Citrus Sinensis ID: 014080

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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-------270-------280-------290-------300-------310-------320-------330-------340-------350-------360-------370-------380-------390-------400-------410-------420-------430-
Protein Sequence
MGWLTKILKGSSRRHYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEVDQKGKKVIENEYDSEDDLQCIKSDDSDEDELDEDEIRAIAQQEEDERRAKAQQEEDERRARARAQLEEDEQLAKAIQDSLRVDSPPRYESGNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGFICFKLIYFVF
Secondary Structure (PSIPRED)
ccccccccccccccccccccccccccccccccccccccccccHHHHHHHHHccccccccccccccccccccHHHHcccccccccccccHHHHHHHHccHHHHHHHHHHHHHHHHHHHHcccccHHHHHHHHHHHccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccEEEcccccccHHHHHHHcccccccccccccccccccccEEEcccEEEEcccccccccccccccccccccccccEEEcccccEEcccccccccccccccccHHHHHHHHHHHccccccccccEEEEcHHHHHHHHHccccccccccccccEEEEEEEEEEEEEEcccccccccEEEEEEcEEcccccEEEEEEEEEccccHHHHHHHHHHHHHHHHHHHccccccEEEEEEc
Secondary Structure Prediction (SSPRO)
ccHHHHHHccccccccccccccccccccccccccccccccccccHHHHHHHHHHHHHccccccccccccccccccccccccccccccccHHHHHHHHHHHHcHHccccHccccccccccccccccHHHcHHccccccccccccccccccccccccccccccccccccccccccEEEEcccccccccEEEcccccccccccEEccccccccHHHHHHHccccccccccccccccccHcccccccccccccccccccccccccccccccccccccEEEcccccEEEHHHHccccccccccHHHHHHHHHHHHHccccccccccEEEEcHHHHHHHHHHcccccccccccccEEEcccEEEEEEEcccccccccEEEEEcccccccccccEEEEEEEEccHHHHHHHHHHHHHHHHHHHHHcccccccEEEEEc
Coil and Loop (DISEMBL)
mgwltkilkgssrrhyharygddrtwderrysaaddssgfdneEIDRAIALSLVEVDQKGKKVieneydseddlqciksddsdedeldEDEIRAIAQQEEDERRAKAQQEEDERRARARAQLEEDEQLAKAIQDslrvdsppryesgnifqpfpffsgyricagcnteighgrYLSCmeafwhpecfrchscnlpitdvefsmsgnrpyhkhcykeqhhpkcdvcqnfiptnsaglieyrahpfwlqkycpsherdgtprccscermeprdtkylsldDGRKLCLECLDsaimdthecqPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAmegeknghhhlpetrglclseeqTVTTVlrrprigagyRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGFICFKLIYFVF
Flexible Loop (DISEMBL)
mgwltkilkgssrrhyharygddrtwderrysaaddssgfdneEIDRAIALSLVEVDQKGKKVieneydseddlqciksddsdedelDEDEIRAIAQQEEDERRAKAQQEEDERRARARAQLEEDEQLAKAIQDSLRVDSPPRYESGNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCScermeprdtkylsldDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTvlrrprigagyrliDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGFICFKLIYFVF
Low Complexity Region (SEG)
MGWLTKILKGSSRRHYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEVDQKGKKVIENEYDSEDDLQCIKsddsdedeldedeIRAIAQQEEDerrakaqqeederrararaqleedeqLAKAIQDSLRVDSPPRYESGNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGFICFKLIYFVF
Disordered region (IsUnstruct)
**********************************************RAIALSLVEV******************************************************************************************GNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQAL****************TRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGFICFKLIYFV*
Disordered Region (DISOPRED)
MGWLTKILKG************************************************************************************************************************************************FFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLL**********************TRGLCLSEEQT*************************LIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGFICFKLIYFVF
Disordered Region (DISEMBL)
MGWLTKILKGSSRRHYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEVDQKGKKVIENEYDSEDDLQCIKSD*********DEIRAIAQQ************************EEDEQLAKAIQDSLRVDSPPRYESGNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGFICFKLIYFVF
Disordered Region (DISPRO)
*GW*********************************S***DNEEIDRAIALSLVEV*******************************************************************************************NIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGFICFKLIYFVF
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
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Transmembrane Helix (MEMSAT)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
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TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MGWLTKILKGSSRRHYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEVDQKGKKVIENEYDSEDDLQCIKSDDSDEDELDEDEIxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxLRVDSPPRYESGNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGFICFKLIYFVF
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	431	2.2.26 [Sep-21-2011]
Q8W4F0	553	Protein DA1-related 1 OS=	yes	no	0.969	0.755	0.696	1e-172
P0C7Q8	532	Protein DA1 OS=Arabidopsi	no	no	0.923	0.748	0.545	1e-137
Q0WSN2	528	Protein DA1-related 2 OS=	no	no	0.758	0.619	0.582	1e-114
Q9FJX9	560	Protein DA1-related 7 OS=	no	no	0.853	0.657	0.443	3e-85
Q9FJX8	644	Protein DA1-related 6 OS=	no	no	0.761	0.509	0.449	6e-83
Q9FKN7	1613	Protein DA1-related 4 OS=	no	no	0.596	0.159	0.541	2e-76
Q9LVR6	450	Protein DA1-related 3 OS=	no	no	0.751	0.72	0.438	4e-73
Q84WJ0	702	Protein DA1-related 5 OS=	no	no	0.573	0.351	0.505	3e-70
P53776	390	LIM/homeobox protein Lhx4	yes	no	0.273	0.302	0.276	9e-07
Q969G2	390	LIM/homeobox protein Lhx4	yes	no	0.273	0.302	0.276	9e-07

>sp|Q8W4F0|DAR1_ARATH Protein DA1-related 1 OS=Arabidopsis thaliana GN=DAR1 PE=2 SV=3

 Score =  604 bits (1558), Expect = e-172,   Method: Compositional matrix adjust.
 Identities = 315/452 (69%), Positives = 358/452 (79%), Gaps = 34/452 (7%)

Query: 1   MGWLTKILKGSSRRHY----HARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEV 56
           MGWLTKILKGSS +      + RY +DR  +  RYSA  + S FD EEI+ AIALSL E 
Sbjct: 1   MGWLTKILKGSSHKFSDGQCNGRYREDRNLEGPRYSA--EGSDFDKEEIECAIALSLSEQ 58

Query: 57  ------DQKGKKVIENEYDSEDDLQC------------IKSDDSDEDELDEDEIRAIA-- 96
                 D KGKK+IE + ++E+D               +++ + +E  + + +I      
Sbjct: 59  EHVIPQDDKGKKIIEYKSETEEDDDDDEDEDEEYMRAQLEAAEEEERRVAQAQIEEEEKR 118

Query: 97  ----QQEEDERR-AKAQQEEDERRARARAQLEEDEQLAKAIQDSLRVDSPPRYESGNIFQ 151
               Q EE E+  AKA+ EE+E R R++AQLEEDE LAKA+Q+S+ V SPPRY+ GNI Q
Sbjct: 119 RAEAQLEETEKLLAKARLEEEEMR-RSKAQLEEDELLAKALQESMNVGSPPRYDPGNILQ 177

Query: 152 PFPFF--SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPY 209
           P+PF   S +RIC GC  EIGHGR+LSCM   WHPECF C++C+ PI D EFSMSGNRPY
Sbjct: 178 PYPFLIPSSHRICVGCQAEIGHGRFLSCMGGVWHPECFCCNACDKPIIDYEFSMSGNRPY 237

Query: 210 HKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEP 269
           HK CYKEQHHPKCDVC NFIPTN AGLIEYRAHPFW+QKYCPSHERDGTPRCCSCERMEP
Sbjct: 238 HKLCYKEQHHPKCDVCHNFIPTNPAGLIEYRAHPFWMQKYCPSHERDGTPRCCSCERMEP 297

Query: 270 RDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQA 329
           +DTKYL LDDGRKLCLECLDSAIMDTHECQPLYLEI+EFYEGL+MKVEQQ+P+LLVER A
Sbjct: 298 KDTKYLILDDGRKLCLECLDSAIMDTHECQPLYLEIREFYEGLHMKVEQQIPMLLVERSA 357

Query: 330 LNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEV 389
           LNEAMEGEK+GHHHLPETRGLCLSEEQTVTTVLRRPRIGAGY+LIDMITEP RLIRRCEV
Sbjct: 358 LNEAMEGEKHGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYKLIDMITEPCRLIRRCEV 417

Query: 390 TAILILYGLPRLLTGSILAHEMMHAWLRLKGF 421
           TAILILYGLPRLLTGSILAHEMMHAWLRL G+
Sbjct: 418 TAILILYGLPRLLTGSILAHEMMHAWLRLNGY 449

Ubiquitin receptor that probably regulates developmental process.
Arabidopsis thaliana (taxid: 3702)

>sp|P0C7Q8|DA1_ARATH Protein DA1 OS=Arabidopsis thaliana GN=DA1 PE=1 SV=1

 Score =  489 bits (1258), Expect = e-137,   Method: Compositional matrix adjust.
 Identities = 247/453 (54%), Positives = 311/453 (68%), Gaps = 55/453 (12%)

Query: 1   MGWLTKILKGSSRRHYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEVDQKG 60
           MGW  KI KGS++R    R G+++  +   Y     ++  D+E        S  + D   
Sbjct: 1   MGWFNKIFKGSNQR---LRVGNNKH-NHNVYYDNYPTASHDDEP-------SAADTD--- 46

Query: 61  KKVIENEYDSEDDLQCIKSDDSDEDELDEDEIRAIAQQEEDERRAKAQQEEDERRARARA 120
               +N+            D++  D+ +ED  RAIA    +E      QE+     +   
Sbjct: 47  ---ADNDEPHHTQEPSTSEDNTSNDQENEDIDRAIALSLLEE-----NQEQTSISGKYSM 98

