL CF C +C + LQKG++F+L+ GQL C+ D
Sbjct:    88 KLFAVKCGGCFEAIAPNEFVMRAQKSVYHLSCFCCCVCERQLQKGDEFVLKEGQLLCKGD 147

Query:    76 FEKEMYLMQQSSP--SDDMMLDEN---CXXXXXXXXXXXXX-----------TILTSAQR 119
             +EKE  L+   SP  SD    D+    C                        TILT+ QR
Sbjct:   148 YEKERELLSLVSPAASDSGKSDDEESLCKSAHGAGKGASEDGKDHKRPKRPRTILTTQQR 207

Query:   120 RQFKSSFEVSPKPCRKV 136
             R FK+SFEVS KPCRKV
Sbjct:   208 RAFKASFEVSSKPCRKV 224

GO:0001558 "regulation of cell growth" evidence=IEA;ISO

GO:0003674 "molecular_function" evidence=ND

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

GO:0005575 "cellular_component" evidence=ND

GO:0005634 "nucleus" evidence=IEA

GO:0007411 "axon guidance" evidence=IEA;ISO

GO:0007417 "central nervous system development" evidence=ISO

GO:0007420 "brain development" evidence=IMP

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0021542 "dentate gyrus development" evidence=IEA;ISO

GO:0021549 "cerebellum development" evidence=IEA;ISO

GO:0021766 "hippocampus development" evidence=ISO

GO:0021953 "central nervous system neuron differentiation" evidence=IEA;ISO

GO:0030182 "neuron differentiation" evidence=ISO

GO:0030901 "midbrain development" evidence=IEA;ISO

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

GO:0045665 "negative regulation of neuron differentiation" evidence=IEA;ISO

GO:0071542 "dopaminergic neuron differentiation" evidence=IEA;ISO

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database

ID	Length	Definition	E-value
Query	267
cd09377	59	cd09377, LIM2_Lhx2_Lhx9, The second LIM domain of	1e-18
cd09378	55	cd09378, LIM2_Lmx1a_Lmx1b, The second LIM domain o	3e-17
cd09374	55	cd09374, LIM2_Isl, The second LIM domain of Isl, a	2e-13
cd09387	55	cd09387, LIM2_LMO4, The second LIM domain of LMO4	2e-13
pfam00412	58	pfam00412, LIM, LIM domain	2e-12
cd09376	56	cd09376, LIM2_Lhx3_Lhx4, The second LIM domain of	5e-12
cd09375	56	cd09375, LIM2_Lhx1_Lhx5, The second LIM domain of	2e-11
cd09475	59	cd09475, LIM2_Lhx9, The second LIM domain of Lhx9	1e-10
cd09471	55	cd09471, LIM2_Isl2, The second LIM domain of Isl2	2e-10
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	2e-10
cd09379	55	cd09379, LIM2_AWH, The second LIM domain of Arrowh	3e-10
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	3e-10
cd09389	55	cd09389, LIM2_LMO1_LMO3, The second LIM domain of	4e-10
cd09473	56	cd09473, LIM2_Lhx4, The second LIM domain of Lhx4	4e-10
cd09472	57	cd09472, LIM2_Lhx3b, The second LIM domain of Lhx3	1e-09
cd09474	59	cd09474, LIM2_Lhx2, The second LIM domain of Lhx2	2e-09
cd09383	55	cd09383, LIM2_Lhx7_Lhx8, The second LIM domain of	4e-09
cd09382	55	cd09382, LIM2_Lhx6, The second LIM domain of Lhx6	5e-09
cd09385	56	cd09385, LIM2_LMO2, The second LIM domain of LMO2	8e-09
cd09331	59	cd09331, LIM1_PINCH, The first LIM domain of prote	3e-08
cd09390	55	cd09390, LIM2_dLMO, The second LIM domain of dLMO	3e-08
cd09372	53	cd09372, LIM2_FBLP-1, The second LIM domain of the	2e-07
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	8e-07
cd09351	54	cd09351, LIM1_LPP, The first LIM domain of lipoma	7e-06
cd09349	87	cd09349, LIM1_Zyxin, The first LIM domain of Zyxin	8e-06
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	9e-06
cd09456	52	cd09456, LIM2_Enigma, The second LIM domain of Eni	3e-05
cd09457	52	cd09457, LIM2_ENH, The second LIM domain of the En	4e-05
cd09327	52	cd09327, LIM1_abLIM, The first LIM domain of actin	1e-04
cd09350	54	cd09350, LIM1_TRIP6, The first LIM domain of Thyro	5e-04
cd09345	54	cd09345, LIM2_FHL, The second LIM domain of Four a	6e-04
cd09352	54	cd09352, LIM1_Ajuba_like, The first LIM domain of	7e-04
cd09461	54	cd09461, LIM3_Enigma_like_1, The third LIM domain	8e-04
cd09328	56	cd09328, LIM2_abLIM, The second LIM domain on acti	0.001
cd09363	54	cd09363, LIM3_Enigma_like, The third LIM domain of	0.001
cd09371	53	cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b	0.001
cd09356	53	cd09356, LIM2_TRIP6, The second LIM domain of Thyr	0.001
cd09459	55	cd09459, LIM3_ENH, The third LIM domain of the Eni	0.002
cd09353	60	cd09353, LIM2_Zyxin, The second LIM domain of Zyxi	0.002
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	0.002
cd09366	55	cd09366, LIM1_Isl, The first LIM domain of Isl, a	0.003
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	0.003
cd09354	60	cd09354, LIM2_LPP, The second LIM domain of lipoma	0.003
cd09426	57	cd09426, LIM2_FHL2, The second LIM domain of Four	0.004

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

 Score = 76.9 bits (190), Expect = 1e-18
 Identities = 25/56 (44%), Positives = 36/56 (64%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          +CARC   +   E+VMRA+  V+HL CF C  C +PL KG+ F +R G ++CR  +
Sbjct: 4  RCARCHLGISASELVMRARDLVFHLNCFTCATCNKPLTKGDHFGMRDGLVYCRLHY 59

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

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

 Score = 73.3 bits (180), Expect = 3e-17
 Identities = 27/55 (49%), Positives = 41/55 (74%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          C+ C +++ P E+VMRA  +VYHL CF C +C + LQKG++F+L+ GQL C+ D+
Sbjct: 1  CSGCLEKIAPSELVMRALENVYHLRCFCCCVCERQLQKGDEFVLKEGQLLCKSDY 55

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

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

 Score = 62.8 bits (153), Expect = 2e-13
 Identities = 22/54 (40%), Positives = 33/54 (61%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
          CA+C      ++ VMRA++ +YH+ CF C  C + L  G++F LR   LFC+ D
Sbjct: 1  CAKCQQSFSKNDFVMRARTKIYHIECFRCSACSRQLIPGDEFALRDDGLFCKAD 54

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

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

 Score = 62.9 bits (153), Expect = 2e-13
 Identities = 25/55 (45%), Positives = 32/55 (58%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          C+ CG  +   E+VMRAQ +VYHL CF C  C   L  G++F   +G LFC  D 
Sbjct: 1  CSACGQSIPASELVMRAQGNVYHLKCFTCSTCHNQLVPGDRFHYVNGSLFCEHDR 55

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

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

 Score = 60.8 bits (148), Expect = 2e-12
 Identities = 23/59 (38%), Positives = 34/59 (57%), Gaps = 1/59 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80
          CA CG  +   E+V RA   V+H  CF C +C +PL  G+ F  + G+L+C+ D+ K  
Sbjct: 1  CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGD-FFEKDGKLYCKHDYFKLF 58

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

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

 Score = 59.3 bits (144), Expect = 5e-12
 Identities = 23/56 (41%), Positives = 37/56 (66%), Gaps = 1/56 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL-RSGQLFCRQDF 76
          CA C + + P ++V RAQ +VYHL CF C +C + L+ G++F L    +L C++D+
Sbjct: 1  CAGCDEGIPPTQVVRRAQDNVYHLECFACFMCKRQLETGDEFYLMEDDRLVCKKDY 56

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

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

 Score = 57.4 bits (139), Expect = 2e-11
 Identities = 21/56 (37%), Positives = 36/56 (64%), Gaps = 1/56 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ-FILRSGQLFCRQDF 76
          CA C   + P+++V RA+  V+HL CF C++C + L  GE+ +IL   +  C++D+
Sbjct: 1  CAGCDQGISPNDLVRRARDKVFHLNCFTCMVCRKQLSTGEELYILDENKFICKEDY 56

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

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

 Score = 55.5 bits (133), Expect = 1e-10
 Identities = 24/56 (42%), Positives = 33/56 (58%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          +CARC   +   EMVMRA+  VYHL CF C  C + L  G+ F ++   ++CR  F
Sbjct: 4  RCARCHLGISASEMVMRARESVYHLSCFTCTTCNKTLTTGDHFGMKDNLVYCRAHF 59

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

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

 Score = 54.9 bits (132), Expect = 2e-10
 Identities = 23/54 (42%), Positives = 33/54 (61%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
          CA+C       ++VMRA+  VYH+ CF C +C + L  G++F LR  +L CR D
Sbjct: 1  CAQCRLGFSSSDLVMRARDSVYHIECFRCSVCSRQLLPGDEFCLREHELLCRAD 54

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

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

 Score = 54.6 bits (132), Expect = 2e-10
 Identities = 18/55 (32%), Positives = 30/55 (54%), Gaps = 2/55 (3%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          CA CG  +   E+ +RA    +H  CF C +C +PL  G+ F  + G+ +C + +
Sbjct: 1  CAGCGKPIEGREL-LRALGKKWHPECFKCSVCGKPLG-GDSFYEKDGKPYCEKCY 53

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

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

 Score = 54.4 bits (131), Expect = 3e-10
 Identities = 21/55 (38%), Positives = 31/55 (56%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          CA+C   +   + V RA+ HVYHL CF C  C + L  GE+F L   ++ C+  +
Sbjct: 1  CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDRVLCKAHY 55

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

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

 Score = 54.3 bits (131), Expect = 3e-10
 Identities = 22/55 (40%), Positives = 31/55 (56%), Gaps = 1/55 (1%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
          KCA CG  +   E V+RA   V+H  CF C  C +PL  G+ F  + G+L+C+  
Sbjct: 1  KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPL-SGDTFFEKDGKLYCKDC 54

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

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

 Score = 54.3 bits (130), Expect = 4e-10
 Identities = 23/55 (41%), Positives = 34/55 (61%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          CA C   +   EMVMRA+ +VYHL CF C +C Q    G++F L++  + C+ D+
Sbjct: 1  CAACSKLIPAFEMVMRAKDNVYHLDCFACQLCNQRFCVGDKFFLKNNMILCQMDY 55

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

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

 Score = 53.9 bits (129), Expect = 4e-10
 Identities = 22/56 (39%), Positives = 36/56 (64%), Gaps = 1/56 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQF-ILRSGQLFCRQDF 76
          C  C   + P ++V +AQ  VYHL CF C+IC + L  G++F ++  G+L C++D+
Sbjct: 1  CTACQQGIPPTQVVRKAQDFVYHLHCFACIICSRQLATGDEFYLMEDGRLVCKEDY 56

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

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

 Score = 52.8 bits (126), Expect = 1e-09
 Identities = 23/57 (40%), Positives = 36/57 (63%), Gaps = 1/57 (1%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQF-ILRSGQLFCRQDF 76
          KCA C   + P ++V RAQ  VYHL CF C++C + L  G++F ++   +L C+ D+
Sbjct: 1  KCAACQQGIPPTQVVRRAQDFVYHLHCFACIVCKRQLATGDEFYLMEDSRLVCKADY 57

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

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

 Score = 52.4 bits (125), Expect = 2e-09
 Identities = 24/56 (42%), Positives = 33/56 (58%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          +CARC   +   EMVMRA+  VYHL CF C  C + L  G+ F ++   ++CR  F
Sbjct: 4  RCARCHLGISASEMVMRARDLVYHLNCFTCTTCNKMLTTGDHFGMKDNLVYCRLHF 59

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

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

 Score = 51.2 bits (122), Expect = 4e-09
 Identities = 22/55 (40%), Positives = 32/55 (58%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          C+RCG  +   + V RA+ +VYHL CF C  C + L  GE+F L   ++ CR  +
Sbjct: 1  CSRCGRHIHSTDWVRRAKGNVYHLACFACFSCKRQLSTGEEFALVEEKVLCRVHY 55

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

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

 Score = 51.2 bits (122), Expect = 5e-09
 Identities = 22/52 (42%), Positives = 31/52 (59%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCR 73
          CARCG ++   + V RA+ + YHL CF C  C + L  GE+F L   ++ CR
Sbjct: 1  CARCGRQIYASDWVRRARGNAYHLACFACFSCKRQLSTGEEFGLVEEKVLCR 52

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

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

 Score = 50.4 bits (120), Expect = 8e-09
 Identities = 21/54 (38%), Positives = 31/54 (57%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
          CA C  R+  +EM MR +  VYHL CF C  C +    G++++L +  + C QD
Sbjct: 1  CASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQD 54

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

>gnl|CDD|188717 cd09331, LIM1_PINCH, The first LIM domain of protein PINCH

 Score = 48.9 bits (117), Expect = 3e-08
 Identities = 20/55 (36%), Positives = 27/55 (49%), Gaps = 1/55 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          C RC +   P E ++ +   +YH  CFVC  C QP   G  F    G+ +C  DF
Sbjct: 1  CERCREGFEPDEKIVNSNGELYHEQCFVCAQCFQPFPDGL-FYEFEGRKYCEHDF 54

The first LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 59

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

 Score = 48.7 bits (116), Expect = 3e-08
 Identities = 22/55 (40%), Positives = 31/55 (56%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          CA C   +   EMVMRA+++VYHL CF C  C      G++F L   ++ C  D+
Sbjct: 1  CAACSKTIPAFEMVMRARTNVYHLECFACQRCNHRFCVGDRFYLCENKILCEYDY 55

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

>gnl|CDD|188758 cd09372, LIM2_FBLP-1, The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1)

 Score = 46.6 bits (111), Expect = 2e-07
 Identities = 18/56 (32%), Positives = 29/56 (51%), Gaps = 4/56 (7%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRS-GQLFCRQDF 76
          CA+C   +  H  ++RA    YH PCF CV C + +   E F +    +++C  D+
Sbjct: 1  CAKCQGVITEH--IIRALGKGYHPPCFTCVTCGRRIGD-ESFAVDEQNEVYCLDDY 53

The second LIM domain of the filamin-binding LIM protein-1 (FBLP-1): Fblp-1 contains a proline-rich domain near its N terminus and two LIM domains at its C terminus. FBLP-1 mRNA was detected in a variety of tissues and cells including platelets and endothelial cells. FBLP-1 binds to Filamins. The association between filamin B and FBLP-1 may play an unknown role in cytoskeletal function, cell adhesion, and cell motility. As in other LIM domains, this domain family is 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188748 cd09362, LIM2_Enigma_like, The second LIM domain of Enigma-like family

 Score = 44.8 bits (106), Expect = 8e-07
 Identities = 20/55 (36%), Positives = 30/55 (54%), Gaps = 3/55 (5%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          CARC  ++L    VM A    +H+ CFVC  C QP+     F +  G+ +C +D+
Sbjct: 1  CARCHKKILGE--VMHALKQTWHVSCFVCAACKQPI-GNSLFHMEDGEPYCEKDY 52

The second LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred partner (LPP)

 Score = 42.0 bits (99), Expect = 7e-06
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 1/55 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          C +CG+++L       A   VYH+ CF C  C   LQ G+ F    G+ +C +D+
Sbjct: 1  CVKCGEKVLGEGSGCTAMDQVYHISCFTCHQCQINLQ-GKPFYALDGKPYCEEDY 54

The first LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188735 cd09349, LIM1_Zyxin, The first LIM domain of Zyxin

 Score = 42.9 bits (101), Expect = 8e-06
 Identities = 20/53 (37%), Positives = 29/53 (54%), Gaps = 1/53 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQ 74
          C  CG  L   +  +RA  H++H+ CF C  C Q LQ G+QF    G+ +C +
Sbjct: 34 CGICGQPLSRTQPAVRALGHLFHVTCFTCHQCEQQLQ-GQQFYSLEGKPYCEE 85

The first LIM domain of Zyxin: Zyxin exhibits three copies of the LIM domain, an extensive proline-rich domain and a nuclear export signal. Localized at sites of cell substratum adhesion in fibroblasts, Zyxin interacts with alpha-actinin, members of the cysteine-rich protein (CRP) family, proteins that display Src homology 3 (SH3) domains and Ena/VASP family members. Zyxin and its partners have been implicated in the spatial control of actin filament assembly as well as in pathways important for cell differentiation. In addition to its functions at focal adhesion plaques, recent work has shown that zyxin moves from the sites of cell contacts to the nucleus, where it directly participates in the regulation of gene expression. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 87

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

 Score = 41.7 bits (98), Expect = 9e-06
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          CA C  ++L  + V  A +  +H  CF C +C   L     +  + G+L+CR+D+
Sbjct: 1  CAGCRGKILDSQYVQ-ALNQDWHCDCFRCSVCSDSLS--NWYFEKDGKLYCRKDY 52

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

>gnl|CDD|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma

 Score = 40.8 bits (95), Expect = 3e-05
 Identities = 15/55 (27%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          CA+C  ++     +M A    +H+ CF C  C  P+ +   F +  G  +C +D+
Sbjct: 1  CAKCKKKITGE--IMHALKMTWHVHCFTCAACKTPI-RNRAFYMEEGAPYCERDY 52

The second LIM domain of Enigma: Enigma was initially characterized in humans as a protein containing three LIM domains at the C-terminus and a PDZ domain at N-terminus. 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. Enigma is expressed in multiple tissues, such as skeletal muscle, heart, bone and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188841 cd09457, LIM2_ENH, The second LIM domain of the Enigma Homolog (ENH) family

 Score = 40.0 bits (93), Expect = 4e-05
 Identities = 19/55 (34%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          C RC  ++L    V+ A    +H+ CFVCV C  P+ +   F L  G+ +C  D+
Sbjct: 1  CGRCQRKILGE--VINALKQTWHVSCFVCVACHNPI-RNNVFHLEDGEPYCETDY 52

The second LIM domain of the Enigma Homolog (ENH) family: ENH was initially identified in rat brain. Same as enigma, it contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. ENH is implicated in signal transduction processes involving protein kinases. It has also been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ENH is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188713 cd09327, LIM1_abLIM, The first LIM domain of actin binding LIM (abLIM) proteins

 Score = 38.8 bits (91), Expect = 1e-04
 Identities = 17/55 (30%), Positives = 29/55 (52%), Gaps = 3/55 (5%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          C +CG +      V+R Q   +H+ CF C +C   L +G  F ++ G+ +C  D+
Sbjct: 1  CYKCGKKCKGE--VLRVQDKYFHIKCFTCKVCGCDLAQGG-FFVKEGEYYCTDDY 52

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

>gnl|CDD|188736 cd09350, LIM1_TRIP6, The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6)

 Score = 37.0 bits (86), Expect = 5e-04
 Identities = 15/51 (29%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFC 72
          C RCG+ ++       A   V+H+ CF C+ C   L +G+ F     + +C
Sbjct: 1  CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKL-RGQPFYAVEKKAYC 50

The first LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188731 cd09345, LIM2_FHL, The second LIM domain of Four and a half LIM domains protein (FHL)

 Score = 36.9 bits (86), Expect = 6e-04
 Identities = 14/51 (27%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFC 72
          C  CG  ++P    M  +   +H  CF C  C +P+   + FI +  +++C
Sbjct: 1  CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIG-TKSFIPKDDKIYC 50

The second LIM domain of Four and a half LIM domains protein (FHL): LIM-only protein family consists of five members, designated FHL1, FHL2, FHL3, FHL5 and LIMPETin. The first four members are composed of four complete LIM domains arranged in tandem and an N-terminal single zinc finger domain with a consensus sequence equivalent to the C-terminal half of a LIM domain. LIMPETin is an exception, containing six LIM domains. FHL1, 2 and 3 are predominantly expressed in muscle tissues, and FHL5 is highly expressed in male germ cells. FHL proteins exert their roles as transcription co-activators or co-repressors through a wide array of interaction partners. For example, FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. FHL3 int eracts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. FHL5 is a tissue-specific coactivator of CREB/CREM family transcription factors. 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|188738 cd09352, LIM1_Ajuba_like, The first LIM domain of Ajuba-like proteins

 Score = 36.6 bits (85), Expect = 7e-04
 Identities = 16/55 (29%), Positives = 30/55 (54%), Gaps = 1/55 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          C +CG  +       +A  ++YH  CF C  C + L +G+ F   +G+++C +D+
Sbjct: 1  CVKCGKGVYGASQACQAMGNLYHTNCFTCCSCGRTL-RGKAFYNVNGKVYCEEDY 54

The first LIM domain of Ajuba-like proteins: Ajuba like LIM protein family includes three highly homologous proteins Ajuba, Limd1, and WTIP. Members of the family contain three tandem C-terminal LIM domains and a proline-rich N-terminal region. This family of proteins functions as scaffolds, participating in the assembly of numerous protein complexes. In the cytoplasm, Ajuba binds Grb2 to modulate serum-stimulated ERK activation. Ajuba also recruits the TNF receptor-associated factor 6 (TRAF6) to p62 and activates PKCKappa activity. Ajuba interacts with alpha-catenin and F-actin to contribute to the formation or stabilization of adheren junctions by linking adhesive receptors to the actin cytoskeleton. Although Ajuba is a cytoplasmic protein, it can shuttle into the nucleus. In nucleus, Ajuba functions as a corepressor for the zinc finger-protein Snail. It binds to the SNAG repression domain of Snail through its LIM region. Arginine methyltransferase-5 (Prmt5), a protein in the complex, is recruited to Snai l through an interaction with Ajuba. This ternary complex functions to repress E-cadherin, a Snail target gene. In addition, Ajuba contains functional nuclear-receptor interacting motifs and selectively interacts with retinoic acid receptors (RARs) and rexinoid receptor (RXRs) to negatively regulate retinoic acid signaling. Wtip, the Wt1-interacting protein, was originally identified as an interaction partner of the Wilms tumour protein 1 (WT1). Wtip is involved in kidney and neural crest development. Wtip interacts with the receptor tyrosine kinase Ror2 and inhibits canonical Wnt signaling. LIMD1 was reported to inhibit cell growth and metastases. The inhibition may be mediated through an interaction with the protein barrier-to-autointegration (BAF), a component of SWI/SNF chromatin-remodeling protein; or through the interaction with retinoblastoma protein (pRB), resulting in inhibition of E2F-mediated transcription, and expression of the majority of genes with E2F1- responsive elements. Recently, Limd1 was shown to interact with the p62/sequestosome protein and influence IL-1 and RANKL signaling by facilitating the assembly of a p62/TRAF6/a-PKC multi-protein complex. The Limd1-p62 interaction affects both NF-kappaB and AP-1 activity in epithelial cells and osteoclasts. Moreover, LIMD1 functions as tumor repressor to block lung tumor cell line in vitro and in vivo. Recent studies revealed that LIM proteins Wtip, LIMD1 and Ajuba interact with components of RNA induced silencing complexes (RISC) as well as eIF4E and the mRNA m7GTP cap-protein complex and are required for microRNA-mediated gene silencing. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 54

>gnl|CDD|188845 cd09461, LIM3_Enigma_like_1, The third LIM domain of an Enigma subfamily with unknown function

 Score = 36.4 bits (84), Expect = 8e-04
 Identities = 16/52 (30%), Positives = 26/52 (50%), Gaps = 1/52 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCR 73
          C  CG  +   +  + A ++ YH  CF C  C   L+ G+ F  + G+ FC+
Sbjct: 1  CVSCGFPIEAGDRWVEALNNNYHSQCFNCTRCNVNLE-GQSFYAKGGRPFCK 51

The third LIM domain of an Enigma subfamily with unknown function: The Enigma LIM domain family is comprised of three characterized 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. They serve as adaptor proteins, where the PDZ domain tethers the protein to the cytoskeleton and the LIM domains, recruit signaling proteins to implement corresponding functions. The members of the enigma family have been implicated in regulating or organizing cytoskeletal structure, as well as involving multiple signaling pathways. 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|188714 cd09328, LIM2_abLIM, The second LIM domain on actin binding LIM (abLIM) proteins

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 18/56 (32%), Positives = 26/56 (46%), Gaps = 2/56 (3%)

Query: 19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQ 74
          G KC  C D +     V+ A    YH  CFVC +C QP   G++      +  C++
Sbjct: 1  GTKCDSCQDFV--EGEVVSALGKTYHPKCFVCSVCRQPFPPGDRVTFNGKECLCQK 54

The second LIM domain of actin binding LIM (abLIM) proteins: Three homologous members of the abLIM protein family have been identified; abLIM-1, abLIM-2 and abLIM-3. The N-terminal of abLIM consists of four tandem repeats of LIM domains and the C-terminal of acting binding LIM protein is a villin headpiece domain, which has strong actin binding activity. The abLIM-1, which is expressed in retina, brain, and muscle tissue, has been indicated to function as a tumor suppressor. AbLIM-2 and -3, mainly expressed in muscle and neuronal tissue, bind to F-actin strongly. They may serve as a scaffold for signaling modules of the actin cytoskeleton and thereby modulate transcription. It has shown that LIM domains of abLIMs interact with STARS (striated muscle activator of Rho signaling), which directly binds actin and stimulates serum-response factor (SRF)-dependent transcription. All LIM domains are 50-60 amino acids in size and share two characteristic highly conserved zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

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

 Score = 35.9 bits (83), Expect = 0.001
 Identities = 14/52 (26%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCR 73
          C  C   +   +  + A  H +H  CFVC +C   L +G+ F  +  +  C+
Sbjct: 1  CHGCDFPIEAGDRFLEALGHTWHDTCFVCAVCHVNL-EGQTFYSKKDKPLCK 51

The third LIM domain of Enigma-like family: The Enigma LIM domain family is comprised of three members: Enigma, ENH, and Cypher (mouse)/ZASP (human). These subfamily members contain a single PDZ domain at the N-terminus and three LIM domains at the C-terminus. Enigma was initially characterized in humans and is expressed in multiple tissues, such as skeletal muscle, heart, bone, and brain. The third LIM domain specifically interacts with the insulin receptor and the second LIM domain interacts with the receptor tyrosine kinase Ret and the adaptor protein APS. Thus Enigma is implicated in signal transduction processes, such as mitogenic activity, insulin related actin organization, and glucose metabolism. The second member, ENH protein, was first identified in rat brain. It has been shown that ENH interacts with protein kinase D1 (PKD1) via its LIM domains and forms a complex with PKD1 and the alpha1C subunit of cardiac L-type voltage-gated calcium channel in rat neonatal cardiomyocytes. The N-terminal PDZ domain interacts with alpha-actinin at the Z-line. ZASP/Cypher is required for maintenance of Z-line structure during muscle contraction, but not required for Z-line assembly. In heart, Cypher/ZASP plays a structural role through its interaction with cytoskeletal Z-line proteins. In addition, there is increasing evidence that Cypher/ZASP also performs signaling functions. Studies reveal that Cypher/ZASP interacts with and directs PKC to the Z-line, where PKC phosphorylates downstream signaling targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

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

 Score = 35.8 bits (83), Expect = 0.001
 Identities = 18/56 (32%), Positives = 28/56 (50%), Gaps = 3/56 (5%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFE 77
          CA C  R +    ++R     +H  C  C +C QPL     F  R  +L+C+QD++
Sbjct: 1  CAGC-QRPISDRYLLRVNERSWHEECLQCSVCQQPLTTSCYF--RDRKLYCKQDYQ 53

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

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          C+ C   ++  E ++RA    YH  CF CV+C + L      +  +GQ+ C +DF
Sbjct: 1  CSVCSKPIM--ERILRATGKAYHPHCFTCVVCHRSLDGIPFTVDATGQIHCIEDF 53

The second LIM domain of Thyroid receptor-interacting protein 6 (TRIP6): TRIP6 is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal. TRIP6 protein localizes to focal adhesion sites and along actin stress fibers. Recruitment of this protein to the plasma membrane occurs in a lysophosphatidic acid (LPA)-dependent manner. TRIP6 recruits a number of molecules involved in actin assembly, cell motility, survival and transcriptional control. The function of TRIP6 in cell motility is regulated by Src-dependent phosphorylation at a Tyr residue. The phosphorylation activates the coupling to the Crk SH2 domain, which is required for the function of TRIP6 in promoting lysophosphatidic acid (LPA)-induced cell migration. TRIP6 can shuttle to the nucleus to serve as a coactivator of AP-1 and NF-kappaB transcriptional factors. Moreover, TRIP6 can form a ternary complex with the NHERF2 PDZ protein and LPA2 receptor to regulate LPA-induced activation of ERK and AKT, rendering cells resistant to chemotherapy. Recent evidence shows that TRIP6 antagonizes Fas-Induced apoptosis by enhancing the antiapoptotic effect of LPA in cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188843 cd09459, LIM3_ENH, The third LIM domain of the Enigma Homolog (ENH) family

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 15/53 (28%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQ 74
          C  C   +   +  + A  H +H  CFVC +CC+ L+ G+ F  +  +  C++
Sbjct: 1  CHGCEFPIEAGDRFLEALGHTWHDTCFVCSVCCESLE-GQTFFSKKDKPLCKK 52

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|188739 cd09353, LIM2_Zyxin, The second LIM domain of Zyxin

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 20/59 (33%), Positives = 33/59 (55%), Gaps = 4/59 (6%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL-RSGQLFCRQDFEKE 79
          CA C  ++   + +++A    YH  CF CV+C  PL+ GE FI+ ++ Q  C  D+ + 
Sbjct: 1  CAVCDQKIT--DRMLKATGKSYHPQCFTCVVCKCPLE-GESFIVDQANQPHCVNDYHRR 56

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

>gnl|CDD|188744 cd09358, LIM_Mical_like, The LIM domain of Mical (molecule interacting with CasL) like family

 Score = 35.3 bits (82), Expect = 0.002
 Identities = 18/55 (32%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          CA CG  + P E +  A   ++H  CF C  C + L+ G  +    G+L+C+  F
Sbjct: 1  CAVCGKTVYPMERL-VADGKLFHKSCFRCSHCNKTLRLGN-YASLEGKLYCKPHF 53

The LIM domain of Mical (molecule interacting with CasL) like family: Known members of this family includes LIM domain containing proteins; Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2) and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth and mobility. Eplin has also found to be tumor suppressor. 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|188752 cd09366, LIM1_Isl, The first LIM domain of Isl, a member of LHX protein family

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 14/55 (25%), Positives = 26/55 (47%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          C  CG ++    ++  A    +H  C  C  C Q L +     +R G+ +C++D+
Sbjct: 1  CVGCGGKIHDQYILRVAPDLEWHAACLKCAECGQYLDETCTCFVRDGKTYCKRDY 55

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

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

 Score = 34.8 bits (80), Expect = 0.003
 Identities = 14/55 (25%), Positives = 23/55 (41%), Gaps = 3/55 (5%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          C  CG R+       R     +H  CF C +C   L     +  + G+L+C + +
Sbjct: 1  CTGCGGRIQDSFHY-RVVQEAWHNSCFQCSVCQDLLTN--WYYEKDGKLYCHKHY 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|188740 cd09354, LIM2_LPP, The second LIM domain of lipoma preferred partner (LPP)

 Score = 34.8 bits (80), Expect = 0.003
 Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKE 79
          C+ C   +L  + ++RA    YH  CF CV+C + L      +  + Q+ C +DF K+
Sbjct: 1  CSVCSKPIL--DRILRATGKPYHPQCFTCVVCGKSLDGIPFTVDATNQIHCIEDFHKK 56

The second LIM domain of lipoma preferred partner (LPP): LPP is a member of the zyxin LIM protein family and contains three LIM zinc-binding domains at the C-terminal and proline-rich region at the N-terminal. LPP initially identified as the most frequent translocation partner of HMGA2 (High Mobility Group A2) in a subgroup of benign tumors of adipose tissue (lipomas). It was also shown to be rearranged in a number of other soft tissues, as well as in a case of acute monoblastic leukemia. In addition to its involvement in tumors, LPP was inedited as a smooth muscle restricted LIM protein that plays an important role in SMC migration. LPP is localized at sites of cell adhesion, cell-cell contacts and transiently in the nucleus. In nucleus, it acts as a coactivator for the ETS domain transcription factor PEA3. In addition to PEA3, it interacts with alpha-actinin,vasodilator stimulated phosphoprotein (VASP),Palladin, and Scrib. The LIM domains are the main focal adhesion targeting elements and that the proline- rich region, which harbors binding sites for alpha-actinin and vasodilator- stimulated phosphoprotein (VASP), has a weak targeting capacity. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 60

>gnl|CDD|188810 cd09426, LIM2_FHL2, The second LIM domain of Four and a half LIM domains protein 2 (FHL2)

 Score = 34.6 bits (79), Expect = 0.004
 Identities = 18/58 (31%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKE 79
          C+ C   ++P    M  + + +H  CF+C  C QP+   + FI +  Q FC   +EK+
Sbjct: 1  CSECKKTIMPGTRKMEYKGNSWHETCFICQRCQQPIGT-KSFIPKDNQNFCVPCYEKQ 57

The second LIM domain of Four and a half LIM domains protein 2 (FHL2): FHL2 is one of the best studied FHL proteins. FHL2 expression is most abundant in the heart, and in brain, liver and lung to a lesser extent. FHL2 participates in a wide range of cellular processes, such as transcriptional regulation, signal transduction, and cell survival by binding to various protein partners. FHL2 has shown to interact with more than 50 different proteins, including receptors, structural proteins, transcription factors and cofactors, signal transducers, splicing factors, DNA replication and repair enzymes, and metabolic enzymes. Although FHL2 is abundantly expressed in heart, the fhl2 null mice are viable and had no detectable abnormal cardiac phenotype. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to s upport the assembly of multimeric protein complexes. Length = 57

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	267
KOG4577|consensus	383		100.0
KOG0484|consensus	125		99.82
KOG0489|consensus	261		99.75
KOG0850|consensus	245		99.69
KOG2251|consensus	228		99.69
KOG0494|consensus	332		99.68
KOG0490|consensus	235		99.66
KOG0488|consensus	309		99.65
KOG0843|consensus	197		99.65
KOG0487|consensus	308		99.64
KOG0492|consensus	246		99.63
KOG0485|consensus	268		99.61
KOG0842|consensus	307		99.6
KOG0848|consensus	317		99.55
KOG0844|consensus	408		99.53
KOG0493|consensus	342		99.5
KOG0486|consensus	351		99.5
KOG0490|consensus	235		99.48
KOG1701|consensus	468		99.48
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.46
PF00046	57	Homeobox: Homeobox domain not present here.; Inter	99.41
TIGR01565	58	homeo_ZF_HD homeobox domain, ZF-HD class. This mod	99.38
COG5576	156	Homeodomain-containing transcription factor [Trans	99.38
KOG4577|consensus	383		99.36
KOG0491|consensus	194		99.36
KOG1701|consensus	468		99.29
KOG0847|consensus	288		99.23
smart00389	56	HOX Homeodomain. DNA-binding factors that are invo	99.2
KOG0483|consensus	198		99.13
cd00086	59	homeodomain Homeodomain; DNA binding domains invol	99.13
KOG1703|consensus	479		99.09
KOG0849|consensus	354		99.09
KOG2272|consensus	332		99.0
KOG3802|consensus	398		98.99
KOG2272|consensus	332		98.98
KOG1044|consensus	670		98.97
KOG1703|consensus	479		98.67
KOG1168|consensus	385		98.59
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.52
KOG1044|consensus	670		98.41
KOG1700|consensus	200		98.0
KOG0775|consensus	304		97.58
KOG1146|consensus	1406		97.54
KOG1702|consensus	264		97.18
KOG0774|consensus	334		97.15
KOG2252|consensus	558		97.07
KOG1700|consensus	200		97.05
PF05920	40	Homeobox_KN: Homeobox KN domain; InterPro: IPR0084	95.93
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	92.5
KOG3623|consensus	1007		91.73
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	82.1

>KOG4577|consensus

Probab=100.00  E-value=5.2e-35  Score=253.35  Aligned_cols=149  Identities=32%  Similarity=0.597  Sum_probs=132.1

Q ss_pred             CcccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEee-CCeecchhhHHHH
Q psy10849          1 STSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILR-SGQLFCRQDFEKE   79 (267)
Q Consensus         1 ~~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~-~~~lyC~~cy~k~   79 (267)
                      ||.|+|.+||+++|.++|+.+|..|...|.+...|-+|.+.+||..||.|.+|++.|.+|++|++. +.++.|+.+|+..
T Consensus        74 CFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~A  153 (383)
T KOG4577|consen   74 CFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETA  153 (383)
T ss_pred             HhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHH
Confidence            899999999999999999999999999999886666789999999999999999999999999987 6899999999874


Q ss_pred             HhhhcCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhh
Q psy10849         80 MYLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQR  153 (267)
Q Consensus        80 f~~~~~~~~~~~~~~~~~~~~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrR  153 (267)
                      -..       ....       -++....||+||.+|..||+.|+.+|...+.|.+.+||+      |..|+|||||||||
T Consensus       154 k~k-------~~~~-------l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRR  219 (383)
T KOG4577|consen  154 KQK-------HCNE-------LEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRR  219 (383)
T ss_pred             Hhc-------cccc-------cccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhh
Confidence            321       1111       133455799999999999999999999999999999999      89999999999999


Q ss_pred             hhhhhhhhhc
Q psy10849        154 RQFKSSFEIS  163 (267)
Q Consensus       154 ak~k~~~~~~  163 (267)
                      ||.||.++.+
T Consensus       220 AKEKRLKKDA  229 (383)
T KOG4577|consen  220 AKEKRLKKDA  229 (383)
T ss_pred             HHHHhhhhhc
Confidence            9999988776

>KOG0484|consensus

Probab=99.82  E-value=3.1e-21  Score=144.09  Aligned_cols=60  Identities=22%  Similarity=0.278  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ++|+||.||.||..||.+||+.|..++|||+.+||+      |+|.+|||||||||||+||+.+..
T Consensus        14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a   79 (125)
T KOG0484|consen   14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA   79 (125)
T ss_pred             HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence            678999999999999999999999999999999999      999999999999999999987655

>KOG0489|consensus

Probab=99.75  E-value=4.4e-19  Score=157.74  Aligned_cols=62  Identities=23%  Similarity=0.211  Sum_probs=56.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhccCC
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISSMP  166 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~~~  166 (267)
                      .+.||.||.||..||.+||++|+.|+|.++..|.+      |+|||||||||||||||||..+.....
T Consensus       157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~  224 (261)
T KOG0489|consen  157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ  224 (261)
T ss_pred             CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence            34799999999999999999999999999999998      999999999999999999977665543

>KOG0850|consensus

Probab=99.69  E-value=7.8e-17  Score=136.78  Aligned_cols=69  Identities=22%  Similarity=0.255  Sum_probs=61.9

Q ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhccC
Q psy10849         97 NCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISSM  165 (267)
Q Consensus        97 ~~~~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~~  165 (267)
                      +.+++...+|.|+.||+|+.-||..|.+.|++++|....+|.+      |+..||||||||||.|+||+++..+.
T Consensus       112 e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~  186 (245)
T KOG0850|consen  112 ERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG  186 (245)
T ss_pred             eeccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence            4566777788899999999999999999999999999888888      99999999999999999999885543

>KOG2251|consensus

Probab=99.69  E-value=3.9e-17  Score=138.03  Aligned_cols=63  Identities=17%  Similarity=0.202  Sum_probs=59.0

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        101 RDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       101 ~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ..+.||.||.||+||..||.+||+.|.+++|||+.+||+      |.|.+|||||.|||||+|++++.+
T Consensus        31 ~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq   99 (228)
T KOG2251|consen   31 SSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ   99 (228)
T ss_pred             CccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence            367889999999999999999999999999999999999      999999999999999999987754

>KOG0494|consensus

Probab=99.68  E-value=1.2e-17  Score=143.52  Aligned_cols=62  Identities=19%  Similarity=0.256  Sum_probs=54.5

Q ss_pred             CCCCCCCC-CCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhcc
Q psy10849        103 GRRGPKRP-RTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISS  164 (267)
Q Consensus       103 ~~~~~kr~-Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~  164 (267)
                      ++++.||. ||.||..|+.+||+.|.+.+|||...||.      |+|-+||||||||||||||.++...
T Consensus       136 kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg  204 (332)
T KOG0494|consen  136 KKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG  204 (332)
T ss_pred             ccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence            34444554 99999999999999999999999999987      9999999999999999999876654

>KOG0490|consensus

Probab=99.66  E-value=2.2e-17  Score=143.89  Aligned_cols=113  Identities=20%  Similarity=0.498  Sum_probs=94.1