Query: 121 QLEEDEQLAKAIQDSLRVDSPPRYESGNIF------------------------------ 150
            ++EDEQLA+A+Q+S+ V + PR++SG+ +                              
Sbjct: 99  PVDEDEQLARALQESMVVGNSPRHKSGSTYDNGNAYGAGDLYGNGHMYGGGNVYANGDIY 158

Query: 151 --QPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRP 208
             +P  F   +RICAGCN EIGHGR+L+C+ + WHPECFRC+ C+ PI++ EFS SGN P
Sbjct: 159 YPRPITFQMDFRICAGCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPISEYEFSTSGNYP 218

Query: 209 YHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERME 268
           +HK CY+E++HPKCDVC +FIPTN AGLIEYRAHPFW+QKYCPSHE D TPRCCSCERME
Sbjct: 219 FHKACYRERYHPKCDVCSHFIPTNHAGLIEYRAHPFWVQKYCPSHEHDATPRCCSCERME 278

Query: 269 PRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQ 328
           PR+T+Y+ L+DGRKLCLECLDSA+MDT +CQPLYL+IQ FYEGLNMKVEQ+VPLLLVERQ
Sbjct: 279 PRNTRYVELNDGRKLCLECLDSAVMDTMQCQPLYLQIQNFYEGLNMKVEQEVPLLLVERQ 338

Query: 329 ALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCE 388
           ALNEA EGEKNGH+H+PETRGLCLSEEQTV+TV +R + G G +    ITEPY+L R+CE
Sbjct: 339 ALNEAREGEKNGHYHMPETRGLCLSEEQTVSTVRKRSKHGTG-KWAGNITEPYKLTRQCE 397

Query: 389 VTAILILYGLPRLLTGSILAHEMMHAWLRLKGF 421
           VTAILIL+GLPRLLTGSILAHEMMHAW+RLKGF
Sbjct: 398 VTAILILFGLPRLLTGSILAHEMMHAWMRLKGF 430

Ubiquitin receptor that limits final seed and organ size by restricting the period of cell proliferation. May act maternally to control seed mass.

Arabidopsis thaliana (taxid: 3702)

>sp|Q0WSN2|DAR2_ARATH Protein DA1-related 2 OS=Arabidopsis thaliana GN=DAR2 PE=2 SV=1

 Score =  410 bits (1055), Expect = e-114,   Method: Compositional matrix adjust.
 Identities = 195/335 (58%), Positives = 246/335 (73%), Gaps = 8/335 (2%)

Query: 89  EDEIRAIAQQEEDERRAKAQQEEDERRARARA-QLEEDEQLAKAIQDSLRVDS-PPRYES 146
           +D  R    +EE +R       ++ +R       ++ +    +     L   S  P YE 
Sbjct: 92  DDRSRGARDKEELDRSISLSLADNTKRPHGYGWSMDNNRDFPRPFHGGLNPSSFIPPYEP 151

Query: 147 GNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGN 206
                 + +    RIC GCN++IG G YL CM  F+HPECFRCHSC   IT+ EFS+SG 
Sbjct: 152 S-----YQYRRRQRICGGCNSDIGSGNYLGCMGTFFHPECFRCHSCGYAITEHEFSLSGT 206

Query: 207 RPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCER 266
           +PYHK C+KE  HPKC+VC +FIPTN AGLIEYR HPFW QKYCPSHE D T RCCSCER
Sbjct: 207 KPYHKLCFKELTHPKCEVCHHFIPTNDAGLIEYRCHPFWNQKYCPSHEYDKTARCCSCER 266

Query: 267 MEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVE 326
           +E  D +Y +L+DGR LCLEC+++AI DT ECQPLY  I+++YEG+ MK++QQ+P+LLV+
Sbjct: 267 LESWDVRYYTLEDGRSLCLECMETAITDTGECQPLYHAIRDYYEGMYMKLDQQIPMLLVQ 326

Query: 327 RQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRR 386
           R+ALN+A+ GEKNG+HH+PETRGLCLSEEQTVT+VLRRPR+GA +RL+ M T+P RL R+
Sbjct: 327 REALNDAIVGEKNGYHHMPETRGLCLSEEQTVTSVLRRPRLGA-HRLVGMRTQPQRLTRK 385

Query: 387 CEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGF 421
           CEVTAIL+LYGLPRLLTG+ILAHE+MH WLRL GF
Sbjct: 386 CEVTAILVLYGLPRLLTGAILAHELMHGWLRLNGF 420

Ubiquitin receptor that probably regulates developmental process.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJX9|DAR7_ARATH Protein DA1-related 7 OS=Arabidopsis thaliana GN=DAR7 PE=2 SV=2

 Score =  315 bits (808), Expect = 3e-85,   Method: Compositional matrix adjust.
 Identities = 173/390 (44%), Positives = 238/390 (61%), Gaps = 22/390 (5%)

Query: 44  EIDRAIALSLVEVDQKGKKVIENEYDSEDDLQCIKSDDSDEDELDEDEIRAIAQQEEDER 103
           E+D+++   + E DQ+  K++E     +      KS   ++D+++ DE +A+  QE    
Sbjct: 84  ELDKSV---VDEEDQQLSKIVEESLKEKG-----KSKQFEDDQVENDEQQALMVQESLYM 135

Query: 104 RAKAQQEEDERRARARAQLEEDEQLAKAIQDSLRVDSP------PRYESGNIFQ-PFPFF 156
              + Q E+++       L ED QL K I +S +          P  E GN+ +      
Sbjct: 136 VELSAQLEEDKNISTIPPLNEDAQLQKVIWESAKGKGQIEHFKDPVEEDGNLPRVDLNVN 195

Query: 157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE 216
             + IC GC + I +GR +  +   WHPECF C  C+ PI   EFS +  R  H  CY E
Sbjct: 196 HPHSICDGCKSAIEYGRSVHALGVNWHPECFCCRYCDKPIAMHEFSNTKGR-CHITCY-E 253

Query: 217 QHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLS 276
           + HP C VC+   P       +Y+ HPFW +KYCP HE DGTP+CCSCER+EP  TKY+ 
Sbjct: 254 RSHPNCHVCKKKFPGR-----KYKEHPFWKEKYCPFHEVDGTPKCCSCERLEPWGTKYVM 308

Query: 277 LDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEG 336
           L D R LC++C++ A+MDT+ECQPL+ EI+EF+  LNMKVE++ PLLLVE++AL +A   
Sbjct: 309 LADNRWLCVKCMECAVMDTYECQPLHFEIREFFGSLNMKVEKEFPLLLVEKEALKKAEAQ 368

Query: 337 EKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILY 396
           EK  + H   TRG+CLSE Q V +V ++P +G    L+ + TEP +++  CEVTAILILY
Sbjct: 369 EKIDNQHGVVTRGICLSEGQIVNSVFKKPTMGPNGELVSLGTEPQKVVGGCEVTAILILY 428

Query: 397 GLPRLLTGSILAHEMMHAWLRLKGFICFKL 426
           GLPRLLTG ILAHEMMHAWLRL G+   KL
Sbjct: 429 GLPRLLTGYILAHEMMHAWLRLNGYRNLKL 458

Ubiquitin receptor that probably regulates developmental process.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FJX8|DAR6_ARATH Protein DA1-related 6 OS=Arabidopsis thaliana GN=DAR6 PE=2 SV=1

 Score =  308 bits (788), Expect = 6e-83,   Method: Compositional matrix adjust.
 Identities = 159/354 (44%), Positives = 223/354 (62%), Gaps = 26/354 (7%)

Query: 78  KSDDSDEDELDEDEIRAIAQQEEDERRAKAQQEEDERRARARAQLEEDEQLAKAIQDSLR 137
           K    +++++ +DE  A+  QE         + E+      RA ++EDEQLAKA+++SL+
Sbjct: 199 KGKQFEDEQVKKDEQLALIVQESLNMVESPPRLEENNNISTRAPVDEDEQLAKAVEESLK 258

Query: 138 VDSPPRYESGNI--------FQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRC 189
                +     +          P P      +C GCN  + HG  ++ +   WHP CF C
Sbjct: 259 GKGQIKQSKDEVEGDGMLLELNPPP-----SLCGGCNFAVEHGGSVNILGVLWHPGCFCC 313

Query: 190 HSCNLPIT--DVEFSMSGNR-PYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWL 246
            +C+ PI   D+E  +S +R  +HK CY+      C VC+         +  Y  HPFW 
Sbjct: 314 RACHKPIAIHDIENHVSNSRGKFHKSCYERY----CYVCK------EKKMKTYNNHPFWE 363

Query: 247 QKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQ 306
           ++YCP HE DGTP+CCSCER+EPR++ Y+ L DGR LCLEC++SA+MD+ ECQPL+ +++
Sbjct: 364 ERYCPVHEADGTPKCCSCERLEPRESNYVMLADGRWLCLECMNSAVMDSDECQPLHFDMR 423

Query: 307 EFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPR 366
           +F+EGLNMK+E++ P LLVE+QALN+A + EK  + +   TRG+CLSEEQ V +V +RP 
Sbjct: 424 DFFEGLNMKIEKEFPFLLVEKQALNKAEKEEKIDYQYEVVTRGICLSEEQIVDSVSQRPV 483

Query: 367 IGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKG 420
            G   +L+ M TE  ++ R CEVTAILILYGLPRLLTG ILAHEMMHA+LRL G
Sbjct: 484 RGPNNKLVGMATESQKVTRECEVTAILILYGLPRLLTGYILAHEMMHAYLRLNG 537

Ubiquitin receptor that probably regulates developmental process.

Arabidopsis thaliana (taxid: 3702)

>sp|Q9FKN7|DAR4_ARATH Protein DA1-related 4 OS=Arabidopsis thaliana GN=DAR4 PE=1 SV=2

 Score =  286 bits (733), Expect = 2e-76,   Method: Compositional matrix adjust.
 Identities = 143/264 (54%), Positives = 184/264 (69%), Gaps = 7/264 (2%)

Query: 162  CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFS-MSGNRPYHKHCYKEQHHP 220
            C  C + I  G  ++   + WHP+CF C  C  PI   E S + G   YHK CYKE  HP
Sbjct: 1240 CKDCKSAIEDGISINAYGSVWHPQCFCCLRCREPIAMNEISDLRGM--YHKPCYKELRHP 1297

Query: 221  KCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDG 280
             C VC+  IP  + GL +Y  HPFW++ YCPSH+ DGTP+CCSCER+E   T+Y+ L D 
Sbjct: 1298 NCYVCEKKIPRTAEGL-KYHEHPFWMETYCPSHDGDGTPKCCSCERLEHCGTQYVMLADF 1356

Query: 281  RKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGE--- 337
            R LC EC+DSAIMD+ ECQPL+ EI+EF+EGL+MK+E++ P+ LVE+ ALN+A + E   
Sbjct: 1357 RWLCRECMDSAIMDSDECQPLHFEIREFFEGLHMKIEEEFPVYLVEKNALNKAEKEEKID 1416

Query: 338  KNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYG 397
            K G   L   RG+CLSEEQ VT+V +  R     +++D +TE  R++R+CEVTAILILYG
Sbjct: 1417 KQGDQCLMVVRGICLSEEQIVTSVSQGVRRMLNKQILDTVTESQRVVRKCEVTAILILYG 1476

Query: 398  LPRLLTGSILAHEMMHAWLRLKGF 421
            LPRLLTG ILAHEMMHA+LRL G+
Sbjct: 1477 LPRLLTGYILAHEMMHAYLRLNGY 1500

Arabidopsis thaliana (taxid: 3702)

>sp|Q9LVR6|DAR3_ARATH Protein DA1-related 3 OS=Arabidopsis thaliana GN=DAR3 PE=2 SV=2

 Score =  275 bits (704), Expect = 4e-73,   Method: Compositional matrix adjust.
 Identities = 153/349 (43%), Positives = 216/349 (61%), Gaps = 25/349 (7%)

Query: 80  DDSDEDELDEDEIRAIAQQEEDERRAKAQQEEDERRARARAQLEEDEQLAKAIQDSLRVD 139
           D+  E E  ++E   +A+Q E++RR +  +E+ +R      Q+++D+      +D  +++
Sbjct: 10  DEKIEIERVKEESLKLAKQAEEKRRLEESKEQGKR-----IQVDDDQLAKTTSKDKGQIN 64

Query: 140 SPPRYESGNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDV 199
                   ++  P P   G        +EIG G  +       +P C  C  C+ P    
Sbjct: 65  HSKDVVEEDV-NPPPSIDG-------KSEIGDGTSV-------NPRCLCCFHCHRPFVMH 109

Query: 200 EFSMSGNRPYHKHCYKEQHHPK-CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGT 258
           E    G   +H  CYKE +  + C VCQ  IP N+ G+ ++  HPFW +KYCP H+ DGT
Sbjct: 110 EILKKGK--FHIDCYKEYYRNRNCYVCQQKIPVNAEGIRKFSEHPFWKEKYCPIHDEDGT 167

Query: 259 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQ 318
            +CCSCER+EPR T Y+ L D R LC+EC+ SA+MDT+E QPL+ EI+EF+EGL +KV++
Sbjct: 168 AKCCSCERLEPRGTNYVMLGDFRWLCIECMGSAVMDTNEVQPLHFEIREFFEGLFLKVDK 227

Query: 319 QVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLI-DMI 377
           +  LLLVE+QALN+A E EK  +H    TRGLC+SEEQ V ++++ PR+G   +LI D++
Sbjct: 228 EFALLLVEKQALNKAEEEEKIDYHRAAVTRGLCMSEEQIVPSIIKGPRMGPDNQLITDIV 287

Query: 378 TEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGFICFKL 426
           TE  R +   EVT ILI+YGLPRLLTG ILAHEMMHAWLRL G+   KL
Sbjct: 288 TESQR-VSGFEVTGILIIYGLPRLLTGYILAHEMMHAWLRLNGYKNLKL 335

Arabidopsis thaliana (taxid: 3702)

>sp|Q84WJ0|DAR5_ARATH Protein DA1-related 5 OS=Arabidopsis thaliana GN=DAR5 PE=2 SV=2

 Score =  266 bits (679), Expect = 3e-70,   Method: Compositional matrix adjust.
 Identities = 133/263 (50%), Positives = 176/263 (66%), Gaps = 16/263 (6%)

Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPIT--DVEFSMSGNR-PYHKHCYKEQ 217
           +C GCN+ + H   ++ +   WHP CF C SC+ PI   ++E  +S +R  +HK CY+  
Sbjct: 346 MCGGCNSAVKHEESVNILGVLWHPGCFCCRSCDKPIAIHELENHVSNSRGKFHKSCYERY 405

Query: 218 HHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSL 277
               C VC+         +  Y  HPFW ++YCP HE DGTP+CCSCER+EPR TKY  L
Sbjct: 406 ----CYVCK------EKKMKTYNIHPFWEERYCPVHEADGTPKCCSCERLEPRGTKYGKL 455

Query: 278 DDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGE 337
            DGR LCLEC  SA MD+ ECQPLY ++++F+E LNMK+E++ PL+LV ++ LN+  + E
Sbjct: 456 SDGRWLCLECGKSA-MDSDECQPLYFDMRDFFESLNMKIEKEFPLILVRKELLNK--KEE 512

Query: 338 KNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYG 397
           K  +H+    R  C+SE++ +T V   PR G   +LIDM TEP  ++  C+VTAILILYG
Sbjct: 513 KIDNHYEVLIRAYCMSEQKIMTYVSEEPRTGQNKQLIDMDTEPQGVVHECKVTAILILYG 572

Query: 398 LPRLLTGSILAHEMMHAWLRLKG 420
           LPRLLTG ILAHEMMHAWLRL G
Sbjct: 573 LPRLLTGYILAHEMMHAWLRLNG 595

Arabidopsis thaliana (taxid: 3702)

>sp|P53776|LHX4_MOUSE LIM/homeobox protein Lhx4 OS=Mus musculus GN=Lhx4 PE=1 SV=4

 Score = 55.5 bits (132), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 36/130 (27%), Positives = 57/130 (43%), Gaps = 12/130 (9%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK 221
           CAGCN  I     L  ++  WH  C +C  C + + D  FS +G+  Y K  + ++   K
Sbjct: 30  CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGS-VYCKEDFFKRFGTK 88

Query: 222 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGR 281
           C  CQ  IP      +  +A  F    +C +        C  C R      ++  ++DGR
Sbjct: 89  CTACQQGIPPTQ---VVRKAQDFVYHLHCFA--------CIICNRQLATGDEFYLMEDGR 137

Query: 282 KLCLECLDSA 291
            +C E  ++A
Sbjct: 138 LVCKEDYETA 147

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

Mus musculus (taxid: 10090)

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

 Score = 55.5 bits (132), Expect = 9e-07,   Method: Compositional matrix adjust.
 Identities = 36/130 (27%), Positives = 57/130 (43%), Gaps = 12/130 (9%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK 221
           CAGCN  I     L  ++  WH  C +C  C + + D  FS +G+  Y K  + ++   K
Sbjct: 30  CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGS-VYCKEDFFKRFGTK 88

Query: 222 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGR 281
           C  CQ  IP      +  +A  F    +C +        C  C R      ++  ++DGR
Sbjct: 89  CTACQQGIPPTQ---VVRKAQDFVYHLHCFA--------CIICNRQLATGDEFYLMEDGR 137

Query: 282 KLCLECLDSA 291
            +C E  ++A
Sbjct: 138 LVCKEDYETA 147

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	431
356496814	546	PREDICTED: protein DA1-related 1-like is	0.969	0.765	0.731	0.0
356537914	563	PREDICTED: protein DA1-related 1-like is	0.955	0.731	0.700	0.0
356496816	528	PREDICTED: protein DA1-related 1-like is	0.937	0.765	0.726	1e-179
356537916	530	PREDICTED: protein DA1-related 1-like is	0.955	0.777	0.733	1e-179
255585154	525	zinc ion binding protein, putative [Rici	0.948	0.779	0.754	1e-178
297798208	558	hypothetical protein ARALYDRAFT_328082 [	0.965	0.745	0.716	1e-176
356502199	531	PREDICTED: protein DA1-related 1-like [G	0.953	0.774	0.735	1e-176
357518461	531	Disease resistance-like protein [Medicag	0.953	0.774	0.737	1e-174
17065046	553	Unknown protein [Arabidopsis thaliana] g	0.969	0.755	0.696	1e-170
240256211	553	LIM domain-containing protein [Arabidops	0.969	0.755	0.696	1e-170

>gi|356496814|ref|XP_003517260.1| PREDICTED: protein DA1-related 1-like isoform 1 [Glycine max]

 Score =  648 bits (1672), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 321/439 (73%), Positives = 361/439 (82%), Gaps = 21/439 (4%)

Query: 1   MGWLTKILKGSS----RRHYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEV 56
           MGW TK+LKGS     R  YH +YG+DR WD   +S+ DD +  + E+IDRAIALSL E 
Sbjct: 1   MGWFTKLLKGSDYKILRGQYHGKYGEDRIWD-NHHSSMDDLTDIEKEDIDRAIALSLSEE 59

Query: 57  DQKGKKVIENEYDSEDDLQCIKSDDSDED----ELDEDEIRAIAQQEEDERRAKAQQEED 112
           D KGKKV++ +  SED+  C   D+ DE      L+E+E  A  QQEE+ER AK QQ  D
Sbjct: 60  DHKGKKVVDYDSQSEDEELCKIDDEEDEHLVKVHLEEEERLAKIQQEEEERLAKIQQ--D 117