Q ss_pred             CCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhhhcCCCCCCCcccCCCCCCCCCC
Q psy10849         25 CGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLMQQSSPSDDMMLDENCRPRDGR  104 (267)
Q Consensus        25 C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~~~~~~~~~~~~~~~~~~~~~~~  104 (267)
                      |+..|.+. ..+.+.+..||..|..|..|...+..+...+..++..||..+|.+                       ..+
T Consensus         2 ~~~~~~~~-~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~-----------------------~~~   57 (235)
T KOG0490|consen    2 CGRQILDR-YLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQR-----------------------EFK   57 (235)
T ss_pred             CCccccch-HHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchh-----------------------hhh
Confidence            66777654 455667899999999999999999533444444899999888755                       123


Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      .+.||.||.|+..|+.+|++.|+.++||+...|+.      ++|.+|||||||||+||+++.+
T Consensus        58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~  120 (235)
T KOG0490|consen   58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER  120 (235)
T ss_pred             ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence            45689999999999999999999999999999887      8999999999999999999764

>KOG0488|consensus

Probab=99.65  E-value=3e-17  Score=148.69  Aligned_cols=62  Identities=13%  Similarity=0.110  Sum_probs=56.5

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        102 DGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       102 ~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      +..+|.|+.||+||+.||.+||+.|++..|.+..+|.+      |+..|||+||||||+||||+....
T Consensus       167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g  234 (309)
T KOG0488|consen  167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG  234 (309)
T ss_pred             CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence            34578888999999999999999999999999998887      999999999999999999987653

>KOG0843|consensus

Probab=99.65  E-value=4.1e-17  Score=133.64  Aligned_cols=58  Identities=22%  Similarity=0.206  Sum_probs=54.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        106 GPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       106 ~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ++||.||+||.+||..||.+|+.++|....+|++      |++.||||||||||.|.||.+...
T Consensus       101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~  164 (197)
T KOG0843|consen  101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED  164 (197)
T ss_pred             CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence            7899999999999999999999999999998888      999999999999999999976553

>KOG0487|consensus

Probab=99.64  E-value=6.7e-17  Score=144.54  Aligned_cols=60  Identities=17%  Similarity=0.112  Sum_probs=54.5

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhcc
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISS  164 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~  164 (267)
                      +..|++|..+|..|+.+||++|-.|.|.++..|-+      ||+|||||||||||+|.||+.+.+.
T Consensus       233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r  298 (308)
T KOG0487|consen  233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR  298 (308)
T ss_pred             cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence            55677899999999999999999999999988887      9999999999999999999886443

>KOG0492|consensus

Probab=99.63  E-value=1.7e-16  Score=132.66  Aligned_cols=62  Identities=18%  Similarity=0.153  Sum_probs=56.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        102 DGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       102 ~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .+++..|..||.||.+||..||+.|...+|.++.+|.+      |+|.||||||||||||.||.++..
T Consensus       139 rKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae  206 (246)
T KOG0492|consen  139 RKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAE  206 (246)
T ss_pred             cccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHH
Confidence            45566788999999999999999999999999999998      999999999999999999987654

>KOG0485|consensus

Probab=99.61  E-value=5.4e-16  Score=130.42  Aligned_cols=58  Identities=22%  Similarity=0.300  Sum_probs=53.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        106 GPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       106 ~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ++|+.||+|+..|+.+||.+|+..+|.+...|..      |+|.||||||||||.||||+....
T Consensus       103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad  166 (268)
T KOG0485|consen  103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD  166 (268)
T ss_pred             ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence            4688999999999999999999999999988877      999999999999999999987554

>KOG0842|consensus

Probab=99.60  E-value=1.4e-15  Score=135.99  Aligned_cols=65  Identities=17%  Similarity=0.224  Sum_probs=58.8

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhcc
Q psy10849        100 PRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISS  164 (267)
Q Consensus       100 ~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~  164 (267)
                      +..+.++.||.|-.|+..|+.|||+.|..++|.+..+||+      ||++||||||||||.|.||++++..
T Consensus       146 ~~t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~  216 (307)
T KOG0842|consen  146 PQTGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA  216 (307)
T ss_pred             CccccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence            3445667788899999999999999999999999999999      9999999999999999999887664

>KOG0848|consensus

Probab=99.55  E-value=1e-15  Score=132.33  Aligned_cols=55  Identities=20%  Similarity=0.200  Sum_probs=49.9

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        109 RPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       109 r~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      +.|.++|+.|+.+||++|..++|..+..+.+      |+||||||||||||||.||+.++.
T Consensus       201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk  261 (317)
T KOG0848|consen  201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK  261 (317)
T ss_pred             ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence            4689999999999999999999998876666      999999999999999999977665

>KOG0844|consensus

Probab=99.53  E-value=4.2e-15  Score=130.65  Aligned_cols=65  Identities=17%  Similarity=0.086  Sum_probs=57.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhccCCCC
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISSMPCR  168 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~~~~~  168 (267)
                      ....||.||.||.+||..||++|.+..|.++..|-+      |+|..|||||||||+|.||+...-.+|..
T Consensus       178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPhp  248 (408)
T KOG0844|consen  178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPHP  248 (408)
T ss_pred             cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCCC
Confidence            344689999999999999999999999988887777      99999999999999999998766556655

>KOG0493|consensus

Probab=99.50  E-value=7.9e-15  Score=126.44  Aligned_cols=57  Identities=25%  Similarity=0.280  Sum_probs=51.4

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      -||.||.||.+||..|+.+|+.++|..-..|.+      |+|.||||||||+|||.||.....
T Consensus       246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgsk  308 (342)
T KOG0493|consen  246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSK  308 (342)
T ss_pred             hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCC
Confidence            478999999999999999999999998887776      999999999999999999965433

>KOG0486|consensus

Probab=99.50  E-value=6.1e-15  Score=130.26  Aligned_cols=59  Identities=17%  Similarity=0.225  Sum_probs=56.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      +|+||.||.||.+||.+||..|+++.||+..+||+      |+|.+|+|||.||||||||.++.+
T Consensus       110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~  174 (351)
T KOG0486|consen  110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQ  174 (351)
T ss_pred             hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhH
Confidence            38999999999999999999999999999999999      999999999999999999987655

>KOG0490|consensus

Probab=99.48  E-value=2.1e-14  Score=125.06  Aligned_cols=160  Identities=24%  Similarity=0.368  Sum_probs=125.0

Q ss_pred             CcccCCcccCcccccc--ccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCC-eecchhhHH
Q psy10849          1 STSHNSHVSCHPRGFR--LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSG-QLFCRQDFE   77 (267)
Q Consensus         1 ~~~~dg~~yC~~cy~~--~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~-~lyC~~cy~   77 (267)
                      ||.++|..||+.+|.+  .+..+|.+|...|...|.+.++..+. |..||.|..|...+..+..+.+... +.+|..++.
T Consensus        39 ~~~~~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~  117 (235)
T KOG0490|consen   39 CFSKDGSIYCKRDYQREFKFSKRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRK  117 (235)
T ss_pred             cccCCCcccccccchhhhhccccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhh
Confidence            5778999999999998  88889999999997777777787777 9999999999998888888988875 888988876


Q ss_pred             HHH--hh--hcCCCCCCCc--ccCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCce
Q psy10849         78 KEM--YL--MQQSSPSDDM--MLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAK  145 (267)
Q Consensus        78 k~f--~~--~~~~~~~~~~--~~~~~~~~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v  145 (267)
                      +.-  ..  +.........  .............+.++.||.++..|+..|+..|..+++|+...+++      +++++|
T Consensus       118 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~  197 (235)
T KOG0490|consen  118 EERPLPEGENLPDLSGTAPPSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVI  197 (235)
T ss_pred             hhccccccccCCCCCCCCCccccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhh
Confidence            542  11  1111111110  00111122334567789999999999999999999999998888877      899999


Q ss_pred             eeecchhhhhhhhhhh
Q psy10849        146 NILTPNQRRQFKSSFE  161 (267)
Q Consensus       146 ~vWFQNrRak~k~~~~  161 (267)
                      +|||||+|++.++...
T Consensus       198 q~~~~~~~~~~~~~~~  213 (235)
T KOG0490|consen  198 QVWFQNRRAKLRKHKR  213 (235)
T ss_pred             hhhcccHHHHHHhhcc
Confidence            9999999999998654

>KOG1701|consensus

Probab=99.48  E-value=2.3e-15  Score=137.74  Aligned_cols=77  Identities=27%  Similarity=0.647  Sum_probs=70.6

Q ss_pred             cccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEee-CCeecchhhHHHHH
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILR-SGQLFCRQDFEKEM   80 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~-~~~lyC~~cy~k~f   80 (267)
                      |.+|+++||+.||+.. ..+|..|++.|.  |+|++|.++.||+.||+|.+|++.| +|..|++. ++++||..||.++|
T Consensus       318 Y~v~~k~~CE~cyq~t-lekC~~Cg~~I~--d~iLrA~GkayHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~kf  393 (468)
T KOG1701|consen  318 YQVDGKPYCEGCYQDT-LEKCNKCGEPIM--DRILRALGKAYHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHKKF  393 (468)
T ss_pred             cccCCcccchHHHHHH-HHHHhhhhhHHH--HHHHHhcccccCCCceEEEEecccc-CCccccccCCCceeeehhhhhhc
Confidence            6789999999999764 469999999999  5799999999999999999999999 58999986 69999999999999


Q ss_pred             hh
Q psy10849         81 YL   82 (267)
Q Consensus        81 ~~   82 (267)
                      +-
T Consensus       394 AP  395 (468)
T KOG1701|consen  394 AP  395 (468)
T ss_pred             Cc
Confidence            85

>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=99.46  E-value=1.1e-13  Score=94.95  Aligned_cols=58  Identities=33%  Similarity=0.875  Sum_probs=53.1

Q ss_pred             CCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHH
Q psy10849         22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM   80 (267)
Q Consensus        22 C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f   80 (267)
                      |.+|+++|.+++.++.+.++.||++||+|..|+++|.. ..|+..++++||..||.++|
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~-~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLND-GDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTT-SSEEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCC-CeeEeECCEEECHHHHhhhC
Confidence            88999999988877789999999999999999999974 45899999999999999876

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 ....

>PF00046 Homeobox: Homeobox domain not present here

Probab=99.41  E-value=4.6e-14  Score=96.65  Aligned_cols=51  Identities=27%  Similarity=0.351  Sum_probs=48.1

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKS  158 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~  158 (267)
                      ||.|+.||.+|+.+|++.|+.++||+...+++      |+..+|++||||||+++||
T Consensus         1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk   57 (57)
T PF00046_consen    1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK   57 (57)
T ss_dssp             SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence            57899999999999999999999999888877      9999999999999999986

; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....

>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class

Probab=99.38  E-value=3.8e-13  Score=92.02  Aligned_cols=46  Identities=20%  Similarity=0.202  Sum_probs=43.6

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCC----CChhhhhh------cCCCceeeecchhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPK----PCRKVSTM------NSKRAKNILTPNQR  153 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~----p~~~~r~~------l~~~~v~vWFQNrR  153 (267)
                      ||.||.||.+|+..|++.|+.++|    |+...+++      |++++|||||||-+
T Consensus         2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k   57 (58)
T TIGR01565         2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK   57 (58)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence            789999999999999999999999    99998888      99999999999954

This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.

>COG5576 Homeodomain-containing transcription factor [Transcription]

Probab=99.38  E-value=3.1e-13  Score=110.85  Aligned_cols=64  Identities=23%  Similarity=0.273  Sum_probs=57.0

Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        100 PRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       100 ~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ..++....++.|++.|..|+.+|++.|+.+++|+...|.+      |+++.|||||||||++.|+.....
T Consensus        44 ~~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~  113 (156)
T COG5576          44 KQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK  113 (156)
T ss_pred             cccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence            3456677888889999999999999999999999999988      899999999999999999976554

>KOG4577|consensus

Probab=99.36  E-value=8e-15  Score=128.03  Aligned_cols=158  Identities=20%  Similarity=0.347  Sum_probs=124.3

Q ss_pred             ccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh----hcCCCC
Q psy10849         13 RGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL----MQQSSP   88 (267)
Q Consensus        13 cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~----~~~~~~   88 (267)
                      ++...--++|+.|.+.|.+. +|++++++.||..|++|+.|..+|  ++.++.+++.+||+++|.++|+.    ++..+|
T Consensus        27 df~~~eip~CagC~q~IlDr-FilKvl~R~wHs~CLkCs~C~~qL--~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIp  103 (383)
T KOG4577|consen   27 DFSNVEIPICAGCDQHILDR-FILKVLDRHWHSSCLKCSDCHDQL--ADRCFSREGSVYCKEDFFKRFGTKCSACQEGIP  103 (383)
T ss_pred             cccccccccccchHHHHHHH-HHHHHHhhhhhhhhcchhhhhhHH--HHHHhhcCCceeehHHHHHHhCCcchhhcCCCC
Confidence            34333456899999999976 788999999999999999999999  57899999999999999999997    567777


Q ss_pred             CCCcc---------cCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh--cCCCceeeecchhhhhhh
Q psy10849         89 SDDMM---------LDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM--NSKRAKNILTPNQRRQFK  157 (267)
Q Consensus        89 ~~~~~---------~~~~~~~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~--l~~~~v~vWFQNrRak~k  157 (267)
                      ++.+|         ++++++...+++........+.++-+.+.+..||....-.-...+.  -.+|...+....+....|
T Consensus       104 PtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK  183 (383)
T KOG4577|consen  104 PTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLK  183 (383)
T ss_pred             hHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHH
Confidence            77655         5667777888888888999999998888899887653222111111  566777777777778888


Q ss_pred             hhhhhccCCCCCCCcC
Q psy10849        158 SSFEISSMPCRKVGVH  173 (267)
Q Consensus       158 ~~~~~~~~~~~~~~~~  173 (267)
                      ..+..+.+|++++++.
T Consensus       184 ~AYn~SpKPARHVREQ  199 (383)
T KOG4577|consen  184 QAYNTSPKPARHVREQ  199 (383)
T ss_pred             HHhcCCCchhHHHHHH
Confidence            8888888888777664

>KOG0491|consensus

Probab=99.36  E-value=5.9e-14  Score=113.48  Aligned_cols=57  Identities=16%  Similarity=0.155  Sum_probs=52.3

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhcc
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISS  164 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~  164 (267)
                      ++.||+|+..|+..|++.|+.++|.+...|.+      |+++|||+||||||+|.||..++..
T Consensus       101 ~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~  163 (194)
T KOG0491|consen  101 RKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ  163 (194)
T ss_pred             hhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence            45799999999999999999999999988888      8999999999999999999876653

>KOG1701|consensus

Probab=99.29  E-value=1.7e-12  Score=119.13  Aligned_cols=79  Identities=24%  Similarity=0.599  Sum_probs=68.8

Q ss_pred             ccCCcccCccccccccCCCCCCCCCcccCCC-----cEEEecCceeecCCcccccccccCC---CCCceEeeCCeecchh
Q psy10849          3 SHNSHVSCHPRGFRLYGVKCARCGDRLLPHE-----MVMRAQSHVYHLPCFVCVICCQPLQ---KGEQFILRSGQLFCRQ   74 (267)
Q Consensus         3 ~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e-----~~~~a~~~~wH~~CF~C~~C~~~L~---~g~~f~~~~~~lyC~~   74 (267)
                      ..++++||..||+++|+++|+.|+++|++.+     ..|.++++.||.+|++|..|+..|.   +|..+|..|+.|+|+.
T Consensus       378 d~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~HllCk~  457 (468)
T KOG1701|consen  378 DSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHLLCKT  457 (468)
T ss_pred             cCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCceeech
Confidence            4678999999999999999999999998643     2245799999999999999999996   4678999999999999


Q ss_pred             hHHHHHh
Q psy10849         75 DFEKEMY   81 (267)
Q Consensus        75 cy~k~f~   81 (267)
                      |+.++..
T Consensus       458 Ch~~Rl~  464 (468)
T KOG1701|consen  458 CHLKRLQ  464 (468)
T ss_pred             hhhhhhc
Confidence            9877654

>KOG0847|consensus

Probab=99.23  E-value=5.1e-12  Score=106.74  Aligned_cols=54  Identities=17%  Similarity=0.223  Sum_probs=48.4

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      +..|..|+-.||..||..|+..+|+-...|.+      +++.+|+|||||||.||||..-
T Consensus       168 k~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA  227 (288)
T KOG0847|consen  168 KQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA  227 (288)
T ss_pred             cccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence            45677899999999999999999998887777      8999999999999999999653

>smart00389 HOX Homeodomain

Probab=99.20  E-value=5.8e-12  Score=85.64  Aligned_cols=50  Identities=28%  Similarity=0.452  Sum_probs=45.5

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFK  157 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k  157 (267)
                      ++.|+.|+.+|+..|++.|+.++||+...+++      |+..+|+.||+|||++.|
T Consensus         1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~   56 (56)
T smart00389        1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK   56 (56)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence            35788899999999999999999999888777      899999999999999864

DNA-binding factors that are involved in the transcriptional regulation of key developmental processes

>KOG0483|consensus

Probab=99.13  E-value=1.2e-11  Score=105.05  Aligned_cols=54  Identities=22%  Similarity=0.182  Sum_probs=44.6

Q ss_pred             CCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        110 PRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       110 ~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .+-+||.+|+..||+.|+...+.....+..      |.+|||.|||||||||||..+...
T Consensus        53 kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~  112 (198)
T KOG0483|consen   53 KKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK  112 (198)
T ss_pred             ccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence            344689999999999999998866554444      999999999999999999965443

>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner

Probab=99.13  E-value=1.8e-11  Score=83.85  Aligned_cols=52  Identities=31%  Similarity=0.447  Sum_probs=47.3

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      ++.|+.|+..|+.+|++.|+.++||+..+++.      |++++|++||+|||++.++.
T Consensus         1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~   58 (59)
T cd00086           1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS   58 (59)
T ss_pred             CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence            35678999999999999999999999888777      99999999999999998864

>KOG1703|consensus

Probab=99.09  E-value=2e-11  Score=117.48  Aligned_cols=77  Identities=25%  Similarity=0.578  Sum_probs=70.9

Q ss_pred             ccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849          3 SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus         3 ~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ..+|++||..||.+.+.+.|.+|+++|.+.  +|.+.+..||++||+|..|+++|. +..|++.++.+||..||.+++.+
T Consensus       347 ~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~--~v~a~~~~wH~~cf~C~~C~~~~~-~~~~~~~~~~pyce~~~~~~~~~  423 (479)
T KOG1703|consen  347 ELDGKILCHECFHAPFRPNCKRCLLPILEE--GVCALGRLWHPECFVCADCGKPLK-NSSFFESDGEPYCEDHYKKLFTT  423 (479)
T ss_pred             ccCCCccHHHHHHHhhCccccccCCchHHh--HhhhccCeechhceeeecccCCCC-CCcccccCCccchhhhHhhhccc
Confidence            568999999999999999999999999964  778889999999999999999995 68899999999999999999863

>KOG0849|consensus

Probab=99.09  E-value=1.2e-10  Score=107.77  Aligned_cols=61  Identities=18%  Similarity=0.260  Sum_probs=55.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        102 DGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       102 ~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      ...++.+|.||+|+..|+..|++.|++++||++..|++      +++.+|+|||+|||+||+|....
T Consensus       171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~  237 (354)
T KOG0849|consen  171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD  237 (354)
T ss_pred             cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence            34566788899999999999999999999999999998      89999999999999999998744

>KOG2272|consensus

Probab=99.00  E-value=4e-11  Score=103.40  Aligned_cols=75  Identities=19%  Similarity=0.471  Sum_probs=69.8

Q ss_pred             cccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHH
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK   78 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k   78 (267)
                      |.+.|.+||+.+|.++||..|..|+.+|.++  ++.|+++.|-++||.|+.|.+.|.-...|+..|-++.|+.||.+
T Consensus       237 YEkkGlaYCe~h~~qLfG~~CF~C~~~i~G~--vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r  311 (332)
T KOG2272|consen  237 YEKKGLAYCETHYHQLFGNLCFICNRVIGGD--VVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR  311 (332)
T ss_pred             hhhcCchhHHHHHHHHhhhhheecCCccCcc--HHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence            6799999999999999999999999999876  77899999999999999999999766789999999999999975

>KOG3802|consensus

Probab=98.99  E-value=8e-10  Score=101.38  Aligned_cols=56  Identities=21%  Similarity=0.236  Sum_probs=50.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        106 GPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       106 ~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      |.|++||.|....+..||+.|.+|+.|+..+...      |.+.+|+|||-|||.|.||...
T Consensus       293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~  354 (398)
T KOG3802|consen  293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP  354 (398)
T ss_pred             cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence            5577899999999999999999999999765544      8999999999999999999654

>KOG2272|consensus

Probab=98.98  E-value=7.2e-11  Score=101.82  Aligned_cols=77  Identities=19%  Similarity=0.423  Sum_probs=70.6

Q ss_pred             cCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhhh
Q psy10849          4 HNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLM   83 (267)
Q Consensus         4 ~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~~   83 (267)
                      .+|.+||..|+.+.--++|..|.++|.  |.++.++++.||.+.|+|+.|-+++. |-.-+.+.|..||+.+|.++||.+
T Consensus       180 vk~eLyClrChD~mgipiCgaC~rpIe--ervi~amgKhWHveHFvCa~CekPFl-GHrHYEkkGlaYCe~h~~qLfG~~  256 (332)
T KOG2272|consen  180 VKGELYCLRCHDKMGIPICGACRRPIE--ERVIFAMGKHWHVEHFVCAKCEKPFL-GHRHYEKKGLAYCETHYHQLFGNL  256 (332)
T ss_pred             hccceeccccccccCCcccccccCchH--HHHHHHhccccchhheeehhcCCccc-chhhhhhcCchhHHHHHHHHhhhh
Confidence            467899999999888889999999998  56888999999999999999999996 788888999999999999999973

>KOG1044|consensus

Probab=98.97  E-value=9.8e-11  Score=111.08  Aligned_cols=74  Identities=23%  Similarity=0.470  Sum_probs=68.4

Q ss_pred             cccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHH
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFE   77 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~   77 (267)
                      +.+||.+||+.||++.|+.+|..|.+.|.+.  |+.|.++.||+.|-+|+.|+..|.+|++-++.+..++-..|-.
T Consensus       175 ~skdg~pyce~dy~~~fgvkc~~c~~fisgk--vLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~q  248 (670)
T KOG1044|consen  175 MSKDGVPYCEKDYQAKFGVKCEECEKFISGK--VLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQ  248 (670)
T ss_pred             eccCCCcchhhhhhhhcCeehHHhhhhhhhh--hhhccCcccCcchhhhhhhccccccchheeeccccccCCcccc
Confidence            4689999999999999999999999999975  8999999999999999999999999999999999988777743

>KOG1703|consensus

Probab=98.67  E-value=4.5e-09  Score=101.33  Aligned_cols=75  Identities=20%  Similarity=0.448  Sum_probs=68.5

Q ss_pred             CcccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhH
Q psy10849          1 STSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF   76 (267)
Q Consensus         1 ~~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy   76 (267)
                      .|.+||.+||+.||.++|.++|..|.++|...+..+++.+..||..||+|..|...|. +..|+...++++|..|+
T Consensus       404 ~~~~~~~pyce~~~~~~~~~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~-~~~~~~~~~~p~c~~~~  478 (479)
T KOG1703|consen  404 FFESDGEPYCEDHYKKLFTTKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLT-KKTFFETLDKPLCQKHF  478 (479)
T ss_pred             ccccCCccchhhhHhhhccccchhccchhHhhhhHhhccCccccccceehhhhhcccc-CCceeecCCccccccCC
Confidence            3689999999999999999999999999886666788999999999999999999996 68899999999999885

>KOG1168|consensus

Probab=98.59  E-value=2e-08  Score=88.39  Aligned_cols=57  Identities=25%  Similarity=0.347  Sum_probs=48.3

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhh----h--cCCCceeeecchhhhhhhhhhhhc
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVST----M--NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~----~--l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .||+||.+-.-..+.||++|..+++|+.....    .  |.+.+|+|||-|+|.|.||.....
T Consensus       309 kKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa  371 (385)
T KOG1168|consen  309 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA  371 (385)
T ss_pred             cccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence            48899999999999999999999999853222    2  999999999999999999965433

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

Probab=98.52  E-value=7e-08  Score=60.07  Aligned_cols=38  Identities=45%  Similarity=0.947  Sum_probs=34.2

Q ss_pred             CCCCCCCcccCCCcEEEecCceeecCCcccccccccCC
Q psy10849         21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQ   58 (267)
Q Consensus        21 ~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~   58 (267)
                      +|.+|++.|.+.+.++.+.++.||..||+|..|+.+|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            58999999998756788899999999999999999984

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

>KOG1044|consensus

Probab=98.41  E-value=9.5e-08  Score=91.12  Aligned_cols=59  Identities=25%  Similarity=0.723  Sum_probs=53.5

Q ss_pred             CCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        21 ~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      .|++|++.|..+ .++.|+++.||..||+|..|...|.  ..|+.+++.+||..||.++|++
T Consensus       135 ~cagc~~~lk~g-q~llald~qwhv~cfkc~~c~~vL~--gey~skdg~pyce~dy~~~fgv  193 (670)
T KOG1044|consen  135 TCAGCGEELKNG-QALLALDKQWHVSCFKCKSCSAVLN--GEYMSKDGVPYCEKDYQAKFGV  193 (670)
T ss_pred             cccchhhhhhcc-ceeeeeccceeeeeeehhhhccccc--ceeeccCCCcchhhhhhhhcCe
Confidence            699999999887 4666999999999999999999994  4688899999999999999987

>KOG1700|consensus

Probab=98.00  E-value=1e-06  Score=75.51  Aligned_cols=58  Identities=31%  Similarity=0.755  Sum_probs=49.3

Q ss_pred             CCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHH
Q psy10849         21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM   80 (267)
Q Consensus        21 ~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f   80 (267)
                      .|..|.+.+.+.|+++ ..+..||..||+|..|+..|. ...+...++.+||..++..+|
T Consensus       110 ~c~~c~k~vy~~Ek~~-~~~~~~hk~cfrc~~~~~~ls-~~~~~~~~g~l~~~~~~~~~~  167 (200)
T KOG1700|consen  110 KCARCQKTVYPLEKVT-GNGLEFHKSCFRCTHCGKKLS-PKNYAALEGVLYCKHHFAQLF  167 (200)
T ss_pred             ccccccceeeehHHHh-hhhhhhhhhheeecccccccC-CcchhhcCCccccchhhheee
Confidence            3999999999877665 778899999999999999996 467888889999988876654

>KOG0775|consensus

Probab=97.58  E-value=0.0002  Score=63.15  Aligned_cols=58  Identities=19%  Similarity=0.214  Sum_probs=44.0

Q ss_pred             CCCCCCCCCCCC---------HHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILT---------SAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       104 ~~~~kr~Rt~ft---------~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      |||.--+||+..         +.-+..|++-|..++||....+.+      |+..||--||.|||.+.|....
T Consensus       164 RrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a  236 (304)
T KOG0775|consen  164 RRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA  236 (304)
T ss_pred             eccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence            344444576654         445678899999999998765544      9999999999999999995433

>KOG1146|consensus

Probab=97.54  E-value=5.4e-05  Score=78.72  Aligned_cols=57  Identities=19%  Similarity=0.173  Sum_probs=50.2

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .|+.||.++..||.+|+..|+...+|...+.|.      ++.|+|+|||||-|+|.|+.....
T Consensus       903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~  965 (1406)
T KOG1146|consen  903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG  965 (1406)
T ss_pred             hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence            466899999999999999999999997665555      899999999999999999987654

>KOG1702|consensus

Probab=97.18  E-value=2.2e-05  Score=66.30  Aligned_cols=60  Identities=23%  Similarity=0.580  Sum_probs=49.8

Q ss_pred             CCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        21 ~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      -|..|++.+.+.|.+ +.+++.||..||.|..|+..|. -..|--.+.++||..+|.+..+.
T Consensus         6 n~~~cgk~vYPvE~v-~cldk~whk~cfkce~c~mtln-mKnyKgy~kkpycn~hYpkq~at   65 (264)
T KOG1702|consen    6 NREDCGKTVYPVEEV-KCLDKVWHKQCFKCEVCGMTLN-MKNYKGYDKKPYCNPHYPKQVAT   65 (264)
T ss_pred             hhhhhccccccHHHH-hhHHHHHHHHhheeeeccCChh-hhhccccccCCCcCcccccceee
Confidence            577899999887644 5889999999999999999996 35565568899999999887655

>KOG0774|consensus

Probab=97.15  E-value=0.0013  Score=57.63  Aligned_cols=57  Identities=14%  Similarity=0.207  Sum_probs=48.3

Q ss_pred             CCCCCCCCCHHHHHHHHHhhh---cCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        107 PKRPRTILTSAQRRQFKSSFE---VSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~---~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ++|+|--|+..-.++|.+.|.   .++||+...+++      ++..||--||-|.|-+.||...+.
T Consensus       188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~  253 (334)
T KOG0774|consen  188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN  253 (334)
T ss_pred             HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence            466777899999999999996   568999888777      899999999999999999965443

>KOG2252|consensus

Probab=97.07  E-value=0.00024  Score=68.19  Aligned_cols=52  Identities=23%  Similarity=0.356  Sum_probs=46.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhh
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQF  156 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~  156 (267)
                      -..|+.|++||+.|++.|.+.|+.+++|+..+.+.      |..+.|.-||-|-|.+.
T Consensus       418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs  475 (558)
T KOG2252|consen  418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS  475 (558)
T ss_pred             ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence            34788899999999999999999999999887776      88999999999988774

>KOG1700|consensus

Probab=97.05  E-value=0.00015  Score=62.18  Aligned_cols=62  Identities=23%  Similarity=0.443  Sum_probs=51.9

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ..+|.+|++.+...+++. ..+..||..||.|..|...|. ...+...++.+||+.||..+++.
T Consensus         7 ~~kc~~c~k~vy~~e~~~-~~g~~~hk~c~~c~~~~k~l~-~~~~~~~e~~~yc~~~~~~~~~~   68 (200)
T KOG1700|consen    7 TDKCNACGKTVYFVEKVQ-KDGVDFHKECFKCEKCKKTLT-LSGYSEHEGVPYCKNCHVAQFGP   68 (200)
T ss_pred             cchhhhccCcchHHHHHh-ccCcchhhhHHhccccccccc-cccccccccccccccchHhhhCc
Confidence            458999999998776554 778999999999999999996 46677789999999987777654

>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants []

Probab=95.93  E-value=0.00077  Score=42.63  Aligned_cols=28  Identities=21%  Similarity=0.258  Sum_probs=21.2

Q ss_pred             cCCCCChhhhhh------cCCCceeeecchhhhh
Q psy10849        128 VSPKPCRKVSTM------NSKRAKNILTPNQRRQ  155 (267)
Q Consensus       128 ~~~~p~~~~r~~------l~~~~v~vWFQNrRak  155 (267)
                      .++||+..++++      |+..||..||-|.|.+
T Consensus         7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR   40 (40)
T PF05920_consen    7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR   40 (40)
T ss_dssp             TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred             CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence            368998887776      9999999999999964

; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.

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

Probab=92.50  E-value=0.058  Score=33.38  Aligned_cols=33  Identities=27%  Similarity=0.755  Sum_probs=25.9

Q ss_pred             CCCCCCcccCCCcEEEecCceeecCCcccccccccC
Q psy10849         22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL   57 (267)
Q Consensus        22 C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L   57 (267)
                      |.-|+..|.+.-.+++..++.||   |.|..|...|
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~---fCC~tC~~~f   33 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYY---FCCPTCLSQF   33 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEE---EECHHHHHHH
Confidence            77899999987677888899998   5666676655

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

>KOG3623|consensus

Probab=91.73  E-value=0.27  Score=49.30  Aligned_cols=46  Identities=9%  Similarity=-0.005  Sum_probs=37.5

Q ss_pred             HHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhcc
Q psy10849        119 RRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISS  164 (267)
Q Consensus       119 l~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~  164 (267)
                      +..|+.+|..+..|.......      |+.++|++||++++++..+..+.-+
T Consensus       568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps  619 (1007)
T KOG3623|consen  568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS  619 (1007)
T ss_pred             HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence            678899999999998654443      9999999999999999887654443

>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=82.10  E-value=1.2  Score=33.45  Aligned_cols=29  Identities=34%  Similarity=0.655  Sum_probs=17.7

Q ss_pred             CCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         20 VKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      ..|..|++.|.....++-..+..+|..|+
T Consensus        79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~  107 (109)
T PF10367_consen   79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCI  107 (109)
T ss_pred             CCccCcCCcCCCceEEEeCCCeEEecccc
Confidence            46777887776653333334566776665

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 [].

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	267
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		2e-10
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		3e-10
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		6e-10
2dfy_X	195	Crystal Structure Of A Cyclized Protein Fusion Of L		6e-09
1rut_X	188	Complex Of Lmo4 Lim Domains 1 And 2 With The Ldb1 L		7e-09
2lxd_A	125	Backbone 1h, 13c, And 15n Chemical Shift Assignment		9e-08
2l6y_B	96	Haddock Model Of Gata1nf:lmo2lim2-Ldb1lid Length =		4e-07
2xjy_A	131	Crystal Structure Of The Lmo2:ldb1-Lid Complex, P21		4e-06
1g47_A	77	1st Lim Domain Of Pinch Protein Length = 77		5e-04
3ixe_B	72	Structural Basis Of Competition Between Pinch1 And		5e-04

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

Iteration: 1
 Score = 63.2 bits (152), Expect = 2e-10,   Method: Compositional matrix adjust.
 Identities = 29/76 (38%), Positives = 45/76 (59%), Gaps = 1/76 (1%)
Query: 3   SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
           S    V C    F+ +G KC  C   + P ++V +AQ  VYHL CF C+IC + L  G++
Sbjct: 49  SRAGSVYCKEDFFKRFGTKCTACQQGIPPTQVVRKAQDFVYHLHCFACIICNRQLATGDE 108
Query: 63  F-ILRSGQLFCRQDFE 77
           F ++  G+L C++D+E
Sbjct: 109 FYLMEDGRLVCKEDYE 124

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

Iteration: 1
 Score = 62.4 bits (150), Expect = 3e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 3   SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
           S    V C    F+ +G KCA C   + P ++V RAQ  VYHL CF CV+C + L  G++
Sbjct: 103 SRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDE 162
Query: 63  F-ILRSGQLFCRQDFE 77
           F ++   +L C+ D+E
Sbjct: 163 FYLMEDSRLVCKADYE 178

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

Iteration: 1
 Score = 61.2 bits (147), Expect = 6e-10,   Method: Compositional matrix adjust.
 Identities = 30/76 (39%), Positives = 44/76 (57%), Gaps = 1/76 (1%)
Query: 3   SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
           S    V C    F+ +G KCA C   + P ++V RAQ  VYHL CF CV+C + L  G++
Sbjct: 49  SRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDE 108
Query: 63  F-ILRSGQLFCRQDFE 77
           F ++   +L C+ D+E
Sbjct: 109 FYLMEDSRLVCKADYE 124

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 1   STSHNSHVSCHPRGFRLYG--VKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQ 58
           S + +  + C     RL+G    C+ CG  +   E+VMRAQ +VYHL CF C  C   L 
Sbjct: 47  SYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLV 106
Query: 59  KGEQFILRSGQLFCRQD 75
            G++F   +G LFC  D
Sbjct: 107 PGDRFHYINGSLFCEHD 123

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

Iteration: 1
 Score = 57.8 bits (138), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 30/77 (38%), Positives = 41/77 (53%), Gaps = 2/77 (2%)
Query: 1   STSHNSHVSCHPRGFRLYG--VKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQ 58
           S + +  + C     RL+G    C+ CG  +   E+VMRAQ +VYHL CF C  C   L 
Sbjct: 49  SYTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLV 108
Query: 59  KGEQFILRSGQLFCRQD 75
            G++F   +G LFC  D
Sbjct: 109 PGDRFHYINGSLFCEHD 125

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

Iteration: 1
 Score = 53.9 bits (128), Expect = 9e-08,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 15 FRLYGVK--CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFC 72
           RL+G    CA C  R+  +EM MR +  VYHL CF C  C +    G++++L +  + C
Sbjct: 4  LRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIVC 63
Query: 73 RQDF 76
           QD 
Sbjct: 64 EQDI 67

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

Iteration: 1
 Score = 52.0 bits (123), Expect = 4e-07,   Method: Compositional matrix adjust.
 Identities = 24/64 (37%), Positives = 35/64 (54%), Gaps = 2/64 (3%)
Query: 15 FRLYGVK--CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFC 72
           RL+G    CA C  R+  +EM MR +  VYHL CF C  C +    G++++L +  + C
Sbjct: 2  LRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFSVGDRYLLINSDIVC 61
Query: 73 RQDF 76
           QD 
Sbjct: 62 EQDI 65

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

Iteration: 1
 Score = 48.5 bits (114), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 25/69 (36%), Positives = 36/69 (52%), Gaps = 2/69 (2%)
Query: 10  CHPRGFRLYGVK--CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRS 67
           C     RL+G    CA C  R+  +EM MR +  VYHL CF C  C +    G++++L +
Sbjct: 55  CRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLIN 114
Query: 68  GQLFCRQDF 76
             + C QD 
Sbjct: 115 SDIVCEQDI 123

>pdb|1G47|A Chain A, 1st Lim Domain Of Pinch Protein Length = 77

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Composition-based stats.
 Identities = 20/61 (32%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDF 76
          L    C RC     P E ++ +   +YH  CFVC  C Q   +G  F    G+ +C  DF
Sbjct: 9  LASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDF 67
Query: 77 E 77
          +
Sbjct: 68 Q 68

>pdb|3IXE|B Chain B, Structural Basis Of Competition Between Pinch1 And Pinch2 For Binding To The Ankyrin Repeat Domain Of Integrin-Linked Kinase Length = 72

Iteration: 1
 Score = 41.6 bits (96), Expect = 5e-04,   Method: Compositional matrix adjust.
 Identities = 20/56 (35%), Positives = 29/56 (51%), Gaps = 1/56 (1%)
Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFE 77
          C RC  R  P E ++ +   +YH  CFVC  C +P  +G  F    G+ +C  DF+
Sbjct: 14 CQRCQARFSPAERIVNSNGELYHEHCFVCAQCFRPFPEG-LFYEFEGRKYCEHDFQ 68

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	267
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	4e-29
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	3e-22
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	9e-07
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	1e-21
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	1e-08
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	3e-20
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	1e-08
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	2e-19
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	5e-07
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	4e-15
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-09
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	7e-14
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	7e-14
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	8e-14
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	2e-13
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	4e-13
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	1e-12
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	5e-12
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	5e-12
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	2e-11
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	5e-11
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	8e-10
2cuq_A	80	Four and A half LIM domains 3; structural genomics	1e-10
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	2e-10
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	5e-10
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	3e-09
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-09
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	8e-09
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	1e-08
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	1e-08
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	2e-08
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	2e-08
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	3e-08
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	3e-08
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	4e-08
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	9e-06
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	5e-08
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	6e-08
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	7e-08
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	1e-07
2co8_A	82	NEDD9 interacting protein with calponin homology a	2e-07
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	2e-07
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	2e-07
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	4e-07
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	4e-07
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	1e-06
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	1e-06
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	3e-06
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	5e-06
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	6e-05
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	6e-05
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	2e-04
2cor_A	79	Pinch protein; LIM domain, particularly interestin	2e-04

>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 = 89.7 bits (222), Expect = 3e-22
 Identities = 35/132 (26%), Positives = 53/132 (40%), Gaps = 9/132 (6%)

Query: 3   SHNSHVSCHPRGFRLYGV--KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKG 60
           + +  + C     RL+G    C+ CG  +   E+VMRAQ +VYHL CF C  C   L  G
Sbjct: 51  TKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPG 110

Query: 61  EQFILRSGQLFCRQDFEKEM------YLMQQSSPSDDMMLDENCRPRD-GRRGPKRPRTI 113
           ++F   +G LFC  D    +            S      +     P   G         +
Sbjct: 111 DRFHYINGSLFCEHDRPTALINGHLNSGGSGGSGGSGGDVMVVGEPTLMGGEFGDEDERL 170

Query: 114 LTSAQRRQFKSS 125
           +T  +  QF ++
Sbjct: 171 ITRLENTQFDAA 182

>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 = 47.3 bits (112), Expect = 9e-07
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 2/61 (3%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL-QKGEQFILRSGQLFCRQDFEKE 79
          +CA CG ++     ++ A    +H  C  C  C   L   G     +SG + CR D+ + 
Sbjct: 7  RCAGCGGKIAD-RFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 65