Query: 113 ERRAR--------ARAQLEEDEQLAKAIQDSLRVDSPPRYESGNIFQPFP--FFSGYRIC 162
           ER A+        A+AQLEEDEQLA+AIQ+SL++ SPPRY++ +    FP  F  GYRIC
Sbjct: 118 ERLAKIQQEDERLAKAQLEEDEQLARAIQESLKIGSPPRYDNDSSILSFPHLFPPGYRIC 177

Query: 163 AGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKC 222
           AGC TEIG GR+LSCM   WHPECF CH+C+LPITD EFSMS NRPYHK CY+E+HHP+C
Sbjct: 178 AGCKTEIGQGRFLSCMGGVWHPECFCCHACHLPITDYEFSMSSNRPYHKACYREKHHPRC 237

Query: 223 DVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRK 282
           DVC+NFIPTNS+GLIEYRAHPFWLQKYCPSHE DGTPRCCSCERME RDTKYL LDDGRK
Sbjct: 238 DVCKNFIPTNSSGLIEYRAHPFWLQKYCPSHELDGTPRCCSCERMESRDTKYLLLDDGRK 297

Query: 283 LCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHH 342
           LCLECLDS+IMDTHECQPLYLEIQEFYEGLNMK+EQQ+P+LLVERQALNEAMEGEKNGHH
Sbjct: 298 LCLECLDSSIMDTHECQPLYLEIQEFYEGLNMKLEQQIPMLLVERQALNEAMEGEKNGHH 357

Query: 343 HLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLL 402
           HLPETRGLCLSEEQTVTT+ RRPRIGAGYR IDMITEPYRLIR CEVTAIL+LYGLPRLL
Sbjct: 358 HLPETRGLCLSEEQTVTTISRRPRIGAGYRAIDMITEPYRLIRHCEVTAILVLYGLPRLL 417

Query: 403 TGSILAHEMMHAWLRLKGF 421
           TGSILAHEMMHAWLRLKG+
Sbjct: 418 TGSILAHEMMHAWLRLKGY 436

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356537914|ref|XP_003537451.1| PREDICTED: protein DA1-related 1-like isoform 1 [Glycine max]

 Score =  639 bits (1649), Expect = 0.0,   Method: Compositional matrix adjust.
 Identities = 323/461 (70%), Positives = 361/461 (78%), Gaps = 49/461 (10%)

Query: 1   MGWLTKILKGSS----RRHYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEV 56
           MGW TK+LKGS     R  YH +YG+DR WD   +S+ DD +  + E+IDRAIALSL E 
Sbjct: 1   MGWFTKLLKGSDHKILRGQYHGKYGEDRIWD-NHHSSMDDLTDIEKEDIDRAIALSLSEE 59

Query: 57  DQKGKKVIENEYDSEDDLQCIKSDDSDEDE------LDEDEIRAIAQQEEDERRAKAQQE 110
           D KGKKV++ E          K DD +EDE      LDEDE  A  QQEE+ER AK QQE
Sbjct: 60  DHKGKKVVDEEL--------CKIDDDEEDEHLVKVHLDEDERLAKIQQEEEERLAKIQQE 111

Query: 111 ----------EDERRAR------------------ARAQLEEDEQLAKAIQDSLRVDSPP 142
                     E+ER A+                  A+AQLEEDEQLA+AIQ+SL++ SPP
Sbjct: 112 DEHLAKIQQEEEERLAKIQQEDECLAKIQQEDERLAKAQLEEDEQLARAIQESLKIGSPP 171

Query: 143 RYESGNIFQPFP--FFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVE 200
           +Y++G+    FP  F  GYRICAGC TEIG GR+LSCM   WHPECF CH+C+LPITD E
Sbjct: 172 QYDNGSSILSFPHLFPPGYRICAGCKTEIGQGRFLSCMGGVWHPECFCCHACHLPITDYE 231

Query: 201 FSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPR 260
           FSMS NRPYHK CY+E+HHP+CDVC+NFIPTNS+GLIEYRAHPFWLQKYCPSHE DGT R
Sbjct: 232 FSMSSNRPYHKSCYREKHHPRCDVCKNFIPTNSSGLIEYRAHPFWLQKYCPSHELDGTSR 291

Query: 261 CCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQV 320
           CCSCERMEPRDTKYL LDDGRKLCLECLDS+IMDTHECQPLYLEIQEFYEGLNMK+EQQ+
Sbjct: 292 CCSCERMEPRDTKYLLLDDGRKLCLECLDSSIMDTHECQPLYLEIQEFYEGLNMKLEQQI 351

Query: 321 PLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEP 380
           P+LLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTT+ RRPRI AGYR IDMITEP
Sbjct: 352 PMLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTISRRPRIAAGYRAIDMITEP 411

Query: 381 YRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGF 421
           YRLIR CEVTAIL+LYGLPRLLTGSILAHEMMHAWLRLKG+
Sbjct: 412 YRLIRCCEVTAILVLYGLPRLLTGSILAHEMMHAWLRLKGY 452

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356496816|ref|XP_003517261.1| PREDICTED: protein DA1-related 1-like isoform 2 [Glycine max]

 Score =  634 bits (1635), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 316/435 (72%), Positives = 353/435 (81%), Gaps = 31/435 (7%)

Query: 1   MGWLTKILKGSS----RRHYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEV 56
           MGW TK+LKGS     R  YH +YG+DR WD   +S+ DD +  + E+IDRAIALSL E 
Sbjct: 1   MGWFTKLLKGSDYKILRGQYHGKYGEDRIWD-NHHSSMDDLTDIEKEDIDRAIALSLSEE 59

Query: 57  DQKGKKVIENEYDSEDDLQCIKSDDSDEDELDEDEIRAIAQQEEDERRAKAQQEEDERRA 116
           D KGKKV+        D   +K        L+E+E  A  QQEE+ER AK QQ  DER A
Sbjct: 60  DHKGKKVV--------DEHLVKV------HLEEEERLAKIQQEEEERLAKIQQ--DERLA 103

Query: 117 R--------ARAQLEEDEQLAKAIQDSLRVDSPPRYESGNIFQPFP--FFSGYRICAGCN 166
           +        A+AQLEEDEQLA+AIQ+SL++ SPPRY++ +    FP  F  GYRICAGC 
Sbjct: 104 KIQQEDERLAKAQLEEDEQLARAIQESLKIGSPPRYDNDSSILSFPHLFPPGYRICAGCK 163

Query: 167 TEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQ 226
           TEIG GR+LSCM   WHPECF CH+C+LPITD EFSMS NRPYHK CY+E+HHP+CDVC+
Sbjct: 164 TEIGQGRFLSCMGGVWHPECFCCHACHLPITDYEFSMSSNRPYHKACYREKHHPRCDVCK 223

Query: 227 NFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLE 286
           NFIPTNS+GLIEYRAHPFWLQKYCPSHE DGTPRCCSCERME RDTKYL LDDGRKLCLE
Sbjct: 224 NFIPTNSSGLIEYRAHPFWLQKYCPSHELDGTPRCCSCERMESRDTKYLLLDDGRKLCLE 283

Query: 287 CLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPE 346
           CLDS+IMDTHECQPLYLEIQEFYEGLNMK+EQQ+P+LLVERQALNEAMEGEKNGHHHLPE
Sbjct: 284 CLDSSIMDTHECQPLYLEIQEFYEGLNMKLEQQIPMLLVERQALNEAMEGEKNGHHHLPE 343

Query: 347 TRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSI 406
           TRGLCLSEEQTVTT+ RRPRIGAGYR IDMITEPYRLIR CEVTAIL+LYGLPRLLTGSI
Sbjct: 344 TRGLCLSEEQTVTTISRRPRIGAGYRAIDMITEPYRLIRHCEVTAILVLYGLPRLLTGSI 403

Query: 407 LAHEMMHAWLRLKGF 421
           LAHEMMHAWLRLKG+
Sbjct: 404 LAHEMMHAWLRLKGY 418

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356537916|ref|XP_003537452.1| PREDICTED: protein DA1-related 1-like isoform 2 [Glycine max]

 Score =  634 bits (1635), Expect = e-179,   Method: Compositional matrix adjust.
 Identities = 314/428 (73%), Positives = 357/428 (83%), Gaps = 16/428 (3%)

Query: 1   MGWLTKILKGSS----RRHYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEV 56
           MGW TK+LKGS     R  YH +YG+DR WD   +S+ DD +  + E+IDRAIALSL E 
Sbjct: 1   MGWFTKLLKGSDHKILRGQYHGKYGEDRIWD-NHHSSMDDLTDIEKEDIDRAIALSLSEE 59

Query: 57  DQKGKKVIENEYDSEDDLQCIKSDDSDEDELDEDEIRAIAQ-QEEDERRAKAQQEEDERR 115
           D KGKKV+E     E+ L  I+ +D    ++ ++E   +A+ Q+EDE  AK QQE DER 
Sbjct: 60  DHKGKKVVE-----EERLAKIQQEDEHLAKIQQEEEERLAKIQQEDECLAKIQQE-DERL 113

Query: 116 ARARAQLEEDEQLAKAIQDSLRVDSPPRYESGNIFQPFP--FFSGYRICAGCNTEIGHGR 173
           A+A  QLEEDEQLA+AIQ+SL++ SPP+Y++G+    FP  F  GYRICAGC TEIG GR
Sbjct: 114 AKA--QLEEDEQLARAIQESLKIGSPPQYDNGSSILSFPHLFPPGYRICAGCKTEIGQGR 171

Query: 174 YLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNS 233
           +LSCM   WHPECF CH+C+LPITD EFSMS NRPYHK CY+E+HHP+CDVC+NFIPTNS
Sbjct: 172 FLSCMGGVWHPECFCCHACHLPITDYEFSMSSNRPYHKSCYREKHHPRCDVCKNFIPTNS 231