Query: 80 M 80
           
Sbjct: 66 F 66

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

 Score = 86.7 bits (215), Expect = 1e-21
 Identities = 24/68 (35%), Positives = 36/68 (52%), Gaps = 2/68 (2%)

Query: 15  FRLYGVK--CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFC 72
            RL+G    CA C  R+  +EM MR +  VYHL CF C  C +    G++++L +  + C
Sbjct: 60  LRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVC 119

Query: 73  RQDFEKEM 80
            QD  +  
Sbjct: 120 EQDIYEWT 127

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

 Score = 51.7 bits (124), Expect = 1e-08
 Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL-QKGEQFILRSGQLFCRQDFEK 78
           C  C   +      ++A    +H  C  C +C   L + G +   + G+  CR+D+ +
Sbjct: 4  TCGGCQQNIGD-RYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 61

>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 = 84.2 bits (208), Expect = 3e-20
 Identities = 27/67 (40%), Positives = 41/67 (61%), Gaps = 1/67 (1%)

Query: 15  FRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQF-ILRSGQLFCR 73
           F+ +G KCA C   + P ++V RAQ  VYHL CF CV+C + L  G++F ++   +L C+
Sbjct: 115 FKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCK 174

Query: 74  QDFEKEM 80
            D+E   
Sbjct: 175 ADYETAK 181

>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 = 52.2 bits (125), Expect = 1e-08
 Identities = 18/76 (23%), Positives = 27/76 (35%), Gaps = 3/76 (3%)

Query: 3   SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
                      G       CA C   +L    +++A    +H  C  C  C  PL   E+
Sbjct: 44  DEGGSGGHMGSGGTPEIPMCAGCDQHIL-DRFILKALDRHWHSKCLKCSDCHVPL--AER 100

Query: 63  FILRSGQLFCRQDFEK 78
              R   ++C+ DF K
Sbjct: 101 CFSRGESVYCKDDFFK 116

>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 = 81.8 bits (202), Expect = 2e-19
 Identities = 30/79 (37%), Positives = 44/79 (55%), Gaps = 1/79 (1%)

Query: 3   SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQ 62
           S    V C    F+ +G KCA C   + P ++V RAQ  VYHL CF CV+C + L  G++
Sbjct: 49  SRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDE 108

Query: 63  F-ILRSGQLFCRQDFEKEM 80
           F ++   +L C+ D+E   
Sbjct: 109 FYLMEDSRLVCKADYETAK 127

>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 = 47.5 bits (113), Expect = 5e-07
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 3/58 (5%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
           CA C   +L    +++A    +H  C  C  C  PL   E+   R   ++C+ DF K
Sbjct: 8  MCAGCDQHIL-DRFILKALDRHWHSKCLKCSDCHVPL--AERCFSRGESVYCKDDFFK 62

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

 Score = 69.0 bits (169), Expect = 4e-15
 Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 3/68 (4%)

Query: 15  FRLYGVKCARCGDRLLPHEMVMRAQSHVYHLP--CFVCVICCQPLQKGEQFILRSGQLFC 72
            + + V C  C + + P    +   +  +H    CF+C  C + L  G++F+   G +FC
Sbjct: 59  VKNHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCL-IGQKFMPVEGMVFC 117

Query: 73  RQDFEKEM 80
             + +K M
Sbjct: 118 SVECKKRM 125

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

 Score = 53.9 bits (130), Expect = 1e-09
 Identities = 16/58 (27%), Positives = 29/58 (50%), Gaps = 2/58 (3%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
          +CA C D L+      +A++  +HL  F C  C   L  GE +++ + +  C+  + K
Sbjct: 5  RCAGC-DELIFSNEYTQAENQNWHLKHFCCFDCDSILA-GEIYVMVNDKPVCKPCYVK 60

>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 = 64.3 bits (157), Expect = 7e-14
 Identities = 19/63 (30%), Positives = 26/63 (41%), Gaps = 1/63 (1%)

Query: 16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
           L    C RC     P E ++ +   +YH  CFVC  C Q       F    G+ +C  D
Sbjct: 8  ALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP-EGLFYEFEGRKYCEHD 66

Query: 76 FEK 78
          F+ 
Sbjct: 67 FQM 69

>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 = 64.4 bits (157), Expect = 7e-14
 Identities = 17/74 (22%), Positives = 28/74 (37%), Gaps = 3/74 (4%)

Query: 6  SHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL 65
          S  S     +  +G  C  C   +      M A    YH  CF C+ C   ++ G+ + L
Sbjct: 2  SSGSSGKDYWGKFGEFCHGCSLLMTG--PFMVAGEFKYHPECFACMSCKVIIEDGDAYAL 59

Query: 66 R-SGQLFCRQDFEK 78
               L+C +   +
Sbjct: 60 VQHATLYCGKCHNE 73

>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 = 64.0 bits (156), Expect = 8e-14
 Identities = 18/63 (28%), Positives = 25/63 (39%), Gaps = 1/63 (1%)

Query: 16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
                C RC     P E ++ +   +YH  CFVC  C Q       F    G+ +C  D
Sbjct: 8  GSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFP-EGLFYEFEGRKYCEHD 66

Query: 76 FEK 78
          F+ 
Sbjct: 67 FQM 69

>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 = 62.8 bits (153), Expect = 2e-13
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
           C  CG+ ++     + A   V+H+ CFVC  C   L+ G+ F     + +C   +  
Sbjct: 7  GCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLR-GQHFYAVERRAYCEGCYVA 63

>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 = 62.4 bits (152), Expect = 4e-13
 Identities = 16/73 (21%), Positives = 25/73 (34%), Gaps = 1/73 (1%)

Query: 6  SHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL 65
          S  S      R    KC  C   ++  +  +  +  V+H  CF C  C Q +     F  
Sbjct: 2  SSGSSGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIG-TGSFFP 60

Query: 66 RSGQLFCRQDFEK 78
          +    +C    E 
Sbjct: 61 KGEDFYCVTCHET 73

>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 = 61.0 bits (148), Expect = 1e-12
 Identities = 18/60 (30%), Positives = 27/60 (45%), Gaps = 2/60 (3%)

Query: 15 FRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQ 74
           RLYG +C  C   +     V+ A    YH  CFVC +C  P   G++      +  C++
Sbjct: 11 QRLYGTRCFSCDQFIE--GEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQK 68

>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 = 59.4 bits (144), Expect = 5e-12
 Identities = 16/75 (21%), Positives = 25/75 (33%), Gaps = 1/75 (1%)

Query: 6  SHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL 65
          S  S  P     +   CA C   +      +  +   +H  CF C  C + L   E F  
Sbjct: 2  SSGSSGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLA-DEPFTC 60

Query: 66 RSGQLFCRQDFEKEM 80
          +  +L C   +    
Sbjct: 61 QDSELLCNDCYCSAF 75

>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 = 58.9 bits (143), Expect = 5e-12
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKE 79
           C  C   ++P    M  +   +H  CF+C  C QP+   + FI +  Q FC   +EK+
Sbjct: 7  GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPI-GTKSFIPKDNQNFCVPCYEKQ 64

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

 Score = 57.4 bits (139), Expect = 2e-11
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
           C+ CG+ ++P    +      +H  CF+C  C QPL     F+   G  +C   +E 
Sbjct: 7  GCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLG-SRSFVPDKGAHYCVPCYEN 63

>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 = 57.4 bits (139), Expect = 5e-11
 Identities = 13/62 (20%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 18 YGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFE 77
              C  C   +      +  ++  +H  CF C  C  PL   E F+ +  ++ C +   
Sbjct: 4  GSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLA-NETFVAKDNKILCNKCTT 62

Query: 78 KE 79
          +E
Sbjct: 63 RE 64

>2cup_A Skeletal muscle LIM-protein 1; four and half LIM domains protein 1, LIM domain, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 Length = 101

 Score = 54.0 bits (130), Expect = 8e-10
 Identities = 9/51 (17%), Positives = 20/51 (39%)

Query: 3   SHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVIC 53
           + ++ + C+    R    KC  C   ++  +  +  +  V+H  CF     
Sbjct: 50  AKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100

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

 Score = 55.8 bits (135), Expect = 1e-10
 Identities = 21/73 (28%), Positives = 30/73 (41%), Gaps = 3/73 (4%)

Query: 6  SHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL 65
          S  S  P     +  +CARC   L   +  +  +   +H  C VC  C  PL  G+QF  
Sbjct: 2  SSGSSGPCYENKFAPRCARCSKTLT--QGGVTYRDQPWHRECLVCTGCQTPLA-GQQFTS 58

Query: 66 RSGQLFCRQDFEK 78
          R    +C   F +
Sbjct: 59 RDEDPYCVACFGE 71

>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 = 55.0 bits (133), Expect = 2e-10
 Identities = 19/73 (26%), Positives = 26/73 (35%), Gaps = 3/73 (4%)

Query: 6  SHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL 65
          S  S       ++  KC  C   +L  E  + A   V+H  CFVC  C         F  
Sbjct: 2  SSGSSGKDFLAMFSPKCGGCNRPVL--ENYLSAMDTVWHPECFVCGDCFTSFS-TGSFFE 58

Query: 66 RSGQLFCRQDFEK 78
            G+ FC   +  
Sbjct: 59 LDGRPFCELHYHH 71

>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 = 54.0 bits (130), Expect = 5e-10
 Identities = 15/67 (22%), Positives = 24/67 (35%), Gaps = 4/67 (5%)

Query: 15 FRLYGVKCARCG---DRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLF 71
                KCA C            V+  +   +H  CF C  C   L   ++F+    Q++
Sbjct: 11 KNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLA-NKRFVFHQEQVY 69

Query: 72 CRQDFEK 78
          C    +K
Sbjct: 70 CPDCAKK 76

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

 Score = 51.5 bits (124), Expect = 3e-09
 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 3/58 (5%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
           C  C   +     V+ A    +H+  FVC  C +P   G +   R G  +C   + +
Sbjct: 7  ICGACRRPIE--GRVVNAMGKQWHVEHFVCAKCEKPFL-GHRHYERKGLAYCETHYNQ 61

>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 = 51.0 bits (122), Expect = 4e-09
 Identities = 13/64 (20%), Positives = 20/64 (31%), Gaps = 3/64 (4%)

Query: 17 LYGVKCARCGD--RLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQ 74
               CA C +    L     +  +   +H  CF C  C   L  G  F+     + C  
Sbjct: 3  SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL-VGRGFLTERDDILCPD 61

Query: 75 DFEK 78
            + 
Sbjct: 62 CGKD 65

>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 = 50.5 bits (121), Expect = 8e-09
 Identities = 18/74 (24%), Positives = 30/74 (40%), Gaps = 4/74 (5%)

Query: 5  NSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFI 64
          +S  S  P   R     CA C + +   +  + A    +H+ CF C  C   L    ++I
Sbjct: 2  SSGSSGKPIKIR-GPSHCAGCKEEIKHGQ-SLLALDKQWHVSCFKCQTCSVIL--TGEYI 57

Query: 65 LRSGQLFCRQDFEK 78
           + G  +C  D+  
Sbjct: 58 SKDGVPYCESDYHA 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 = 50.5 bits (121), Expect = 1e-08
 Identities = 16/79 (20%), Positives = 25/79 (31%), Gaps = 4/79 (5%)

Query: 1  STSHNSHVSCHPRGFR-LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQK 59
          S   ++ V              CA C   +      + A    +H   F C  C   +  
Sbjct: 6  SGDQDTLVQRAEHIPAGKRTPMCAHCNQVIR--GPFLVALGKSWHPEEFNCAHCKNTMA- 62

Query: 60 GEQFILRSGQLFCRQDFEK 78
             F+   G L+C   +EK
Sbjct: 63 YIGFVEEKGALYCELCYEK 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 = 50.1 bits (120), Expect = 1e-08
 Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 2/58 (3%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
          KCA C   +L  + ++RA    YH  CF CV+C + L      +  + Q+ C +DF +
Sbjct: 17 KCATCSQPIL--DRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHR 72

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

 Score = 49.3 bits (118), Expect = 2e-08
 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 3/58 (5%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
           C +C   +      +  +   +H  CFVC  C + L  G++F  R    +C   F  
Sbjct: 7  GCVQCKKPIT--TGGVTYREQPWHKECFVCTACRKQLS-GQRFTARDDFAYCLNCFCD 61

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

 Score = 49.7 bits (119), Expect = 2e-08
 Identities = 14/58 (24%), Positives = 26/58 (44%), Gaps = 2/58 (3%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
          KC  CG  +   E V       +H  CF+C++C + L       +   +++C+  + K
Sbjct: 9  KCGACGRTVYHAEEVQ-CDGRSFHRCCFLCMVCRKNLDSTT-VAIHDAEVYCKSCYGK 64

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

 Score = 48.9 bits (117), Expect = 3e-08
 Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 3/58 (5%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
           C +C   +      +  Q   +H  CFVCV C + L  G++F     Q +C   ++ 
Sbjct: 7  GCVKCNKAIT--SGGITYQDQPWHADCFVCVTCSKKLA-GQRFTAVEDQYYCVDCYKN 61

>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 = 48.6 bits (116), Expect = 3e-08
 Identities = 16/60 (26%), Positives = 31/60 (51%), Gaps = 3/60 (5%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80
           C +CG+ ++    V++A ++ +H  CF C +C + L     F+  +G+  CR    +E 
Sbjct: 7  GCHQCGEFII--GRVIKAMNNSWHPECFRCDLCQEVLADIG-FVKNAGRHLCRPCHNREK 63

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

 Score = 51.2 bits (122), Expect = 4e-08
 Identities = 15/70 (21%), Positives = 27/70 (38%), Gaps = 2/70 (2%)

Query: 9   SCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSG 68
           +            C RCG  +   E V+      +H  CF C  C + L+       + G
Sbjct: 105 ASRMAQKVGGSDGCPRCGQAVYAAEKVI-GAGKSWHKSCFRCAKCGKSLE-STTLADKDG 162

Query: 69  QLFCRQDFEK 78
           +++C+  + K
Sbjct: 163 EIYCKGCYAK 172

>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 = 44.2 bits (104), Expect = 9e-06
 Identities = 13/59 (22%), Positives = 28/59 (47%), Gaps = 2/59 (3%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKE 79
          KC  C   +   E V + +   +H  CF+C++C + L       +   +++C+  + K+
Sbjct: 9  KCGVCQKAVYFAEEV-QCEGSSFHKSCFLCMVCKKNLD-STTVAVHGDEIYCKSCYGKK 65

>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 = 49.6 bits (118), Expect = 5e-08
 Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 2/63 (3%)

Query: 17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL-QKGEQFILRSGQLFCRQD 75
          L   +CA CG ++     ++ A    +H  C  C  C   L   G     +SG + CR D
Sbjct: 3  LSWKRCAGCGGKIA-DRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRND 61

Query: 76 FEK 78
          + +
Sbjct: 62 YIR 64

>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 = 47.9 bits (114), Expect = 6e-08
 Identities = 14/65 (21%), Positives = 24/65 (36%), Gaps = 3/65 (4%)

Query: 17 LYGVKCARCGD--RLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQ 74
               C  C      L     +  Q   +H  CF C  C   L  G+ F+ ++ ++FC++
Sbjct: 3  SGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLV-GKGFLTQNKEIFCQK 61

Query: 75 DFEKE 79
               
Sbjct: 62 CGSGM 66

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

 Score = 48.3 bits (115), Expect = 7e-08
 Identities = 16/58 (27%), Positives = 27/58 (46%), Gaps = 2/58 (3%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
           C  C   + P E ++ A   V+H+ CF C  C   L  G  +    G+++C+  F +
Sbjct: 17 TCVECQKTVYPMERLL-ANQQVFHISCFRCSYCNNKLSLGT-YASLHGRIYCKPHFNQ 72

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

 Score = 47.4 bits (113), Expect = 1e-07
 Identities = 12/58 (20%), Positives = 25/58 (43%), Gaps = 3/58 (5%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
           C +CG  ++   + ++ +    H  C+VC  C   L K +       Q++C +   +
Sbjct: 17 MCDKCGTGIV--GVFVKLRDRHRHPECYVCTDCGTNL-KQKGHFFVEDQIYCEKHARE 71

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

 Score = 47.3 bits (112), Expect = 2e-07
 Identities = 17/61 (27%), Positives = 23/61 (37%), Gaps = 2/61 (3%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGE-QFILRSGQLFCRQDFEKE 79
           CA CG+ L   E +     H +H  CF C  C   L  G  +     G  +C Q   + 
Sbjct: 17 LCALCGEHLYVLERLC-VNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQT 75

Query: 80 M 80
           
Sbjct: 76 D 76

>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 = 48.2 bits (114), Expect = 2e-07
 Identities = 19/79 (24%), Positives = 29/79 (36%), Gaps = 2/79 (2%)

Query: 1   STSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL-QK 59
           S         H     L   +CA CG ++     ++ A    +H  C  C  C   L   
Sbjct: 43  SKLGGGGSGGHMGSGGLSWKRCAGCGGKIADRF-LLYAMDSYWHSRCLKCSSCQAQLGDI 101

Query: 60  GEQFILRSGQLFCRQDFEK 78
           G     +SG + CR D+ +
Sbjct: 102 GTSSYTKSGMILCRNDYIR 120

>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 = 46.7 bits (111), Expect = 2e-07
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 3/58 (5%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
           C +CG  ++    V++A+    H  CFVC  C   L K + +    G+L+C      
Sbjct: 27 LCDKCGSGIV--GAVVKARDKYRHPECFVCADCNLNL-KQKGYFFVEGELYCETHARA 81

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

 Score = 45.8 bits (109), Expect = 4e-07
 Identities = 14/61 (22%), Positives = 22/61 (36%), Gaps = 2/61 (3%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80
          KC +C   +   E V  +    +H PC  C  C + L          G+ +C       M
Sbjct: 2  KCPKCDKEVYFAERVT-SLGKDWHRPCLKCEKCGKTL-TSGGHAEHEGKPYCNHPCYSAM 59

Query: 81 Y 81
          +
Sbjct: 60 F 60

>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 = 46.6 bits (110), Expect = 4e-07
 Identities = 13/59 (22%), Positives = 25/59 (42%), Gaps = 2/59 (3%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPL-QKGEQFILRSGQLFCRQDFEK 78
           C  C   +      ++A    +H  C  C +C   L + G +   + G+  CR+D+ +
Sbjct: 5  TCGGCQQNIG-DRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLR 62

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 80

 Score = 44.4 bits (105), Expect = 1e-06
 Identities = 9/35 (25%), Positives = 15/35 (42%)

Query: 102 DGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKV 136
           +  +  KR RT +T  Q       + +   P RK+
Sbjct: 12  EEPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKM 46

>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 = 44.3 bits (105), Expect = 1e-06
 Identities = 14/55 (25%), Positives = 21/55 (38%), Gaps = 2/55 (3%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQD 75
          KC +C   +   E V  +    +H  C  C  C + L  G       G+ FC + 
Sbjct: 11 KCPKCDKTVYFAEKVS-SLGKDWHKFCLKCERCSKTLTPGG-HAEHDGKPFCHKP 63

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens} Length = 70

 Score = 43.1 bits (102), Expect = 3e-06
 Identities = 10/34 (29%), Positives = 16/34 (47%)

Query: 103 GRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKV 136
                KRPRT +T  Q R  +  F+++  P  + 
Sbjct: 3   SGSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQ 36

>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 = 42.5 bits (100), Expect = 5e-06
 Identities = 17/65 (26%), Positives = 31/65 (47%), Gaps = 3/65 (4%)

Query: 18 YGVKCARCGDRLLPHEMVMRAQSHVYHLP--CFVCVICCQPLQKGEQFILRSGQLFCRQD 75
          + V C  C + + P    +   +  +H    CF+C  C + L  G++F+   G +FC  +
Sbjct: 1  HAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI-GQKFMPVEGMVFCSVE 59

Query: 76 FEKEM 80
           +K M
Sbjct: 60 CKKRM 64

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1 Length = 146

 Score = 41.1 bits (96), Expect = 6e-05
 Identities = 11/119 (9%), Positives = 29/119 (24%), Gaps = 12/119 (10%)

Query: 21  KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEM 80
           K  R         +     +          +   + LQ               ++  K  
Sbjct: 13  KVRRIKLGYTQTNVGEALAAVHGSEFSQTTICRFENLQLS------------FKNACKLK 60

Query: 81  YLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM 139
            ++ +     + +              ++ RT ++ A +   +  F    KP  +    
Sbjct: 61  AILSKWLEEAEQVGALYNEKVGANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMR 119

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

 Score = 39.3 bits (91), Expect = 6e-05
 Identities = 14/52 (26%), Positives = 22/52 (42%), Gaps = 2/52 (3%)

Query: 21 KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFC 72
           C  C   +     V+ A    YH  C +CV C Q   +GE+  L+   ++ 
Sbjct: 7  GCDSCEKYIT--GRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWH 56

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1 Length = 66

 Score = 38.1 bits (89), Expect = 2e-04
 Identities = 7/30 (23%), Positives = 14/30 (46%)

Query: 107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKV 136
             R RT+L   Q    ++ +  +P+P   +
Sbjct: 3   TTRVRTVLNEKQLHTLRTCYAANPRPDALM 32

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

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 13/57 (22%), Positives = 22/57 (38%), Gaps = 4/57 (7%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEK 78
          C +C   +   E  +  ++  YH   F C  C + L          G+L+C    +K
Sbjct: 18 CQKCHAIID--EQPLIFKNDPYHPDHFNCANCGKEL--TADARELKGELYCLPCHDK 70

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	267
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.86
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.78
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.78
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.76
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.76
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.75
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.75
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.74
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.73
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.73
2dms_A	80	Homeobox protein OTX2; homeobox domain, three heli	99.72
2dmt_A	80	Homeobox protein BARH-like 1; homeobox domain, thr	99.71
2cra_A	70	Homeobox protein HOX-B13; DNA-binding, transcripti	99.71
1wh5_A	80	ZF-HD homeobox family protein; structural genomics	99.71
2dmq_A	80	LIM/homeobox protein LHX9; homeobox domain, three	99.7
2cue_A	80	Paired box protein PAX6; homeobox domain, transcri	99.7
2kt0_A	84	Nanog, homeobox protein nanog; homeodomain, struct	99.7
1nk2_P	77	Homeobox protein VND; homeodomain, DNA-binding pro	99.7
2da2_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.7
1wh7_A	80	ZF-HD homeobox family protein; homeobox domain, st	99.7
2da1_A	70	Alpha-fetoprotein enhancer binding protein; homeob	99.7
2djn_A	70	Homeobox protein DLX-5; structural genomics, NPPSF	99.69
2dmu_A	70	Homeobox protein goosecoid; homeobox domain, three	99.69
1ahd_P	68	Antennapedia protein mutant; DNA binding protein/D	99.69
2da4_A	80	Hypothetical protein DKFZP686K21156; homeobox doma	99.69
1puf_A	77	HOX-1.7, homeobox protein HOX-A9; homeodomian, pro	99.68
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.68
2l7z_A	73	Homeobox protein HOX-A13; gene regulation; NMR {Ho	99.68
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.68
2vi6_A	62	Homeobox protein nanog; homeodomain, DNA-binding,	99.68
1zq3_P	68	PRD-4, homeotic bicoid protein; protein-DNA comple	99.68
2h1k_A	63	IPF-1, pancreatic and duodenal homeobox 1, homeodo	99.68
2da3_A	80	Alpha-fetoprotein enhancer binding protein; homeob	99.68
2hdd_A	61	Protein (engrailed homeodomain Q50K); DNA binding,	99.67
2e1o_A	70	Homeobox protein PRH; DNA binding protein, structu	99.67
1ig7_A	58	Homeotic protein MSX-1; helix-turn-helix, transcri	99.67
1yz8_P	68	Pituitary homeobox 2; DNA binding protein, transcr	99.66
1bw5_A	66	ISL-1HD, insulin gene enhancer protein ISL-1; DNA-	99.66
3a01_A	93	Homeodomain-containing protein; homeodomain, prote	99.66
1b8i_A	81	Ultrabithorax, protein (ultrabithorax homeotic pro	99.66
2r5y_A	88	Homeotic protein sex combs reduced; homeodomain; H	99.66
1fjl_A	81	Paired protein; DNA-binding protein, paired BOX, t	99.66
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.66
2dn0_A	76	Zinc fingers and homeoboxes protein 3; triple home	99.65
2m0c_A	75	Homeobox protein aristaless-like 4; structural gen	99.65
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.65
1ftt_A	68	TTF-1 HD, thyroid transcription factor 1 homeodoma	99.65
1jgg_A	60	Segmentation protein EVEN-skipped; homeodomain, pr	99.65
2hi3_A	73	Homeodomain-only protein; transcription; NMR {Mus	99.64
1wi3_A	71	DNA-binding protein SATB2; homeodomain, helix-turn	99.64
2ly9_A	74	Zinc fingers and homeoboxes protein 1; structural	99.63
2k40_A	67	Homeobox expressed in ES cells 1; thermostable hom	99.63
2cuf_A	95	FLJ21616 protein; homeobox domain, hepatocyte tran	99.63
1uhs_A	72	HOP, homeodomain only protein; structural genomics	99.63
1b72_A	97	Protein (homeobox protein HOX-B1); homeodomain, DN	99.63
2ecc_A	76	Homeobox and leucine zipper protein homez; homeobo	99.63
3a02_A	60	Homeobox protein aristaless; homeodomain, developm	99.63
2da5_A	75	Zinc fingers and homeoboxes protein 3; homeobox do	99.63
1akh_A	61	Protein (mating-type protein A-1); complex (TWO DN	99.62
2ecb_A	89	Zinc fingers and homeoboxes protein 1; homeobox do	99.61
3rkq_A	58	Homeobox protein NKX-2.5; helix-turn-helix, DNA bi	99.61
3a03_A	56	T-cell leukemia homeobox protein 2; homeodomain, d	99.6
1x2n_A	73	Homeobox protein pknox1; homeobox domain, structur	99.6
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.59
3nar_A	96	ZHX1, zinc fingers and homeoboxes protein 1; corep	99.59
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.59
1puf_B	73	PRE-B-cell leukemia transcription factor-1; homeod	99.57
2da6_A	102	Hepatocyte nuclear factor 1-beta; homeobox domain,	99.57
2xsd_C	164	POU domain, class 3, transcription factor 1; trans	99.56
1au7_A	146	Protein PIT-1, GHF-1; complex (DNA-binding protein	99.56
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.56
1e3o_C	160	Octamer-binding transcription factor 1; transcript	99.56
2dmn_A	83	Homeobox protein TGIF2LX; TGFB-induced factor 2-li	99.55
2cqx_A	72	LAG1 longevity assurance homolog 5; homeodomain, D	99.55
1b72_B	87	Protein (PBX1); homeodomain, DNA, complex, DNA-bin	99.55
2dmp_A	89	Zinc fingers and homeoboxes protein 2; homeobox do	99.54
1lfb_A	99	Liver transcription factor (LFB1); transcription r	99.54
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.54
1du6_A	64	PBX1, homeobox protein PBX1; homeodomain, gene reg	99.54
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.53
2l9r_A	69	Homeobox protein NKX-3.1; structural genomics, nor	99.53
3d1n_I	151	POU domain, class 6, transcription factor 1; prote	99.53
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.52
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.51
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.51
3l1p_A	155	POU domain, class 5, transcription factor 1; POU,	99.51
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.51
1k61_A	60	Mating-type protein alpha-2; protein-DNA complex,	99.51
3nau_A	66	Zinc fingers and homeoboxes protein 2; ZHX2, corep	99.51
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.5
1mnm_C	87	Protein (MAT alpha-2 transcriptional repressor); t	99.5
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.49
2e19_A	64	Transcription factor 8; homeobox domain, structura	99.49
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.48
1le8_B	83	Mating-type protein alpha-2; matalpha2, isothermal	99.47
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.47
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.47
2d5v_A	164	Hepatocyte nuclear factor 6; transcription factor,	99.46
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.45
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.45
1x2m_A	64	LAG1 longevity assurance homolog 6; homeobox domai	99.45
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.44
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.4
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.38
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.38
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.38
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.37
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.36
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.36
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.35
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.35
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.33
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.33
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.32
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.3
3k2a_A	67	Homeobox protein MEIS2; homeobox domain, DNA-bindi	99.29
1ic8_A	194	Hepatocyte nuclear factor 1-alpha; transcription r	99.29
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.25
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.22
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.19
2h8r_A	221	Hepatocyte nuclear factor 1-beta; trasncription fa	99.14
2da7_A	71	Zinc finger homeobox protein 1B; homeobox domain,	99.14
2nzz_A	37	Penetratin conjugated GAS (374-394) peptide; confo	99.13
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.08
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.08
1mh3_A	421	Maltose binding-A1 homeodomain protein chimera; MA	99.0
2lk2_A	89	Homeobox protein TGIF1; NESG, structural genomics,	98.9
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	98.74
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	98.42
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	97.55
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	96.64
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	96.41
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	96.05
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	95.11
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	95.07
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	95.01
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	94.91
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	94.51
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	91.84
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	90.74
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	89.89

>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=99.86  E-value=2.5e-23  Score=172.51  Aligned_cols=116  Identities=30%  Similarity=0.600  Sum_probs=96.6

Q ss_pred             cccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEe-eCCeecchhhHHHHH
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL-RSGQLFCRQDFEKEM   80 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~-~~~~lyC~~cy~k~f   80 (267)
                      |.+||++||+.||.++|+++|.+|+++|.+.+.++.+.++.||++||+|..|++.|..|..|+. .++++||..||.+++
T Consensus        48 f~~~g~~yC~~~y~~~f~~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~  127 (169)
T 2rgt_A           48 FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK  127 (169)
T ss_dssp             EESSSCEECHHHHHHHHSCBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHH
T ss_pred             cccCCeeeecccccccccccccccccccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHh
Confidence            6799999999999999999999999999988888899999999999999999999976777765 589999999999987


Q ss_pred             hhhcCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChh
Q psy10849         81 YLMQQSSPSDDMMLDENCRPRDGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRK  135 (267)
Q Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~  135 (267)
                      ..-.                 + ..+.||.||.|+.+||++|++.|+.+++|+..
T Consensus       128 ~~~~-----------------~-~~~~~rprt~~~~~q~~~l~~~f~~~~~~~~~  164 (169)
T 2rgt_A          128 QGGS-----------------G-GSGGSGGGTPMVAASPERHDGGLQANPVEVQS  164 (169)
T ss_dssp             HCC----------------------------EEEECCCCEECCSSCCCCCCCCCC
T ss_pred             hccC-----------------C-CCCCcCCCCcccHHHHHHHHHHHhCCCCcccc
Confidence            6310                 1 13468999999999999999999999999754

>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=99.78  E-value=6.1e-20  Score=134.06  Aligned_cols=77  Identities=21%  Similarity=0.392  Sum_probs=71.5

Q ss_pred             CCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849          5 NSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus         5 dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ||++||+.||.++|+++|.+|+++|.+.+.++.+.++.||++||+|..|+++|. +..|+.+++++||+.||.++|+.
T Consensus         1 ~g~~yC~~~y~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~f~~~~~~~~C~~c~~~~~~~   77 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLA-DEPFTCQDSELLCNDCYCSAFSS   77 (82)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCS-SCCEEEETTEEEETTTSSCCGGG
T ss_pred             CCceechhHhCcccCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccC-CCccEeeCCEEECHHHHhhhcCC
Confidence            689999999999999999999999996567888999999999999999999996 67899999999999999998874

>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=99.78  E-value=2.6e-19  Score=130.62  Aligned_cols=77  Identities=21%  Similarity=0.376  Sum_probs=71.3

Q ss_pred             CCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849          5 NSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus         5 dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ++.+||+.||.++|+++|.+|+++|.+.+.++.+.++.||++||+|..|+++|. +..|+.+++++||+.||.++|+.
T Consensus         1 ~~~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~~   77 (82)
T 1x63_A            1 GSSGSSGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIG-TGSFFPKGEDFYCVTCHETKFAS   77 (82)
T ss_dssp             CCSCCCCCCCSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCT-TSCEEEETTEEEEHHHHHHHTSC
T ss_pred             CCCcCchhHHccccCCcCccCCcccccCceEEEECccccccccCchhhCCCccC-CCccEeeCCEEECHHHHHHHhCC
Confidence            478999999999999999999999998778899999999999999999999996 45799999999999999999864

>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=99.76  E-value=5.3e-19  Score=127.46  Aligned_cols=74  Identities=23%  Similarity=0.415  Sum_probs=67.6

Q ss_pred             CCcccCccccccccCCCCCCCCCcccC---CCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHH
Q psy10849          5 NSHVSCHPRGFRLYGVKCARCGDRLLP---HEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKE   79 (267)
Q Consensus         5 dg~~yC~~cy~~~f~~~C~~C~~~I~~---~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~   79 (267)
                      ++++||+.||.++|+++|.+|+++|.+   .+.++.+.++.||++||+|..|+++|. +..|+.+++++||..||.++
T Consensus         1 g~~~yC~~cy~~~~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~f~~~~~~~yC~~cy~~l   77 (77)
T 2egq_A            1 GSSGSSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLA-NKRFVFHQEQVYCPDCAKKL   77 (77)
T ss_dssp             CCSSCCTTCCCSCCCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCT-TSCCCEETTEECCHHHHHHC
T ss_pred             CCCeEchhHhchhhCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCC-CCccEeECCEEEChHHhccC
Confidence            478999999999999999999999996   446888999999999999999999996 67899999999999999763

>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=99.76  E-value=5.1e-19  Score=128.49  Aligned_cols=75  Identities=28%  Similarity=0.510  Sum_probs=69.5

Q ss_pred             CCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849          5 NSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus         5 dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      +|++||+.||.++|+++|.+|+++|.+.  ++.+.++.||++||+|..|+++|. +..|+.+++++||+.||.++|+.
T Consensus         1 gg~~yC~~cy~~~~~~~C~~C~~~I~~~--~v~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~~   75 (80)
T 2cuq_A            1 GSSGSSGPCYENKFAPRCARCSKTLTQG--GVTYRDQPWHRECLVCTGCQTPLA-GQQFTSRDEDPYCVACFGELFAS   75 (80)
T ss_dssp             CCCCSCCCCCCCCSSCCCTTTCCCCCSC--CEESSSSEECTTTCBCSSSCCBCT-TCCEEECSSSEEEHHHHHHHTTC
T ss_pred             CCcEEcHHHHccccCCcCCCCCCEecCc--EEEECCchhhhhhCCcccCCCcCC-CCeeEeECCEEECHHHHHHHcCC
Confidence            5899999999999999999999999864  678999999999999999999995 67899999999999999999874

>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=99.75  E-value=8.5e-19  Score=127.28  Aligned_cols=75  Identities=24%  Similarity=0.492  Sum_probs=68.9

Q ss_pred             CCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849          5 NSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus         5 dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      +|++||+.||.++|+++|.+|+++|.+.  ++.+.++.||++||+|..|+++|. +..|+.+++++||+.||.++|+.
T Consensus         1 gg~~yC~~~y~~~~~~~C~~C~~~I~~~--~v~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~~y~~~f~~   75 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFSPKCGGCNRPVLEN--YLSAMDTVWHPECFVCGDCFTSFS-TGSFFELDGRPFCELHYHHRRGS   75 (80)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSS--CEEETTEEECTTTCBCSSSCCBSC-SSCCEESSSCEECHHHHHHHHSS
T ss_pred             CCCccchhHHhhhcCCccccCCCeecce--eEEECCCeEecCcCChhhCCCCCC-CCcEEeECCEEECHHHHHHHcCC
Confidence            5899999999999999999999999963  678999999999999999999996 45788999999999999999874

>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=99.75  E-value=6.2e-19  Score=128.40  Aligned_cols=76  Identities=22%  Similarity=0.440  Sum_probs=69.0

Q ss_pred             CCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEe-eCCeecchhhHHHHHhh
Q psy10849          5 NSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL-RSGQLFCRQDFEKEMYL   82 (267)
Q Consensus         5 dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~-~~~~lyC~~cy~k~f~~   82 (267)
                      .+.+||+.||.++|+++|.+|+++|.+  .++.+.++.||++||+|..|+++|..|..|.+ +++++||+.||.++|+.
T Consensus         1 g~~~yC~~~y~~~~~~~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~   77 (81)
T 1x6a_A            1 GSSGSSGKDYWGKFGEFCHGCSLLMTG--PFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSG   77 (81)
T ss_dssp             CCCCCCCCCSSCCSSCBCTTTCCBCCS--CCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCT
T ss_pred             CCCccchhHHhhhcCCcCccCCCCcCc--eEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcC
Confidence            468999999999999999999999993  47789999999999999999999976788884 89999999999999874

>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=99.74  E-value=2.1e-19  Score=151.26  Aligned_cols=81  Identities=36%  Similarity=0.778  Sum_probs=74.9

Q ss_pred             cccCCcccCccccccccCC--CCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHH
Q psy10849          2 TSHNSHVSCHPRGFRLYGV--KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKE   79 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~--~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~   79 (267)
                      |.+||++||+.||.++|++  +|..|+++|.+.|.++.+.++.||+.||+|..|++.|..|..|+..++++||..||.++
T Consensus        50 ~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~  129 (188)
T 1rut_X           50 YTKSGMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTA  129 (188)
T ss_dssp             EEETTEEECHHHHHHHHSCCEECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTT
T ss_pred             EEeCCccccccccccccccCCccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHH
Confidence            6799999999999999999  79999999998778899999999999999999999996678899999999999999988


Q ss_pred             Hhh
Q psy10849         80 MYL   82 (267)
Q Consensus        80 f~~   82 (267)
                      |+.
T Consensus       130 ~~~  132 (188)
T 1rut_X          130 LIN  132 (188)
T ss_dssp             TC-
T ss_pred             hcc
Confidence            765

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

Probab=99.73  E-value=1.7e-18  Score=137.22  Aligned_cols=81  Identities=31%  Similarity=0.664  Sum_probs=75.9

Q ss_pred             cccCCcccCccccccccCC--CCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHH
Q psy10849          2 TSHNSHVSCHPRGFRLYGV--KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKE   79 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~--~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~   79 (267)
                      |.+||++||+.||.++|++  +|..|+++|.+.|.++.+.++.||++||+|..|+++|..|..|+..++++||..||.++
T Consensus        47 ~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~  126 (131)
T 2xjy_A           47 YYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEW  126 (131)
T ss_dssp             EEETTEEECHHHHHHHHCCCEECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHH
T ss_pred             EEECCEEeecCchhhhCCCccChhhcCCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHH
Confidence            5789999999999999999  99999999998778899999999999999999999996678899999999999999999


Q ss_pred             Hhh
Q psy10849         80 MYL   82 (267)
Q Consensus        80 f~~   82 (267)
                      |+.
T Consensus       127 ~~~  129 (131)
T 2xjy_A          127 TKI  129 (131)
T ss_dssp             HHH
T ss_pred             hhc
Confidence            874

>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=99.73  E-value=3.9e-18  Score=124.19  Aligned_cols=74  Identities=31%  Similarity=0.608  Sum_probs=67.4

Q ss_pred             CCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEee-CCeecchhhHHHHHhh
Q psy10849          5 NSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILR-SGQLFCRQDFEKEMYL   82 (267)
Q Consensus         5 dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~-~~~lyC~~cy~k~f~~   82 (267)
                      ||++||+.||. +++++|.+|+++|.+  .++.+.++.||++||+|..|+++|. +..|+.. ++++||+.||.++|+.
T Consensus         2 ~g~~yC~~~y~-~~~~~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L~-~~~f~~~~~g~~yC~~cy~~~f~~   76 (81)
T 2dlo_A            2 SSGSSGEGCYV-ATLEKCATCSQPILD--RILRAMGKAYHPGCFTCVVCHRGLD-GIPFTVDATSQIHCIEDFHRKFAS   76 (81)
T ss_dssp             CCCCCCCCCCC-SSCCBCTTTCCBCCS--CCEEETTEEECTTTCBCSSSCCBCT-TSCEECCTTCCCEEHHHHHHHTTS
T ss_pred             cCCEECHHHhh-cCCCccccCCCeecc--eeEEECCccccHHhcCcccCCCccC-CCeeEECCCCEEECHHHHHHHhcC
Confidence            78999999998 799999999999984  4788999999999999999999996 6778876 6899999999999874

>2dms_A Homeobox protein OTX2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Mus musculus}

Probab=99.72  E-value=1.9e-18  Score=125.92  Aligned_cols=60  Identities=17%  Similarity=0.155  Sum_probs=54.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ..+.||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+..
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~rk~~~~~   69 (80)
T 2dms_A            4 GSSGRRERTTFTRAQLDVLEALFAKTRYPDIFMREEVALKINLPESRVQVWFKNRRAKCRQQQQQQ   69 (80)
T ss_dssp             CCCCCCCCSSCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHTHHHHTTCSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHhhhhhHHHhHHhhHHHHcc
Confidence            456789999999999999999999999999988887      999999999999999999976544