Query: 234 AGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIM 293
           +GLIEYRAHPFWLQKYCPSHE DGT RCCSCERMEPRDTKYL LDDGRKLCLECLDS+IM
Sbjct: 232 SGLIEYRAHPFWLQKYCPSHELDGTSRCCSCERMEPRDTKYLLLDDGRKLCLECLDSSIM 291

Query: 294 DTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLS 353
           DTHECQPLYLEIQEFYEGLNMK+EQQ+P+LLVERQALNEAMEGEKNGHHHLPETRGLCLS
Sbjct: 292 DTHECQPLYLEIQEFYEGLNMKLEQQIPMLLVERQALNEAMEGEKNGHHHLPETRGLCLS 351

Query: 354 EEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMH 413
           EEQTVTT+ RRPRI AGYR IDMITEPYRLIR CEVTAIL+LYGLPRLLTGSILAHEMMH
Sbjct: 352 EEQTVTTISRRPRIAAGYRAIDMITEPYRLIRCCEVTAILVLYGLPRLLTGSILAHEMMH 411

Query: 414 AWLRLKGF 421
           AWLRLKG+
Sbjct: 412 AWLRLKGY 419

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255585154|ref|XP_002533282.1| zinc ion binding protein, putative [Ricinus communis] gi|223526907|gb|EEF29114.1| zinc ion binding protein, putative [Ricinus communis]

 Score =  632 bits (1630), Expect = e-178,   Method: Compositional matrix adjust.
 Identities = 320/424 (75%), Positives = 355/424 (83%), Gaps = 15/424 (3%)

Query: 1   MGWLTKILKGSSRR-HYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEVDQK 59
           MGWLTKI KGSS +  YH R+G+DR W+E  + +ADD S FD EE+D AIALSL E DQK
Sbjct: 1   MGWLTKIFKGSSYKGQYHGRFGEDRYWEEP-HRSADDLSDFDREELDCAIALSLSEEDQK 59

Query: 60  GKKVIENEYDSEDDLQCIKSDDSDEDELDEDEIRAIAQQEEDERRAKAQQEEDERRARAR 119
           GKKVIE + DS+          S+EDE          +   +E   +A+ EEDE+RA+A 
Sbjct: 60  GKKVIEEDNDSQQ---------SEEDERRARAEEEEKRTTAEEEEKRARAEEDEKRAKA- 109

Query: 120 AQLEEDEQLAKAIQDSLRVDSPPRYESGNIFQPFP--FFSGYRICAGCNTEIGHGRYLSC 177
            QLEEDEQLAKA+Q++L V+SPPRY+  N F P+P  F SGYRICAGCNT IGHGR+LSC
Sbjct: 110 -QLEEDEQLAKALQETLTVNSPPRYDFENAFSPYPVLFPSGYRICAGCNTVIGHGRFLSC 168

Query: 178 MEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLI 237
           M A WHP CFRC++CN PI+D EFSMSGNRP+HK CYKE+HHPKCDVC NFIPTNS+GLI
Sbjct: 169 MGAVWHPVCFRCNACNQPISDYEFSMSGNRPFHKSCYKERHHPKCDVCNNFIPTNSSGLI 228

Query: 238 EYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHE 297
           EYRAHPFWLQKYCPSHERDGTPRCCSCERME  DT+YLSLDDGRKLCLECLDSAIMDTHE
Sbjct: 229 EYRAHPFWLQKYCPSHERDGTPRCCSCERMESTDTRYLSLDDGRKLCLECLDSAIMDTHE 288

Query: 298 CQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQT 357
           CQPLY EI+EFYEGLNMKVEQ+VPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEE T
Sbjct: 289 CQPLYFEIREFYEGLNMKVEQEVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEHT 348

Query: 358 VTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLR 417
           +TTV RRPRIGAGYR ID+ITEPYRL RRCEVTAILILYGLPRLLTGSILAHEMMHAWLR
Sbjct: 349 ITTVSRRPRIGAGYRFIDLITEPYRLSRRCEVTAILILYGLPRLLTGSILAHEMMHAWLR 408

Query: 418 LKGF 421
           LKG+
Sbjct: 409 LKGY 412

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297798208|ref|XP_002866988.1| hypothetical protein ARALYDRAFT_328082 [Arabidopsis lyrata subsp. lyrata] gi|297312824|gb|EFH43247.1| hypothetical protein ARALYDRAFT_328082 [Arabidopsis lyrata subsp. lyrata]

 Score =  623 bits (1607), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 326/455 (71%), Positives = 362/455 (79%), Gaps = 39/455 (8%)

Query: 1   MGWLTKILKGSSRR----HYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEV 56
           MGWLTKILKGSS +      + RY +DR  +  RYSA  + S FD EEI+ AIALSL E 
Sbjct: 1   MGWLTKILKGSSHKFSDGQCNGRYREDRNLEGPRYSA--EGSDFDKEEIECAIALSLSEQ 58

Query: 57  ------DQKGKKVIENEYDSEDDLQCIKSDDSDEDEL---------------------DE 89
                 D KGKKVIE  Y SE +      D+ +++E                      +E
Sbjct: 59  EHVIPQDDKGKKVIE--YKSETEEDDDDEDEDEDEEYMRAQLEAAEEEERRVAQAQIKEE 116

Query: 90  DEIRAIAQQEEDERR-AKAQQEEDERRARARAQLEEDEQLAKAIQDSLRVDSPPRYESGN 148
           ++ RA AQ EE E++ AKA+ EE+E R RA+AQLEEDEQLAKAIQ+S+ V SPPRY+ GN
Sbjct: 117 EKRRAEAQLEEIEKQLAKARLEEEEMR-RAKAQLEEDEQLAKAIQESMNVGSPPRYDLGN 175

Query: 149 IFQPFPFF--SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGN 206
           I QP+PF   S +RICAGC  EIGHGR+LSCM   WHPECF CH+C+ PI D EFSMSGN
Sbjct: 176 ILQPYPFLIPSSHRICAGCQAEIGHGRFLSCMGGVWHPECFCCHACDKPIIDYEFSMSGN 235

Query: 207 RPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCER 266
           RPYHK CYKEQHHPKCDVC NFIPTN AGLIEYRAHPFW+QKYCPSHERDGTPRCCSCER
Sbjct: 236 RPYHKLCYKEQHHPKCDVCHNFIPTNPAGLIEYRAHPFWMQKYCPSHERDGTPRCCSCER 295

Query: 267 MEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVE 326
           MEP+DTKYL LDDGRKLCLECLDSAIMDTHECQPLYLEI+EFYEGL+MKVEQQ+P+LLVE
Sbjct: 296 MEPKDTKYLILDDGRKLCLECLDSAIMDTHECQPLYLEIREFYEGLHMKVEQQIPMLLVE 355

Query: 327 RQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRR 386
           R ALNEAMEGEK+GHHHLPETRGLCLSEEQTVTTVLRRPRIGAGY+LIDMITEP RLIRR
Sbjct: 356 RSALNEAMEGEKHGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYKLIDMITEPCRLIRR 415

Query: 387 CEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGF 421
           CEVTAILILYGLPRLLTGSILAHEMMHAWLRL G+
Sbjct: 416 CEVTAILILYGLPRLLTGSILAHEMMHAWLRLNGY 450

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356502199|ref|XP_003519908.1| PREDICTED: protein DA1-related 1-like [Glycine max]

 Score =  622 bits (1605), Expect = e-176,   Method: Compositional matrix adjust.
 Identities = 314/427 (73%), Positives = 353/427 (82%), Gaps = 16/427 (3%)

Query: 1   MGWLTKILKGSSRR----HYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEV 56
           MGW TK+LKGS+R+     YH +Y DDR  D    SA DD +  + EEI RAIALSL E 
Sbjct: 1   MGWFTKLLKGSNRKSSGGRYHGKYEDDRISDNLDCSA-DDLTDIEKEEIGRAIALSLSEA 59

Query: 57  DQKGKKVIENEYDSEDDLQCIKSDDSDEDELDEDEIRAIAQQEEDERRAKAQQEEDERRA 116
           D+KGKKVIE++ +SEDD  C  SD+       E E     QQ+ED+  AK QQ+ED  + 
Sbjct: 60  DKKGKKVIEDDSESEDDELCPLSDE-------EAESVGEVQQDEDDHHAKIQQDED--KH 110

Query: 117 RARAQLEEDEQLAKAIQDSLRVDSPPRYESGNIFQPFP--FFSGYRICAGCNTEIGHGRY 174
               QLEEDEQLA+AIQ+SL + SPPR E+ ++FQPF   F   YRIC+GCN EIGHGR+
Sbjct: 111 LDEVQLEEDEQLARAIQESLSISSPPRSETDSLFQPFAHLFPPVYRICSGCNAEIGHGRF 170

Query: 175 LSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSA 234
           LSCM  +WHPECF CH+C LPITD EFSMSGNR YHK CYKE HHP+CDVC+NFIP NSA
Sbjct: 171 LSCMGGYWHPECFCCHACKLPITDYEFSMSGNRRYHKSCYKELHHPRCDVCKNFIPPNSA 230

Query: 235 GLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMD 294
           GLIEYRAHPFWLQKYCPSHERDGTPRCCSC+R+E  DTKYL LDDGRKLCLECLDSAIMD
Sbjct: 231 GLIEYRAHPFWLQKYCPSHERDGTPRCCSCQRLESVDTKYLLLDDGRKLCLECLDSAIMD 290

Query: 295 THECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSE 354
           THECQPLY+EIQEFYEGL+MK+EQQVP+LLVERQALNEAMEGEKNGHHHLPETRGLCLSE
Sbjct: 291 THECQPLYVEIQEFYEGLHMKIEQQVPMLLVERQALNEAMEGEKNGHHHLPETRGLCLSE 350

Query: 355 EQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHA 414
           EQTV T+LRRPRIGAGY+LIDMITEP+RL+RRCEVTAIL+LYGLPRLLTGSILAHEMMHA
Sbjct: 351 EQTVPTILRRPRIGAGYQLIDMITEPFRLVRRCEVTAILVLYGLPRLLTGSILAHEMMHA 410

Query: 415 WLRLKGF 421
           WLRLKG+
Sbjct: 411 WLRLKGY 417

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|357518461|ref|XP_003629519.1| Disease resistance-like protein [Medicago truncatula] gi|355523541|gb|AET03995.1| Disease resistance-like protein [Medicago truncatula]

 Score =  616 bits (1588), Expect = e-174,   Method: Compositional matrix adjust.
 Identities = 318/431 (73%), Positives = 352/431 (81%), Gaps = 20/431 (4%)

Query: 1   MGWLTKILKGSSRRH----YHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEV 56
           MGWLTK LKGS+ +H    Y  +YG DR  D    +AADD + F+ EEIDRAIA+SL EV
Sbjct: 1   MGWLTKFLKGSNHKHSGRGYTGKYGHDRDSDNHD-NAADDLNDFEREEIDRAIAISLSEV 59

Query: 57  ---DQKGKKVIENEYDSEDDLQCIKSDDSDEDELDEDEIRAIAQQEEDERRAKAQQEEDE 113
              D KGKKVIE + +SEDD  C   D+ D      D +  + Q EED   AK QQEEDE
Sbjct: 60  SEEDHKGKKVIEEDSESEDDELCPLDDEED------DHVGDVEQDEED-HVAKIQQEEDE 112

Query: 114 RRARARAQLEEDEQLAKAIQDSLRVDSPPRYESGNIFQPFP--FFSGYRICAGCNTEIGH 171
             +    QLEEDEQLA+AIQ+SL +DS P  ++ +IFQPF   F   YRICAGCN EIGH
Sbjct: 113 --SLDEVQLEEDEQLARAIQESLSIDSSPPSQTDSIFQPFTNLFSPVYRICAGCNVEIGH 170

Query: 172 GRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPT 231
           GR+LSCM A WHPECF CH+C LPITD E+SMSGNRPYHK CYKE HHP+CDVC+ FIP 
Sbjct: 171 GRFLSCMGAVWHPECFCCHACKLPITDYEYSMSGNRPYHKSCYKELHHPRCDVCKIFIPQ 230

Query: 232 NSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 291
           NSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSC+RME  DTKYL LDDGRKLCLECLDSA
Sbjct: 231 NSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCQRMESTDTKYLLLDDGRKLCLECLDSA 290

Query: 292 IMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGH-HHLPETRGL 350
           IMDTHECQPLYLEIQEFYEGL+MK+EQQ+P+LLVERQALNEAMEGEKNGH HHLPETRGL
Sbjct: 291 IMDTHECQPLYLEIQEFYEGLHMKIEQQIPMLLVERQALNEAMEGEKNGHNHHLPETRGL 350

Query: 351 CLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHE 410
           CLSEEQTV T+LRRP IGAGYR+IDMITEP+RLIRRCEVTAIL+LYGLPRLLTGSILAHE
Sbjct: 351 CLSEEQTVPTILRRPSIGAGYRVIDMITEPFRLIRRCEVTAILVLYGLPRLLTGSILAHE 410

Query: 411 MMHAWLRLKGF 421
           MMHAWLRLKG+
Sbjct: 411 MMHAWLRLKGY 421

Source: Medicago truncatula

Species: Medicago truncatula

Genus: Medicago

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|17065046|gb|AAL32677.1| Unknown protein [Arabidopsis thaliana] gi|21387149|gb|AAM47978.1| unknown protein [Arabidopsis thaliana]

 Score =  604 bits (1558), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 315/452 (69%), Positives = 358/452 (79%), Gaps = 34/452 (7%)

Query: 1   MGWLTKILKGSSRRHY----HARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEV 56
           MGWLTKILKGSS +      + RY +DR  +  RYSA  + S FD EEI+ AIALSL E 
Sbjct: 1   MGWLTKILKGSSHKFSDGQCNGRYREDRNLEGPRYSA--EGSDFDKEEIECAIALSLSEQ 58

Query: 57  ------DQKGKKVIENEYDSEDDLQC------------IKSDDSDEDELDEDEIRAIA-- 96
                 D KGKK+IE + ++E+D               +++ + +E  + + +I      
Sbjct: 59  EHVIPQDDKGKKIIEYKSETEEDDDDDEDEDEEYMRAQLEAAEEEERRVAQAQIEEEEKR 118

Query: 97  ----QQEEDERR-AKAQQEEDERRARARAQLEEDEQLAKAIQDSLRVDSPPRYESGNIFQ 151
               Q EE E+  AKA+ EE+E R R++AQLEEDE LAKA+Q+S+ V SPPRY+ GNI Q
Sbjct: 119 RAEAQLEETEKLLAKARLEEEEMR-RSKAQLEEDELLAKALQESMNVGSPPRYDPGNILQ 177

Query: 152 PFPFF--SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPY 209
           P+PF   S +RIC GC  EIGHGR+LSCM   WHPECF C++C+ PI D EFSMSGNRPY
Sbjct: 178 PYPFLIPSSHRICVGCQAEIGHGRFLSCMGGVWHPECFCCNACDKPIIDYEFSMSGNRPY 237

Query: 210 HKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEP 269
           HK CYKEQHHPKCDVC NFIPTN AGLIEYRAHPFW+QKYCPSHERDGTPRCCSCERMEP
Sbjct: 238 HKLCYKEQHHPKCDVCHNFIPTNPAGLIEYRAHPFWMQKYCPSHERDGTPRCCSCERMEP 297

Query: 270 RDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQA 329
           +DTKYL LDDGRKLCLECLDSAIMDTHECQPLYLEI+EFYEGL+MKVEQQ+P+LLVER A
Sbjct: 298 KDTKYLILDDGRKLCLECLDSAIMDTHECQPLYLEIREFYEGLHMKVEQQIPMLLVERSA 357

Query: 330 LNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEV 389
           LNEAMEGEK+GHHHLPETRGLCLSEEQTVTTVLRRPRIGAGY+LIDMITEP RLIRRCEV
Sbjct: 358 LNEAMEGEKHGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYKLIDMITEPCRLIRRCEV 417

Query: 390 TAILILYGLPRLLTGSILAHEMMHAWLRLKGF 421
           TAILILYGLPRLLTGSILAHEMMHAWLRL G+
Sbjct: 418 TAILILYGLPRLLTGSILAHEMMHAWLRLNGY 449

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|240256211|ref|NP_195404.6| LIM domain-containing protein [Arabidopsis thaliana] gi|334302915|sp|Q8W4F0.3|DAR1_ARATH RecName: Full=Protein DA1-related 1 gi|332661310|gb|AEE86710.1| LIM domain-containing protein [Arabidopsis thaliana]

 Score =  604 bits (1558), Expect = e-170,   Method: Compositional matrix adjust.
 Identities = 315/452 (69%), Positives = 358/452 (79%), Gaps = 34/452 (7%)

Query: 1   MGWLTKILKGSSRRHY----HARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEV 56
           MGWLTKILKGSS +      + RY +DR  +  RYSA  + S FD EEI+ AIALSL E 
Sbjct: 1   MGWLTKILKGSSHKFSDGQCNGRYREDRNLEGPRYSA--EGSDFDKEEIECAIALSLSEQ 58

Query: 57  ------DQKGKKVIENEYDSEDDLQC------------IKSDDSDEDELDEDEIRAIA-- 96
                 D KGKK+IE + ++E+D               +++ + +E  + + +I      
Sbjct: 59  EHVIPQDDKGKKIIEYKSETEEDDDDDEDEDEEYMRAQLEAAEEEERRVAQAQIEEEEKR 118

Query: 97  ----QQEEDERR-AKAQQEEDERRARARAQLEEDEQLAKAIQDSLRVDSPPRYESGNIFQ 151
               Q EE E+  AKA+ EE+E R R++AQLEEDE LAKA+Q+S+ V SPPRY+ GNI Q
Sbjct: 119 RAEAQLEETEKLLAKARLEEEEMR-RSKAQLEEDELLAKALQESMNVGSPPRYDPGNILQ 177

Query: 152 PFPFF--SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPY 209
           P+PF   S +RIC GC  EIGHGR+LSCM   WHPECF C++C+ PI D EFSMSGNRPY
Sbjct: 178 PYPFLIPSSHRICVGCQAEIGHGRFLSCMGGVWHPECFCCNACDKPIIDYEFSMSGNRPY 237

Query: 210 HKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEP 269
           HK CYKEQHHPKCDVC NFIPTN AGLIEYRAHPFW+QKYCPSHERDGTPRCCSCERMEP
Sbjct: 238 HKLCYKEQHHPKCDVCHNFIPTNPAGLIEYRAHPFWMQKYCPSHERDGTPRCCSCERMEP 297

Query: 270 RDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQA 329
           +DTKYL LDDGRKLCLECLDSAIMDTHECQPLYLEI+EFYEGL+MKVEQQ+P+LLVER A
Sbjct: 298 KDTKYLILDDGRKLCLECLDSAIMDTHECQPLYLEIREFYEGLHMKVEQQIPMLLVERSA 357

Query: 330 LNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEV 389
           LNEAMEGEK+GHHHLPETRGLCLSEEQTVTTVLRRPRIGAGY+LIDMITEP RLIRRCEV
Sbjct: 358 LNEAMEGEKHGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYKLIDMITEPCRLIRRCEV 417

Query: 390 TAILILYGLPRLLTGSILAHEMMHAWLRLKGF 421
           TAILILYGLPRLLTGSILAHEMMHAWLRL G+
Sbjct: 418 TAILILYGLPRLLTGSILAHEMMHAWLRLNGY 449