>2dmt_A Homeobox protein BARH-like 1; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.71  E-value=1.8e-18  Score=126.00  Aligned_cols=60  Identities=20%  Similarity=0.139  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        102 DGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       102 ~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      ...++.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+||...
T Consensus        12 ~~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~~   77 (80)
T 2dmt_A           12 TKAKKGRRSRTVFTELQLMGLEKRFEKQKYLSTPDRIDLAESLGLSQLQVKTWYQNRRMKWKKSGP   77 (80)
T ss_dssp             CCCCCCCCSCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHSCCCS
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHeeeccHHHHHHhhcccC
Confidence            44567789999999999999999999999999998887      9999999999999999999654

>2cra_A Homeobox protein HOX-B13; DNA-binding, transcription regulation, helix-turn-helix, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.71  E-value=2e-18  Score=122.62  Aligned_cols=58  Identities=17%  Similarity=0.143  Sum_probs=53.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      ..+.||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~   67 (70)
T 2cra_A            4 GSSGRKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKKSGP   67 (70)
T ss_dssp             SCCCCCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTSSCT
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhhHhhHhHHHHhcccCC
Confidence            345688999999999999999999999999998887      9999999999999999999654

>1wh5_A ZF-HD homeobox family protein; structural genomics, zinc finger homeobox family protein, riken structural genomics/proteomics initiative; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.71  E-value=2e-18  Score=125.73  Aligned_cols=56  Identities=20%  Similarity=0.154  Sum_probs=52.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhc----CCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849        103 GRRGPKRPRTILTSAQRRQFKSSFEV----SPKPCRKVSTM------NSKRAKNILTPNQRRQFKS  158 (267)
Q Consensus       103 ~~~~~kr~Rt~ft~~Ql~~L~~~f~~----~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~  158 (267)
                      +.++.||.||.||.+|+.+||..|+.    ++||+...|++      |++++|||||||||+|+|+
T Consensus        13 ~~~~~rR~Rt~ft~~Ql~~Le~~f~~~~~~~~yp~~~~r~~La~~lgL~~~~VkvWFqNrRaK~~~   78 (80)
T 1wh5_A           13 GGGIRKRHRTKFTAEQKERMLALAERIGWRIQRQDDEVIQRFCQETGVPRQVLKVWLHNNKHSGPS   78 (80)
T ss_dssp             CCCCSCCCSCCCCHHHHHHHHHHHHHHTSCCCTTTHHHHHHHHHHSCCCHHHHHHHHHHHSSSSSC
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHHhccCcCCCcCHHHHHHHHHHhCCCcccccCCccccCcCCCC
Confidence            44667899999999999999999999    99999998887      9999999999999999986

>2dmq_A LIM/homeobox protein LHX9; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.70  E-value=5.9e-18  Score=123.20  Aligned_cols=59  Identities=27%  Similarity=0.309  Sum_probs=54.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .+.||.||.||.+|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+.....
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~   69 (80)
T 2dmq_A            5 SSGKRMRTSFKHHQLRTMKSYFAINHNPDAKDLKQLAQKTGLTKRVLQVWFQNARAKFRRNLLRQ   69 (80)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHHHHSS
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHhhHccHHHHHHHHHHHHHH
Confidence            45689999999999999999999999999988887      999999999999999999976544

>2cue_A Paired box protein PAX6; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.70  E-value=2.6e-18  Score=125.12  Aligned_cols=59  Identities=17%  Similarity=0.204  Sum_probs=54.1

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .+.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+..
T Consensus         5 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~~   69 (80)
T 2cue_A            5 SSGQRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKLR   69 (80)
T ss_dssp             CSSCCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHHHHHHHHHHHHHhhhh
Confidence            45688999999999999999999999999988877      999999999999999999977654

>2kt0_A Nanog, homeobox protein nanog; homeodomain, structural genomics, protein structure initiative, PSI, center for eukaryotic structural genomics; NMR {Homo sapiens}

Probab=99.70  E-value=5.7e-18  Score=124.43  Aligned_cols=60  Identities=17%  Similarity=0.047  Sum_probs=54.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        103 GRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       103 ~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      ...+.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+.
T Consensus        18 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~k~   83 (84)
T 2kt0_A           18 VPVKKQKTRTVFSSTQLCVLNDRFQRQKYLSLQQMQELSNILNLSYKQVKTWFQNQRMKSKRWQKN   83 (84)
T ss_dssp             CCSCSCCCSSCCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHTTTSCCCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHHhhc
Confidence            3456789999999999999999999999999998887      99999999999999999997643

>1nk2_P Homeobox protein VND; homeodomain, DNA-binding protein, embryonic development, complex (homeodomain/DNA); HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1nk3_P* 1vnd_A 1qry_A

Probab=99.70  E-value=6e-18  Score=122.33  Aligned_cols=61  Identities=15%  Similarity=0.102  Sum_probs=55.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        103 GRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       103 ~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ...+.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+.....
T Consensus         5 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kr~~~~~   71 (77)
T 1nk2_P            5 LPNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNEK   71 (77)
T ss_dssp             CSCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhcchhhhhccc
Confidence            3456788999999999999999999999999998887      999999999999999999976654

>2da2_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.70  E-value=3.5e-18  Score=121.27  Aligned_cols=59  Identities=19%  Similarity=0.147  Sum_probs=53.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      ..+.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+....
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da2_A            4 GSSGRSSRTRFTDYQLRVLQDFFDANAYPKDDEFEQLSNLLNLPTRVIVVWFQNARQKARKSGPS   68 (70)
T ss_dssp             SCCSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHHCCCSSC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHhHHhhHhhhHHHhhcccc
Confidence            355788999999999999999999999999998887      99999999999999999996543

>1wh7_A ZF-HD homeobox family protein; homeobox domain, structural genomics, riken structural genomics/proteomics initiative, RSGI; NMR {Arabidopsis thaliana} SCOP: a.4.1.1

Probab=99.70  E-value=2.9e-18  Score=124.80  Aligned_cols=57  Identities=19%  Similarity=0.147  Sum_probs=52.0

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHhhhc-----CCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849        101 RDGRRGPKRPRTILTSAQRRQFKSSFEV-----SPKPCRKVSTM------NSKRAKNILTPNQRRQFKS  158 (267)
Q Consensus       101 ~~~~~~~kr~Rt~ft~~Ql~~L~~~f~~-----~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~  158 (267)
                      .+...+.||.||.||.+|+.+|| +|+.     ++||+...|++      |++++|||||||||+|+|+
T Consensus        11 ~~~~~~~rR~Rt~ft~~Ql~~Le-~F~~~~~w~~~yp~~~~r~~La~~lgL~e~qVkvWFqNrR~k~~~   78 (80)
T 1wh7_A           11 SSSGGTTKRFRTKFTAEQKEKML-AFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCCCSSCCCCCCCHHHHHHHH-HHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCCCCCCCCCCccCCHHHHHHHH-HHHHHcCcCCCCCCHHHHHHHHHHhCcCcCcccccccccccCCCC
Confidence            34456789999999999999999 8999     99999998887      9999999999999999987

>2da1_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.70  E-value=3.1e-18  Score=121.54  Aligned_cols=59  Identities=20%  Similarity=0.200  Sum_probs=53.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      ..+.+|.||.||.+|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+.
T Consensus         4 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~~~   68 (70)
T 2da1_A            4 GSSGKRPRTRITDDQLRVLRQYFDINNSPSEEQIKEMADKSGLPQKVIKHWFRNTLFKERQSGPS   68 (70)
T ss_dssp             SCCCCSCSCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHCCCHHHHHHHHHHHHHHHHCCCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHHhhhhhHHHhhhccc
Confidence            345788999999999999999999999999888877      99999999999999999997543

>2djn_A Homeobox protein DLX-5; structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.69  E-value=3.8e-18  Score=121.14  Aligned_cols=58  Identities=21%  Similarity=0.208  Sum_probs=53.0

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      ..+.||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+||...
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   67 (70)
T 2djn_A            4 GSSGRKPRTIYSSFQLAALQRRFQKTQYLALPERAELAASLGLTQTQVKIWFQNKRSKIKKSGP   67 (70)
T ss_dssp             CCCCCCSSCSSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHSSCCHHHHHHHHHHHHHTCSSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCHHHHHHHHHHHhhhhcccCC
Confidence            345688999999999999999999999999998887      9999999999999999999653

>2dmu_A Homeobox protein goosecoid; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=4.7e-18  Score=120.62  Aligned_cols=57  Identities=19%  Similarity=0.234  Sum_probs=52.6

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      .+.+|.||.||.+|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+...
T Consensus         5 ~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2dmu_A            5 SSGRRHRTIFTDEQLEALENLFQETKYPDVGTREQLARKVHLREEKVEVWFKNRRAKWRRSGP   67 (70)
T ss_dssp             TSSCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTST
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCCCHHHeehccccccccccccCC
Confidence            45688999999999999999999999999988887      9999999999999999999654

>1ahd_P Antennapedia protein mutant; DNA binding protein/DNA; HET: DNA; NMR {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 2hoa_A 1hom_A 1ftz_A

Probab=99.69  E-value=4.6e-18  Score=120.06  Aligned_cols=57  Identities=21%  Similarity=0.228  Sum_probs=52.4

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~~~~   64 (68)
T 1ahd_P            2 RKRGRQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKENKTK   64 (68)
T ss_dssp             CSCTTCCCCHHHHHHHHHHHHHCSSCCTTHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHSCCC
T ss_pred             CCCCCCCcCHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHhhhhHHhHHHHhHHhHhcccc
Confidence            478999999999999999999999999988877      999999999999999999976544

>2da4_A Hypothetical protein DKFZP686K21156; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.69  E-value=4e-18  Score=124.13  Aligned_cols=58  Identities=17%  Similarity=0.242  Sum_probs=53.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcC----CCCChhhhhh------cCCCceeeecchhhhhhhhhh
Q psy10849        103 GRRGPKRPRTILTSAQRRQFKSSFEVS----PKPCRKVSTM------NSKRAKNILTPNQRRQFKSSF  160 (267)
Q Consensus       103 ~~~~~kr~Rt~ft~~Ql~~L~~~f~~~----~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~  160 (267)
                      +..+.||.||.||.+|+.+||..|+.+    +||+...+++      |++++|+|||||||+|+|+..
T Consensus         4 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~~~~~yp~~~~r~~La~~lgL~~~qV~vWFqNrR~k~rk~~   71 (80)
T 2da4_A            4 GSSGALQDRTQFSDRDLATLKKYWDNGMTSLGSVCREKIEAVATELNVDCEIVRTWIGNRRRKYRLMG   71 (80)
T ss_dssp             CCCCCCCSSCCCCHHHHHHHHHHHTTTTTCCSHHHHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhCCCCCCCcCHHHHHHHHHHhCCCHHHhhHhHHHHHHHHhhcc
Confidence            456678999999999999999999999    9999988877      999999999999999999954

>1puf_A HOX-1.7, homeobox protein HOX-A9; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Mus musculus} SCOP: a.4.1.1 PDB: 1san_A

Probab=99.68  E-value=6.6e-18  Score=122.14  Aligned_cols=60  Identities=18%  Similarity=0.149  Sum_probs=54.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .++.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+..
T Consensus        10 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~k~~   75 (77)
T 1puf_A           10 ARSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             CCTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhhhhc
Confidence            455788999999999999999999999999998887      999999999999999999987654

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

Probab=99.68  E-value=1.3e-17  Score=131.17  Aligned_cols=78  Identities=26%  Similarity=0.582  Sum_probs=72.9

Q ss_pred             cccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceee--cCCcccccccccCCCCCceEeeCCeecchhhHHHH
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYH--LPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKE   79 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH--~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~   79 (267)
                      +.+||++||+.||.++|+++|.+|+++|.+++.+|.+.++.||  ++||+|..|+++|. |..|++.++++||..+|.++
T Consensus        46 ~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l~-~~~f~~~~~~~yC~~~~~~~  124 (126)
T 2xqn_T           46 VMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI-GQKFMPVEGMVFCSVECKKR  124 (126)
T ss_dssp             EEETTEEEEHHHHHHHSCCBCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBCT-TSEEEEETTEEESSHHHHHS
T ss_pred             EeECCEEechHHhCcCcCccCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCCCCccC-CCeeEeECCEEcchHHhhhh
Confidence            4789999999999999999999999999987788999999999  99999999999996 78999999999999888876


Q ss_pred             H
Q psy10849         80 M   80 (267)
Q Consensus        80 f   80 (267)
                      |
T Consensus       125 f  125 (126)
T 2xqn_T          125 M  125 (126)
T ss_dssp             C
T ss_pred             c
Confidence            5

>2l7z_A Homeobox protein HOX-A13; gene regulation; NMR {Homo sapiens} PDB: 2ld5_A*

Probab=99.68  E-value=1.2e-17  Score=119.52  Aligned_cols=59  Identities=15%  Similarity=0.127  Sum_probs=53.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      ..+.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+....
T Consensus         4 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   68 (73)
T 2l7z_A            4 MLEGRKKRVPYTKVQLKELEREYATNKFITKDKRRRISATTNLSERQVTIWFQNRRVKEKKVINK   68 (73)
T ss_dssp             SSCCCCCCCCSCHHHHHHHHHHHHHTSCCCHHHHHHHHHHHTSCSHHHHHHHHHHHHHHTTSSSS
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHhhCCCcCHHHHHHHHHHHCCCHHHHHHHHHHHhHHHHHHhcc
Confidence            345688999999999999999999999999998887      99999999999999999996543

>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=99.68  E-value=2.7e-17  Score=119.69  Aligned_cols=74  Identities=27%  Similarity=0.522  Sum_probs=64.8

Q ss_pred             CcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849          6 SHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus         6 g~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      +.+||+.||.++|+++|.+|+++|.+  .++.+.++.||++||+|..|+++|..+..|...++.+||..||.++++
T Consensus         2 ~~~yC~~dy~~~~~~~C~~C~~~I~~--~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~   75 (81)
T 1v6g_A            2 SSGSSGLDYQRLYGTRCFSCDQFIEG--EVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSV   75 (81)
T ss_dssp             CCCCCCSCGGGSCCCBCTTTCCBCCS--CCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSS
T ss_pred             CCCcchHHHHhHhCCcCccccCEecc--ceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCC
Confidence            56899999999999999999999994  478899999999999999999999766666666667899999977654

>2vi6_A Homeobox protein nanog; homeodomain, DNA-binding, transcription, transcription facto developmental protein, transcription regulation, NUC homeobox; 2.6A {Mus musculus}

Probab=99.68  E-value=4.9e-18  Score=117.69  Aligned_cols=54  Identities=20%  Similarity=0.136  Sum_probs=46.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        106 GPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       106 ~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      +.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+.
T Consensus         2 ~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~   61 (62)
T 2vi6_A            2 TKQKMRTVFSQAQLCALKDRFQKQKYLSLQQMQELSSILNLSYKQVKTWFQNQRMKCKRW   61 (62)
T ss_dssp             ------CCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCGGG
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHHhHHhhcchhhc
Confidence            3578999999999999999999999999998887      99999999999999999985

>1zq3_P PRD-4, homeotic bicoid protein; protein-DNA complex, double helix, helix-turn-helix; NMR {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.68  E-value=1e-17  Score=118.20  Aligned_cols=57  Identities=23%  Similarity=0.209  Sum_probs=52.7

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      +||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+.....
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNRR~k~kk~~~~~   64 (68)
T 1zq3_P            2 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH   64 (68)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             cCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHhhHHHHHHHHHHhccc
Confidence            578999999999999999999999999988877      999999999999999999976544

>2h1k_A IPF-1, pancreatic and duodenal homeobox 1, homeodomain; protein-DNA complex, transcription/DNA complex; 2.42A {Mesocricetus auratus}

Probab=99.68  E-value=6.3e-18  Score=117.53  Aligned_cols=54  Identities=26%  Similarity=0.235  Sum_probs=49.4

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhh
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSF  160 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~  160 (267)
                      .||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kk~~   62 (63)
T 2h1k_A            3 NKRTRTAYTRAQLLELEKEFLFNKYISRPRRVELAVMLNLTERHIKIWFQNRRMKWKKEE   62 (63)
T ss_dssp             --CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCcCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcCHHHhhHHHHhhhhhhhhhc
Confidence            578999999999999999999999999998887      999999999999999999863

>2da3_A Alpha-fetoprotein enhancer binding protein; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics; NMR {Homo sapiens}

Probab=99.68  E-value=5.4e-18  Score=123.33  Aligned_cols=59  Identities=24%  Similarity=0.245  Sum_probs=53.7

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        103 GRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       103 ~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      ...+.||.||.||.+|+.+||..|+.++||+...+++      |++++|+|||||||+|+||...
T Consensus        13 ~~~~~rr~Rt~ft~~Ql~~Le~~f~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~   77 (80)
T 2da3_A           13 EPQRDKRLRTTITPEQLEILYQKYLLDSNPTRKMLDHIAHEVGLKKRVVQVWFQNTRARERKSGP   77 (80)
T ss_dssp             CCCCCTTCCSSCCTTTHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhHHHhHHHHHhHhhhcc
Confidence            3466789999999999999999999999999988877      9999999999999999999653

>2hdd_A Protein (engrailed homeodomain Q50K); DNA binding, complex (DNA binding protein/DNA), transcription/DNA complex; HET: DNA; 1.90A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 1hdd_C* 2jwt_A 3hdd_A 1p7j_A* 1p7i_A* 2hos_A 2hot_A 1du0_A* 1ztr_A 1enh_A 2p81_A

Probab=99.67  E-value=6.2e-18  Score=116.80  Aligned_cols=52  Identities=25%  Similarity=0.305  Sum_probs=46.5

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKS  158 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~  158 (267)
                      .||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+||
T Consensus         3 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk   60 (61)
T 2hdd_A            3 EKRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFKNKRAKIKK   60 (61)
T ss_dssp             ----CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHhhhhcccccc
Confidence            478999999999999999999999999998887      9999999999999999997

>2e1o_A Homeobox protein PRH; DNA binding protein, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.67  E-value=1.3e-17  Score=118.43  Aligned_cols=57  Identities=16%  Similarity=0.131  Sum_probs=52.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      .+.++.||.||.+|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+...
T Consensus         5 ~~~~r~R~~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rr~~~   67 (70)
T 2e1o_A            5 SSGKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRSGP   67 (70)
T ss_dssp             CCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHSC
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCCCHHHhhHhhHhhHhhcCCCCC
Confidence            34678899999999999999999999999988887      9999999999999999999754

>1ig7_A Homeotic protein MSX-1; helix-turn-helix, transcription/DNA complex; 2.20A {Mus musculus} SCOP: a.4.1.1

Probab=99.67  E-value=1.1e-17  Score=114.31  Aligned_cols=52  Identities=21%  Similarity=0.202  Sum_probs=49.0

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      ||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+||.
T Consensus         1 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   58 (58)
T 1ig7_A            1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL   58 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhhhhhHhhhhhccC
Confidence            57899999999999999999999999998887      99999999999999999973

>1yz8_P Pituitary homeobox 2; DNA binding protein, transcription/DNA complex; NMR {Homo sapiens} SCOP: a.4.1.1 PDB: 2l7f_P 2lkx_A* 2l7m_P

Probab=99.66  E-value=1.1e-17  Score=118.01  Aligned_cols=57  Identities=21%  Similarity=0.288  Sum_probs=52.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        106 GPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       106 ~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      +.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+.
T Consensus         2 ~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~~~   64 (68)
T 1yz8_P            2 SQRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKREEF   64 (68)
T ss_dssp             CSSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHHTTT
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHccCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhHHHHHHhhc
Confidence            3588999999999999999999999999888877      99999999999999999997654

>1bw5_A ISL-1HD, insulin gene enhancer protein ISL-1; DNA-binding protein, homeodomain, LIM domain; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.66  E-value=1.1e-17  Score=117.37  Aligned_cols=55  Identities=22%  Similarity=0.301  Sum_probs=51.1

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhh
Q psy10849        106 GPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSF  160 (267)
Q Consensus       106 ~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~  160 (267)
                      +.+|.||.||.+|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..
T Consensus         2 k~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~   62 (66)
T 1bw5_A            2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCCCCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHHHHHhHHHHHHHhHHh
Confidence            4688999999999999999999999999988877      999999999999999999854

>3a01_A Homeodomain-containing protein; homeodomain, protein-DNA complex, DNA-binding, homeobox, NUC developmental protein; 2.70A {Drosophila melanogaster}

Probab=99.66  E-value=2.2e-17  Score=123.65  Aligned_cols=60  Identities=15%  Similarity=0.165  Sum_probs=54.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ..+.||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+.....
T Consensus        14 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~~   79 (93)
T 3a01_A           14 PPKRKKPRTSFTRIQVAELEKRFHKQKYLASAERAALARGLKMTDAQVKTWFQNRRTKWRRQTAEE   79 (93)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHTTTCCHHHHHHHHHHHHHHHHHHHTCC
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCChhhcccccHhhhhhhhhhhHHH
Confidence            355688999999999999999999999999998887      999999999999999999976554

>1b8i_A Ultrabithorax, protein (ultrabithorax homeotic protein IV); DNA binding, homeodomain, homeotic proteins, development, specificity; HET: DNA; 2.40A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 9ant_A*

Probab=99.66  E-value=1.2e-17  Score=121.92  Aligned_cols=58  Identities=19%  Similarity=0.210  Sum_probs=47.9

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      ..+.||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+||..+
T Consensus        17 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~   80 (81)
T 1b8i_A           17 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALSLTERQIKIWFQNRRMKLKKEIQ   80 (81)
T ss_dssp             -------CCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTTC-
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHHhHHhhhhhhhhcc
Confidence            345688999999999999999999999999998887      9999999999999999999653

>2r5y_A Homeotic protein sex combs reduced; homeodomain; HET: DNA; 2.60A {Drosophila melanogaster} PDB: 2r5z_A*

Probab=99.66  E-value=1.3e-17  Score=123.57  Aligned_cols=57  Identities=23%  Similarity=0.254  Sum_probs=48.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSF  160 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~  160 (267)
                      ..+.||.||.||..|+.+||..|+.++||+...|++      |++++|+|||||||+|+||..
T Consensus        25 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~vWFqNRR~k~kk~~   87 (88)
T 2r5y_A           25 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKEH   87 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHTTC
T ss_pred             CCCCCCCCCCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCcCHHHhhHHhHHHHHHhHhhc
Confidence            445788999999999999999999999999998887      999999999999999999864

>1fjl_A Paired protein; DNA-binding protein, paired BOX, transcription regulation; HET: DNA; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1 PDB: 3a01_B

Probab=99.66  E-value=1.9e-17  Score=120.86  Aligned_cols=58  Identities=17%  Similarity=0.291  Sum_probs=52.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      .++.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+...
T Consensus        15 ~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~rk~~~   78 (81)
T 1fjl_A           15 KRKQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   78 (81)
T ss_dssp             --CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             cCCCCCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHHHHHHhhhhhhhcc
Confidence            566789999999999999999999999999988877      9999999999999999999764

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

Probab=99.66  E-value=4.5e-17  Score=136.29  Aligned_cols=79  Identities=39%  Similarity=0.833  Sum_probs=71.9

Q ss_pred             cccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEe-eCCeecchhhHHHHH
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFIL-RSGQLFCRQDFEKEM   80 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~-~~~~lyC~~cy~k~f   80 (267)
                      |.+||++||+.||.++|+++|..|+++|.+.+.++.+.++.||+.||+|..|+++|..|..|+. .++++||..||.++.
T Consensus       102 f~~~g~~yC~~~y~~~f~~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~~~  181 (182)
T 2jtn_A          102 FSRGESVYCKDDFFKRFGTKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK  181 (182)
T ss_dssp             EEETTEEECHHHHHHTTSCCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHHHT
T ss_pred             eeECCEeeecCccccccccccccCCCccCCCceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHHhh
Confidence            6789999999999999999999999999987778889999999999999999999976777765 589999999998763

>2dn0_A Zinc fingers and homeoboxes protein 3; triple homeobox 1 protein, KIAA0395, TIX1, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.65  E-value=2.3e-17  Score=118.96  Aligned_cols=59  Identities=15%  Similarity=0.071  Sum_probs=52.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ..+.+.||.||.+|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+..
T Consensus         6 ~~~~~~R~~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~kk~~~~~   70 (76)
T 2dn0_A            6 SGASIYKNKKSHEQLSALKGSFCRNQFPGQSEVEHLTKVTGLSTREVRKWFSDRRYHCRNLKGSR   70 (76)
T ss_dssp             SCCCCCCCCCCHHHHHHHHHHHHHSSSCCSHHHHHHHHHHCCCHHHHHHHHHHHHHHSSSCCSSS
T ss_pred             CCCCCCCccCCHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChHHhhHHhHHHhHHHHHhcccC
Confidence            34566799999999999999999999999988887      999999999999999999976544

>2m0c_A Homeobox protein aristaless-like 4; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.65  E-value=2.7e-17  Score=118.11  Aligned_cols=61  Identities=16%  Similarity=0.220  Sum_probs=54.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        102 DGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       102 ~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      +...+.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+.
T Consensus         4 ~~~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~r~   70 (75)
T 2m0c_A            4 SNKGKKRRNRTTFTSYQLEELEKVFQKTHYPDVYAREQLAMRTDLTEARVQVWFQNRRAKWRKRERF   70 (75)
T ss_dssp             CCCSCCCSCSCSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTCCCCC
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHHHHHHHHHHHhh
Confidence            34456788999999999999999999999999988877      89999999999999999996544

>1ftt_A TTF-1 HD, thyroid transcription factor 1 homeodomain; DNA binding protein; NMR {Rattus norvegicus} SCOP: a.4.1.1

Probab=99.65  E-value=2.2e-17  Score=116.52  Aligned_cols=57  Identities=14%  Similarity=0.147  Sum_probs=52.3

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+..
T Consensus         2 ~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~~~~~   64 (68)
T 1ftt_A            2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK   64 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCccCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhHHHhHHHhhhhhhhhhHh
Confidence            478899999999999999999999999988877      999999999999999999976543

>1jgg_A Segmentation protein EVEN-skipped; homeodomain, protein-DNA complex, transcription/DNA complex; 2.00A {Drosophila melanogaster} SCOP: a.4.1.1

Probab=99.65  E-value=2.1e-17  Score=113.70  Aligned_cols=52  Identities=19%  Similarity=0.149  Sum_probs=48.7

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      ||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|++
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~   59 (60)
T 1jgg_A            2 RRYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   59 (60)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHCcCHHHHHHhhHHHHhHhhcc
Confidence            67899999999999999999999999988877      99999999999999999985

>2hi3_A Homeodomain-only protein; transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.64  E-value=3.9e-17  Score=116.84  Aligned_cols=56  Identities=9%  Similarity=0.071  Sum_probs=50.9

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhc-CCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEV-SPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~-~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      .++.||.||..|+.+||..|+. ++||+...+++      |++++|+|||||||+|+|+..+.
T Consensus         2 ~~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~~~l~~~qV~~WFqNRR~k~rk~~~~   64 (73)
T 2hi3_A            2 SAQTVSGPTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL   64 (73)
T ss_dssp             CCSCCSSCCHHHHHHHHHHHHHTTSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhccC
Confidence            4578999999999999999995 99999998887      99999999999999999997643

>1wi3_A DNA-binding protein SATB2; homeodomain, helix-turn-helix, riken structural genomics/proteomics initiative, RSGI, structural genomics; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.64  E-value=3.2e-17  Score=113.54  Aligned_cols=57  Identities=18%  Similarity=0.090  Sum_probs=51.7

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhc-CCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849        102 DGRRGPKRPRTILTSAQRRQFKSSFEV-SPKPCRKVSTM------NSKRAKNILTPNQRRQFKS  158 (267)
Q Consensus       102 ~~~~~~kr~Rt~ft~~Ql~~L~~~f~~-~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~  158 (267)
                      ++.++.||.||.|+.+||.+|+..|+. ++||+..+|++      |++++|||||||||.-.|-
T Consensus         2 ~~~~~~kR~RT~~s~eQL~~Lqs~f~~~~~yPd~~~r~~La~~tGL~~~~IqVWFQNrR~~~~~   65 (71)
T 1wi3_A            2 SSGSSGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKH   65 (71)
T ss_dssp             CCCCCCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCS
T ss_pred             CCCCCCCCCCccCCHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCCHHHHHHhhccceeeecC
Confidence            345678999999999999999999999 99999999988      9999999999999987554

>2ly9_A Zinc fingers and homeoboxes protein 1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.63  E-value=7.6e-17  Score=115.55  Aligned_cols=58  Identities=16%  Similarity=0.011  Sum_probs=52.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        106 GPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       106 ~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ..++.||.||.+|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+.....
T Consensus         5 ~~~~~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kk~~~~~   68 (74)
T 2ly9_A            5 DSFGIRAKKTKEQLAELKVSYLKNQFPHDSEIIRLMKITGLTKGEIKKWFSDTRYNQRNSKSNQ   68 (74)
T ss_dssp             CCCCTTCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTTTTTCSC
T ss_pred             CCCCCCcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHeeeCChhHhHHHHhhCcCC
Confidence            3578899999999999999999999999998877      999999999999999999976443

>2k40_A Homeobox expressed in ES cells 1; thermostable homeodomain variant, DNA binding protein, developmental protein, disease mutation, DNA-binding; NMR {Homo sapiens}

Probab=99.63  E-value=3.8e-17  Score=114.91  Aligned_cols=55  Identities=25%  Similarity=0.278  Sum_probs=51.1

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      ||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+....
T Consensus         2 rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~kr~~~~   62 (67)
T 2k40_A            2 RRPRTAFTQNQIEVLENVFRVNCYPGIDILEDLAQKLNLELDRIQIWFQNRRAKLKRSHRE   62 (67)
T ss_dssp             CCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHCSCCT
T ss_pred             cCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCcCHHHhhHhhHhHHHHHhHhchh
Confidence            78899999999999999999999999988877      99999999999999999996544

>2cuf_A FLJ21616 protein; homeobox domain, hepatocyte transcription factor, structural genomics, loop insertion, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.63  E-value=1e-16  Score=120.41  Aligned_cols=60  Identities=13%  Similarity=0.071  Sum_probs=53.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh---------------------cCCCceeeecchhhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM---------------------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~---------------------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      ..+.||.||.||..|+.+||+.|+.++||+...+++                     |++++|+|||||||+|+|+..+.
T Consensus         4 ~~~~rr~R~~ft~~ql~~Le~~F~~~~yP~~~~r~~lA~~l~~~~~~~~~~~~~~~~ls~~qV~~WFqNRR~k~kr~~~~   83 (95)
T 2cuf_A            4 GSSGRGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANI   83 (95)
T ss_dssp             SSCCCCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCchhhcccccccccCcCCHHHHHHHHHHHHHHHHHHhhc
Confidence            456789999999999999999999999999887776                     67899999999999999998765


Q ss_pred             c
Q psy10849        163 S  163 (267)
Q Consensus       163 ~  163 (267)
                      .
T Consensus        84 ~   84 (95)
T 2cuf_A           84 A   84 (95)
T ss_dssp             C
T ss_pred             c
Confidence            4

>1uhs_A HOP, homeodomain only protein; structural genomics, cardiac development, riken structural genomics/proteomics initiative, RSGI, transcription; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.63  E-value=6.5e-17  Score=115.36  Aligned_cols=55  Identities=9%  Similarity=0.114  Sum_probs=50.1

Q ss_pred             CCCCCCCCHHHHHHHHHhhhc-CCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEV-SPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~-~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      .+.||.||..|+.+||..|+. ++||+...+++      |++++|+|||||||+|+|+..+.
T Consensus         2 ~k~Rt~ft~~Q~~~Le~~F~~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~rk~~~~   63 (72)
T 1uhs_A            2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSEGL   63 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHCC
T ss_pred             CCCCccCCHHHHHHHHHHHHccCCCCCHHHHHHHHHHHCcCHHHhhHHhHHHHHHHhhhccC
Confidence            457899999999999999997 99999988877      99999999999999999997643

>1b72_A Protein (homeobox protein HOX-B1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1

Probab=99.63  E-value=4.5e-17  Score=122.87  Aligned_cols=58  Identities=19%  Similarity=0.149  Sum_probs=50.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      .+.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+.
T Consensus        32 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNRR~k~kk~~~~   95 (97)
T 1b72_A           32 GSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRERE   95 (97)
T ss_dssp             -----CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCcCcCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhHHHHHHHhHHHhHHhcc
Confidence            45688999999999999999999999999998887      99999999999999999997654

>2ecc_A Homeobox and leucine zipper protein homez; homeobox domain, transcription factor, leucine zipper- containing factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.63  E-value=8.4e-17  Score=115.33  Aligned_cols=53  Identities=15%  Similarity=-0.074  Sum_probs=48.5

Q ss_pred             CCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        110 PRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       110 ~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      .|+.||.+||.+||+.|+.++||+..+|++      |++++|+|||||||+|+|+....
T Consensus         6 ~r~kfT~~Ql~~Le~~F~~~~YPs~~er~~LA~~tgLte~qIkvWFqNrR~k~Kk~~l~   64 (76)
T 2ecc_A            6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQLK   64 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTCCS
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhHHhHhhHHHHHHHHHH
Confidence            466799999999999999999999999888      99999999999999999996543

>3a02_A Homeobox protein aristaless; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.00A {Drosophila melanogaster} PDB: 3lnq_A 3cmy_A

Probab=99.63  E-value=3.5e-17  Score=112.61  Aligned_cols=52  Identities=13%  Similarity=0.152  Sum_probs=43.7

Q ss_pred             CCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        110 PRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       110 ~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      .||.||.+|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+
T Consensus         2 ~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~rk~~k   59 (60)
T 3a02_A            2 SHMTFTSFQLEELEKAFSRTHYPDVFTREELAMKIGLTEARIQVWFQNRRAKWRKQEK   59 (60)
T ss_dssp             ---CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHC----
T ss_pred             CCcccCHHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHhhhhhhhhHhhcc
Confidence            589999999999999999999999988877      9999999999999999999653

>2da5_A Zinc fingers and homeoboxes protein 3; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.63  E-value=9.8e-17  Score=115.37  Aligned_cols=55  Identities=16%  Similarity=0.180  Sum_probs=49.6

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        109 RPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       109 r~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      +.|+.||.+|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..+..
T Consensus         9 ~kr~~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kk~~~~~   69 (75)
T 2da5_A            9 TKYKERAPEQLRALESSFAQNPLPLDEELDRLRSETKMTRREIDSWFSERRKKVNAEETKK   69 (75)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHTTHHHHSSCSS
T ss_pred             CCCccCCHHHHHHHHHHHhccCCCCHHHHHHHHHHhCCCHHHhhHhhHHHHHHHHHhhhcc
Confidence            4567799999999999999999999998877      999999999999999999976544

>1akh_A Protein (mating-type protein A-1); complex (TWO DNA-binding proteins/DNA), complex, DNA- binding protein, DNA; HET: DNA; 2.50A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1f43_A 1yrn_A*

Probab=99.62  E-value=4.2e-17  Score=112.53  Aligned_cols=54  Identities=11%  Similarity=0.101  Sum_probs=41.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFK  157 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k  157 (267)
                      +++.+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|
T Consensus         2 k~k~rr~Rt~ft~~q~~~Le~~f~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~k~k   61 (61)
T 1akh_A            2 KEKSPKGKSSISPQARAFLEEVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   61 (61)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHC-
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHhCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhccC
Confidence            356788999999999999999999999999988877      999999999999999986

>2ecb_A Zinc fingers and homeoboxes protein 1; homeobox domain, transcription factor, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.61  E-value=1.6e-16  Score=117.65  Aligned_cols=51  Identities=16%  Similarity=0.042  Sum_probs=47.1

Q ss_pred             CCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        113 ILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       113 ~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .||.+||.+||+.|+.++||+...|++      |++++|+|||||||+|||+..+..
T Consensus        17 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgLte~qVkvWFqNRR~k~rk~~~~~   73 (89)
T 2ecb_A           17 EKTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEKM   73 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSCC
T ss_pred             cCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCcChHHCeecccccchHHHHHHHHh
Confidence            689999999999999999999998888      999999999999999999966544

>3rkq_A Homeobox protein NKX-2.5; helix-turn-helix, DNA binding, nucleus, transcription-DNA CO; 1.70A {Homo sapiens}

Probab=99.61  E-value=9.5e-17  Score=109.44  Aligned_cols=51  Identities=18%  Similarity=0.229  Sum_probs=47.7

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhh
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFK  157 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k  157 (267)
                      .+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|
T Consensus         2 ~rr~Rt~~t~~q~~~Le~~F~~~~yp~~~~r~~La~~l~l~~~qV~~WFqNrR~k~k   58 (58)
T 3rkq_A            2 RRKPRVLFSQAQVYELERRFKQQRYLSAPERDQLASVLKLTSTQVKIWFQNRRYKSK   58 (58)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHC
T ss_pred             cCCCCCCcCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHHHhhHHhhccCC
Confidence            367899999999999999999999999988877      999999999999999986

>3a03_A T-cell leukemia homeobox protein 2; homeodomain, developmental protein, DNA-binding, N gene regulation; 1.54A {Homo sapiens}

Probab=99.60  E-value=8.6e-17  Score=109.15  Aligned_cols=48  Identities=10%  Similarity=0.108  Sum_probs=44.2

Q ss_pred             CCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        112 TILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       112 t~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      |.||..|+.+||..|+.++||+...|++      |++++|+|||||||+|+||+
T Consensus         2 T~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~~WFqNRR~k~kr~   55 (56)
T 3a03_A            2 TSFSRSQVLELERRFLRQKYLASAERAALAKALRMTDAQVKTWFQNRRTKWRRQ   55 (56)
T ss_dssp             --CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHH
T ss_pred             CccCHHHHHHHHHHHHhcCCcCHHHHHHHHHHhCcCHHHhhHhhHHhhhhhccc
Confidence            7899999999999999999999998887      99999999999999999985

>1x2n_A Homeobox protein pknox1; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens} SCOP: a.4.1.1

Probab=99.60  E-value=2.6e-16  Score=112.45  Aligned_cols=59  Identities=19%  Similarity=0.090  Sum_probs=53.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhc---CCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEV---SPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~---~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      ..+.+|.||.|+..|+.+||..|..   ++||+...+++      |++++|+|||||||+|+|+....
T Consensus         4 ~~~~rr~R~~~~~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   71 (73)
T 1x2n_A            4 GSSGKNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRILQSGPS   71 (73)
T ss_dssp             CSSSCCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHHHhCCCCCCCHHHHHHHHHHHCcCHHHHHHHhHHHHhhccccccc
Confidence            3456889999999999999999987   99999998887      99999999999999999997644

>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=99.59  E-value=9.6e-16  Score=108.42  Aligned_cols=66  Identities=29%  Similarity=0.679  Sum_probs=60.1

Q ss_pred             ccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         15 FRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        15 ~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      ...++++|.+|+++|.+.+.++.+.++.||++||+|..|+++|..+ .|+.+++++||+.||.++||
T Consensus         7 ~~~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~-~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B            7 QGSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEG-LFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             CCCTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGG-CCEEETTEEECHHHHHHHTC
T ss_pred             cCcCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCC-CeEeECCeEeCHHHHHHhhC
Confidence            4478889999999999888888999999999999999999999754 78899999999999999885

>3nar_A ZHX1, zinc fingers and homeoboxes protein 1; corepressor, homeodomain, structural genomics, oxford production facility, OPPF, transcription; 2.60A {Homo sapiens}

Probab=99.59  E-value=1.7e-16  Score=119.52  Aligned_cols=57  Identities=16%  Similarity=0.094  Sum_probs=49.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSF  160 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~  160 (267)
                      ....+|.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+..
T Consensus        22 ~~~~~r~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kk~~   84 (96)
T 3nar_A           22 KSGSTGKICKKTPEQLHMLKSAFVRTQWPSPEEYDKLAKESGLARTDIVSWFGDTRYAWKNGN   84 (96)
T ss_dssp             -----CCSSSSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTTC
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHeeecchhhhhHhhhhc
Confidence            455678999999999999999999999999998887      999999999999999999964

>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=99.59  E-value=6.3e-16  Score=130.33  Aligned_cols=79  Identities=25%  Similarity=0.626  Sum_probs=70.7

Q ss_pred             cccCCcccCccccccccCCC------------------------------------------------CCCCCCcccCCC
Q psy10849          2 TSHNSHVSCHPRGFRLYGVK------------------------------------------------CARCGDRLLPHE   33 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~------------------------------------------------C~~C~~~I~~~e   33 (267)
                      |.+||++||+.||.++|+++                                                |.+|+++|.+.+
T Consensus        50 ~~~~g~~yC~~cy~~~f~~~c~~c~~~~g~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~C~~C~~~I~~~~  129 (192)
T 1b8t_A           50 AVHGDEIYCKSCYGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAE  129 (192)
T ss_dssp             EEETTEEEEHHHHHHHHSCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECTTTSCEECSSS
T ss_pred             EecCCEeeChhhhHhhcCccccccccccccEecCCCcccccccccccccCCCCcCccccccccCCCCcCCCCCCEecCcE
Confidence            56899999999999999876                                                778999998776