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

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	431
TAIR|locus:2115290	553	AT4G36860 [Arabidopsis thalian	0.682	0.531	0.851	3.3e-160
TAIR|locus:2202175	532	DA1 "DA1" [Arabidopsis thalian	0.642	0.520	0.746	3e-127
TAIR|locus:2063932	528	DAR2 "DA1-related protein 2" [	0.628	0.513	0.677	8.9e-113
TAIR|locus:2154880	644	DAR6 "DA1-related protein 6" [	0.649	0.434	0.496	7.5e-78
TAIR|locus:2170338	1613	DAR4 "DA1-related protein 4" [	0.596	0.159	0.541	3.4e-73
TAIR|locus:2154890	702	DAR5 "DA1-related protein 5" [	0.573	0.351	0.509	1e-68
WB|WBGene00012379	192	Y1A5A.1 [Caenorhabditis elegan	0.299	0.671	0.305	4.1e-10
UNIPROTKB|F6QGM2	214	LHX3 "LIM/homeobox protein Lhx	0.280	0.565	0.270	6.2e-08
UNIPROTKB|F1PCI5	395	LHX4 "Uncharacterized protein"	0.296	0.324	0.274	1.3e-07
UNIPROTKB|F1MFM7	390	LHX4 "Uncharacterized protein"	0.273	0.302	0.276	2.1e-07

TAIR|locus:2115290 AT4G36860 [Arabidopsis thaliana (taxid:3702)]

 Score = 1417 (503.9 bits), Expect = 3.3e-160, Sum P(2) = 3.3e-160
 Identities = 252/296 (85%), Positives = 271/296 (91%)

Query:   128 LAKAIQDSLRVDSPPRYESGNIFQPFPFF--SGYRICAGCNTEIGHGRYLSCMEAFWHPE 185
             LAKA+Q+S+ V SPPRY+ GNI QP+PF   S +RIC GC  EIGHGR+LSCM   WHPE
Sbjct:   154 LAKALQESMNVGSPPRYDPGNILQPYPFLIPSSHRICVGCQAEIGHGRFLSCMGGVWHPE 213

Query:   186 CFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFW 245
             CF C++C+ PI D EFSMSGNRPYHK CYKEQHHPKCDVC NFIPTN AGLIEYRAHPFW
Sbjct:   214 CFCCNACDKPIIDYEFSMSGNRPYHKLCYKEQHHPKCDVCHNFIPTNPAGLIEYRAHPFW 273

Query:   246 LQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEI 305
             +QKYCPSHERDGTPRCCSCERMEP+DTKYL LDDGRKLCLECLDSAIMDTHECQPLYLEI
Sbjct:   274 MQKYCPSHERDGTPRCCSCERMEPKDTKYLILDDGRKLCLECLDSAIMDTHECQPLYLEI 333

Query:   306 QEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRP 365
             +EFYEGL+MKVEQQ+P+LLVER ALNEAMEGEK+GHHHLPETRGLCLSEEQTVTTVLRRP
Sbjct:   334 REFYEGLHMKVEQQIPMLLVERSALNEAMEGEKHGHHHLPETRGLCLSEEQTVTTVLRRP 393

Query:   366 RIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGF 421
             RIGAGY+LIDMITEP RLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRL G+
Sbjct:   394 RIGAGYKLIDMITEPCRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLNGY 449

GO:0005886 "plasma membrane" evidence=ISM;IDA

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2202175 DA1 "DA1" [Arabidopsis thaliana (taxid:3702)]

 Score = 1198 (426.8 bits), Expect = 3.0e-127, Sum P(2) = 3.0e-127
 Identities = 209/280 (74%), Positives = 245/280 (87%)

Query:   144 YESGNIFQPFP--FFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEF 201
             Y +G+I+ P P  F   +RICAGCN EIGHGR+L+C+ + WHPECFRC+ C+ PI++ EF
Sbjct:   152 YANGDIYYPRPITFQMDFRICAGCNMEIGHGRFLNCLNSLWHPECFRCYGCSQPISEYEF 211

Query:   202 SMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRC 261
             S SGN P+HK CY+E++HPKCDVC +FIPTN AGLIEYRAHPFW+QKYCPSHE D TPRC
Sbjct:   212 STSGNYPFHKACYRERYHPKCDVCSHFIPTNHAGLIEYRAHPFWVQKYCPSHEHDATPRC 271

Query:   262 CSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVP 321
             CSCERMEPR+T+Y+ L+DGRKLCLECLDSA+MDT +CQPLYL+IQ FYEGLNMKVEQ+VP
Sbjct:   272 CSCERMEPRNTRYVELNDGRKLCLECLDSAVMDTMQCQPLYLQIQNFYEGLNMKVEQEVP 331

Query:   322 LLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPY 381
             LLLVERQALNEA EGEKNGH+H+PETRGLCLSEEQTV+TV +R + G G +    ITEPY
Sbjct:   332 LLLVERQALNEAREGEKNGHYHMPETRGLCLSEEQTVSTVRKRSKHGTG-KWAGNITEPY 390

Query:   382 RLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGF 421
             +L R+CEVTAILIL+GLPRLLTGSILAHEMMHAW+RLKGF
Sbjct:   391 KLTRQCEVTAILILFGLPRLLTGSILAHEMMHAWMRLKGF 430

GO:0005634 "nucleus" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043130 "ubiquitin binding" evidence=IDA;IPI

GO:0046621 "negative regulation of organ growth" evidence=IMP

GO:0048317 "seed morphogenesis" evidence=IMP

GO:0048482 "ovule morphogenesis" evidence=IMP

TAIR|locus:2063932 DAR2 "DA1-related protein 2" [Arabidopsis thaliana (taxid:3702)]

 Score = 1073 (382.8 bits), Expect = 8.9e-113, Sum P(2) = 8.9e-113
 Identities = 185/273 (67%), Positives = 228/273 (83%)

Query:   150 FQP-FPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRP 208
             ++P + +    RIC GCN++IG G YL CM  F+HPECFRCHSC   IT+ EFS+SG +P
Sbjct:   149 YEPSYQYRRRQRICGGCNSDIGSGNYLGCMGTFFHPECFRCHSCGYAITEHEFSLSGTKP 208

Query:   209 YHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERME 268
             YHK C+KE  HPKC+VC +FIPTN AGLIEYR HPFW QKYCPSHE D T RCCSCER+E
Sbjct:   209 YHKLCFKELTHPKCEVCHHFIPTNDAGLIEYRCHPFWNQKYCPSHEYDKTARCCSCERLE 268

Query:   269 PRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQ 328
               D +Y +L+DGR LCLEC+++AI DT ECQPLY  I+++YEG+ MK++QQ+P+LLV+R+
Sbjct:   269 SWDVRYYTLEDGRSLCLECMETAITDTGECQPLYHAIRDYYEGMYMKLDQQIPMLLVQRE 328

Query:   329 ALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCE 388
             ALN+A+ GEKNG+HH+PETRGLCLSEEQTVT+VLRRPR+GA +RL+ M T+P RL R+CE
Sbjct:   329 ALNDAIVGEKNGYHHMPETRGLCLSEEQTVTSVLRRPRLGA-HRLVGMRTQPQRLTRKCE 387

Query:   389 VTAILILYGLPRLLTGSILAHEMMHAWLRLKGF 421
             VTAIL+LYGLPRLLTG+ILAHE+MH WLRL GF
Sbjct:   388 VTAILVLYGLPRLLTGAILAHELMHGWLRLNGF 420

GO:0008270 "zinc ion binding" evidence=IEA

GO:0010088 "phloem development" evidence=IMP

GO:0048364 "root development" evidence=IMP

TAIR|locus:2154880 DAR6 "DA1-related protein 6" [Arabidopsis thaliana (taxid:3702)]

 Score = 749 (268.7 bits), Expect = 7.5e-78, Sum P(2) = 7.5e-78
 Identities = 150/302 (49%), Positives = 204/302 (67%)

Query:   128 LAKAIQDSLR-----VDSPPRYES-GNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAF 181
             LAKA+++SL+       S    E  G + +  P  S   +C GCN  + HG  ++ +   
Sbjct:   249 LAKAVEESLKGKGQIKQSKDEVEGDGMLLELNPPPS---LCGGCNFAVEHGGSVNILGVL 305

Query:   182 WHPECFRCHSCNLPIT--DVEFSMSGNR-PYHKHCYKEQHHPKCDVCQNFIPTNSAGLIE 238
             WHP CF C +C+ PI   D+E  +S +R  +HK CY E++   C VC+         +  
Sbjct:   306 WHPGCFCCRACHKPIAIHDIENHVSNSRGKFHKSCY-ERY---CYVCKE------KKMKT 355

Query:   239 YRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHEC 298
             Y  HPFW ++YCP HE DGTP+CCSCER+EPR++ Y+ L DGR LCLEC++SA+MD+ EC
Sbjct:   356 YNNHPFWEERYCPVHEADGTPKCCSCERLEPRESNYVMLADGRWLCLECMNSAVMDSDEC 415

Query:   299 QPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTV 358
             QPL+ ++++F+EGLNMK+E++ P LLVE+QALN+A + EK  + +   TRG+CLSEEQ V
Sbjct:   416 QPLHFDMRDFFEGLNMKIEKEFPFLLVEKQALNKAEKEEKIDYQYEVVTRGICLSEEQIV 475

Query:   359 TTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRL 418
              +V +RP  G   +L+ M TE  ++ R CEVTAILILYGLPRLLTG ILAHEMMHA+LRL
Sbjct:   476 DSVSQRPVRGPNNKLVGMATESQKVTRECEVTAILILYGLPRLLTGYILAHEMMHAYLRL 535

Query:   419 KG 420
              G
Sbjct:   536 NG 537

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

TAIR|locus:2170338 DAR4 "DA1-related protein 4" [Arabidopsis thaliana (taxid:3702)]

 Score = 751 (269.4 bits), Expect = 3.4e-73, P = 3.4e-73
 Identities = 143/264 (54%), Positives = 184/264 (69%)