Q ss_pred             cEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         34 MVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        34 ~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      .+ .+.++.||.+||+|..|+++|. +..|+.+++++||+.||.++|+.
T Consensus       130 ~v-~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~cy~~~f~~  176 (192)
T 1b8t_A          130 KV-IGAGKSWHKSCFRCAKCGKSLE-STTLADKDGEIYCKGCYAKNFGP  176 (192)
T ss_dssp             CE-EETTEEECTTTCBCTTTCCBCC-SSSEEEETTEEEEHHHHHHHTCC
T ss_pred             EE-ecCCCccchhcCCccccCCCCC-CCcccccCCEEeCHHHHHHhcCC
Confidence            55 5999999999999999999996 45799999999999999999875

>1puf_B PRE-B-cell leukemia transcription factor-1; homeodomian, protein-DNA complex, HOX hexapeptide, TALE homeodomain, homeodomain interaction; 1.90A {Homo sapiens} SCOP: a.4.1.1 PDB: 1b8i_B* 2r5y_B* 2r5z_B*

Probab=99.57  E-value=5.2e-16  Score=110.90  Aligned_cols=56  Identities=14%  Similarity=0.195  Sum_probs=51.3

Q ss_pred             CCCCCCCCCHHHHHHHHHhh---hcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        107 PKRPRTILTSAQRRQFKSSF---EVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f---~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      +||.||.||..|+.+|+..|   ..++||+...+++      |++++|+|||||||+|+|+....
T Consensus         1 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk~~~~   65 (73)
T 1puf_B            1 ARRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGK   65 (73)
T ss_dssp             CCCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCTTT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccccccc
Confidence            37889999999999999999   8999999988877      99999999999999999996544

>2da6_A Hepatocyte nuclear factor 1-beta; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.57  E-value=5.5e-16  Score=116.97  Aligned_cols=60  Identities=10%  Similarity=0.116  Sum_probs=52.8

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh----c-----------------------CCCceeeecchhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM----N-----------------------SKRAKNILTPNQRRQF  156 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~----l-----------------------~~~~v~vWFQNrRak~  156 (267)
                      .++.||.||.|+..|+.+||+.|+.++||+...|++    |                       ++.+|+|||||||+|+
T Consensus         3 ~~~~Rr~Rt~ft~~ql~~Le~~F~~~~yPs~~~Re~LA~~ln~~~c~q~g~~~~~~~GL~~~~lte~~V~~WFqNRR~k~   82 (102)
T 2da6_A            3 SGSSGRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRKEE   82 (102)
T ss_dssp             TCCSCCCCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHHHTSCCTTCGGGGGGGCCCHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCccCCHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHhhhcccccccchhcccccccccccceeeeecchHHHH
Confidence            356789999999999999999999999999888877    4                       4678999999999999


Q ss_pred             hhhhhhc
Q psy10849        157 KSSFEIS  163 (267)
Q Consensus       157 k~~~~~~  163 (267)
                      |+..+..
T Consensus        83 kr~~~~~   89 (102)
T 2da6_A           83 AFRQKLA   89 (102)
T ss_dssp             HHHHHHH
T ss_pred             HHhhHhh
Confidence            9976654

>2xsd_C POU domain, class 3, transcription factor 1; transcription-DNA complex, SOX; 2.05A {Mus musculus}

Probab=99.56  E-value=2.9e-16  Score=129.29  Aligned_cols=59  Identities=20%  Similarity=0.209  Sum_probs=45.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      .++.||.||.||..|+.+||+.|+.++||+...|++      |++++|+|||||||+|+||..+.
T Consensus        96 ~~~~rr~Rt~ft~~Ql~~LE~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~~~~  160 (164)
T 2xsd_C           96 QGRKRKKRTSIEVGVKGALESHFLKCPKPSAHEITGLADSLQLEKEVVRVWFCNRRQKEKRMTPA  160 (164)
T ss_dssp             ----------CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTBSCC-
T ss_pred             cccCCCCceeccHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCCChhhhhhhhHHhhHHHhhccCC
Confidence            456788999999999999999999999999998887      99999999999999999997643

>1au7_A Protein PIT-1, GHF-1; complex (DNA-binding protein/DNA), pituitary, CPHD, POU domain, transcription factor, transcription/DNA complex; HET: DNA; 2.30A {Rattus norvegicus} SCOP: a.4.1.1 a.35.1.1

Probab=99.56  E-value=4.1e-16  Score=126.09  Aligned_cols=57  Identities=18%  Similarity=0.229  Sum_probs=49.0

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        103 GRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       103 ~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      ..++.||.||.||..|+.+||..|+.++||+...|++      |++++|+|||||||+|+||+
T Consensus        83 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  145 (146)
T 1au7_A           83 ANERKRKRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV  145 (146)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCCCcCccHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCCChhhchhhhHhhhhhhhcc
Confidence            3456788999999999999999999999999998887      99999999999999999985

>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=99.56  E-value=4.4e-15  Score=105.27  Aligned_cols=66  Identities=27%  Similarity=0.589  Sum_probs=60.2

Q ss_pred             cccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        16 ~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ++|+++|.+|+++|.+.+.++.+.++.||++||+|..|+++|. +..|+.+++++||..||.++|+.
T Consensus         2 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~~   67 (72)
T 1x4k_A            2 SSGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIG-TKSFIPKDNQNFCVPCYEKQHAS   67 (72)
T ss_dssp             CSCCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCC-SSSEEEETTEEEEHHHHHHHTSS
T ss_pred             CccCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccC-CCccCccCCeEECHHHHhHHhCC
Confidence            4688999999999998777899999999999999999999996 45899999999999999998864

>1e3o_C Octamer-binding transcription factor 1; transcription factor, POU domain, dimer, DNA binding; 1.9A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1 PDB: 1gt0_C 1hf0_A* 1cqt_A* 1o4x_A 1oct_C* 1pou_A 1pog_A 1hdp_A

Probab=99.56  E-value=4.5e-16  Score=127.75  Aligned_cols=57  Identities=23%  Similarity=0.288  Sum_probs=48.2

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        103 GRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       103 ~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      +..+.||.||.||..|+.+||+.|+.++||+...|++      |++++|+|||||||+|+||.
T Consensus        97 ~~~~~rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNRR~k~kr~  159 (160)
T 1e3o_C           97 GLSRRRKKRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI  159 (160)
T ss_dssp             -------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCCcCccccCHHHHHHHHHHHhhcCCCCHHHHHHHHHHHCCChHHhhHhhHHhhhhhhcc
Confidence            3456788999999999999999999999999998887      99999999999999999985

>2dmn_A Homeobox protein TGIF2LX; TGFB-induced factor 2-like protein, X-linked TGF(beta) induced transcription factor 2-like protein, TGIF-like on the X; NMR {Homo sapiens}

Probab=99.55  E-value=2e-15  Score=110.53  Aligned_cols=60  Identities=13%  Similarity=0.070  Sum_probs=52.9

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhc---CCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhcc
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEV---SPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEISS  164 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~---~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~~  164 (267)
                      .+.|+.|+.|+.+|+.+|+..|..   ++||+..++++      |+++||+|||||||+|+|+......
T Consensus         5 ~~~rk~R~~~s~~q~~~L~~~f~~~~~~pYPs~~~r~~LA~~~gLs~~qV~~WFqNrR~r~k~~~~~~~   73 (83)
T 2dmn_A            5 SSGKKRKGNLPAESVKILRDWMYKHRFKAYPSEEEKQMLSEKTNLSLLQISNWFINARRRILPDMLQQR   73 (83)
T ss_dssp             CCCCCCCSSCCHHHHHHHHHHHHHTTTTCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHTHHHHTCCC
T ss_pred             CCCCCCCCcCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHhhHHhhhhHhhhcHHHHHhc
Confidence            345788999999999999999977   69999998888      9999999999999999998765543

>2cqx_A LAG1 longevity assurance homolog 5; homeodomain, DNA binding domain, transcription, structural genomics, NPPSFA; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.55  E-value=2.8e-16  Score=112.04  Aligned_cols=53  Identities=19%  Similarity=0.080  Sum_probs=47.7

Q ss_pred             CCCCCCCCHHHHHHHHHhh-hcCCCCChhhhhh------cCCCceeeecchhhhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSF-EVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSF  160 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f-~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~  160 (267)
                      .+.|+.++.+|+.+||+.| +.++||+...|++      |++++|+|||||||+|+|+..
T Consensus         9 ~k~r~r~~~~ql~~LE~~F~~~~~yp~~~~r~~LA~~l~l~e~qVqvWFqNRR~k~r~~~   68 (72)
T 2cqx_A            9 IKDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDKPSG   68 (72)
T ss_dssp             CCCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHSSCC
T ss_pred             CCCCCCCCHHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCCChhhcchhhhhcccCCCCCC
Confidence            4566778899999999999 9999999998877      999999999999999999854

>1b72_B Protein (PBX1); homeodomain, DNA, complex, DNA-binding protein, protein/DNA complex; HET: DNA; 2.35A {Homo sapiens} SCOP: a.4.1.1 PDB: 1lfu_P

Probab=99.55  E-value=9.9e-16  Score=113.12  Aligned_cols=56  Identities=14%  Similarity=0.176  Sum_probs=50.8

Q ss_pred             CCCCCCCCHHHHHHHHHhh---hcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        108 KRPRTILTSAQRRQFKSSF---EVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f---~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ||.||.||..|+.+||..|   ..++||+...+++      |++++|+|||||||+|+|+.....
T Consensus         2 rr~R~~ft~~q~~~Le~~f~~h~~~~yp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   66 (87)
T 1b72_B            2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNIGKF   66 (87)
T ss_dssp             -CCCCCCCHHHHHHHHHHHHTTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCGGGG
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhccccc
Confidence            6889999999999999999   8999999988887      999999999999999999976544

>2dmp_A Zinc fingers and homeoboxes protein 2; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.54  E-value=1.6e-15  Score=112.48  Aligned_cols=51  Identities=20%  Similarity=0.099  Sum_probs=46.8

Q ss_pred             CCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        113 ILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       113 ~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .||.+||.+||..|+.++||+...|++      |++++|+|||||||+|+|+..+..
T Consensus        19 ~~t~~Ql~~Le~~F~~~~yp~~~~r~~La~~~~l~~~qV~vWFqNRR~k~r~~~~~~   75 (89)
T 2dmp_A           19 EKTQGQVKILEDSFLKSSFPTQAELDRLRVETKLSRREIDSWFSERRKLRDSMEQAV   75 (89)
T ss_dssp             CCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHTSCSCC
T ss_pred             cCCHHHHHHHHHHHccCCCCCHHHHHHHHHHhCCCHHhccHhhHhHHHHHHHHhHhh
Confidence            389999999999999999999998887      999999999999999999976554

>1lfb_A Liver transcription factor (LFB1); transcription regulation; 2.80A {Rattus norvegicus} SCOP: a.4.1.1 PDB: 2lfb_A

Probab=99.54  E-value=7e-16  Score=116.52  Aligned_cols=61  Identities=13%  Similarity=0.157  Sum_probs=45.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh---------------------------cCCCceeeecchhhh
Q psy10849        102 DGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM---------------------------NSKRAKNILTPNQRR  154 (267)
Q Consensus       102 ~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~---------------------------l~~~~v~vWFQNrRa  154 (267)
                      +..++.||.||.||..|+.+||..|+.++||+...|++                           |++++|+|||||||+
T Consensus         4 ~~~~k~rr~Rt~ft~~Ql~~LE~~F~~~~yP~~~~R~eLA~~~n~~~~~~~g~~~~~~~~lg~~~lse~qV~vWFqNRR~   83 (99)
T 1lfb_A            4 DPTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRK   83 (99)
T ss_dssp             ---------CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCcCcCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhccccccccccccccccccCccccCcceeeeccHHHHH
Confidence            34567899999999999999999999999999877654                           678899999999999


Q ss_pred             hhhhhhhh
Q psy10849        155 QFKSSFEI  162 (267)
Q Consensus       155 k~k~~~~~  162 (267)
                      |+|+..+.
T Consensus        84 k~k~k~~~   91 (99)
T 1lfb_A           84 EEAFRHKL   91 (99)
T ss_dssp             TTSCCC--
T ss_pred             HHHHhchh
Confidence            99886543

>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=99.54  E-value=7.3e-15  Score=104.13  Aligned_cols=66  Identities=24%  Similarity=0.608  Sum_probs=59.7

Q ss_pred             cccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        16 ~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ++|+++|.+|+++|.+.+.++.+.++.||++||+|..|+++|. +..|+.+++++||..||.++|+.
T Consensus         2 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~~   67 (72)
T 1wyh_A            2 SSGSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLG-SRSFVPDKGAHYCVPCYENKFAS   67 (72)
T ss_dssp             CCCCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTT-TSCEEEETTEEEEHHHHHHHTSC
T ss_pred             CccCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCC-CCccCCcCCeEECHHHHHHHccC
Confidence            4688999999999997667889999999999999999999996 56799999999999999998864

>1du6_A PBX1, homeobox protein PBX1; homeodomain, gene regulation; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.54  E-value=6.7e-16  Score=107.47  Aligned_cols=52  Identities=12%  Similarity=0.118  Sum_probs=48.9

Q ss_pred             CCCCCCCCCHHHHHHHHHhh---hcCCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849        107 PKRPRTILTSAQRRQFKSSF---EVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKS  158 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f---~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~  158 (267)
                      .++.|+.|+..|+.+||..|   ..++||+...+++      |++++|+|||||||+|+||
T Consensus         3 ~rr~R~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~~L~~~qV~~WFqNrR~r~kk   63 (64)
T 1du6_A            3 GHIEGRHMNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKK   63 (64)
T ss_dssp             CCCCCCSSTTTHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHTTTSSC
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHcccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhcc
Confidence            57889999999999999999   8999999988877      9999999999999999987

>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=99.53  E-value=1.1e-14  Score=103.33  Aligned_cols=67  Identities=22%  Similarity=0.526  Sum_probs=60.4

Q ss_pred             ccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhhhc
Q psy10849         17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYLMQ   84 (267)
Q Consensus        17 ~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~~~   84 (267)
                      .++++|.+|+++|.+.+.++.+.++.||++||+|..|+++|. +..|+.+++++||+.||.++|+...
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~~~~~~   69 (72)
T 1x61_A            3 SGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLR-GQHFYAVERRAYCEGCYVATLESGP   69 (72)
T ss_dssp             SCCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCT-TSCEEESSSCEEEHHHHHHHHHTCS
T ss_pred             CCCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCC-cCcCEeeCCeEECHHHHHHHHccCC
Confidence            467899999999997667888999999999999999999995 7889999999999999999997543

>2l9r_A Homeobox protein NKX-3.1; structural genomics, northeast structural genomics consortiu PSI-biology, protein structure initiative; NMR {Homo sapiens}

Probab=99.53  E-value=8.8e-16  Score=108.43  Aligned_cols=52  Identities=12%  Similarity=0.047  Sum_probs=47.2

Q ss_pred             CCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        111 RTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       111 Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      -...|..|+.+||+.|+.++||+...|++      |++++|+|||||||+|+||....
T Consensus         8 ~~~~t~~ql~~LE~~F~~~~yp~~~~r~~LA~~l~Lte~qVqvWFqNRRak~kr~~~~   65 (69)
T 2l9r_A            8 HSHMSHTQVIELERKFSHQKYLSAPERAHLAKNLKLTETQVKIWFQNRRYKTKRKQLS   65 (69)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHSCCSSSS
T ss_pred             CCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCChhheeecchhhhhhhhhhhhh
Confidence            35789999999999999999999998887      99999999999999999996543

>3d1n_I POU domain, class 6, transcription factor 1; protein-DNA complex, helix-turn-helix (HTH), DNA-binding, homeobox, nucleus, transcription regulation; 2.51A {Homo sapiens}

Probab=99.53  E-value=2e-15  Score=122.67  Aligned_cols=55  Identities=20%  Similarity=0.306  Sum_probs=51.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKS  158 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~  158 (267)
                      ..+.||.||.||..|+.+||+.|+.++||+...+++      |++++|+|||||||+|+||
T Consensus        90 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~LA~~l~L~~~qV~vWFqNrR~k~Kk  150 (151)
T 3d1n_I           90 PSKKRKRRTSFTPQAIEALNAYFEKNPLPTGQEITEMAKELNYDREVVRVWFSNRRQTLKN  150 (151)
T ss_dssp             CCCCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHhHHHHHHHHhccCC
Confidence            345688999999999999999999999999998887      9999999999999999997

>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=99.52  E-value=1.5e-14  Score=107.17  Aligned_cols=75  Identities=19%  Similarity=0.274  Sum_probs=65.0

Q ss_pred             CCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849          5 NSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus         5 dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      +....++..+...+.++|.+|+++|.+  .++.+.++.||++||+|..|+++|. +..|+.+++++||+.||.++|+.
T Consensus        11 ~~~~~~~~~~~~~~~~~C~~C~~~I~~--~~v~a~~~~~H~~CF~C~~C~~~L~-~~~f~~~~g~~yC~~cy~~~f~~   85 (90)
T 2dar_A           11 TLVQRAEHIPAGKRTPMCAHCNQVIRG--PFLVALGKSWHPEEFNCAHCKNTMA-YIGFVEEKGALYCELCYEKFFAS   85 (90)
T ss_dssp             CSCBCCEEECTTTCCCBBSSSCCBCCS--CEEEETTEEECTTTCBCSSSCCBCS-SSCBEESSSCEECHHHHHHHTSC
T ss_pred             chhhhcccCCCCCCCCCCccCCCEecc--eEEEECCccccccCCccCCCCCCCC-CCEeEeECCEEECHHHHHHHcCC
Confidence            344566777788899999999999974  4778999999999999999999996 57799999999999999999864

>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=99.51  E-value=7.2e-15  Score=105.52  Aligned_cols=66  Identities=20%  Similarity=0.383  Sum_probs=59.5

Q ss_pred             cccCCCCCCCCCcccC--CCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         16 RLYGVKCARCGDRLLP--HEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        16 ~~f~~~C~~C~~~I~~--~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ++|+++|.+|+++|.+  .+.++.+.++.||++||+|..|+++|. +..|+.+++++||+.||.++|+.
T Consensus         2 ~~~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~-~~~f~~~~g~~yC~~cy~~~f~~   69 (76)
T 1x68_A            2 SSGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLV-GKGFLTQNKEIFCQKCGSGMDTD   69 (76)
T ss_dssp             TTCCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCS-SSCEEEETTEEEETTTTCCCCCC
T ss_pred             CccCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCC-CCceEeECCEEECHHHhhhhhCC
Confidence            4688999999999996  446888999999999999999999996 68899999999999999998865

>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=99.51  E-value=7.2e-15  Score=104.85  Aligned_cols=65  Identities=22%  Similarity=0.398  Sum_probs=58.1

Q ss_pred             cccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        16 ~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      .+|+++|.+|+++|.+  .++.++++.||++||+|..|+.+|..+..|+.+++++||..||.++++.
T Consensus         2 s~~~~~C~~C~~~I~~--~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~   66 (73)
T 1wig_A            2 SSGSSGCDSCEKYITG--RVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTE   66 (73)
T ss_dssp             CCSCCSCSSSCCCCSS--CCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSS
T ss_pred             CcCcCCcccCCCEecC--eeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhcc
Confidence            3688999999999986  3678999999999999999999997678899999999999999887753

>3l1p_A POU domain, class 5, transcription factor 1; POU, transcription factor DNA complex, pore, stem cells; HET: DNA; 2.80A {Mus musculus} PDB: 1ocp_A

Probab=99.51  E-value=2.4e-15  Score=122.75  Aligned_cols=55  Identities=29%  Similarity=0.333  Sum_probs=50.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      ++.||.||.||..|+.+||..|+.++||+...+++      |++++|+|||||||+|+||.
T Consensus        94 ~~~rr~Rt~ft~~Q~~~Le~~F~~~~yps~~~r~~LA~~l~L~~~qV~vWFqNRR~k~Kr~  154 (155)
T 3l1p_A           94 QARKRKRTSIENRVRWSLETMFLKSPKPSLQQITHIANQLGLEKDVVRVWFSNRRQKGKRS  154 (155)
T ss_dssp             CCSCCCCCCCCHHHHHHHHTTTTTCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHC-
T ss_pred             cCCCCCCcccCHHHHHHHHHHHccCCCCCHHHHHHHHHHcCCChhheeeccccccccccCC
Confidence            45688999999999999999999999999998877      89999999999999999984

>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=99.51  E-value=8.3e-15  Score=103.97  Aligned_cols=64  Identities=19%  Similarity=0.383  Sum_probs=57.9

Q ss_pred             ccCCCCCCCCCcccC--CCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         17 LYGVKCARCGDRLLP--HEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        17 ~f~~~C~~C~~~I~~--~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      .++++|.+|+++|.+  .+.++.+.++.||++||+|..|+++|. +..|+.+++++||..||.++|+
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~-~~~f~~~~g~~yC~~c~~~~~~   68 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLV-GRGFLTERDDILCPDCGKDISG   68 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCT-TSCCEECSSSEECHHHHHTCCC
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCC-CCccEeECCEEEChhHcCcccC
Confidence            467899999999996  456888999999999999999999996 7889999999999999998875

>1k61_A Mating-type protein alpha-2; protein-DNA complex, homeodomain, hoogsteen base PAIR, transcription/DNA complex; HET: 5IU; 2.10A {Synthetic} SCOP: a.4.1.1

Probab=99.51  E-value=2.4e-15  Score=103.35  Aligned_cols=49  Identities=22%  Similarity=0.112  Sum_probs=46.2

Q ss_pred             CCCCCHHHHHHHHHhhhc---CCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        111 RTILTSAQRRQFKSSFEV---SPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       111 Rt~ft~~Ql~~L~~~f~~---~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      |+.||.+|+.+||..|+.   ++||+...+++      |++++|+|||||||+|+|+.
T Consensus         2 r~~ft~~q~~~Le~~f~~~~~~~yp~~~~r~~La~~~gl~~~qV~~WFqNrR~r~kk~   59 (60)
T 1k61_A            2 GHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCSCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             cCcCCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHcccccC
Confidence            689999999999999999   99999988877      99999999999999999984

>3nau_A Zinc fingers and homeoboxes protein 2; ZHX2, corepressor, homeodomain, domain swapping, structural oxford protein production facility, OPPF; 2.70A {Homo sapiens}

Probab=99.51  E-value=1.6e-15  Score=105.16  Aligned_cols=45  Identities=18%  Similarity=0.106  Sum_probs=42.9

Q ss_pred             CHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        115 TSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       115 t~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      |.+||.+||+.|..++||+..++++      |++++|+|||||||+|||+.
T Consensus        12 ~~~Ql~~LE~~F~~~~YPs~~er~eLA~~tgLt~~qVkvWFqNRR~k~Kkg   62 (66)
T 3nau_A           12 TKEQIAHLKASFLQSQFPDDAEVYRLIEVTGLARSEIKKWFSDHRYRCQRG   62 (66)
T ss_dssp             CHHHHHHHHHHHHGGGSCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
T ss_pred             hHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCcCHHHhhHhcccchhhhhcc
Confidence            6899999999999999999999888      99999999999999999984

>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=99.50  E-value=1.1e-14  Score=101.65  Aligned_cols=63  Identities=22%  Similarity=0.511  Sum_probs=57.0

Q ss_pred             cccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        16 ~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      ++|+++|.+|+++|. + .++.+.++.||++||+|..|+++|. +..|+.+++++||..||.++|+
T Consensus         2 ~~~~~~C~~C~~~I~-~-~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~~y~~~f~   64 (66)
T 1nyp_A            2 SMGVPICGACRRPIE-G-RVVNAMGKQWHVEHFVCAKCEKPFL-GHRHYERKGLAYCETHYNQLFG   64 (66)
T ss_dssp             CCCCCEETTTTEECC-S-CEECCTTSBEETTTCBCTTTCCBCS-SSCCEEETTEEECHHHHHHHCS
T ss_pred             CcCCCCCcccCCEec-c-eEEEECccccccCcCEECCCCCCCC-CCceEeECCcEECHHHHHHHhC
Confidence            467889999999999 3 3778999999999999999999996 6789999999999999999886

>1mnm_C Protein (MAT alpha-2 transcriptional repressor); transcription regulation, transcriptional repression, DNA- binding protein; HET: DNA; 2.25A {Saccharomyces cerevisiae} SCOP: a.4.1.1

Probab=99.50  E-value=3.8e-15  Score=110.01  Aligned_cols=53  Identities=21%  Similarity=0.083  Sum_probs=48.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhc---CCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849        106 GPKRPRTILTSAQRRQFKSSFEV---SPKPCRKVSTM------NSKRAKNILTPNQRRQFKS  158 (267)
Q Consensus       106 ~~kr~Rt~ft~~Ql~~L~~~f~~---~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~  158 (267)
                      +.++.|+.||..|+.+||..|..   ++||+...+++      |++++|+|||||||+|+|.
T Consensus        26 ~~~k~r~~ft~~q~~~Le~~f~~~~~~~yP~~~~r~~La~~~gL~~~qV~~WFqNrR~r~k~   87 (87)
T 1mnm_C           26 TKPYRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKT   87 (87)
T ss_dssp             SSCCTTCCCCHHHHHHHHHHHHHTTSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCCcCCHHHHHHHHHHHHHhCCCCCcCHHHHHHHHHHHCcCHHHHHHHHHHHHhhccC
Confidence            34567999999999999999999   99999988887      9999999999999999984

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

Probab=99.49  E-value=1.7e-14  Score=103.50  Aligned_cols=66  Identities=29%  Similarity=0.676  Sum_probs=59.2

Q ss_pred             cccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        16 ~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ..++.+|.+|+++|.+.+.++.+.++.||.+||+|..|+++|.. ..|+.+++++||+.||.++|+.
T Consensus         8 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~-~~~~~~~g~~yC~~~y~~~f~~   73 (77)
T 1g47_A            8 ALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPE-GLFYEFEGRKYCEHDFQMLFAP   73 (77)
T ss_dssp             CCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGG-GCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCC-CCeEeECCeEeCHHHHHHHhhc
Confidence            45678999999999877788999999999999999999999974 4688999999999999998863

>2e19_A Transcription factor 8; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Homo sapiens}

Probab=99.49  E-value=3.6e-15  Score=103.82  Aligned_cols=49  Identities=6%  Similarity=-0.063  Sum_probs=44.4

Q ss_pred             CCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        111 RTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       111 Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      +..++.+|+.+||+.|+.++||+...|++      |++++|+|||||||||.++.
T Consensus         7 ~~~p~~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~L~e~qVqvWFqNRRak~~~~   61 (64)
T 2e19_A            7 GQPPLKNLLSLLKAYYALNAQPSAEELSKIADSVNLPLDVVKKWFEKMQAGQISV   61 (64)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTCSCS
T ss_pred             CCCccHHHHHHHHHHHhcCCCcCHHHHHHHHHHhCcChhhcCcchhcccCCCCCC
Confidence            34567999999999999999999998887      99999999999999998874

>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=99.48  E-value=4.5e-14  Score=99.30  Aligned_cols=63  Identities=24%  Similarity=0.560  Sum_probs=56.9

Q ss_pred             ccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        17 ~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      +++++|.+|+++|.+.  ++.+.++.||.+||+|..|+++|. +..|+.+++++||..||.++|+.
T Consensus         3 ~~~~~C~~C~~~I~~~--~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~~   65 (69)
T 2cur_A            3 SGSSGCVKCNKAITSG--GITYQDQPWHADCFVCVTCSKKLA-GQRFTAVEDQYYCVDCYKNFVSG   65 (69)
T ss_dssp             CCCCCCSSSCCCCCTT--CEEETTEEECTTTTBCTTTCCBCT-TSCEEECSSCEEEHHHHHHHHTC
T ss_pred             CCcCCCcccCCEeCcc--eEEECccccccCcCEECCCCCCCC-CCccEeECCEEECHHHhHHHhcC
Confidence            5678999999999853  577999999999999999999996 67899999999999999999874

>1le8_B Mating-type protein alpha-2; matalpha2, isothermal titration calorimetry, protein-DNA complex, transcription/DNA complex; 2.30A {Saccharomyces cerevisiae} SCOP: a.4.1.1 PDB: 1akh_B* 1apl_C* 1yrn_B*

Probab=99.47  E-value=7e-15  Score=107.65  Aligned_cols=52  Identities=17%  Similarity=0.013  Sum_probs=47.0

Q ss_pred             CCCCCCCHHHHHHHHHhhhc---CCCCChhhhhh------cCCCceeeecchhhhhhhhhh
Q psy10849        109 RPRTILTSAQRRQFKSSFEV---SPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSF  160 (267)
Q Consensus       109 r~Rt~ft~~Ql~~L~~~f~~---~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~  160 (267)
                      +.|+.||..|+.+||..|..   ++||+...+++      |++++|+|||||||+|+|+..
T Consensus         4 krr~rft~~q~~~Le~~f~~h~~~~yP~~~~r~~La~~~gLt~~qV~~WFqNrR~r~kk~~   64 (83)
T 1le8_B            4 YRGHRFTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVAARRAKEKTIT   64 (83)
T ss_dssp             -CCCCCCHHHHHHHHHHHHHTSSSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHhhCCCCCcCHHHHHHHHHHHCCCHHHcccccHHHHccccccc
Confidence            34666999999999999999   99999988887      999999999999999999964

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

Probab=99.47  E-value=3.5e-14  Score=98.90  Aligned_cols=61  Identities=25%  Similarity=0.601  Sum_probs=54.2

Q ss_pred             cCCCCCCCCCcccCCCcEEEecCceee--cCCcccccccccCCCCCceEeeCCeecc-hhhHHHH
Q psy10849         18 YGVKCARCGDRLLPHEMVMRAQSHVYH--LPCFVCVICCQPLQKGEQFILRSGQLFC-RQDFEKE   79 (267)
Q Consensus        18 f~~~C~~C~~~I~~~e~~~~a~~~~wH--~~CF~C~~C~~~L~~g~~f~~~~~~lyC-~~cy~k~   79 (267)
                      |+++|.+|+++|.+++.++.+.++.||  ++||+|..|+++|. +..|+.+++++|| ..||.++
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 HAVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLI-GQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             -CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCT-TSCCEEETTEEESSHHHHHTT
T ss_pred             CcCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCC-CCceEEECCEEecCHHHhhhh
Confidence            577999999999975568889999999  99999999999996 7889999999999 8888764

>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=99.47  E-value=5.2e-14  Score=99.21  Aligned_cols=63  Identities=22%  Similarity=0.493  Sum_probs=56.7

Q ss_pred             ccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        17 ~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      +|+++|.+|+++|.+.  .+.+.++.||++||+|..|+++|. +..|+.+++++||..||.++|+.
T Consensus         3 ~~~~~C~~C~~~I~~~--~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~~   65 (70)
T 2d8z_A            3 SGSSGCVQCKKPITTG--GVTYREQPWHKECFVCTACRKQLS-GQRFTARDDFAYCLNCFCDLYAS   65 (70)
T ss_dssp             CCCCBCSSSCCBCCSS--EEESSSSEEETTTSBCSSSCCBCT-TSCCEESSSSEECHHHHHHHTCC
T ss_pred             CCCCCCcccCCeeccc--eEEECccccCCCCCccCCCCCcCC-cCceEeeCCeEECHHHHHHHhcc
Confidence            5788999999999854  578999999999999999999995 67899999999999999998864

>2d5v_A Hepatocyte nuclear factor 6; transcription factor, transcription-DNA complex; 2.00A {Rattus norvegicus} PDB: 1s7e_A

Probab=99.46  E-value=7.9e-15  Score=120.72  Aligned_cols=58  Identities=22%  Similarity=0.386  Sum_probs=48.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      ..+.||.||.||..|+.+||+.|+.++||+...|++      |++++|+|||||||+|+|+...
T Consensus        94 ~~~~rr~Rt~ft~~q~~~Le~~F~~~~yp~~~~r~~la~~l~L~~~qV~~WFqNrR~r~k~~~~  157 (164)
T 2d5v_A           94 GNTPKKPRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNARRRSLDKWL  157 (164)
T ss_dssp             ------CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHTSSCC--
T ss_pred             CCCCCCCCCcCCHHHHHHHHHHHhcCCCCCHHHHHHHHHHHCcCHHHhhhcChhhhccccccCC
Confidence            345788999999999999999999999999998887      9999999999999999998654

>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=99.45  E-value=4.6e-14  Score=110.82  Aligned_cols=65  Identities=26%  Similarity=0.600  Sum_probs=57.4

Q ss_pred             cccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCC-CCceEeeCCeecchhhHHHHHh
Q psy10849         16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQK-GEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        16 ~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~-g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      ..+.++|.+|+++|.+. .++.+.++.||.+||+|..|+.+|.. |..|+.+++++||+.||.++||
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 GLSWKRCAGCGGKIADR-FLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             CSSCSBBSSSSSBCCSS-SEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             CccCCcCcCCCCCcCCc-EEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            34567999999999965 46789999999999999999999962 5789999999999999999985

>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=99.45  E-value=9.6e-14  Score=97.88  Aligned_cols=63  Identities=25%  Similarity=0.593  Sum_probs=55.9

Q ss_pred             ccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        17 ~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      .+..+|..|+++|.+  .++.+.++.||++||+|..|+++|.. ..|+.+++++||+.||.++|+.
T Consensus         3 ~~~~~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L~~-~~f~~~~g~~yC~~c~~~~~~~   65 (70)
T 2d8x_A            3 SGSSGCHQCGEFIIG--RVIKAMNNSWHPECFRCDLCQEVLAD-IGFVKNAGRHLCRPCHNREKAS   65 (70)
T ss_dssp             CCSSBCSSSCCBCCS--CCEEETTEEECTTTSBCSSSCCBCSS-SCCEEETTEEECHHHHHHHHCC
T ss_pred             CCCCcCccCCCEecc--eEEEECcccccccCCEeCCCCCcCCC-CccEeECCeEECHHHhhhhcCC
Confidence            356799999999985  36789999999999999999999974 5788899999999999999875

>1x2m_A LAG1 longevity assurance homolog 6; homeobox domain, structural genomics, NPPSFA, national project on protein structural and functional analyses; NMR {Mus musculus} SCOP: a.4.1.1

Probab=99.45  E-value=7.1e-15  Score=101.89  Aligned_cols=44  Identities=18%  Similarity=0.138  Sum_probs=39.6

Q ss_pred             HHHHHHHHHhh-hcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        116 SAQRRQFKSSF-EVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       116 ~~Ql~~L~~~f-~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      ..|+.+||+.| ..++||+...|++      |+++||||||||||+|+|+.
T Consensus         9 ~~~~~~LE~~F~~~~~yp~~~~r~~LA~~l~LterQVkvWFqNRR~k~k~~   59 (64)
T 1x2m_A            9 AQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKPS   59 (64)
T ss_dssp             SCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCCS
T ss_pred             chHHHHHHHHHHHcCCCcCHHHHHHHHHHhCCCHHHHHHHHHHHHhccCCC
Confidence            45799999999 5789999988887      99999999999999999974

>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=99.44  E-value=1.1e-13  Score=99.27  Aligned_cols=66  Identities=18%  Similarity=0.372  Sum_probs=58.1

Q ss_pred             ccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecch-hhHHHHHhh
Q psy10849         15 FRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCR-QDFEKEMYL   82 (267)
Q Consensus        15 ~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~-~cy~k~f~~   82 (267)
                      ...++++|.+|+++|..++ .+.+.++.||++||+|..|+++|. +..|+.+++++||. .||.++|+.
T Consensus         5 ~~~~~~~C~~C~~~I~~~~-~v~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~~cy~~~f~~   71 (76)
T 2cu8_A            5 SSGMASKCPKCDKTVYFAE-KVSSLGKDWHKFCLKCERCSKTLT-PGGHAEHDGKPFCHKPCYATLFGS   71 (76)
T ss_dssp             CCCCCCBCTTTCCBCCTTT-EEEETTEEEETTTCBCSSSCCBCC-TTSCEEETTEEECTTTHHHHHSCS
T ss_pred             cCCCCCCCcCCCCEeECCe-EEEECCeEeeCCCCCCCCCCCccC-CCceEeECCEEecchHHHHHhccc
Confidence            4567889999999999765 456999999999999999999996 57799999999999 799998863

>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=99.40  E-value=2.6e-13  Score=98.48  Aligned_cols=61  Identities=25%  Similarity=0.655  Sum_probs=54.3

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      .++|.+|+++|..++ ++.++++.||++||+|..|+.+|. + .|+.+++++||+.||.++|+.
T Consensus        15 ~~~C~~C~~~I~~~~-~v~a~~~~wH~~CF~C~~C~~~L~-~-~~~~~~g~~yC~~~y~~~fg~   75 (80)
T 2dj7_A           15 PSHCAGCKEEIKHGQ-SLLALDKQWHVSCFKCQTCSVILT-G-EYISKDGVPYCESDYHAQFGS   75 (80)
T ss_dssp             CSCCTTTCCCCSSSC-CEEETTEEECTTTCBCSSSCCBCS-S-CCEEETTEEECTTHHHHHTTC
T ss_pred             CCCCcCcCCeeCCCe-EEEECCcccccccCCcCcCCCCcC-C-CeEEECCEEECHHHHHHHcCC
Confidence            458999999998765 567999999999999999999996 4 588999999999999999874

>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=99.38  E-value=3.3e-13  Score=99.72  Aligned_cols=61  Identities=25%  Similarity=0.606  Sum_probs=54.4

Q ss_pred             cCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         18 YGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        18 f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      ...+|.+|++.|.+  .++.+.++.||.+||+|..|++.|. +..|+.+++++||+.||.++|+
T Consensus        24 ~~~~C~~C~~~I~~--~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~~y~~~f~   84 (89)
T 1x64_A           24 RMPLCDKCGSGIVG--AVVKARDKYRHPECFVCADCNLNLK-QKGYFFVEGELYCETHARARTS   84 (89)
T ss_dssp             SCCBCTTTCCBCCS--CCEESSSCEECTTTCCCSSSCCCTT-TSCCEEETTEEECHHHHHHHSS
T ss_pred             cCCCcccCCCEecc--cEEEECCceECccCCEecCCCCCCC-CCCeEeECCEEECHHHHHHHhC
Confidence            34589999999996  3678999999999999999999996 4578889999999999999886

>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=99.38  E-value=2.8e-13  Score=98.26  Aligned_cols=63  Identities=22%  Similarity=0.645  Sum_probs=54.7

Q ss_pred             cCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         18 YGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        18 f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ..++|.+|+++|...+ ++.+.++.||++||+|..|+++|. +..|+.+++++||+.||.++|+.
T Consensus         6 ~~~~C~~C~~~I~~~~-~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~~~~yC~~cy~~~f~~   68 (81)
T 1a7i_A            6 GGNKCGACGRTVYHAE-EVQCDGRSFHRCCFLCMVCRKNLD-STTVAIHDAEVYCKSCYGKKYGP   68 (81)
T ss_dssp             --CBCSSSCCBCSSTT-EEEETTEEEESSSEECSSSCCEEC-SSCCEEETTEEECSHHHHHHCC-
T ss_pred             CCCcCcCcCccccCce-eEEeCCcccccccCccCCCCCCCC-CCCeEeeCCEEECHHHHHHHhCC
Confidence            4679999999998765 568999999999999999999996 45789999999999999999875

>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=99.38  E-value=1.4e-13  Score=99.45  Aligned_cols=60  Identities=18%  Similarity=0.532  Sum_probs=54.3

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      .++|.+|++.|.+.  ++.+.++.||++||+|..|++.|. +..|+.+++++||+.||.++|+
T Consensus        15 ~~~C~~C~~~I~~~--~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~cy~~~~~   74 (79)
T 1x62_A           15 LPMCDKCGTGIVGV--FVKLRDRHRHPECYVCTDCGTNLK-QKGHFFVEDQIYCEKHARERVS   74 (79)
T ss_dssp             CCCCSSSCCCCCSS--CEECSSCEECTTTTSCSSSCCCHH-HHCCEESSSCEECHHHHHHHHS
T ss_pred             CCccccCCCCccCc--EEEECcceeCcCcCeeCCCCCCCC-CCCeEeECCEEECHHHHHHHhC
Confidence            46999999999963  778999999999999999999995 5678899999999999999986

>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=99.37  E-value=4e-13  Score=99.70  Aligned_cols=65  Identities=23%  Similarity=0.612  Sum_probs=56.6

Q ss_pred             cccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        16 ~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      .....+|.+|++.|.+.+. +.+.++.||++||+|..|+.+|.. ..|+.+++++||..||.++|+.
T Consensus        12 ~~~~~~C~~C~~~I~~~~~-v~a~~~~~H~~CF~C~~C~~~L~~-~~~~~~~g~~yC~~~y~~~f~~   76 (91)
T 2d8y_A           12 APARETCVECQKTVYPMER-LLANQQVFHISCFRCSYCNNKLSL-GTYASLHGRIYCKPHFNQLFKS   76 (91)
T ss_dssp             SSSSCBCTTTCCBCCTTSE-EECSSSEEETTTCBCTTTCCBCCT-TTCCCSSSCCCCHHHHHHHSCC
T ss_pred             CCCCCcCccCCCccCCcee-EEECCCEECCCCCeeCCCCCCCCC-CCcEeECCEEECHHHHHHHhCC
Confidence            3456799999999997764 579999999999999999999974 4588899999999999999874

>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=99.36  E-value=3.4e-13  Score=97.58  Aligned_cols=63  Identities=21%  Similarity=0.342  Sum_probs=53.9

Q ss_pred             cccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        16 ~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ..+.++|.+|+++|.+  .++.++++.||++||+|..|+.+|. +.. +.+++++||..||.++|+.
T Consensus        12 ~~~~~~C~~C~~~I~~--~~v~a~~~~~H~~CF~C~~C~~~L~-~~~-f~~~g~~yC~~cy~~~f~p   74 (79)
T 2cor_A           12 GLGKYICQKCHAIIDE--QPLIFKNDPYHPDHFNCANCGKELT-ADA-RELKGELYCLPCHDKMGVS   74 (79)
T ss_dssp             CCCCCBCTTTCCBCCS--CCCCCSSSCCCTTTSBCSSSCCBCC-TTC-EEETTEEECHHHHHTTSCC
T ss_pred             ccCCCCCccCCCEecc--eEEEECcceeCCCCCEeCCCCCccC-CCC-EeECCEEeCHHHHHHhCCC
Confidence            3456799999999993  3678999999999999999999996 444 4889999999999998764

>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=99.36  E-value=2.9e-13  Score=102.11  Aligned_cols=53  Identities=17%  Similarity=0.349  Sum_probs=49.9

Q ss_pred             cccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCccccccc
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICC   54 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~   54 (267)
                      +.+||++||+.||.++|+++|.+|+++|.++|.++.+.++.||++||+|..|+
T Consensus        49 ~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           49 VAKDNKILCNKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             EEETTEEECHHHHTTCCCCBCSSSCCBCCSSSCEEESSSCEEETTTCCCTTCC
T ss_pred             ECcCCEEEChhHhhhhcCCccccCCCccccCCeEEEeCCcchHHhCCCCCCCC
Confidence            46899999999999999999999999999777889999999999999999986

>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=99.35  E-value=6.9e-13  Score=102.52  Aligned_cols=63  Identities=21%  Similarity=0.526  Sum_probs=56.4

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCC-CCceEeeCCeecchhhHHHHHhh
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQK-GEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~-g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      .++|.+|+++|.+. .++.+.++.||++||+|..|+.+|.. |..|+.+++++||+.||.++|+.
T Consensus         3 ~~~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~   66 (114)
T 1j2o_A            3 LLTCGGCQQNIGDR-YFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGS   66 (114)
T ss_dssp             CBCBSSSCSCBCSS-EEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTS
T ss_pred             CCCCcCCCCeeCCc-EEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCc
Confidence            35899999999965 47889999999999999999999963 56899999999999999999986

>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=99.35  E-value=6.7e-13  Score=100.07  Aligned_cols=65  Identities=20%  Similarity=0.503  Sum_probs=58.4

Q ss_pred             ccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        17 ~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      .++++|.+|+++|...+.++.+.++.||++||+|..|+++|. +..|+.+++++||+.||.++|+.
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~cy~~~~~~   67 (101)
T 2cup_A            3 SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLA-NETFVAKDNKILCNKCTTREDSP   67 (101)
T ss_dssp             SCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTT-SSCCEEETTEEECHHHHTTCCCC
T ss_pred             CCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCC-cCeeECcCCEEEChhHhhhhcCC
Confidence            567899999999986446888999999999999999999995 67899999999999999998865

>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=99.33  E-value=1.1e-12  Score=93.86  Aligned_cols=61  Identities=20%  Similarity=0.489  Sum_probs=54.1

Q ss_pred             CCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecch-hhHHHHHhh
Q psy10849         20 VKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCR-QDFEKEMYL   82 (267)
Q Consensus        20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~-~cy~k~f~~   82 (267)
                      ++|.+|+++|..++ .+.+.++.||++||+|..|+.+|. +..|+.+++++||. .||.++|+.
T Consensus         1 p~C~~C~~~I~~~~-~v~a~~~~~H~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~~cy~~~f~~   62 (76)
T 1iml_A            1 PKCPKCDKEVYFAE-RVTSLGKDWHRPCLKCEKCGKTLT-SGGHAEHEGKPYCNHPCYSAMFGP   62 (76)
T ss_dssp             CBCTTTSSBCCGGG-EEEETTEEEETTTCBCTTTCCBCC-TTTEEEETTEEEETTTHHHHHSSC
T ss_pred             CcCCCCCCEEECce-EEEECCccccCCCCCccccCccCC-CCceECcCCeEeeCHHHHHHHhCc
Confidence            47999999998665 567999999999999999999996 45799999999999 699999874

>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=99.33  E-value=3e-13  Score=98.52  Aligned_cols=62  Identities=27%  Similarity=0.567  Sum_probs=52.9

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceE--eeCCeecchhhHHHHHhh
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFI--LRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~--~~~~~lyC~~cy~k~f~~   82 (267)
                      ..+|.+|++.|...+.+ .+.++.||.+||+|..|++.|. +..|+  .+++++||+.||.++|+.
T Consensus        15 ~~~C~~C~~~I~~~e~v-~a~~~~wH~~CF~C~~C~~~L~-~~~~~~~~~~g~~yC~~~y~~~~~~   78 (82)
T 2co8_A           15 GDLCALCGEHLYVLERL-CVNGHFFHRSCFRCHTCEATLW-PGGYEQHPGDGHFYCLQHLPQTDSG   78 (82)
T ss_dssp             SCBCSSSCCBCCTTTBC-CBTTBCCBTTTCBCSSSCCBCC-TTSEECCTTTCCCEETTTCCCCCCC
T ss_pred             CCCCcccCCCcccceEE-EECCCeeCCCcCEEcCCCCCcC-CCceeEeCcCCEEEChHHHHhhhcC
Confidence            45899999999877655 4999999999999999999996 45566  368999999999988764

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

Probab=99.32  E-value=1.4e-12  Score=102.28  Aligned_cols=64  Identities=23%  Similarity=0.545  Sum_probs=57.7

Q ss_pred             ccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        17 ~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      +|+++|.+|+++|.+++ ++.++++.||++||+|..|+++|. +..|+.+++++||+.||.++|+.
T Consensus         1 ~~~~~C~~C~~~I~~~~-~~~a~~~~~H~~CF~C~~C~~~L~-~~~f~~~~g~~yC~~cy~~~~~~   64 (126)
T 2xqn_T            1 SEKPRCAGCDELIFSNE-YTQAENQNWHLKHFCCFDCDSILA-GEIYVMVNDKPVCKPCYVKNHAV   64 (126)
T ss_dssp             -CCCBBTTTSSBCCSSC-EEEETTEEECGGGSBCTTTCCBCT-TSEEEEETTEEEEHHHHHHHSCC
T ss_pred             CcCCCCccCCCEeCCce-EEeeCCCCccCCCCCcCCCCCCCC-cCEEEeECCEEechHHhCcCcCc
Confidence            36789999999999764 778999999999999999999996 67899999999999999999875

>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=99.30  E-value=8e-13  Score=103.37  Aligned_cols=65  Identities=26%  Similarity=0.562  Sum_probs=57.7

Q ss_pred             ccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCC-CCceEeeCCeecchhhHHHHHhh
Q psy10849         17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQK-GEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        17 ~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~-g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ++.++|.+|+++|.+.+ ++.+.++.||++||+|..|+.+|.+ +..|+.+++++||+.||.++|+.
T Consensus         3 ~~~~~C~~C~~~I~~~~-~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~   68 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADRF-LLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGN   68 (122)
T ss_dssp             SCCCCBSSSSSCCCSSC-CEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCC
T ss_pred             CCCCCCcccCCEeCCcE-EEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCC
Confidence            46789999999999764 5779999999999999999999952 46799999999999999999985

>3k2a_A Homeobox protein MEIS2; homeobox domain, DNA-binding, transcription, nucleus, phosphoprotein, DNA bindi protein; 1.95A {Homo sapiens} SCOP: a.4.1.1

Probab=99.29  E-value=3.6e-13  Score=94.51  Aligned_cols=51  Identities=14%  Similarity=0.096  Sum_probs=43.7

Q ss_pred             CCCHHHHHHHHHhhh---cCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        113 ILTSAQRRQFKSSFE---VSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       113 ~ft~~Ql~~L~~~f~---~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .|+.+|+.+|+..|.   .++||+...+++      |++++|+|||||||+|+|+.....
T Consensus         4 ~f~~~~~~~L~~~f~~h~~~pyp~~~~r~~La~~~~l~~~qV~~WFqNrR~r~kk~~~~~   63 (67)
T 3k2a_A            4 IFPKVATNIMRAWLFQHLTHPYPSEEQKKQLAQDTGLTILQVNNWFINARRRIVQPMIDQ   63 (67)
T ss_dssp             --CHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHSCC---
T ss_pred             cCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHhCcCHHHhhhhhHHHHHHHhHHHHHH
Confidence            689999999999999   999999998887      999999999999999999865443

>1ic8_A Hepatocyte nuclear factor 1-alpha; transcription regulation, DNA-binding, POU domain, diabetes, disease mutation, MODY3, transcription/DNA comple; 2.60A {Homo sapiens} SCOP: a.4.1.1 a.35.1.1

Probab=99.29  E-value=2.8e-13  Score=114.05  Aligned_cols=56  Identities=13%  Similarity=0.121  Sum_probs=45.3

Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh---------------------------cCCCceeeecchhhhh
Q psy10849        103 GRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM---------------------------NSKRAKNILTPNQRRQ  155 (267)
Q Consensus       103 ~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~---------------------------l~~~~v~vWFQNrRak  155 (267)
                      ..++.||.||.|+..|+.+||+.|+.++||+...|++                           |++.+|+|||||||+|
T Consensus       111 ~~~k~rr~R~~ft~~ql~~Le~~F~~~~yp~~~~Re~la~~~~~~~~~~~G~~~~~~~glg~~~lte~~V~~WFqNRR~~  190 (194)
T 1ic8_A          111 PTKKGRRNRFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKE  190 (194)
T ss_dssp             ------CCCCCCCHHHHHHHHHHHHHHCCCCTTTTHHHHHHHHHHHHHHSSCCCTTCCTTGGGCCCHHHHHHHHHHHHHH
T ss_pred             ccccCCCCCcccCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCchhhccccccccccccccccccCccccchhchhhhhh
Confidence            4567899999999999999999999999999877765                           5678899999999999


Q ss_pred             hhh
Q psy10849        156 FKS  158 (267)
Q Consensus       156 ~k~  158 (267)
                      +|.
T Consensus       191 ~k~  193 (194)
T 1ic8_A          191 EAF  193 (194)
T ss_dssp             CC-
T ss_pred             hhc
Confidence            874

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

Probab=99.25  E-value=8.2e-12  Score=98.41  Aligned_cols=62  Identities=21%  Similarity=0.588  Sum_probs=55.9

Q ss_pred             CCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCC-CCceEeeCCeecchhhHHHHHhh
Q psy10849         20 VKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQK-GEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~-g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ++|.+|+++|.+. .++.|+++.||++||+|..|+.+|.. |..|+.+++++||+.||.++|+.
T Consensus         3 ~~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~   65 (131)
T 2xjy_A            3 LTCGGCQQNIGDR-YFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQ   65 (131)
T ss_dssp             CBBTTTCCBCCSS-EEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCC
T ss_pred             ccCcCCCCEeCCc-EEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCC
Confidence            5899999999965 46789999999999999999999963 57899999999999999999985

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

Probab=99.22  E-value=1e-11  Score=103.52  Aligned_cols=75  Identities=23%  Similarity=0.452  Sum_probs=63.4

Q ss_pred             CCcccCccccc---cccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849          5 NSHVSCHPRGF---RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus         5 dg~~yC~~cy~---~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      ++..||...+.   ....++|.+|+++|.+. .++.+.++.||++||+|..|+.+|. +..| .+++++||+.||.++|+
T Consensus        43 ~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~L~-~~~f-~~~g~~yC~~~y~~~f~  119 (182)
T 2jtn_A           43 DDEGGSGGHMGSGGTPEIPMCAGCDQHILDR-FILKALDRHWHSKCLKCSDCHVPLA-ERCF-SRGESVYCKDDFFKRFG  119 (182)
T ss_dssp             SSSCSSSSSCCCCCCCSCCBCBTSSSBCCCS-EEEEETTEEECSSTTSCTTTCCCCS-SCCE-EETTEEECHHHHHHTTS
T ss_pred             ccccccccccccCCCCCCCcCccCCCCccCc-eeEEecCCeEccccCccCCCCCccC-CCce-eECCEeeecCccccccc
Confidence            56678988775   44456999999999975 4678999999999999999999996 4445 68999999999999987


Q ss_pred             h
Q psy10849         82 L   82 (267)
Q Consensus        82 ~   82 (267)
                      .
T Consensus       120 ~  120 (182)
T 2jtn_A          120 T  120 (182)
T ss_dssp             C
T ss_pred             c
Confidence            5

>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=99.19  E-value=8.9e-12  Score=104.48  Aligned_cols=65  Identities=26%  Similarity=0.590  Sum_probs=57.7

Q ss_pred             ccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCC-CCceEeeCCeecchhhHHHHHhh
Q psy10849         17 LYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQK-GEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        17 ~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~-g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      ++.++|.+|+++|.+. .++.|+++.||++||+|..|+.+|.. |..|+.+++++||+.||.++|+.
T Consensus         3 l~~~~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~   68 (188)
T 1rut_X            3 LSWKRCAGCGGKIADR-FLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGN   68 (188)
T ss_dssp             -CCCBBTTTCCBCCCS-EEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSC
T ss_pred             CCCCcCccCCCEeCCc-eeEEecCcEecccCcccCCCCcccccCCceEEEeCCcccccccccccccc
Confidence            4567999999999965 46789999999999999999999964 57899999999999999999985

>2h8r_A Hepatocyte nuclear factor 1-beta; trasncription factor, POU, homeo, protein-DNA, human disease; 3.20A {Homo sapiens}

Probab=99.14  E-value=7.7e-12  Score=106.50  Aligned_cols=55  Identities=11%  Similarity=0.141  Sum_probs=45.6

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh---------------------------cCCCceeeecchhhh
Q psy10849        102 DGRRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM---------------------------NSKRAKNILTPNQRR  154 (267)
Q Consensus       102 ~~~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~---------------------------l~~~~v~vWFQNrRa  154 (267)
                      ...++.||.||.|+..|+.+|++.|+.++||+...|++                           |++.+|+|||||||+
T Consensus       137 ~~~~k~RR~R~~ft~~ql~~Le~~F~~~~YP~~~~ReeLA~~~n~~~~~~rg~~~~~~~~L~~~~lte~~V~~WFqNRR~  216 (221)
T 2h8r_A          137 PTNKKMRRNRFKWGPASQQILYQAYDRQKNPSKEEREALVEECNRAECLQRGVSPSKAHGLGSNLVTEVRVYNWFANRRK  216 (221)
T ss_dssp             -----CCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHHHHTTCCSTTGGGGTTSCCCHHHHHHHHHHHHT
T ss_pred             cccCCCCCCCcCCCHHHHHHHHHHHHcCCCCCHHHHHHHHHHHChhhhcccccccchhccccccccCHHHHHHHhHHhhh
Confidence            34677899999999999999999999999999888876                           256789999999998


Q ss_pred             hh
Q psy10849        155 QF  156 (267)
Q Consensus       155 k~  156 (267)
                      +.
T Consensus       217 ~~  218 (221)
T 2h8r_A          217 EE  218 (221)
T ss_dssp             TC
T ss_pred             hh
Confidence            74

>2da7_A Zinc finger homeobox protein 1B; homeobox domain, three helices with the DNA binding helix- turn-helix motif, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.14  E-value=5e-12  Score=88.10  Aligned_cols=40  Identities=5%  Similarity=-0.006  Sum_probs=37.3

Q ss_pred             HHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhh
Q psy10849        116 SAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQ  155 (267)
Q Consensus       116 ~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak  155 (267)
                      .+|+..||++|+.+++|+..++++      |++++|||||||||++
T Consensus        14 k~ql~~Lk~yF~~n~~Ps~eei~~LA~~lgL~~~VVrVWFqNrRa~   59 (71)
T 2da7_A           14 KDHMSVLKAYYAMNMEPNSDELLKISIAVGLPQEFVKEWFEQRKVY   59 (71)
T ss_dssp             THHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHHHHHHhhcccc
Confidence            578999999999999999988887      9999999999999984

>2nzz_A Penetratin conjugated GAS (374-394) peptide; conformational analysis, G protein, GAS subunit, A2A adenosine receptor, cell-penetrating peptides; NMR {Synthetic} PDB: 2o00_A

Probab=99.13  E-value=1e-11  Score=76.06  Aligned_cols=22  Identities=23%  Similarity=0.238  Sum_probs=19.3

Q ss_pred             Cceeeecchhhhhhhhhhhhcc
Q psy10849        143 RAKNILTPNQRRQFKSSFEISS  164 (267)
Q Consensus       143 ~~v~vWFQNrRak~k~~~~~~~  164 (267)
                      +||+||||||||||||......
T Consensus         1 rQVkIWFQNRRaK~Kk~~~~~~   22 (37)
T 2nzz_A            1 RQIKIWFQNRRMKWKKRVFNDA   22 (37)
T ss_dssp             CCTTTTTTCSHHHHTSSHHHHT
T ss_pred             CCceeccHHHHHHHHHHhHHHH
Confidence            6899999999999999877643

>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=99.08  E-value=7.8e-11  Score=97.04  Aligned_cols=61  Identities=28%  Similarity=0.642  Sum_probs=53.1

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      .++|.+|+++|.+. .++.++++.||++||+|..|+.+|. +..| .++|++||+.||.++|+.
T Consensus         6 ~~~C~~C~~~I~~~-~~~~a~~~~wH~~CF~C~~C~~~L~-~~~f-~~~g~~yC~~~y~~~f~~   66 (169)
T 2rgt_A            6 IPMCAGCDQHILDR-FILKALDRHWHSKCLKCSDCHVPLA-ERCF-SRGESVYCKDDFFKRFGT   66 (169)
T ss_dssp             -CBBSSSSSBCCSS-SCEECSSCEECTTTSBCTTTCCBCC-SCCE-ESSSCEECHHHHHHHHSC
T ss_pred             CCccccCCCccCCc-EEEEECCcEEccccCccCCCCCcCC-CCCc-ccCCeeeecccccccccc
Confidence            46899999999975 4678999999999999999999996 3444 789999999999999976

>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=99.08  E-value=8.6e-11  Score=98.73  Aligned_cols=62  Identities=21%  Similarity=0.632  Sum_probs=55.1

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      .++|.+|+++|..++. +.+.++.||++||+|..|+.+|. +..|+.+++++||+.||.++|+.
T Consensus         7 ~~~C~~C~~~I~~~~~-v~a~g~~wH~~CF~C~~C~~~L~-~~~~~~~~g~~yC~~cy~~~f~~   68 (192)
T 1b8t_A            7 GKKCGVCQKAVYFAEE-VQCEGSSFHKSCFLCMVCKKNLD-STTVAVHGDEIYCKSCYGKKYGP   68 (192)
T ss_dssp             CEECTTTCCEECSSCC-EEETTEEECTTTCBCTTTCCBCC-SSSEEEETTEEEEHHHHHHHHSC
T ss_pred             CCcCccCCCeecceeE-EEeCCceecCCCCcCcccCCcCC-CCeeEecCCEeeChhhhHhhcCc
Confidence            3589999999987664 56999999999999999999996 45799999999999999999974

>1mh3_A Maltose binding-A1 homeodomain protein chimera; MATA1, binding cooperativity, maltose binding protein, MBP, sugar binding, DNA binding protein; 2.10A {Escherichia coli} SCOP: a.4.1.1 c.94.1.1 PDB: 1mh4_A 1le8_A

Probab=99.00  E-value=2.1e-11  Score=112.76  Aligned_cols=51  Identities=12%  Similarity=0.064  Sum_probs=47.4

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhh
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFK  157 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k  157 (267)
                      .++.|+.|+..|+.+||+.|+.++||+...|++      |+++||||||||||+|+|
T Consensus       365 ~~~~~~~~~~~q~~~Le~~f~~~~yp~~~~~~~la~~~~l~~~qv~~wf~n~r~~~~  421 (421)
T 1mh3_A          365 QTAAAAAISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK  421 (421)
T ss_dssp             HHHHHCSSCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHCCCC
T ss_pred             hhhhhhhhcchHHHHHHHHHhcCCCcCHHHHHHHHHHHCcCHHHhhHhhhhcccccC
Confidence            356688999999999999999999999999888      999999999999999986

>2lk2_A Homeobox protein TGIF1; NESG, structural genomics, northeast structural genomics CON PSI-biology, transcription; NMR {Homo sapiens}

Probab=98.90  E-value=2.1e-10  Score=84.24  Aligned_cols=52  Identities=12%  Similarity=0.071  Sum_probs=46.3

Q ss_pred             CCCCHHHHHHHHHhhhc---CCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        112 TILTSAQRRQFKSSFEV---SPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       112 t~ft~~Ql~~L~~~f~~---~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      ..|+.+++.+|+.-|..   ++||+..++++      |+++||++||||||+|+++.....
T Consensus        10 ~~l~~~~~~iL~~W~~~h~~npYPs~~ek~~LA~~tgLt~~QV~~WF~NrR~R~kk~~~~~   70 (89)
T 2lk2_A           10 HMLPKESVQILRDWLYEHRYNAYPSEQEKALLSQQTHLSTLQVCNWFINARRRLLPDMLRK   70 (89)
T ss_dssp             CCCCHHHHHHHHHHHHHTSGGGSCCHHHHHHHHHHSSSCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             ccCCHHHHHHHHHHHHHhccCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHhhhHHHHh
Confidence            47899999999999977   89999998887      999999999999999999876544

>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=98.74  E-value=8.9e-10  Score=85.91  Aligned_cols=64  Identities=17%  Similarity=0.171  Sum_probs=52.4

Q ss_pred             cccCCcccCccccccccCC--CCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHH
Q psy10849          2 TSHNSHVSCHPRGFRLYGV--KCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKE   79 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~--~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~   79 (267)
                      |.+||++||+.||.++|++  +|.+|+++|.+++ + .+.++             ..| .|+.|+++++++||..||.+.
T Consensus        50 ~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~~-~-~~~g~-------------~~l-~g~~f~~~~~~~yC~~~~~~~  113 (122)
T 1m3v_A           50 YTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGGD-V-MVVGE-------------PTL-MGGEFGDEDERLITRLENTQF  113 (122)
T ss_dssp             EEETTEEECHHHHHHHHCCCCSSSCSSCCSCCEE-S-SSSSS-------------SSC-CSCTTCCTTCCCCEECTTTTT
T ss_pred             EEECCeeecHHHHHHHcCCCCccccCCCCcCchh-e-EEcCC-------------cCC-CCCccEecCCEeEccCcchhc
Confidence            6799999999999999999  9999999998753 2 23332             234 589999999999999999876


Q ss_pred             Hh
Q psy10849         80 MY   81 (267)
Q Consensus        80 f~   81 (267)
                      +.
T Consensus       114 ~~  115 (122)
T 1m3v_A          114 DA  115 (122)
T ss_dssp             TC
T ss_pred             hh
Confidence            53

>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=98.42  E-value=2.7e-08  Score=76.50  Aligned_cols=60  Identities=18%  Similarity=0.111  Sum_probs=47.9

Q ss_pred             cccCCcccCccccccccCCCCCCCCCcccCCCcEEEecCceeecCCcccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCFVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      |.+||++||+.||.++|+++|..|..    + .+|               .|+..+..|+.|+++++++||..||.++.+
T Consensus        48 ~~~~g~~yC~~~y~~~f~~~c~~c~~----~-~~~---------------~~~~~~~~g~~f~~~~~~~~C~~~~~~~~~  107 (114)
T 1j2o_A           48 YYKLGRKLCRRDYLRLGGSGGHMGSG----G-DVM---------------VVGEPTLMGGEFGDEDERLITRLENTQFDA  107 (114)
T ss_dssp             CCBTTBCCCHHHHHHHHTSCCSSCBS----C-SCC---------------CSSCSSTTSSBCCCSSSCCCEEEECTTCCC
T ss_pred             EEECCeeechHHHHHHhCcccCcCCC----C-cee---------------EcCCccCCCCeeEEcCCEeecchhhhcccc
Confidence            68999999999999999999998862    1 132               144665568999999999999999877543

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

Probab=97.55  E-value=1.8e-05  Score=46.36  Aligned_cols=29  Identities=38%  Similarity=0.846  Sum_probs=25.5

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      ..+|..|++.|...|.++ +.++.||..||
T Consensus         3 ~~~C~~C~k~Vy~~Ek~~-~~g~~~Hk~CF   31 (31)
T 1zfo_A            3 NPNCARCGKIVYPTEKVN-CLDKFWHKACF   31 (31)
T ss_dssp             CCBCSSSCSBCCGGGCCC-SSSSCCCGGGC
T ss_pred             CCcCCccCCEEecceeEE-ECCeEecccCC
Confidence            358999999999887665 89999999998

>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=96.64  E-value=0.00039  Score=48.75  Aligned_cols=29  Identities=21%  Similarity=0.292  Sum_probs=25.8

Q ss_pred             cccCCcccCc-cccccccCCCCCCCCCccc
Q psy10849          2 TSHNSHVSCH-PRGFRLYGVKCARCGDRLL   30 (267)
Q Consensus         2 ~~~dg~~yC~-~cy~~~f~~~C~~C~~~I~   30 (267)
                      +.+||++||+ .||.++|+++|.+|++.+.
T Consensus        43 ~~~~g~~yC~~~cy~~~f~~~C~~C~~~~~   72 (76)
T 1iml_A           43 AEHEGKPYCNHPCYSAMFGPKGFGRGGAES   72 (76)
T ss_dssp             EEETTEEEETTTHHHHHSSCCCSSCCCSSS
T ss_pred             ECcCCeEeeCHHHHHHHhCccCCCcCCcee
Confidence            5689999999 6999999999999997664

>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=96.41  E-value=0.00044  Score=49.12  Aligned_cols=28  Identities=25%  Similarity=0.324  Sum_probs=16.8

Q ss_pred             cccCCcccCccccccccCCCCCCCCCcc
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCARCGDRL   29 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~I   29 (267)
                      +.+||++||+.||.++|+++|.+|++..
T Consensus        50 ~~~~~~~yC~~cy~~~f~~~c~gcg~g~   77 (81)
T 1a7i_A           50 AIHDAEVYCKSCYGKKYGPKGYGYGQGA   77 (81)
T ss_dssp             EEETTEEECSHHHHHHCC----------
T ss_pred             EeeCCEEECHHHHHHHhCCcccccCCcc
Confidence            5689999999999999999999999764

>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=96.05  E-value=0.0017  Score=45.44  Aligned_cols=25  Identities=12%  Similarity=0.173  Sum_probs=22.7

Q ss_pred             cccCCcccCccccccccCCCCCCCC
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCARCG   26 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~C~   26 (267)
                      +.+||++||+.||.++|+++|..+.
T Consensus        51 ~~~~g~~yC~~cy~~~f~~~C~~~s   75 (76)
T 1x68_A           51 LTQNKEIFCQKCGSGMDTDISGPSS   75 (76)
T ss_dssp             EEETTEEEETTTTCCCCCCSSSSSC
T ss_pred             EeECCEEECHHHhhhhhCCcCCCCC
Confidence            4689999999999999999998875

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

Probab=95.11  E-value=0.0033  Score=42.97  Aligned_cols=23  Identities=9%  Similarity=-0.021  Sum_probs=20.6

Q ss_pred             cccCCcccCccccccccCCCCCC
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCAR   24 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~   24 (267)
                      +.+||++||+.||.++|+++|.+
T Consensus        47 ~~~~~~~yC~~cy~~~f~~~C~g   69 (69)
T 2cur_A           47 TAVEDQYYCVDCYKNFVSGPSSG   69 (69)
T ss_dssp             EECSSCEEEHHHHHHHHTCSCCC
T ss_pred             EeECCEEECHHHhHHHhcCCCCC
Confidence            46899999999999999999964

>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=95.07  E-value=0.0043  Score=42.46  Aligned_cols=23  Identities=17%  Similarity=0.193  Sum_probs=20.6

Q ss_pred             cccCCcccCccccccccCCCCCC
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCAR   24 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~   24 (267)
                      +.+||++||+.||.++|+++|..
T Consensus        47 ~~~~~~~yC~~cy~~~f~~~c~~   69 (70)
T 2d8z_A           47 TARDDFAYCLNCFCDLYASGPSS   69 (70)
T ss_dssp             EESSSSEECHHHHHHHTCCCCTT
T ss_pred             EeeCCeEECHHHHHHHhccccCC
Confidence            46899999999999999999964

>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=95.01  E-value=0.0037  Score=42.98  Aligned_cols=23  Identities=9%  Similarity=0.057  Sum_probs=20.6

Q ss_pred             cccCCcccCccccccccCCCCCC
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCAR   24 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~   24 (267)
                      +.+||++||+.||.++|+++|+.
T Consensus        49 ~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1wyh_A           49 VPDKGAHYCVPCYENKFASGPSS   71 (72)
T ss_dssp             EEETTEEEEHHHHHHHTSCCCCC
T ss_pred             CCcCCeEECHHHHHHHccCcCCC
Confidence            46899999999999999999964

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

Probab=94.91  E-value=0.0041  Score=42.73  Aligned_cols=23  Identities=9%  Similarity=0.028  Sum_probs=20.6

Q ss_pred             cccCCcccCccccccccCCCCCC
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCAR   24 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~   24 (267)
                      +.+||++||+.||.++|+++|..
T Consensus        49 ~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1x4k_A           49 IPKDNQNFCVPCYEKQHASGPSS   71 (72)
T ss_dssp             EEETTEEEEHHHHHHHTSSCCCC
T ss_pred             CccCCeEECHHHHhHHhCCCCCC
Confidence            46899999999999999999964

>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=94.51  E-value=0.011  Score=42.78  Aligned_cols=22  Identities=23%  Similarity=0.391  Sum_probs=20.6

Q ss_pred             cccCCcccCccccccccCCCCC
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCA   23 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~   23 (267)
                      |.+||++||+.||.++|+++|.
T Consensus        58 ~~~~g~~yC~~~y~~~f~~kc~   79 (91)
T 2d8y_A           58 ASLHGRIYCKPHFNQLFKSKGN   79 (91)
T ss_dssp             CCSSSCCCCHHHHHHHSCCCSC
T ss_pred             EeECCEEECHHHHHHHhCCCcC
Confidence            6789999999999999999997

>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=90.74  E-value=0.034  Score=37.97  Aligned_cols=23  Identities=4%  Similarity=-0.048  Sum_probs=19.1

Q ss_pred             cccCCcccCccccccccCCCCCCC
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCARC   25 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~C   25 (267)
                      |.+||++||+.||.++|+ +|..+
T Consensus        49 ~~~~~~~yC~~cy~~~~~-~~~~~   71 (72)
T 1x61_A           49 YAVERRAYCEGCYVATLE-SGPSS   71 (72)
T ss_dssp             EESSSCEEEHHHHHHHHH-TCSSC
T ss_pred             EeeCCeEECHHHHHHHHc-cCCCC
Confidence            578999999999999885 66654

>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=89.89  E-value=0.059  Score=36.58  Aligned_cols=22  Identities=14%  Similarity=0.110  Sum_probs=18.6

Q ss_pred             cccCCcccCccccccccCCCCC
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCA   23 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~   23 (267)
                      +.+||++||+.||.++|++++.
T Consensus        47 ~~~~g~~yC~~c~~~~~~~~~~   68 (70)
T 2d8x_A           47 VKNAGRHLCRPCHNREKASGPS   68 (70)
T ss_dssp             EEETTEEECHHHHHHHHCCCSC
T ss_pred             EeECCeEECHHHhhhhcCCCCC
Confidence            3579999999999999987653

---

Homologous Structure Domains

Structure Domains Detected by RPS-BLAST

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

ID	Length	Definition	E-value
Query	267
d1rutx3	31	g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus	5e-09

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]} Length = 31

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

 Score = 48.6 bits (116), Expect = 5e-09
 Identities = 15/27 (55%), Positives = 19/27 (70%)

Query: 22 CARCGDRLLPHEMVMRAQSHVYHLPCF 48
          C+ CG  +   E+VMRAQ +VYHL CF
Sbjct: 5  CSACGQSIPASELVMRAQGNVYHLKCF 31

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	267
d2craa1	58	Homeobox protein hox-b13 {Human (Homo sapiens) [Ta	99.76
d1zq3p1	67	Homeotic bicoid protein {Fruit fly (Drosophila mel	99.75
d1ig7a_	58	Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10	99.75
d9anta_	56	Antennapedia Homeodomain {Drosophila melanogaster	99.74
d1pufa_	77	Homeobox protein hox-a9 {Mouse (Mus musculus) [Tax	99.74
d1jgga_	57	Even-skipped homeodomain {Fruit fly (Drosophila me	99.73
d2e1oa1	57	Homeobox protein prh {Human (Homo sapiens) [TaxId:	99.73
d1vnda_	77	VND/NK-2 protein {Fruit fly (Drosophila melanogast	99.71
d1uhsa_	72	Homeodomain-only protein, Hop {Mouse (Mus musculus	99.71
d1fjla_	65	Paired protein {Fruit fly (Drosophila melanogaster	99.71
d1p7ia_	53	Engrailed Homeodomain {Drosophila melanogaster [Ta	99.71
d2cuea1	68	Paired box protein pax6 {Human (Homo sapiens) [Tax	99.7
d1b72a_	88	Homeobox protein hox-b1 {Human (Homo sapiens) [Tax	99.7
d1ftta_	68	Thyroid transcription factor 1 homeodomain {Rat (R	99.7
d1yz8p1	60	Pituitary homeobox 2 {Human (Homo sapiens) [TaxId:	99.7
d2cufa1	82	Homeobox-containing protein 1, HMBOX1 (Flj21616) {	99.66
d1bw5a_	66	Insulin gene enhancer protein isl-1 {Rat (Rattus n	99.65
d1ocpa_	67	Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId	99.65
d1au7a1	58	Pit-1 POU homeodomain {Rat (Rattus norvegicus) [Ta	99.63
d1le8a_	53	Mating type protein A1 Homeodomain {Baker's yeast	99.6
d1wi3a_	71	DNA-binding protein SATB2 {Human (Homo sapiens) [T	99.6
d1wh7a_	80	ZF-HD homeobox protein At4g24660 {Thale cress (Ara	99.58
d1e3oc1	57	Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId	99.57
d1s7ea1	50	Hepatocyte nuclear factor 6 {Mouse (Mus musculus)	99.52
d2ecba1	76	Zinc fingers and homeoboxes protein 1, ZHX1 {Human	99.5
d2ecca1	76	Homeobox-leucine zipper protein Homez {Human (Homo	99.48
d1pufb_	73	pbx1 {Human (Homo sapiens) [TaxId: 9606]}	99.44
d1lfba_	78	Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rat	99.44
d1x2ma1	52	Lag1 longevity assurance homolog 6, LASS6 {Mouse (	99.38
d2cqxa1	59	LAG1 longevity assurance homolog 5, LASS5 {Mouse (	99.29
d1k61a_	60	mat alpha2 Homeodomain {Baker's yeast (Saccharomyc	99.27
d1x2na1	62	Homeobox protein pknox1 {Human (Homo sapiens) [Tax	99.19
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.08
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.87
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.78
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.47
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.37
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.33
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.26
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.23
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.07
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.06
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.06
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.89
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.79
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	97.73
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.73
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	97.72
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.72
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	97.71
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	97.68
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.67
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.65
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	97.64
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.62
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	97.58
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.56
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.56
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.55
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.55
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.46
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.44
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	97.41
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	97.4
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.38
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.34
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.34
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.32
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.28
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.27
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.25
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.24
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.2
d2co8a2	36	Nedd9 interacting protein with calponin homology,	97.19
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.12
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.1
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	97.07
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.04
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.03
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.86
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	96.77
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	96.75
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	96.66
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.55
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	96.54
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	96.45
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	96.35
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.14
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.11
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	95.83
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.52
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	95.26
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	95.2
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	94.89
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	94.85
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	94.41
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	94.4
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	93.98
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	93.86
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	93.43
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	93.41
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	92.33
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	91.76
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	91.41
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	91.31
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	91.24
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	90.72
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	90.0
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	89.85
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	87.97
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	85.94

>d2craa1 a.4.1.1 (A:7-64) Homeobox protein hox-b13 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b13
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.76  E-value=4.8e-20  Score=124.19  Aligned_cols=51  Identities=18%  Similarity=0.201  Sum_probs=48.7

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKS  158 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~  158 (267)
                      ||.||.||.+|+.+||+.|+.++||+...+++      |++++|+|||||||+|+||
T Consensus         2 rr~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~qV~vWFqNrR~k~kk   58 (58)
T d2craa1           2 RKKRIPYSKGQLRELEREYAANKFITKDKRRKISAATSLSERQITIWFQNRRVKEKK   58 (58)
T ss_dssp             CCSCCCSCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHTTTS
T ss_pred             CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCHHHeeecccchhhhccC
Confidence            67899999999999999999999999999888      9999999999999999986

>d1zq3p1 a.4.1.1 (P:2-68) Homeotic bicoid protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeotic bicoid protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.75  E-value=9.5e-20  Score=126.44  Aligned_cols=57  Identities=23%  Similarity=0.209  Sum_probs=52.3

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      +||.||+||.+|+.+||+.|+.++||+...+++      |++++|+|||||||+|+|+.....
T Consensus         1 Prr~Rt~ft~~Ql~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFqNrR~k~kk~~~~~   63 (67)
T d1zq3p1           1 PRRTRTTFTSSQIAELEQHFLQGRYLTAPRLADLSAKLALGTAQVKIWFKNRRRRHKIQSDQH   63 (67)
T ss_dssp             CSCCSCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHHHHTT
T ss_pred             CCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeccccHHHhHhhhhhhc
Confidence            478899999999999999999999999998888      999999999999999999966443

>d1ig7a_ a.4.1.1 (A:) Msx-1 homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Msx-1 homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.75  E-value=9.7e-20  Score=122.96  Aligned_cols=52  Identities=21%  Similarity=0.202  Sum_probs=49.3

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      ||.||.||.+|+.+||+.|+.++||+...+++      |++++|+|||||||+|+||+
T Consensus         1 rr~Rt~ft~~Ql~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   58 (58)
T d1ig7a_           1 RKPRTPFTTAQLLALERKFRQKQYLSIAERAEFSSSLSLTETQVKIWFQNRRAKAKRL   58 (58)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhheeecCcchHhHhccC
Confidence            57899999999999999999999999999888      99999999999999999984

>d9anta_ a.4.1.1 (A:) Antennapedia Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Antennapedia Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.74  E-value=1e-19  Score=121.52  Aligned_cols=49  Identities=20%  Similarity=0.244  Sum_probs=47.1

Q ss_pred             CCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        111 RTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       111 Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      ||.||.+|+.+||+.|+.++||+...|++      |++++|+|||||||+|+||.
T Consensus         1 Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~l~l~~~~V~iWFQNrRak~kk~   55 (56)
T d9anta_           1 RQTYTRYQTLELEKEFHFNRYLTRRRRIEIAHALSLTERQIKIWFQNRRMKWKKE   55 (56)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHC
T ss_pred             CCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCChhHeeeccccchhhhhhc
Confidence            79999999999999999999999998888      99999999999999999985

>d1pufa_ a.4.1.1 (A:) Homeobox protein hox-a9 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-a9
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.74  E-value=2.1e-19  Score=127.90  Aligned_cols=59  Identities=19%  Similarity=0.155  Sum_probs=53.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        105 RGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       105 ~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      +..||.||.||.+|+.+||..|+.++||+...|++      |++++|+|||||||+|+|+..+..
T Consensus        11 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~l~~~qV~iWFqNrR~k~kr~~~~~   75 (77)
T d1pufa_          11 RSTRKKRCPYTKHQTLELEKEFLFNMYLTRDRRYEVARLLNLTERQVKIWFQNRRMKMKKINKDR   75 (77)
T ss_dssp             CTTSCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CcCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHhhhhhhhhHHHHHHHHHHh
Confidence            34578899999999999999999999999999888      999999999999999999976654

>d1jgga_ a.4.1.1 (A:) Even-skipped homeodomain {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Even-skipped homeodomain
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.73  E-value=1.8e-19  Score=121.14  Aligned_cols=51  Identities=20%  Similarity=0.134  Sum_probs=48.5

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        109 RPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       109 r~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      |.||.||.+|+.+||+.|+.++||+...+++      |++++|+|||||||+|+||+
T Consensus         1 R~Rt~fT~~Ql~~Le~~F~~~~yp~~~~r~~LA~~lgl~~~qV~vWFqNrR~k~kk~   57 (57)
T d1jgga_           1 RYRTAFTRDQLGRLEKEFYKENYVSRPRRCELAAQLNLPESTIKVWFQNRRMKDKRQ   57 (57)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHC
T ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhHhhhcchhhhhhhhcC
Confidence            6799999999999999999999999998888      99999999999999999973

>d2e1oa1 a.4.1.1 (A:8-64) Homeobox protein prh {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein prh
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.73  E-value=2.9e-19  Score=120.10  Aligned_cols=51  Identities=16%  Similarity=0.178  Sum_probs=48.5

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKS  158 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~  158 (267)
                      |+.||.||..|+.+||+.|+.++||+...+++      |++++|+|||||||+|+||
T Consensus         1 k~~R~~ft~~Q~~~Le~~F~~n~yp~~~~r~~LA~~l~L~~~qV~~WFqNrR~k~kk   57 (57)
T d2e1oa1           1 KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRR   57 (57)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHH
T ss_pred             CCCCccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhCCCHHHhhHhhhhhhhhccC
Confidence            57899999999999999999999999998888      9999999999999999986

>d1vnda_ a.4.1.1 (A:) VND/NK-2 protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: VND/NK-2 protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.71  E-value=3.7e-19  Score=126.70  Aligned_cols=59  Identities=15%  Similarity=0.129  Sum_probs=53.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      ..+.+|.||.||.+|+.+||+.|+.++||+...+++      |++++|+|||||||+|+|+....
T Consensus         6 p~k~rr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~   70 (77)
T d1vnda_           6 PNKKRKRRVLFTKAQTYELERRFRQQRYLSAPEREHLASLIRLTPTQVKIWFQNHRYKTKRAQNE   70 (77)
T ss_dssp             SSSSCSSCCCCCTTHHHHHHHHHHHCSCCCHHHHHHHHHHHTCCHHHHHHHHHHSSSSCSSSCCC
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChhhhhhcchhHHHHHHHHhhc
Confidence            355678999999999999999999999999998888      99999999999999999986543

>d1uhsa_ a.4.1.1 (A:) Homeodomain-only protein, Hop {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeodomain-only protein, Hop
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.71  E-value=9.6e-19  Score=122.71  Aligned_cols=53  Identities=9%  Similarity=0.105  Sum_probs=49.4

Q ss_pred             CCCCCCCCHHHHHHHHHhhhc-CCCCChhhhhh------cCCCceeeecchhhhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEV-SPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSF  160 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~-~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~  160 (267)
                      ++.|+.||.+||.+||.+|++ ++||+...+++      |++++|+|||||||||+||..
T Consensus         2 ~~~r~~fT~~Ql~~Le~~F~~~n~yP~~~~r~~LA~~lgL~~~~VqvWFqNrRak~rk~~   61 (72)
T d1uhsa_           2 SEGAATMTEDQVEILEYNFNKVNKHPDPTTLCLIAAEAGLTEEQTQKWFKQRLAEWRRSE   61 (72)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHSSCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHccccCCHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHhcc
Confidence            678999999999999999986 78999999888      999999999999999999864

>d1fjla_ a.4.1.1 (A:) Paired protein {Fruit fly (Drosophila melanogaster) [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired protein
species: Fruit fly (Drosophila melanogaster) [TaxId: 7227]

Probab=99.71  E-value=8.5e-19  Score=120.90  Aligned_cols=56  Identities=16%  Similarity=0.258  Sum_probs=52.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        106 GPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       106 ~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      |.||.||.||.+|+.+||+.|+.++||+...+++      |++++|+|||||||+|+|+...
T Consensus         1 k~rr~Rt~ft~~Q~~~Le~~F~~n~yPs~~~r~~LA~~lgl~~~~V~~WFqNrR~k~kk~~~   62 (65)
T d1fjla_           1 KQRRSRTTFSASQLDELERAFERTQYPDIYTREELAQRTNLTEARIQVWFQNRRARLRKQHT   62 (65)
T ss_dssp             CCCCCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHhCCCHHHhhHhhhhHHHHHHhccc
Confidence            4588999999999999999999999999998888      9999999999999999998654

>d1p7ia_ a.4.1.1 (A:) Engrailed Homeodomain {Drosophila melanogaster [TaxId: 7227]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Engrailed Homeodomain
species: Drosophila melanogaster [TaxId: 7227]

Probab=99.71  E-value=5.9e-19  Score=116.85  Aligned_cols=47  Identities=23%  Similarity=0.279  Sum_probs=45.1

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhh
Q psy10849        109 RPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQ  155 (267)
Q Consensus       109 r~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak  155 (267)
                      |.||.||.+|+.+||+.|+.++||+...|++      |++++|+|||||||||
T Consensus         1 R~Rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~LA~~lgL~~~qV~vWFqNrRaK   53 (53)
T d1p7ia_           1 RPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNARAK   53 (53)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHC
T ss_pred             CCCccCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCChHHhhhcccccCCC
Confidence            5799999999999999999999999999888      9999999999999997

>d2cuea1 a.4.1.1 (A:7-74) Paired box protein pax6 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Paired box protein pax6
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=9.5e-19  Score=121.68  Aligned_cols=55  Identities=18%  Similarity=0.228  Sum_probs=51.4

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      ||.||+||.+|+.+||+.|+.++||+..++++      |++++|+|||||||+|+|+..+.
T Consensus         2 rR~Rt~ft~~Ql~~Le~~F~~n~yP~~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kr~~~~   62 (68)
T d2cuea1           2 QRNRTSFTQEQIEALEKEFERTHYPDVFARERLAAKIDLPEARIQVWFSNRRAKWRREEKL   62 (68)
T ss_dssp             CCCCCCSCHHHHHHHHHHHTTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCcCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHhCcChhheeecCcchhHHHHhhhhh
Confidence            67899999999999999999999999999988      99999999999999999986543

>d1b72a_ a.4.1.1 (A:) Homeobox protein hox-b1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein hox-b1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=7.8e-19  Score=128.03  Aligned_cols=58  Identities=19%  Similarity=0.151  Sum_probs=49.5

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhh
Q psy10849        104 RRGPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFE  161 (267)
Q Consensus       104 ~~~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~  161 (267)
                      ..+++|.||.||.+|+.+||+.|+.++||+...+++      |++++|+|||||||+|+||..+
T Consensus        24 ~~~~kr~Rt~ft~~Ql~~Le~~F~~n~yPs~~~r~~LA~~l~l~~~~V~vWFqNrR~k~Kk~~~   87 (88)
T d1b72a_          24 LGSPSGLRTNFTTRQLTELEKEFHFNKYLSRARRVEIAATLELNETQVKIWFQNRRMKQKKRER   87 (88)
T ss_dssp             ------CCCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHHHHHT
T ss_pred             CCCCCCCCcCCCHHHHHHHHHHHHhCCCCchHHHHHHHHHcCCCHHHeeeccHhHHHHHHHhcc
Confidence            345688999999999999999999999999999888      9999999999999999999654

>d1ftta_ a.4.1.1 (A:) Thyroid transcription factor 1 homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Thyroid transcription factor 1 homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.70  E-value=1.1e-18  Score=121.30  Aligned_cols=57  Identities=14%  Similarity=0.147  Sum_probs=52.2

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhhc
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEIS  163 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~~  163 (267)
                      .||.||.||..|+.+||+.|+.++||+...+++      |++++|+|||||||+|+|+..+..
T Consensus         2 krr~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~l~L~~~~V~~WFqNrR~k~kk~~~~~   64 (68)
T d1ftta_           2 RRKRRVLFSQAQVYELERRFKQQKYLSAPEREHLASMIHLTPTQVKIWFQNHRYKMKRQAKDK   64 (68)
T ss_dssp             CSSSCSSCCHHHHHHHHHHHHHSSSCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHTTSCC
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCccceeeecccHHHHHhhcccch
Confidence            367999999999999999999999999998888      999999999999999999865443

>d1yz8p1 a.4.1.1 (P:1-60) Pituitary homeobox 2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pituitary homeobox 2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.70  E-value=1e-18  Score=118.71  Aligned_cols=53  Identities=21%  Similarity=0.303  Sum_probs=49.9

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      +||.||.||.+|+.+||+.|..++||+...+++      |++++|+|||||||+|+|+.
T Consensus         1 Qrr~Rt~ft~~Q~~~Le~~F~~~~yP~~~~r~~LA~~l~l~~~~V~~WFqNrR~k~kr~   59 (60)
T d1yz8p1           1 QRRQRTHFTSQQLQQLEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR   59 (60)
T ss_dssp             SSCSCCCCCHHHHHHHHHHHTTCSSCCTTTTTHHHHHTTSCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHcCCCChHHHHHHHHHHCCChHHHHHHhHHHHHHHHhc
Confidence            478899999999999999999999999988887      99999999999999999985

>d2cufa1 a.4.1.1 (A:8-89) Homeobox-containing protein 1, HMBOX1 (Flj21616) {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-containing protein 1, HMBOX1 (Flj21616)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.66  E-value=8.4e-18  Score=121.13  Aligned_cols=57  Identities=14%  Similarity=0.095  Sum_probs=50.9

Q ss_pred             CCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh---------------------cCCCceeeecchhhhhhhhhhhhcc
Q psy10849        108 KRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM---------------------NSKRAKNILTPNQRRQFKSSFEISS  164 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~---------------------l~~~~v~vWFQNrRak~k~~~~~~~  164 (267)
                      ||.||.||.+||.+||+.|+.++||+...|++                     |++.+|+|||||||+|+|+......
T Consensus         1 Rr~R~~ft~~Ql~~LE~~F~~n~yP~~~~R~~LA~~~~~~~~~~~~~~~~~~~l~~~~V~vWFqNRR~k~kk~~~~a~   78 (82)
T d2cufa1           1 RGSRFTWRKECLAVMESYFNENQYPDEAKREEIANACNAVIQKPGKKLSDLERVTSLKVYNWFANRRKEIKRRANIAA   78 (82)
T ss_dssp             CCCSCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHHHHHCCTTCCCCTTTCCCHHHHHHHHHHHHHHHHHHHHCCC
T ss_pred             CcCCCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccccccccchhccCCCHHHHHHHHhhhHHHHHHhhhHHH
Confidence            57899999999999999999999999888766                     5778999999999999999765543

>d1bw5a_ a.4.1.1 (A:) Insulin gene enhancer protein isl-1 {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Insulin gene enhancer protein isl-1
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.65  E-value=6.9e-18  Score=116.57  Aligned_cols=55  Identities=22%  Similarity=0.301  Sum_probs=51.5

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhh
Q psy10849        106 GPKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSF  160 (267)
Q Consensus       106 ~~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~  160 (267)
                      +.+|.||.||.+|+.+||..|+.++||+...+++      |++++|+|||||||+|.|+..
T Consensus         2 k~kR~Rt~~t~~Q~~~Le~~F~~n~~Ps~~~~~~LA~~l~l~~~~V~~WFqNrR~k~kk~~   62 (66)
T d1bw5a_           2 KTTRVRTVLNEKQLHTLRTCYAANPRPDALMKEQLVEMTGLSPRVIRVWFQNKRCKDKKRS   62 (66)
T ss_dssp             CCSCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHCSSCC
T ss_pred             CCCCCCcCcCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCcCHHHhhhhhHhHHHHHHHHH
Confidence            4689999999999999999999999999998887      999999999999999998854

>d1ocpa_ a.4.1.1 (A:) Oct-3 POU Homeodomain {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-3 POU Homeodomain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.65  E-value=6.9e-18  Score=116.82  Aligned_cols=53  Identities=28%  Similarity=0.298  Sum_probs=49.9

Q ss_pred             CCCCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        107 PKRPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       107 ~kr~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      .||.||.||.+|+..|++.|+.++||+...+++      |++++|+|||||||+|+||.
T Consensus         8 ~rr~Rt~~t~~q~~~Le~~F~~n~~P~~~~r~~La~~~~l~~~~V~~WFqNrR~k~Kk~   66 (67)
T d1ocpa_           8 RKRKRTSIENRVRWSLETMFLKCPKPSLQQITHIANQLGLEKDVVRVWFCNRRQKGKRS   66 (67)
T ss_dssp             SSSCCSSCCHHHHHHHHHHHSSCSCCCHHHHHHHHHHHTCCHHHHHHHHHHHHSSSSSC
T ss_pred             cCCCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHHcCCHHHHHHHhHHHHHHHhcC
Confidence            467899999999999999999999999998888      99999999999999999984

>d1au7a1 a.4.1.1 (A:103-160) Pit-1 POU homeodomain {Rat (Rattus norvegicus) [TaxId: 10116]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Pit-1 POU homeodomain
species: Rat (Rattus norvegicus) [TaxId: 10116]

Probab=99.63  E-value=1.7e-17  Score=111.67  Aligned_cols=51  Identities=20%  Similarity=0.240  Sum_probs=48.3

Q ss_pred             CCCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        109 RPRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       109 r~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      |.||.|+.+|+.+||..|+.++||+...+++      |++++|+|||||||+|+|+.
T Consensus         1 r~Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kr~   57 (58)
T d1au7a1           1 KRRTTISIAAKDALERHFGEHSKPSSQEIMRMAEELNLEKEVVRVWFCNRRQREKRV   57 (58)
T ss_dssp             CCCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHTTSC
T ss_pred             CCCCCCCHHHHHHHHHHHHHccCCCHHHHHHHHHHhCCCHHHHHHHHHHHhHHHHhc
Confidence            5799999999999999999999999988887      99999999999999999985

>d1le8a_ a.4.1.1 (A:) Mating type protein A1 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Mating type protein A1 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.60  E-value=5.4e-17  Score=107.20  Aligned_cols=47  Identities=13%  Similarity=0.095  Sum_probs=44.8

Q ss_pred             CCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhh
Q psy10849        111 RTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFK  157 (267)
Q Consensus       111 Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k  157 (267)
                      ||.||.+|+.+||+.|+.++||+...+++      |++++|+|||||||+|.|
T Consensus         1 Rt~~s~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgl~~~qV~~WFqNrR~k~K   53 (53)
T d1le8a_           1 KSSISPQARAFLEQVFRRKQSLNSKEKEEVAKKCGITPLQVRVWFINKRMRSK   53 (53)
T ss_dssp             CCCCCHHHHHHHHHHHHHCSCCCHHHHHHHHHHTTSCHHHHHHHHHHHHHTTC
T ss_pred             CCCCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCCCHHHHHHHHHhhhhccC
Confidence            79999999999999999999999998887      999999999999999976

>d1wi3a_ a.4.1.1 (A:) DNA-binding protein SATB2 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: DNA-binding protein SATB2
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.60  E-value=7.8e-17  Score=112.91  Aligned_cols=54  Identities=22%  Similarity=0.149  Sum_probs=49.0

Q ss_pred             CCCCCCCCCCHHHHHHHHHhhh-cCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        106 GPKRPRTILTSAQRRQFKSSFE-VSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       106 ~~kr~Rt~ft~~Ql~~L~~~f~-~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      ..+|.||.||.+|+.+|++.|+ .++||+..++++      |++++|+|||||||+|+|+.
T Consensus         6 ~~~r~R~~~t~~Q~~~Le~~F~~~~~~P~~~~~~~La~~lgl~~~qV~~WFqNrR~k~kk~   66 (71)
T d1wi3a_           6 SGPRSRTKISLEALGILQSFIHDVGLYPDQEAIHTLSAQLDLPKHTIIKFFQNQRYHVKHS   66 (71)
T ss_dssp             CCCCCCCCCCSHHHHHHHHHHHHHCSCCCHHHHHHHHHHSCCCHHHHHHHHHHHHHHCCSS
T ss_pred             CCCCCCccCCHHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCHHHHHHHhHhhHhhhccc
Confidence            3578899999999999999997 589999988877      99999999999999999873

>d1wh7a_ a.4.1.1 (A:) ZF-HD homeobox protein At4g24660 {Thale cress (Arabidopsis thaliana) [TaxId: 3702]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: ZF-HD homeobox protein At4g24660
species: Thale cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=99.58  E-value=1.6e-16  Score=113.79  Aligned_cols=57  Identities=19%  Similarity=0.098  Sum_probs=50.0

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHHHhhhc----CCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849        102 DGRRGPKRPRTILTSAQRRQFKSSFEV----SPKPCRKVSTM------NSKRAKNILTPNQRRQFKS  158 (267)
Q Consensus       102 ~~~~~~kr~Rt~ft~~Ql~~L~~~f~~----~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~  158 (267)
                      ....+.||.||.||.+|+++|+..|++    ++||+...+++      |++++|+|||||+|+++|+
T Consensus        12 ~~~~~~kR~Rt~ft~~Q~~~L~~~fe~~~~~~~~p~~~~~~~la~~~gl~~~~i~vWFqN~R~~~k~   78 (80)
T d1wh7a_          12 SSGGTTKRFRTKFTAEQKEKMLAFAERLGWRIQKHDDVAVEQFCAETGVRRQVLKIWMHNNKNSGPS   78 (80)
T ss_dssp             CCCCCSSCCCCCCCHHHHHHHHHHHHHHTSCCCSSTTHHHHHHHHHSCCCHHHHHHHHHTTSCCSCC
T ss_pred             CCccCCCCccccCCHHHHHHHHHHHHHhcccccCcCHHHHHHHHHHHCCCHHHeeeecccCcCCCCC
Confidence            334556789999999999999988886    89999988887      9999999999999999876

>d1e3oc1 a.4.1.1 (C:104-160) Oct-1 POU Homeodomain {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Oct-1 POU Homeodomain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.57  E-value=1.5e-16  Score=106.56  Aligned_cols=50  Identities=24%  Similarity=0.277  Sum_probs=47.3

Q ss_pred             CCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        110 PRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       110 ~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      .||.|+.+|+..||..|+.++||+...+++      |++++|+|||||||+|+||.
T Consensus         1 kRT~~~~~q~~~Le~~F~~~~~P~~~~~~~LA~~lgL~~~qV~~WFqNrR~k~kk~   56 (57)
T d1e3oc1           1 KRTSIETNIRVALEKSFMENQKPTSEDITLIAEQLNMEKEVIRVWFSNRRQKEKRI   56 (57)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHTSC
T ss_pred             CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHcc
Confidence            489999999999999999999999988887      99999999999999999984

>d1s7ea1 a.4.1.1 (A:103-152) Hepatocyte nuclear factor 6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.52  E-value=6.9e-16  Score=100.63  Aligned_cols=44  Identities=23%  Similarity=0.399  Sum_probs=42.1

Q ss_pred             CCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhh
Q psy10849        110 PRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQR  153 (267)
Q Consensus       110 ~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrR  153 (267)
                      +||.||.+|+.+||+.|+.++||+...+++      |++++|+|||||||
T Consensus         1 PRt~ft~~Q~~~Le~~F~~n~~P~~~~~~~LA~~l~l~~~~V~~WFqNrR   50 (50)
T d1s7ea1           1 PRLVFTDVQRRTLHAIFKENKRPSKELQITISQQLGLELSTVSNFFMNAR   50 (50)
T ss_dssp             CCSCCCHHHHHHHHHHTTSSCSSTHHHHHHHHTTSCSSSHHHHHHHHHCC
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHCcCHHHhhhcCCcCc
Confidence            589999999999999999999999998888      99999999999998

>d2ecba1 a.4.1.1 (A:8-83) Zinc fingers and homeoboxes protein 1, ZHX1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Zinc fingers and homeoboxes protein 1, ZHX1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.50  E-value=2.4e-15  Score=106.52  Aligned_cols=49  Identities=16%  Similarity=0.071  Sum_probs=44.6

Q ss_pred             CCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhhhh
Q psy10849        114 LTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSFEI  162 (267)
Q Consensus       114 ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~~~  162 (267)
                      +|.+|+.+|++.|+.++||+...+++      |++++|+|||||||+|.|+..+.
T Consensus        11 ~T~~Q~~~Le~~F~~~~~P~~~~r~~LA~~l~l~~~~V~~WFqNrR~r~k~~~~~   65 (76)
T d2ecba1          11 KTAEQLRVLQASFLNSSVLTDEELNRLRAQTKLTRREIDAWFTEKKKSKALKEEK   65 (76)
T ss_dssp             CCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHSCCSC
T ss_pred             CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHhCCCHHHHHHhHHHHHHHHHHHhHh
Confidence            48999999999999999999998888      99999999999999998875543

>d2ecca1 a.4.1.1 (A:1-76) Homeobox-leucine zipper protein Homez {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox-leucine zipper protein Homez
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.48  E-value=4.8e-15  Score=105.00  Aligned_cols=51  Identities=16%  Similarity=-0.045  Sum_probs=46.2

Q ss_pred             CCCCCCHHHHHHHHHhhhcCCCCChhhhhh------cCCCceeeecchhhhhhhhhh
Q psy10849        110 PRTILTSAQRRQFKSSFEVSPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSF  160 (267)
Q Consensus       110 ~Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~  160 (267)
                      .++.+|.+|+.+||+.|..++||+..++++      |++++|++||||||+|+|+..
T Consensus         6 ~~~r~T~eQ~~~Le~~F~~n~~Ps~~~~~~La~~~gL~~~qV~~WF~NrR~k~k~~~   62 (76)
T d2ecca1           6 SGKRKTKEQLAILKSFFLQCQWARREDYQKLEQITGLPRPEIIQWFGDTRYALKHGQ   62 (76)
T ss_dssp             CCCCCCHHHHHHHHHHHHHCSSCCHHHHHHHHHHTCCCHHHHHHHHHHHHHHHHHTC
T ss_pred             CCCCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHccCHHHHHHHHHHHHHHHHhch
Confidence            345679999999999999999999988887      999999999999999999854

>d1pufb_ a.4.1.1 (B:) pbx1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: pbx1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.44  E-value=9e-15  Score=102.74  Aligned_cols=53  Identities=15%  Similarity=0.223  Sum_probs=48.3

Q ss_pred             CCCCCCCCHHHHHHHHHhhhc---CCCCChhhhhh------cCCCceeeecchhhhhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEV---SPKPCRKVSTM------NSKRAKNILTPNQRRQFKSSF  160 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~---~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~~  160 (267)
                      ||.|+.||.+|+.+|++.|..   ++||+...+++      |++++|+|||||+|+|+|+..
T Consensus         2 rk~R~~~t~~q~~~Le~~f~~~~~~pYPs~~~k~~La~~~gl~~~qv~~WF~N~R~r~k~~~   63 (73)
T d1pufb_           2 RRKRRNFNKQATEILNEYFYSHLSNPYPSEEAKEELAKKCGITVSQVSNWFGNKRIRYKKNI   63 (73)
T ss_dssp             CCCCCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTSCHHHHHHHHHHHHHHHHHCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhcccc
Confidence            678999999999999999974   78999998887      999999999999999998754

>d1lfba_ a.4.1.1 (A:) Hepatocyte nuclear factor 1a (LFB1/HNF1) {Rat (Rattus rattus) [TaxId: 10117]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Hepatocyte nuclear factor 1a (LFB1/HNF1)
species: Rat (Rattus rattus) [TaxId: 10117]

Probab=99.44  E-value=6.1e-15  Score=104.61  Aligned_cols=50  Identities=12%  Similarity=0.102  Sum_probs=44.7

Q ss_pred             CCCCCHHHHHHHHHhhhcCCCCChhhhhh---------------------------cCCCceeeecchhhhhhhhhh
Q psy10849        111 RTILTSAQRRQFKSSFEVSPKPCRKVSTM---------------------------NSKRAKNILTPNQRRQFKSSF  160 (267)
Q Consensus       111 Rt~ft~~Ql~~L~~~f~~~~~p~~~~r~~---------------------------l~~~~v~vWFQNrRak~k~~~  160 (267)
                      |+.||.+|+.+||+.|+.++||+...|++                           |++.+|++||||||+|.|+..
T Consensus         1 R~~~tp~Ql~~Le~~F~~n~yPs~~~Re~LA~~ln~~~~~~~~~~~~~~~~~~~~~vt~~~V~~WF~NRR~~~kr~~   77 (78)
T d1lfba_           1 RFKWGPASQQILFQAYERQKNPSKEERETLVEECNRAECIQRGVSPSQAQGLGSNLVTEVRVYNWFANRRKEEAFRH   77 (78)
T ss_dssp             CCCCCHHHHHHHHHHHTTCSSCCHHHHHHHHHHHHHHHHTTTTCCTTCTTTTGGGCCCHHHHHHHHHHHHHTTSCCC
T ss_pred             CccCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHhchhhhccccccccccccccccCCCHHHHHHHHHHHHHHHHHhc
Confidence            78999999999999999999999988877                           355679999999999999854

>d1x2ma1 a.4.1.1 (A:8-59) Lag1 longevity assurance homolog 6, LASS6 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Lag1 longevity assurance homolog 6, LASS6
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.38  E-value=1e-14  Score=95.55  Aligned_cols=44  Identities=18%  Similarity=0.117  Sum_probs=40.0

Q ss_pred             CHHHHHHHHHhhhc-CCCCChhhhhh------cCCCceeeecchhhhhhhh
Q psy10849        115 TSAQRRQFKSSFEV-SPKPCRKVSTM------NSKRAKNILTPNQRRQFKS  158 (267)
Q Consensus       115 t~~Ql~~L~~~f~~-~~~p~~~~r~~------l~~~~v~vWFQNrRak~k~  158 (267)
                      |.+|+.+||..|.. ++||+...+++      |++++|+|||||||+|.|+
T Consensus         1 T~~q~~iLE~~F~~~~~~P~~~~~~~LA~~~~ls~~qV~~WFqNrR~k~k~   51 (52)
T d1x2ma1           1 TAQPNAILEKVFTAITKHPDEKRLEGLSKQLDWDVRSIQRWFRQRRNQEKP   51 (52)
T ss_dssp             SSCHHHHHHHHHHTTCSSCCHHHHHHHHHHHCSCHHHHHHHHHHHHHHSCC
T ss_pred             ChhHHHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccCc
Confidence            56799999999987 78999988887      9999999999999999886

>d2cqxa1 a.4.1.1 (A:8-66) LAG1 longevity assurance homolog 5, LASS5 {Mouse (Mus musculus) [TaxId: 10090]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: LAG1 longevity assurance homolog 5, LASS5
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=99.29  E-value=6.6e-14  Score=94.04  Aligned_cols=49  Identities=16%  Similarity=0.074  Sum_probs=43.7

Q ss_pred             CCCCCCCHHHHHHHHHhhhc-CCCCChhhhhh------cCCCceeeecchhhhhhh
Q psy10849        109 RPRTILTSAQRRQFKSSFEV-SPKPCRKVSTM------NSKRAKNILTPNQRRQFK  157 (267)
Q Consensus       109 r~Rt~ft~~Ql~~L~~~f~~-~~~p~~~~r~~------l~~~~v~vWFQNrRak~k  157 (267)
                      +.++.++.+|..+||+.|+. ++||+...+++      |++++|+|||||||+|+|
T Consensus         3 k~~~~~k~~~~~iLE~~F~~~~~yPs~~~~~~LA~~lgls~~qV~~WFqNrR~k~r   58 (59)
T d2cqxa1           3 KDSPVNKVEPNDTLEKVFVSVTKYPDEKRLKGLSKQLDWSVRKIQCWFRHRRNQDK   58 (59)
T ss_dssp             CCCCCSCSCSTTHHHHHHHHTCSSCCHHHHHHHHHHTTCCHHHHHHHHHHHHHHHS
T ss_pred             CCCCCCCccccHHHHHHHHHcCCCcCHHHHHHHHHHHCcCHHHHHHHHHhhhcccC
Confidence            45777888899999999986 68999988887      999999999999999976

>d1k61a_ a.4.1.1 (A:) mat alpha2 Homeodomain {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: mat alpha2 Homeodomain
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=99.27  E-value=3.5e-13  Score=90.82  Aligned_cols=46  Identities=24%  Similarity=0.145  Sum_probs=41.9

Q ss_pred             CCHHHHHHHHHhhhcC---CCCChhhhhh------cCCCceeeecchhhhhhhhh
Q psy10849        114 LTSAQRRQFKSSFEVS---PKPCRKVSTM------NSKRAKNILTPNQRRQFKSS  159 (267)
Q Consensus       114 ft~~Ql~~L~~~f~~~---~~p~~~~r~~------l~~~~v~vWFQNrRak~k~~  159 (267)
                      ||.+|+.+|+..|..+   +||+...+++      |++++|++||||+|+|.|+.
T Consensus         5 ft~~q~~~L~~~f~~~~~~pyPs~~e~~~La~~~gL~~~qV~~WF~N~R~r~K~~   59 (60)
T d1k61a_           5 FTKENVRILESWFAKNIENPYLDTKGLENLMKNTSLSRIQIKNWVSNRRRKEKTI   59 (60)
T ss_dssp             CCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHCC
T ss_pred             CCHHHHHHHHHHHHHcCCCCCcCHHHHHHHHHHHCcCHHHHhHHhHhhccccccC
Confidence            8999999999999765   7999998887      99999999999999998763

>d1x2na1 a.4.1.1 (A:6-67) Homeobox protein pknox1 {Human (Homo sapiens) [TaxId: 9606]}

class: All alpha proteins
fold: DNA/RNA-binding 3-helical bundle
superfamily: Homeodomain-like
family: Homeodomain
domain: Homeobox protein pknox1
species: Human (Homo sapiens) [TaxId: 9606]

Probab=99.19  E-value=1.9e-12  Score=87.71  Aligned_cols=50  Identities=20%  Similarity=0.155  Sum_probs=44.7

Q ss_pred             CCCCCCCCHHHHHHHHHhhhc---CCCCChhhhhh------cCCCceeeecchhhhhhh
Q psy10849        108 KRPRTILTSAQRRQFKSSFEV---SPKPCRKVSTM------NSKRAKNILTPNQRRQFK  157 (267)
Q Consensus       108 kr~Rt~ft~~Ql~~L~~~f~~---~~~p~~~~r~~------l~~~~v~vWFQNrRak~k  157 (267)
                      |+.|+.|+.+|+.+|++.|..   ++||+..++++      |+.++|++||||+|+|..
T Consensus         3 krkR~~~~~~~~~iL~~wf~~~~~nPyPs~~e~~~La~~~~l~~~qI~~WF~N~R~R~l   61 (62)
T d1x2na1           3 KNKRGVLPKHATNVMRSWLFQHIGHPYPTEDEKKQIAAQTNLTLLQVNNWFINARRRIL   61 (62)
T ss_dssp             CCSSCCCCHHHHHHHHHHHHHTTTSCCCCHHHHHHHHHHHTCCHHHHHHHHHHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHHHHHHhccCCCcCHHHHHHHHHHHCcCHHHhHHHHHHHHHHhc
Confidence            566889999999999999984   78999888877      999999999999998864

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

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

Probab=99.08  E-value=2.6e-11  Score=72.11  Aligned_cols=35  Identities=26%  Similarity=0.624  Sum_probs=32.5

Q ss_pred             cccccccCCCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         12 PRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        12 ~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      .||.++|+++|..|+++|.+.  +|.|+++.||++||
T Consensus         1 ~DY~~~fapkC~~C~~~I~g~--~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           1 KDFLAMFSPKCGGCNRPVLEN--YLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCCCCCSCBCTTTCCBCCSS--CEEETTEEECTTTC
T ss_pred             CcHHHHhChhhhhcCCcccch--heeecCCccCcccC
Confidence            489999999999999999864  88899999999998

>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=98.87  E-value=7.2e-10  Score=66.05  Aligned_cols=37  Identities=22%  Similarity=0.404  Sum_probs=35.5

Q ss_pred             cccccccCCCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         12 PRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        12 ~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      .||.+.|+++|..|+++|.++++-|.+.++.||..||
T Consensus         1 kCy~~~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           1 KCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCCSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             CccccccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            4899999999999999999999999999999999998

>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=98.78  E-value=1.5e-09  Score=62.73  Aligned_cols=35  Identities=23%  Similarity=0.499  Sum_probs=32.4

Q ss_pred             cccccccCCCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         12 PRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        12 ~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      +||+++|+++|..|+++|..+  -+...++.||.+||
T Consensus         1 PCyE~kfa~~C~~Ckk~It~G--GvtY~dqpWHkeCF   35 (35)
T d2cuqa2           1 PCYENKFAPRCARCSKTLTQG--GVTYRDQPWHRECL   35 (35)
T ss_dssp             CCCCCCSSCCCTTTCCCCCSC--CEESSSSEECTTTC
T ss_pred             CchHHHHHHHHhhcCCccccC--ceeecCCcchhhhC
Confidence            599999999999999999977  66799999999998

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.47  E-value=3.8e-08  Score=57.02  Aligned_cols=35  Identities=31%  Similarity=0.597  Sum_probs=30.3

Q ss_pred             ccccccccCCCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         11 HPRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        11 ~~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      ++||+.. ..+|..|+++|.  |++++|.++.||+.||
T Consensus         1 E~Cy~~t-lEkC~~C~~~I~--driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           1 EGCYVAT-LEKCATCSQPIL--DRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCCCCSS-CCBCTTTCCBCC--SCCEEETTEEECTTTC
T ss_pred             ChhHHHH-HHHHHHhchHHH--HHHHHHhCCCCCCCCC
Confidence            4688664 469999999999  5699999999999998

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.37  E-value=9.9e-08  Score=57.43  Aligned_cols=34  Identities=32%  Similarity=0.614  Sum_probs=31.2

Q ss_pred             cccccccCCCCCCCCCcccCCCcEEEecCceeecCC
Q psy10849         12 PRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPC   47 (267)
Q Consensus        12 ~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~C   47 (267)
                      .||+++|+.+|..|++.|.+.  ||.|.++.||++|
T Consensus         8 ~DYq~~fG~~C~~C~~~ItG~--V~~Ag~~~yHP~C   41 (41)
T d1v6ga1           8 LDYQRLYGTRCFSCDQFIEGE--VVSALGKTYHPDC   41 (41)
T ss_dssp             SCGGGSCCCBCTTTCCBCCSC--CEEETTEEECTTT
T ss_pred             ccHHHHhCcccccccCEeeee--eeEecCcccCCCC
Confidence            589999999999999999754  8899999999988

>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=98.33  E-value=8e-08  Score=56.57  Aligned_cols=33  Identities=30%  Similarity=0.659  Sum_probs=30.8

Q ss_pred             cccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         48 FVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        48 F~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      |+|..|+++|. +..|++++|++||..||.++|+
T Consensus         1 F~C~~C~~~f~-~~~F~e~~G~pYCe~~Y~~lFA   33 (35)
T d1g47a2           1 FVCAQCFQQFP-EGLFYEFEGRKYCEHDFQMLFA   33 (35)
T ss_dssp             CCCTTTCCCCG-GGCSEEETTEEECHHHHHHHCC
T ss_pred             CCCCCCcCCCC-CCCeEEECCEecChHhHHhhcC
Confidence            78999999997 6789999999999999999986

>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=98.26  E-value=1.9e-07  Score=52.97  Aligned_cols=32  Identities=28%  Similarity=0.590  Sum_probs=29.6

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      +|..|..+|. |++|..+|+++||..||..+||
T Consensus         1 ~C~~C~~~L~-GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQLS-GQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBCT-TSCCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCcccc-CceeeecCCCeehHHhhHhhcC
Confidence            4889999996 8999999999999999999985

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=98.23  E-value=2.8e-07  Score=52.02  Aligned_cols=28  Identities=54%  Similarity=1.137  Sum_probs=27.1

Q ss_pred             CCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         21 KCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        21 ~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      .|.+|++.|.+.|+|++|.+++||..||
T Consensus         4 ~Ca~C~~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3           4 ACSACGQSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             ECTTTCCEECTTSEEEEETTEEECGGGC
T ss_pred             ccccccCcCChhHhheecccceeeeccC
Confidence            6999999999999999999999999998

>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=98.06  E-value=1.1e-06  Score=49.05  Aligned_cols=32  Identities=34%  Similarity=0.671  Sum_probs=29.6

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      +|..|+.+|. |+.|..++..+||..||..+|+
T Consensus         1 vCt~Ck~~La-GqrFTSrde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1           1 VCTGCQTPLA-GQQFTSRDEDPYCVACFGELFA   32 (32)
T ss_dssp             BCSSSCCBCT-TCCEEECSSSEEEHHHHHHHTT
T ss_pred             CccccCcccc-CCccccCCCCccHHHHhHhhcC
Confidence            5899999996 8999999999999999999885

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.06  E-value=1.2e-06  Score=53.61  Aligned_cols=28  Identities=21%  Similarity=0.381  Sum_probs=25.2

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      .++|..|+++|.+.  ++.|+++.||++||
T Consensus        18 ~P~C~~C~~pI~g~--~vtAlgk~WHPEhF   45 (45)
T d2dara2          18 TPMCAHCNQVIRGP--FLVALGKSWHPEEF   45 (45)
T ss_dssp             CCBBSSSCCBCCSC--EEEETTEEECTTTC
T ss_pred             CeeccccCCcccCc--eeeecCCccCcCCC
Confidence            45899999999864  88999999999998

>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=97.89  E-value=4.2e-06  Score=44.64  Aligned_cols=27  Identities=26%  Similarity=0.738  Sum_probs=25.7

Q ss_pred             CCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         22 CARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        22 C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      |..|.+.|.++..-|+..+..||..||
T Consensus         1 C~~C~ktiMPGsrKme~kG~~WHEtCF   27 (27)
T d1x4ka2           1 CQECKKTIMPGTRKMEYKGSSWHETCF   27 (27)
T ss_dssp             BSSSCCCCCSSSCEEEETTEEEETTTT
T ss_pred             CccccccccCCceeecccCCccccccC
Confidence            789999999999999999999999998

>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=97.79  E-value=5.9e-06  Score=43.96  Aligned_cols=27  Identities=26%  Similarity=0.821  Sum_probs=25.6

Q ss_pred             CCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         22 CARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        22 C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      |..|.+.|.++..-++..+..||..||
T Consensus         1 C~~C~ktiMPGsrKmey~G~sWHE~CF   27 (27)
T d1wyha2           1 CSACGETVMPGSRKLEYGGQTWHEHCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEECSTTCCEETTTC
T ss_pred             CccccceecCCcccccccCcccccccC
Confidence            789999999999999999999999998

>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=97.73  E-value=5e-06  Score=46.44  Aligned_cols=30  Identities=17%  Similarity=0.280  Sum_probs=25.9

Q ss_pred             cccCCCCCCCCCcccCCCcEEEecCceeecCC
Q psy10849         16 RLYGVKCARCGDRLLPHEMVMRAQSHVYHLPC   47 (267)
Q Consensus        16 ~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~C   47 (267)
                      +++.++|+.|.++|.+  .++.|+++.||++.
T Consensus         2 kmg~p~C~~C~~PI~~--~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           2 SMGVPICGACRRPIEG--RVVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCCCEETTTTEECCS--CEECCTTSBEETTT
T ss_pred             CcCCcchhhcCCchhh--hHhhhhccccCCCC
Confidence            4567899999999996  49999999999874

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

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

Probab=97.73  E-value=8e-06  Score=45.61  Aligned_cols=28  Identities=25%  Similarity=0.737  Sum_probs=25.1

Q ss_pred             CCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         20 VKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      ..|++|+++|.+. +++++.++.||..|.
T Consensus         3 ~~CaGC~~~I~DR-flL~v~dr~WH~~CL   30 (30)
T d1rutx1           3 KRCAGCGGKIADR-FLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CBBTTTCCBCCCS-EEEEETTEEECGGGC
T ss_pred             cccCCCCCccchh-hhhccchhhhhhhhC
Confidence            4799999999987 789999999999884

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

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

Probab=97.72  E-value=9.8e-06  Score=45.77  Aligned_cols=34  Identities=26%  Similarity=0.658  Sum_probs=31.3

Q ss_pred             cccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         48 FVCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        48 F~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      |+|..|.+++. |...+.+.|..||+.+|.++|+.
T Consensus         1 FvCA~CekPF~-G~rhyE~~g~ayCe~Hy~qLfg~   34 (35)
T d1u5sb2           1 FVCAKCEKPFL-GHRHYERKGLAYCETHYNQLFGD   34 (35)
T ss_dssp             CBCTTTCCBCS-SSCCEEETTEEECHHHHHHHCSC
T ss_pred             CcccccCCccC-CchhhhhcCchHHHHHHHHHhcc
Confidence            78999999996 88999999999999999999874

>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=97.71  E-value=3.9e-06  Score=46.08  Aligned_cols=28  Identities=39%  Similarity=0.901  Sum_probs=25.0

Q ss_pred             CCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         20 VKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      +.|++|++.+.+.|++ ..+++.||+.||
T Consensus         3 ~~CaRC~k~VYp~Ekl-~ClDk~WHK~CF   30 (30)
T d1zfoa_           3 PNCARCGKIVYPTEKV-NCLDKFWHKACF   30 (30)
T ss_dssp             CBCSSSCSBCCGGGCC-CSSSSCCCGGGC
T ss_pred             CcccccCCccccHHHh-hhhHHHHhhccC
Confidence            5799999999998765 589999999998

>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=97.68  E-value=1.3e-05  Score=44.63  Aligned_cols=31  Identities=23%  Similarity=0.639  Sum_probs=27.3

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      +|..|+..|.  .+|.-++|.+||+.||..+|+
T Consensus         1 kC~~C~~vL~--gEYm~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVILT--GEYISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBCS--SCCEEETTEEECTTHHHHHTT
T ss_pred             CccccCcccc--ceeecCCCCcccHHHHHHhcC
Confidence            5889999994  468889999999999999885

>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=97.67  E-value=9.3e-06  Score=44.32  Aligned_cols=30  Identities=23%  Similarity=0.754  Sum_probs=26.8

Q ss_pred             cccccccccCCCCCceEeeCCeecchhhHHH
Q psy10849         48 FVCVICCQPLQKGEQFILRSGQLFCRQDFEK   78 (267)
Q Consensus        48 F~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k   78 (267)
                      |+|..|++.|. .....-++|.+||+.||.+
T Consensus         1 frca~cgk~le-stt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLE-STTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEEC-SSCSEEETTEEECHHHHHH
T ss_pred             CccccccCccc-cceeeccCCcEEEeeeeec
Confidence            78999999995 6788889999999999965

>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=1.7e-05  Score=44.42  Aligned_cols=32  Identities=34%  Similarity=0.697  Sum_probs=28.8

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      .|..|.++|+ ...|..+++..||..||+++|+
T Consensus         1 ~C~~C~qPIG-tksfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           1 ICHRCQQPIG-TKSFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CCSSSCCCCC-SSSEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCccc-ccccccCCCCceEeecchhhcC
Confidence            4889999997 4789999999999999999985

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.64  E-value=1.4e-05  Score=45.26  Aligned_cols=31  Identities=23%  Similarity=0.551  Sum_probs=27.5

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHHHH
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKEM   80 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f   80 (267)
                      +|..|.+++. +..|+..+|++||..||.++.
T Consensus         1 VC~~C~~PF~-~~~Fy~~~g~PyCe~HyH~~~   31 (32)
T d1x3ha2           1 VCGDCFTSFS-TGSFFELDGRPFCELHYHHRR   31 (32)
T ss_dssp             BCSSSCCBSC-SSCCEESSSCEECHHHHHHHH
T ss_pred             CcCccCCcCC-CCCeEeECCccchHHhhhhhc
Confidence            5899999997 678999999999999998764

>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=97.62  E-value=1.7e-05  Score=44.09  Aligned_cols=27  Identities=19%  Similarity=0.587  Sum_probs=24.4

Q ss_pred             CCCCCCCCcccCCCcEEEecCceeecCC
Q psy10849         20 VKCARCGDRLLPHEMVMRAQSHVYHLPC   47 (267)
Q Consensus        20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~C   47 (267)
                      ..|++|+++|.+. +++++.++.||..|
T Consensus         4 ~~CaGC~~~I~DR-flL~a~Dr~WH~~C   30 (30)
T d1j2oa1           4 LTCGGCQQNIGDR-YFLKAIDQYWHEDC   30 (30)
T ss_dssp             BCBSSSCSCBCSS-EEEECSSSEECTTT
T ss_pred             cccCCCCCcchHH-HHHHHHHHHHhcCC
Confidence            4799999999987 78899999999987

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.58  E-value=1.3e-05  Score=45.39  Aligned_cols=34  Identities=24%  Similarity=0.390  Sum_probs=30.1

Q ss_pred             cccccccCCCCCCCCCcccCCCcEEEecCceeecCC
Q psy10849         12 PRGFRLYGVKCARCGDRLLPHEMVMRAQSHVYHLPC   47 (267)
Q Consensus        12 ~cy~~~f~~~C~~C~~~I~~~e~~~~a~~~~wH~~C   47 (267)
                      .||..+|+..|..|.+.|.+  .+|.|.+..||++|
T Consensus         1 kdYw~kfge~C~~C~~~itG--pvMvAG~~K~HPEC   34 (34)
T d1x6aa1           1 KDYWGKFGEFCHGCSLLMTG--PFMVAGEFKYHPEC   34 (34)
T ss_dssp             CCSSCCSSCBCTTTCCBCCS--CCBCCTTCCBCTTS
T ss_pred             CcHHHHHHHHhhhhHhhccc--ceeeecccccCCCC
Confidence            47999999999999998874  58889999999998

>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=97.56  E-value=2.7e-05  Score=43.22  Aligned_cols=29  Identities=24%  Similarity=0.541  Sum_probs=25.0

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      .++|.+|++++...|.+ ..+++.||..|+
T Consensus         2 ~~~CprC~K~VYfaEk~-~~lgk~WHk~Cl   30 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEKV-SSLGKDWHKFCL   30 (30)
T ss_dssp             CCBCTTTCCBCCTTTEE-EETTEEEETTTC
T ss_pred             CCcCCCCCCceeeHHhh-ccCCcccccccC
Confidence            35899999999999866 488999999884

>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=97.56  E-value=2.8e-05  Score=43.44  Aligned_cols=32  Identities=28%  Similarity=0.667  Sum_probs=28.7

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      .|..|.++++ ...|..+++..||..||+++|+
T Consensus         1 ~C~~C~qPIG-tkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           1 LCSGCEQPLG-SRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             BCTTTCCBTT-TSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCccc-ccccccCCCcEEEEeccccccC
Confidence            3888999997 5789999999999999999985

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

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

Probab=97.55  E-value=2.3e-05  Score=48.91  Aligned_cols=33  Identities=18%  Similarity=0.566  Sum_probs=29.1

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      +|..|++.|. ......+|+++||+.||.++|+.
T Consensus         1 KC~~C~k~Ld-s~t~~ehdg~~YCk~CY~k~fGP   33 (49)
T d1b8ta4           1 RCAKCGKSLE-STTLADKDGEIYCKGCYAKNFGP   33 (49)
T ss_dssp             BCTTTCCBCC-SSSEEEETTEEEEHHHHHHHTCC
T ss_pred             ChhhcCCccC-CCcccccCCcccchhhhhhccCC
Confidence            5899999995 56788899999999999999974

>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=97.46  E-value=2.4e-05  Score=47.77  Aligned_cols=28  Identities=32%  Similarity=0.803  Sum_probs=25.3

Q ss_pred             CCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         20 VKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      .+|..|++.+...|.++ +.++.||..||
T Consensus        16 ~kC~~C~k~VY~~E~~~-~~g~~~Hk~CF   43 (43)
T d1b8ta3          16 DGCPRCGQAVYAAEKVI-GAGKSWHKSCF   43 (43)
T ss_dssp             EECTTTSCEECSSSCEE-ETTEEECTTTC
T ss_pred             CcCccCCCEeeHHHHhh-cCCCccccCCC
Confidence            48999999999998765 89999999998

>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=97.44  E-value=3.7e-05  Score=43.57  Aligned_cols=32  Identities=31%  Similarity=0.809  Sum_probs=28.4

Q ss_pred             ccccccccCCCCCceEee-CCeecchhhHHHHHh
Q psy10849         49 VCVICCQPLQKGEQFILR-SGQLFCRQDFEKEMY   81 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~-~~~lyC~~cy~k~f~   81 (267)
                      .|..|++.| +|..|.+. ++++||..+|.++|+
T Consensus         1 tCvvC~~~L-DGvPFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           1 TCVVCHRGL-DGIPFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             BCSSSCCBC-TTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             CeeEcCccc-CCCcEEEcCCCCEeehhhhhhhcC
Confidence            488999999 58999987 599999999999985

>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=97.41  E-value=3.8e-05  Score=43.84  Aligned_cols=28  Identities=25%  Similarity=0.675  Sum_probs=24.5

Q ss_pred             CCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         20 VKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      ..|++|++.|..+. .+.|+++.||..||
T Consensus         9 ~~CagCg~eik~gQ-aL~ALdkqWH~~CF   36 (36)
T d2dj7a2           9 SHCAGCKEEIKHGQ-SLLALDKQWHVSCF   36 (36)
T ss_dssp             SCCTTTCCCCSSSC-CEEETTEEECTTTC
T ss_pred             ccccccchhhhCCc-eeeeeecceeeeeC
Confidence            37999999999874 56699999999998

>d1x6aa2 g.39.1.3 (A:42-75) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.40  E-value=6.3e-05  Score=42.39  Aligned_cols=32  Identities=22%  Similarity=0.647  Sum_probs=29.3

Q ss_pred             cccccccccCCCCCceEeeC-CeecchhhHHHH
Q psy10849         48 FVCVICCQPLQKGEQFILRS-GQLFCRQDFEKE   79 (267)
Q Consensus        48 F~C~~C~~~L~~g~~f~~~~-~~lyC~~cy~k~   79 (267)
                      |.|..|+..+++|+.|.+.+ .++||..||.+.
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            78999999999999999987 799999999874

>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=97.38  E-value=5.8e-05  Score=43.79  Aligned_cols=29  Identities=31%  Similarity=0.808  Sum_probs=25.6

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      ..+|..|++.+..-|.+ .+.++.||..||
T Consensus         7 ~~kC~~C~K~VY~~E~~-~a~g~~~Hk~CF   35 (35)
T d2d8ya1           7 RETCVECQKTVYPMERL-LANQQVFHISCF   35 (35)
T ss_dssp             SCBCTTTCCBCCTTSEE-ECSSSEEETTTC
T ss_pred             CcccccCCCEEeeeeeE-ecCCeehhhccC
Confidence            45899999999998755 599999999998

>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=97.34  E-value=5.9e-05  Score=42.10  Aligned_cols=31  Identities=26%  Similarity=0.576  Sum_probs=27.1

Q ss_pred             cccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         50 CVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        50 C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      |..|+.+|.+ ..|...+|.+||..||++-|+
T Consensus         2 Ca~C~~sL~d-~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           2 CAHCKNTMAY-IGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             CSSSCCBCSS-SCBEESSSCEECHHHHHHHTS
T ss_pred             cccccccHhh-cceeeecCcEeHHHHHHHhcC
Confidence            8899999974 778888999999999998764

>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=97.34  E-value=4e-05  Score=42.38  Aligned_cols=31  Identities=16%  Similarity=0.634  Sum_probs=27.5

Q ss_pred             cccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         50 CVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        50 C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      |..|.+.| +......+++.+||+.||.++|+
T Consensus         2 C~~C~K~L-dStTva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNL-DSTTVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEE-CSSCCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhcc-CcceeeeecceEEehhhccccCC
Confidence            77899999 47889999999999999999875

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

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

Probab=97.32  E-value=3.4e-05  Score=46.58  Aligned_cols=33  Identities=18%  Similarity=0.537  Sum_probs=29.0

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      +|..|++.|.. ..|...+|.+||+.||.++|..
T Consensus         1 rC~~C~~~Ls~-~~yas~~G~lYCkpHf~qLF~~   33 (42)
T d2d8ya2           1 RCSYCNNKLSL-GTYASLHGRIYCKPHFNQLFKS   33 (42)
T ss_dssp             BCTTTCCBCCT-TTCCCSSSCCCCHHHHHHHSCC
T ss_pred             CcCcCCCCccC-CcchhhCCEeccHHHHHHHHHh
Confidence            58999999974 5788889999999999999864

>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=97.28  E-value=5.8e-05  Score=40.54  Aligned_cols=27  Identities=37%  Similarity=0.848  Sum_probs=23.8

Q ss_pred             CCCCCCCCcccCCCcEEEecCceeecCC
Q psy10849         20 VKCARCGDRLLPHEMVMRAQSHVYHLPC   47 (267)
Q Consensus        20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~C   47 (267)
                      .+|.+|++.+...|+++ ..++.||..|
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            47999999999999888 6688999987

>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=97.27  E-value=0.00011  Score=38.79  Aligned_cols=27  Identities=19%  Similarity=0.567  Sum_probs=24.1

Q ss_pred             CCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         22 CARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        22 C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      |..|.++|....+-+...++.||..||
T Consensus         1 c~ecrkpigad~ke~h~knr~wh~~cf   27 (27)
T d2cupa3           1 CVECRKPIGADSKEVHYKNRFWHDTCF   27 (27)
T ss_dssp             CSSSCCBCCSSSCEEEETTEEEETTTC
T ss_pred             CccccCCcCcchHHhhccccccccccC
Confidence            789999998776778889999999998

>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=97.25  E-value=8.7e-05  Score=40.77  Aligned_cols=29  Identities=31%  Similarity=0.797  Sum_probs=26.3

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHH
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEK   78 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k   78 (267)
                      +|..|.+.|. |..|...++++||.+||..
T Consensus         1 vC~~C~K~La-g~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKLA-GQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBCT-TSCEEECSSCEEEHHHHHH
T ss_pred             Ccccccchhc-CceeEEecceEEEeeeecc
Confidence            4899999996 8999999999999999964

>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=97.24  E-value=8.8e-05  Score=41.86  Aligned_cols=27  Identities=19%  Similarity=0.625  Sum_probs=24.9

Q ss_pred             CCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         20 VKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      +.|.+|+..|.+.  ++++.++.+|++||
T Consensus         9 p~CdkCg~GIVG~--~VK~rDk~rHPeCf   35 (35)
T d1x62a2           9 PMCDKCGTGIVGV--FVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCSSSCCCCCSS--CEECSSCEECTTTT
T ss_pred             ccccccCCCcEeE--EEEeccccCCCCCC
Confidence            5899999999975  88999999999998

>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=97.20  E-value=9.5e-05  Score=40.16  Aligned_cols=27  Identities=22%  Similarity=0.564  Sum_probs=23.3

Q ss_pred             CCCCCCcccC--CCcEEEecCceeecCCc
Q psy10849         22 CARCGDRLLP--HEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        22 C~~C~~~I~~--~e~~~~a~~~~wH~~CF   48 (267)
                      |+.|.++|.+  +.+++...++.||..||
T Consensus         1 C~~C~kPItg~gg~kyisFE~R~WH~~CF   29 (29)
T d1x4la1           1 CAGCTNPISGLGGTKYISFEERQWHNDCF   29 (29)
T ss_dssp             BTTTTBCCCCSSSCSCEECSSCEECTTTC
T ss_pred             CCccCCcccccCCceEEEeecccccccCC
Confidence            8899999964  44788899999999998

>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=97.19  E-value=7.7e-05  Score=43.45  Aligned_cols=29  Identities=38%  Similarity=0.823  Sum_probs=25.8

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      ..+|..|++.+..-|.+ .+.++.||..||
T Consensus         8 ~~~C~~C~K~VY~~Erl-~a~g~~yHk~CF   36 (36)
T d2co8a2           8 GDLCALCGEHLYVLERL-CVNGHFFHRSCF   36 (36)
T ss_dssp             SCBCSSSCCBCCTTTBC-CBTTBCCBTTTC
T ss_pred             CCcccccCCEEeeeeEE-EecCcEeccccC
Confidence            45899999999998866 599999999998

>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=97.12  E-value=0.00015  Score=47.71  Aligned_cols=33  Identities=15%  Similarity=0.583  Sum_probs=29.2

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHHHHhh
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKEMYL   82 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~~   82 (267)
                      .|..|++.|. ...+..+++++||+.||.++|+-
T Consensus         1 ~C~~C~K~Ld-S~~~~eh~~e~YCk~CY~k~fGP   33 (65)
T d1b8ta2           1 LCMVCKKNLD-STTVAVHGDEIYCKSCYGKKYGP   33 (65)
T ss_dssp             BCTTTCCBCC-SSSEEEETTEEEEHHHHHHHHSC
T ss_pred             CchhcCCccC-CCccccCCCcccchhhhccccCC
Confidence            4889999995 57788999999999999999985

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

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

Probab=97.10  E-value=3.2e-05  Score=48.26  Aligned_cols=27  Identities=15%  Similarity=0.262  Sum_probs=24.1

Q ss_pred             cccCCcccCccccccccCCCCCCCCCc
Q psy10849          2 TSHNSHVSCHPRGFRLYGVKCARCGDR   28 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~~C~~C~~~   28 (267)
                      .++||++||+.||.++|+++....+..
T Consensus        15 ~ehdg~~YCk~CY~k~fGPKG~g~G~g   41 (49)
T d1b8ta4          15 ADKDGEIYCKGCYAKNFGPKGFGFGQG   41 (49)
T ss_dssp             EEETTEEEEHHHHHHHTCCCCCCCCCC
T ss_pred             cccCCcccchhhhhhccCCCccCcccC
Confidence            468999999999999999999888753

>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=97.07  E-value=0.00016  Score=44.54  Aligned_cols=33  Identities=15%  Similarity=0.349  Sum_probs=28.9

Q ss_pred             ccccccccCCCCCceEeeCCeecc-hhhHHHHHhh
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFC-RQDFEKEMYL   82 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC-~~cy~k~f~~   82 (267)
                      +|..|++.|. ......+++++|| +.||.++|+.
T Consensus         1 kC~~C~K~L~-sg~~aeHdg~pYC~k~CY~~~FGP   34 (48)
T d1imla2           1 KCEKCGKTLT-SGGHAEHEGKPYCNHPCYSAMFGP   34 (48)
T ss_dssp             BCTTTCCBCC-TTTEEEETTEEEETTTHHHHHSSC
T ss_pred             CchhcCcCcC-CCChhhcCCcccccccchhhccCC
Confidence            5889999996 5678999999999 7799999974

>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=97.04  E-value=0.00016  Score=43.44  Aligned_cols=27  Identities=30%  Similarity=0.757  Sum_probs=24.9

Q ss_pred             CCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         20 VKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      +.|.+|+..|.+.  ++++.++.+|++||
T Consensus        19 P~CdkCg~GIVG~--~VK~rDK~rHPeCf   45 (45)
T d1x64a1          19 PLCDKCGSGIVGA--VVKARDKYRHPECF   45 (45)
T ss_dssp             CBCTTTCCBCCSC--CEESSSCEECTTTC
T ss_pred             ccccccCCCcEEE--EEEeccccCCCCCC
Confidence            5899999999976  88999999999998

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

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

Probab=97.03  E-value=0.00021  Score=38.68  Aligned_cols=27  Identities=22%  Similarity=0.549  Sum_probs=23.2

Q ss_pred             CCCCCCcccC--CCcEEEecCceeecCCc
Q psy10849         22 CARCGDRLLP--HEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        22 C~~C~~~I~~--~e~~~~a~~~~wH~~CF   48 (267)
                      |..|.++|.+  +.+++...++.||.+||
T Consensus         1 C~~C~kPItg~gG~k~isFedR~WH~~CF   29 (29)
T d1x68a1           1 CVACSKPISGLTGAKFICFQDSQWHSECF   29 (29)
T ss_dssp             CTTTCCCCCTTTTCCEEEETTEEEEGGGC
T ss_pred             CccccccccccCCceEEEeehhhcccccC
Confidence            7899999964  45788899999999998

>d1x61a2 g.39.1.3 (A:35-66) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.86  E-value=0.00042  Score=38.08  Aligned_cols=30  Identities=23%  Similarity=0.615  Sum_probs=26.7

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHHH
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKE   79 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~   79 (267)
                      .|..|+..|. |+.|+..+.+.||+.||...
T Consensus         1 vC~tC~~kLR-GqpFYAvekkayCE~CYi~t   30 (32)
T d1x61a2           1 VCSTCRAQLR-GQHFYAVERRAYCEGCYVAT   30 (32)
T ss_dssp             BCSSSCCBCT-TSCEEESSSCEEEHHHHHHH
T ss_pred             CeeEeCceec-CCcceEeeccccccceeeee
Confidence            4889999997 89999999999999999653

>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=96.77  E-value=8.5e-05  Score=43.20  Aligned_cols=19  Identities=11%  Similarity=0.095  Sum_probs=17.4

Q ss_pred             cccCCcccCccccccccCC
Q psy10849          2 TSHNSHVSCHPRGFRLYGV   20 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~   20 (267)
                      |++||++||+.||.++|++
T Consensus        16 ~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2          16 YEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             EEETTEEECHHHHHHHCCC
T ss_pred             EEECCEecChHhHHhhcCC
Confidence            5799999999999999985

>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=96.75  E-value=0.00045  Score=38.53  Aligned_cols=32  Identities=19%  Similarity=0.427  Sum_probs=26.7

Q ss_pred             ccccccccCCCCCceEeeCCeecchh-hHHHHHh
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQ-DFEKEMY   81 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~-cy~k~f~   81 (267)
                      +|..|++.|.. .....++|++||.. ||..+|+
T Consensus         1 kCekC~ktL~~-G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTP-GGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCT-TSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCC-CCccccCCCcCcCcchHHhhcC
Confidence            58899999975 45788899999965 9998885

>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=96.66  E-value=0.00012  Score=40.55  Aligned_cols=18  Identities=17%  Similarity=0.307  Sum_probs=16.0

Q ss_pred             cccCCcccCccccccccC
Q psy10849          2 TSHNSHVSCHPRGFRLYG   19 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~   19 (267)
                      +.+||.|||+.||+.+|+
T Consensus        14 m~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1          14 ISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             EEETTEEECTTHHHHHTT
T ss_pred             ecCCCCcccHHHHHHhcC
Confidence            368999999999999886

>d1rutx4 g.39.1.3 (X:114-146) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=96.55  E-value=0.00089  Score=36.89  Aligned_cols=28  Identities=36%  Similarity=0.802  Sum_probs=25.2

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhH
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDF   76 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy   76 (267)
                      .|+.|...|.+|+.|...+|.+||+.+-
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            4889999999999999999999998773

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.54  E-value=0.00072  Score=38.19  Aligned_cols=28  Identities=29%  Similarity=0.802  Sum_probs=26.1

Q ss_pred             CCCCCCCCcccCCCcEEEecCceeecCC
Q psy10849         20 VKCARCGDRLLPHEMVMRAQSHVYHLPC   47 (267)
Q Consensus        20 ~~C~~C~~~I~~~e~~~~a~~~~wH~~C   47 (267)
                      ..|.+|+....+.|+++...+..||..|
T Consensus         8 ~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           8 ATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHccCCCchHHhhcCCCccccccC
Confidence            4799999999999999999999999987

>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=96.45  E-value=0.0012  Score=35.73  Aligned_cols=32  Identities=19%  Similarity=0.471  Sum_probs=27.6

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHHHHh
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      .|+.|++.++. ..|+.+...+||..|++.+|+
T Consensus         1 tcs~ckq~igs-gsffpkg~d~ycvtche~kfa   32 (32)
T d1x63a2           1 TCSNCKQVIGT-GSFFPKGEDFYCVTCHETKFA   32 (32)
T ss_dssp             CCSSSCCCCTT-SCEEEETTEEEEHHHHHHHTS
T ss_pred             Ccchhhhhccc-ccccCCCCcEEEEEeeccccC
Confidence            48899999974 568899999999999999875

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

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

Probab=96.35  E-value=0.00091  Score=37.32  Aligned_cols=29  Identities=31%  Similarity=0.707  Sum_probs=24.9

Q ss_pred             CCCCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         19 GVKCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        19 ~~~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      +.+|..|.+.+.-.|.+ ...++.||+.||
T Consensus         7 g~kcg~c~ktvy~aeev-qc~g~sfhk~cf   35 (35)
T d1b8ta1           7 GKKCGVCQKAVYFAEEV-QCEGSSFHKSCF   35 (35)
T ss_dssp             CEECTTTCCEECSSCCE-EETTEEECTTTC
T ss_pred             CceeccccceEeeeeee-eecCcccccccC
Confidence            45899999999887755 489999999998

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=96.14  E-value=0.0011  Score=37.24  Aligned_cols=33  Identities=27%  Similarity=0.585  Sum_probs=27.8

Q ss_pred             ccccccccCCC-CCceEeeCCeecchhhHHHHHh
Q psy10849         49 VCVICCQPLQK-GEQFILRSGQLFCRQDFEKEMY   81 (267)
Q Consensus        49 ~C~~C~~~L~~-g~~f~~~~~~lyC~~cy~k~f~   81 (267)
                      +|..|+..|.+ |...+.+.+.++|+.+|.++|+
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            47778887753 7788999999999999999985

>d1a7ia1 g.39.1.3 (A:8-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=96.11  E-value=0.0021  Score=33.96  Aligned_cols=27  Identities=33%  Similarity=0.794  Sum_probs=23.5

Q ss_pred             CCCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         21 KCARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        21 ~C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      +|..|.+.+.-.|.+ ...++.||..||
T Consensus         2 kcg~c~ktvy~aeev-qc~grsfhk~cf   28 (28)
T d1a7ia1           2 KCGACGRTVYHAEEV-QCDGRSFHRCCF   28 (28)
T ss_dssp             BCSSSCCBCSSTTEE-EETTEEEESSSE
T ss_pred             ccccccceEeeeeee-eecCceeccccC
Confidence            799999999887655 589999999997

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

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

Probab=95.83  E-value=0.0032  Score=32.54  Aligned_cols=27  Identities=30%  Similarity=0.787  Sum_probs=22.5

Q ss_pred             CCCCCCcccCCCcEEEecCceeecCCc
Q psy10849         22 CARCGDRLLPHEMVMRAQSHVYHLPCF   48 (267)
Q Consensus        22 C~~C~~~I~~~e~~~~a~~~~wH~~CF   48 (267)
                      |..|++.+.+...-+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            788999887655556699999999998

>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=95.52  E-value=0.0021  Score=35.08  Aligned_cols=25  Identities=28%  Similarity=0.667  Sum_probs=22.6

Q ss_pred             CCCCCCCcccCCCcEEEecCceeecCC
Q psy10849         21 KCARCGDRLLPHEMVMRAQSHVYHLPC   47 (267)
Q Consensus        21 ~C~~C~~~I~~~e~~~~a~~~~wH~~C   47 (267)
                      -|..|.+.|.+.  +++|.++.||+.|
T Consensus         7 gC~~C~~~ItGk--VLEAG~khYHP~C   31 (32)
T d1wiga1           7 GCDSCEKYITGR--VLEAGEKHYHPSC   31 (32)
T ss_dssp             SCSSSCCCCSSC--CBCCSSCCBCTTT
T ss_pred             hhhhhhhhhhhh--hhhccccccCCCC
Confidence            599999999975  9999999999987

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=95.26  E-value=0.0083  Score=32.65  Aligned_cols=29  Identities=24%  Similarity=0.653  Sum_probs=23.9

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHH
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEK   78 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k   78 (267)
                      .|..|+..|. ...+++.++++||+.|-..
T Consensus         1 vC~dCg~NLK-qrG~Ffv~~~lyCE~HAr~   29 (31)
T d1x64a2           1 VCADCNLNLK-QKGYFFVEGELYCETHARA   29 (31)
T ss_dssp             CCSSSCCCTT-TSCCEEETTEEECHHHHHH
T ss_pred             CccccccChh-hcceEEeccEEeehhhhhc
Confidence            4899999995 5778888999999988543

>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=95.20  E-value=0.0014  Score=40.19  Aligned_cols=21  Identities=29%  Similarity=0.501  Sum_probs=18.3

Q ss_pred             ccCCcccC-ccccccccCCCCC
Q psy10849          3 SHNSHVSC-HPRGFRLYGVKCA   23 (267)
Q Consensus         3 ~~dg~~yC-~~cy~~~f~~~C~   23 (267)
                      .+||+||| +.||.++|+++=.
T Consensus        16 eHdg~pYC~k~CY~~~FGPkG~   37 (48)
T d1imla2          16 EHEGKPYCNHPCYSAMFGPKGF   37 (48)
T ss_dssp             EETTEEEETTTHHHHHSSCCCS
T ss_pred             hcCCcccccccchhhccCCCcc
Confidence            58999999 8899999998643

>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=94.89  E-value=0.0016  Score=42.69  Aligned_cols=23  Identities=22%  Similarity=0.274  Sum_probs=19.4

Q ss_pred             ccCCcccCccccccccCCCCCCC
Q psy10849          3 SHNSHVSCHPRGFRLYGVKCARC   25 (267)
Q Consensus         3 ~~dg~~yC~~cy~~~f~~~C~~C   25 (267)
                      .+|+++||+.||.++|+++=..=
T Consensus        16 eh~~e~YCk~CY~k~fGPkG~G~   38 (65)
T d1b8ta2          16 VHGDEIYCKSCYGKKYGPKGKGK   38 (65)
T ss_dssp             EETTEEEEHHHHHHHHSCCCCCC
T ss_pred             cCCCcccchhhhccccCCCcccc
Confidence            57899999999999999875443

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.85  E-value=0.0064  Score=35.42  Aligned_cols=27  Identities=30%  Similarity=0.676  Sum_probs=18.3

Q ss_pred             CCCCCCCcccCCCcEEEecCceeecCC
Q psy10849         21 KCARCGDRLLPHEMVMRAQSHVYHLPC   47 (267)
Q Consensus        21 ~C~~C~~~I~~~e~~~~a~~~~wH~~C   47 (267)
                      .|.+|++....+|......+.+||+.|
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~IWHP~C   27 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSSIWHPAC   27 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTEEECTTH
T ss_pred             CcchhhccccccceeeecCCceeCCcc
Confidence            377888877766544435677888776

>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=94.41  E-value=0.0028  Score=35.40  Aligned_cols=18  Identities=22%  Similarity=0.325  Sum_probs=15.8

Q ss_pred             cccCCcccCccccccccC
Q psy10849          2 TSHNSHVSCHPRGFRLYG   19 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~   19 (267)
                      +.||++|||-.||..+|+
T Consensus        15 ~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2          15 TARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             EESSSSEECHHHHHHHTC
T ss_pred             eecCCCeehHHhhHhhcC
Confidence            368999999999998875

>d1v6ga2 g.39.1.3 (A:42-81) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.40  E-value=0.016  Score=33.36  Aligned_cols=29  Identities=24%  Similarity=0.733  Sum_probs=26.6

Q ss_pred             cccccccccCCCCCceEeeCCeecchhhH
Q psy10849         48 FVCVICCQPLQKGEQFILRSGQLFCRQDF   76 (267)
Q Consensus        48 F~C~~C~~~L~~g~~f~~~~~~lyC~~cy   76 (267)
                      |+|..|..++..|+...+......|..|-
T Consensus         1 FvC~vCr~pFP~GDRVTFnGKeC~CQ~Cs   29 (40)
T d1v6ga2           1 FVCAVCRLPFPPGDRVTFNGKECMCQKCS   29 (40)
T ss_dssp             SSCSSSCCCCCSSSCEEEETTEEEEHHHH
T ss_pred             CcccccCCCCCCCCeEEEcCceeehhhcC
Confidence            78999999999999999988999999885

>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=93.98  E-value=0.0054  Score=36.59  Aligned_cols=19  Identities=26%  Similarity=0.482  Sum_probs=16.8

Q ss_pred             ccCCcccCccccccccCCC
Q psy10849          3 SHNSHVSCHPRGFRLYGVK   21 (267)
Q Consensus         3 ~~dg~~yC~~cy~~~f~~~   21 (267)
                      ..+|++||++||.++|.++
T Consensus        16 s~~G~lYCkpHf~qLF~~k   34 (42)
T d2d8ya2          16 SLHGRIYCKPHFNQLFKSK   34 (42)
T ss_dssp             CSSSCCCCHHHHHHHSCCC
T ss_pred             hhCCEeccHHHHHHHHHhh
Confidence            5799999999999999864

>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=93.86  E-value=0.0042  Score=34.04  Aligned_cols=17  Identities=29%  Similarity=0.501  Sum_probs=14.9

Q ss_pred             ccCCcccCccccccccC
Q psy10849          3 SHNSHVSCHPRGFRLYG   19 (267)
Q Consensus         3 ~~dg~~yC~~cy~~~f~   19 (267)
                      .+++.+||+.||.++|+
T Consensus        16 ~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2          16 IHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             EETTEEECSHHHHHHCC
T ss_pred             eecceEEehhhccccCC
Confidence            47899999999998875

>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=93.43  E-value=0.0061  Score=33.82  Aligned_cols=17  Identities=35%  Similarity=0.724  Sum_probs=14.4

Q ss_pred             ccCCcccCc-cccccccC
Q psy10849          3 SHNSHVSCH-PRGFRLYG   19 (267)
Q Consensus         3 ~~dg~~yC~-~cy~~~f~   19 (267)
                      .+||+|||. +||..+|+
T Consensus        16 EH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2          16 EHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             EETTEEECTTTHHHHHSC
T ss_pred             ccCCCcCcCcchHHhhcC
Confidence            589999995 69998885

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

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

Probab=93.41  E-value=0.0083  Score=32.72  Aligned_cols=29  Identities=21%  Similarity=0.567  Sum_probs=23.4

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHHH
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFEK   78 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~k   78 (267)
                      .|..|+..|. ...+++.++++||+.|-..
T Consensus         1 vC~dCg~NLK-qrG~Ffve~~lyCE~HAr~   29 (31)
T d1x62a1           1 VCTDCGTNLK-QKGHFFVEDQIYCEKHARE   29 (31)
T ss_dssp             SCSSSCCCHH-HHCCEESSSCEECHHHHHH
T ss_pred             CccccccChh-hcceEEeccEEehhhhhhh
Confidence            4899999995 4667788999999988644

>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=92.33  E-value=0.009  Score=33.38  Aligned_cols=17  Identities=6%  Similarity=-0.048  Sum_probs=14.7

Q ss_pred             cccCCcccCcccccccc
Q psy10849          2 TSHNSHVSCHPRGFRLY   18 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f   18 (267)
                      |+.||+|||+.+|..+.
T Consensus        15 y~~~g~PyCe~HyH~~~   31 (32)
T d1x3ha2          15 FELDGRPFCELHYHHRR   31 (32)
T ss_dssp             EESSSCEECHHHHHHHH
T ss_pred             EeECCccchHHhhhhhc
Confidence            67999999999998754

>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=91.76  E-value=0.0096  Score=32.94  Aligned_cols=17  Identities=12%  Similarity=0.133  Sum_probs=15.3

Q ss_pred             ccCCcccCccccccccC
Q psy10849          3 SHNSHVSCHPRGFRLYG   19 (267)
Q Consensus         3 ~~dg~~yC~~cy~~~f~   19 (267)
                      .+|+..||..||+++|+
T Consensus        16 pk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1          16 PKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             EETTEEEEHHHHHHHTS
T ss_pred             cCCCCceEeecchhhcC
Confidence            58999999999999885

>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=91.41  E-value=0.014  Score=32.58  Aligned_cols=19  Identities=16%  Similarity=0.286  Sum_probs=17.2

Q ss_pred             cccCCcccCccccccccCC
Q psy10849          2 TSHNSHVSCHPRGFRLYGV   20 (267)
Q Consensus         2 ~~~dg~~yC~~cy~~~f~~   20 (267)
                      |.+.|..||+.+|.++|+.
T Consensus        16 yE~~g~ayCe~Hy~qLfg~   34 (35)
T d1u5sb2          16 YERKGLAYCETHYNQLFGD   34 (35)
T ss_dssp             EEETTEEECHHHHHHHCSC
T ss_pred             hhhcCchHHHHHHHHHhcc
Confidence            6789999999999999974

>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=91.31  E-value=0.01  Score=33.08  Aligned_cols=19  Identities=26%  Similarity=0.557  Sum_probs=17.3

Q ss_pred             CcccCCcccCccccccccC
Q psy10849          1 STSHNSHVSCHPRGFRLYG   19 (267)
Q Consensus         1 ~~~~dg~~yC~~cy~~~f~   19 (267)
                      ||.|.|.++|+.||.++|+
T Consensus        16 ~ytk~~mILCk~DY~rlFG   34 (34)
T d1rutx2          16 SYTKSGMILCRNDYIRLFG   34 (34)
T ss_dssp             EEEETTEEECHHHHHHHHS
T ss_pred             heecCCEEEEchhHHHhcC
Confidence            6889999999999999886

>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=91.24  E-value=0.071  Score=28.70  Aligned_cols=27  Identities=26%  Similarity=0.540  Sum_probs=21.2

Q ss_pred             cccccccCCCCCceEeeCCeecchhhHHH
Q psy10849         50 CVICCQPLQKGEQFILRSGQLFCRQDFEK   78 (267)
Q Consensus        50 C~~C~~~L~~g~~f~~~~~~lyC~~cy~k   78 (267)
                      |..|++.|.  ..-....|.+||..|+.+
T Consensus         2 C~~Cgkelt--adArEl~geLyCLpChdK   28 (31)
T d2cora1           2 CANCGKELT--ADARELKGELYCLPCHDK   28 (31)
T ss_dssp             CSSSCCBCC--TTCEEETTEEECHHHHHT
T ss_pred             ccccccccc--hhHHHhcCCEEEEecccc
Confidence            788999984  334556899999999876

>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=90.72  E-value=0.089  Score=28.31  Aligned_cols=28  Identities=25%  Similarity=0.723  Sum_probs=23.4

Q ss_pred             ccccccccCCCCCceEeeCCeecchhhHH
Q psy10849         49 VCVICCQPLQKGEQFILRSGQLFCRQDFE   77 (267)
Q Consensus        49 ~C~~C~~~L~~g~~f~~~~~~lyC~~cy~   77 (267)
                      +|..|-.+|. .+.|..++++++|..|--
T Consensus         1 RCaKC~hpLA-~E~F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPLA-NETFVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCTT-SSCCEEETTEEECHHHHT
T ss_pred             Cchhhccccc-cCcccccCCeEeeccccc
Confidence            4778888996 688999999999988853

>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=90.00  E-value=0.018  Score=31.79  Aligned_cols=17  Identities=12%  Similarity=0.161  Sum_probs=15.0

Q ss_pred             ccCCcccCccccccccC
Q psy10849          3 SHNSHVSCHPRGFRLYG   19 (267)
Q Consensus         3 ~~dg~~yC~~cy~~~f~   19 (267)
                      .+++..||.+||+++|+
T Consensus        16 p~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1          16 PDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             EETTEEEEHHHHHHHTS
T ss_pred             cCCCcEEEEeccccccC
Confidence            57899999999999885

>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=89.85  E-value=0.02  Score=31.44  Aligned_cols=17  Identities=18%  Similarity=0.180  Sum_probs=15.0

Q ss_pred             ccCCcccCccccccccC
Q psy10849          3 SHNSHVSCHPRGFRLYG   19 (267)
Q Consensus         3 ~~dg~~yC~~cy~~~f~   19 (267)
                      .+|.+|||..||..+|+
T Consensus        16 Srde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1          16 SRDEDPYCVACFGELFA   32 (32)
T ss_dssp             ECSSSEEEHHHHHHHTT
T ss_pred             cCCCCccHHHHhHhhcC
Confidence            58999999999988874

>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=87.97  E-value=0.19  Score=27.29  Aligned_cols=31  Identities=26%  Similarity=0.686  Sum_probs=23.5

Q ss_pred             ccccccccCCC-CCceEeeCCeecchhhHHHH
Q psy10849         49 VCVICCQPLQK-GEQFILRSGQLFCRQDFEKE   79 (267)
Q Consensus        49 ~C~~C~~~L~~-g~~f~~~~~~lyC~~cy~k~   79 (267)
                      +|.-|+..|+. |...+.+.+.++|+.+|.++
T Consensus         2 kC~cC~cRLGEVG~tlytk~nliLCkrDYlRl   33 (33)
T d1j2oa2           2 SCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL   33 (33)
T ss_dssp             CCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHH
T ss_pred             ccccccccccchhhHHHhhcceeeehhhhhcC
Confidence            56677777743 56677788999999999764

>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=85.94  E-value=0.27  Score=26.63  Aligned_cols=25  Identities=28%  Similarity=0.780  Sum_probs=21.1

Q ss_pred             cccccccCCCCCceEeeCCeecchhh
Q psy10849         50 CVICCQPLQKGEQFILRSGQLFCRQD   75 (267)
Q Consensus        50 C~~C~~~L~~g~~f~~~~~~lyC~~c   75 (267)
                      |..|+..|. |+.|.-....++|..|
T Consensus         2 cgkcsvslv-g~gfltq~~~i~c~~c   26 (34)
T d1x68a2           2 CGKCSVSLV-GKGFLTQNKEIFCQKC   26 (34)
T ss_dssp             CTTTCCBCS-SSCEEEETTEEEETTT
T ss_pred             CccceEEEE-eeeeeeccCcEEehhc
Confidence            667888885 7889888899999888