Query:   162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFS-MSGNRPYHKHCYKEQHHP 220
             C  C + I  G  ++   + WHP+CF C  C  PI   E S + G   YHK CYKE  HP
Sbjct:  1240 CKDCKSAIEDGISINAYGSVWHPQCFCCLRCREPIAMNEISDLRGM--YHKPCYKELRHP 1297

Query:   221 KCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDG 280
              C VC+  IP  + GL +Y  HPFW++ YCPSH+ DGTP+CCSCER+E   T+Y+ L D 
Sbjct:  1298 NCYVCEKKIPRTAEGL-KYHEHPFWMETYCPSHDGDGTPKCCSCERLEHCGTQYVMLADF 1356

Query:   281 RKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEK-- 338
             R LC EC+DSAIMD+ ECQPL+ EI+EF+EGL+MK+E++ P+ LVE+ ALN+A + EK  
Sbjct:  1357 RWLCRECMDSAIMDSDECQPLHFEIREFFEGLHMKIEEEFPVYLVEKNALNKAEKEEKID 1416

Query:   339 -NGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYG 397
               G   L   RG+CLSEEQ VT+V +  R     +++D +TE  R++R+CEVTAILILYG
Sbjct:  1417 KQGDQCLMVVRGICLSEEQIVTSVSQGVRRMLNKQILDTVTESQRVVRKCEVTAILILYG 1476

Query:   398 LPRLLTGSILAHEMMHAWLRLKGF 421
             LPRLLTG ILAHEMMHA+LRL G+
Sbjct:  1477 LPRLLTGYILAHEMMHAYLRLNGY 1500

GO:0005634 "nucleus" evidence=ISM

GO:0006952 "defense response" evidence=IEA;ISS;IMP

GO:0008270 "zinc ion binding" evidence=IEA

GO:0009409 "response to cold" evidence=IMP

GO:0043531 "ADP binding" evidence=IEA

TAIR|locus:2154890 DAR5 "DA1-related protein 5" [Arabidopsis thaliana (taxid:3702)]

 Score = 697 (250.4 bits), Expect = 1.0e-68, P = 1.0e-68
 Identities = 134/263 (50%), Positives = 178/263 (67%)

Query:   161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPIT--DVEFSMSGNR-PYHKHCYKEQ 217
             +C GCN+ + H   ++ +   WHP CF C SC+ PI   ++E  +S +R  +HK CY E+
Sbjct:   346 MCGGCNSAVKHEESVNILGVLWHPGCFCCRSCDKPIAIHELENHVSNSRGKFHKSCY-ER 404

Query:   218 HHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSL 277
             +   C VC+         +  Y  HPFW ++YCP HE DGTP+CCSCER+EPR TKY  L
Sbjct:   405 Y---CYVCKE------KKMKTYNIHPFWEERYCPVHEADGTPKCCSCERLEPRGTKYGKL 455

Query:   278 DDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGE 337
              DGR LCLEC  SA MD+ ECQPLY ++++F+E LNMK+E++ PL+LV ++ LN+  + E
Sbjct:   456 SDGRWLCLECGKSA-MDSDECQPLYFDMRDFFESLNMKIEKEFPLILVRKELLNK--KEE 512

Query:   338 KNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILILYG 397
             K  +H+    R  C+SE++ +T V   PR G   +LIDM TEP  ++  C+VTAILILYG
Sbjct:   513 KIDNHYEVLIRAYCMSEQKIMTYVSEEPRTGQNKQLIDMDTEPQGVVHECKVTAILILYG 572

Query:   398 LPRLLTGSILAHEMMHAWLRLKG 420
             LPRLLTG ILAHEMMHAWLRL G
Sbjct:   573 LPRLLTGYILAHEMMHAWLRLNG 595

GO:0008270 "zinc ion binding" evidence=IEA

GO:0043531 "ADP binding" evidence=IEA

WB|WBGene00012379 Y1A5A.1 [Caenorhabditis elegans (taxid:6239)]

 Score = 151 (58.2 bits), Expect = 4.1e-10, P = 4.1e-10
 Identities = 47/154 (30%), Positives = 65/154 (42%)

Query:   142 PRYESGNIFQPFPFFS--------GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCN 193
             P +ES +I  P  +F+          R+C  C+  IG    L  M   WHP+ F C SC 
Sbjct:    39 PLFESKSIITPVFYFNCKRMDRSIDRRLCGHCHQSIG-SEALVAMNRLWHPDHFTCSSCK 97

Query:   194 LPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSH 253
              PI    F  + N  Y   C+ ++++PKC  C   +      L+    H  W       H
Sbjct:    98 RPIKQT-FQAADNHAYCVQCFAQKYNPKCAGCMETLVDTC--LLALDRH--W-------H 145

Query:   254 ERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLEC 287
              R  T  C SC R  P    YL +DD +   L+C
Sbjct:   146 PRCFT--CSSCNRPLPNGEFYL-VDD-KPYDLDC 175

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|F6QGM2 LHX3 "LIM/homeobox protein Lhx3" [Gallus gallus (taxid:9031)]

 Score = 143 (55.4 bits), Expect = 6.2e-08, P = 6.2e-08
 Identities = 36/133 (27%), Positives = 56/133 (42%)

Query:   152 PFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHK 211
             PFP      +CAGCN  I     L  ++  WH +C +C  C   + +  FS  G+  Y K
Sbjct:    18 PFPRSPEIPLCAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAEKCFSR-GDGVYCK 76

Query:   212 HCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRD 271
               + ++   KC  CQ  IP      +  RA  F    +C +        C  C+R     
Sbjct:    77 EDFFKRFGTKCAACQQGIPPTQ---VVRRAQDFVYHLHCFA--------CIVCKRQLATG 125

Query:   272 TKYLSLDDGRKLC 284
              ++  ++D R +C
Sbjct:   126 DEFYLMEDSRLVC 138

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

GO:0001890 "placenta development" evidence=IEA

GO:0005667 "transcription factor complex" evidence=IEA

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

GO:0021520 "spinal cord motor neuron cell fate specification" evidence=IEA

GO:0021521 "ventral spinal cord interneuron specification" evidence=IEA

GO:0021526 "medial motor column neuron differentiation" evidence=IEA

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

GO:0021983 "pituitary gland development" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

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

GO:0048839 "inner ear development" evidence=IEA

UNIPROTKB|F1PCI5 LHX4 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 149 (57.5 bits), Expect = 1.3e-07, P = 1.3e-07
 Identities = 39/142 (27%), Positives = 61/142 (42%)

Query:   150 FQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPY 209
             F P P  +    CAGCN  I     L  ++  WH  C +C  C + + D  FS +G+  Y
Sbjct:    25 FSPLP--AEIPQCAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGS-VY 81

Query:   210 HKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEP 269
              K  + ++   KC  CQ  IP      +  +A  F    +C +        C  C R   
Sbjct:    82 CKEDFFKRFGTKCTACQQGIPPTQ---VVRKAQDFVYHLHCFA--------CIICNRQLA 130

Query:   270 RDTKYLSLDDGRKLCLECLDSA 291
                ++  ++DGR +C E  ++A
Sbjct:   131 TGDEFYLMEDGRLVCKEDYETA 152

GO:0005634 "nucleus" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0021526 "medial motor column neuron differentiation" evidence=IEA

GO:0009887 "organ morphogenesis" evidence=IEA

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

GO:0001890 "placenta development" 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|F1MFM7 LHX4 "Uncharacterized protein" [Bos taurus (taxid:9913)]

 Score = 147 (56.8 bits), Expect = 2.1e-07, P = 2.1e-07
 Identities = 36/130 (27%), Positives = 57/130 (43%)

Query:   162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK 221
             CAGCN  I     L  ++  WH  C +C  C + + D  FS +G+  Y K  + ++   K
Sbjct:    30 CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGS-VYCKEDFFKRFGTK 88

Query:   222 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGR 281
             C  CQ  IP      +  +A  F    +C +        C  C R      ++  ++DGR
Sbjct:    89 CTACQQGIPPTQ---VVRKAQDFVYHLHCFA--------CIICNRQLATGDEFYLMEDGR 137

Query:   282 KLCLECLDSA 291
              +C E  ++A
Sbjct:   138 LVCKEDYETA 147

GO:0005634 "nucleus" evidence=IEA

GO:0043066 "negative regulation of apoptotic process" evidence=IEA

GO:0021526 "medial motor column neuron differentiation" evidence=IEA

GO:0009887 "organ morphogenesis" evidence=IEA

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

GO:0001890 "placenta development" 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

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
Q8W4F0	DAR1_ARATH	No assigned EC number	0.6969	0.9698	0.7558	yes	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	431
pfam12315	212	pfam12315, DUF3633, Protein of unknown function (D	2e-77
cd09396	53	cd09396, LIM_DA1, The Lim domain of DA1	7e-28
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	3e-12
cd09332	52	cd09332, LIM2_PINCH, The second LIM domain of prot	9e-09
pfam00412	58	pfam00412, LIM, LIM domain	9e-09
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	1e-08
cd09338	53	cd09338, LIM3_Paxillin_like, The third LIM domain	3e-07
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	4e-07
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	5e-07
cd09410	53	cd09410, LIM3_Leupaxin, The third LIM domain of Le	8e-07
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	2e-06
cd09454	52	cd09454, LIM1_ZASP_Cypher, The first LIM domain of	6e-06
cd09341	56	cd09341, LIM2_Testin_like, The second LIM domain o	2e-05
cd09409	53	cd09409, LIM3_Paxillin, The third LIM domain of pa	2e-05
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	8e-05
cd09468	52	cd09468, LIM1_Lhx4, The first LIM domain of Lhx4	1e-04
cd09397	58	cd09397, LIM1_UF1, LIM domain in proteins of unkno	1e-04
cd09421	59	cd09421, LIM3_LIMPETin, The third LIM domain of pr	1e-04
cd09434	56	cd09434, LIM4_FHL3, The fourth LIM domain of Four	2e-04
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	2e-04
cd09339	52	cd09339, LIM4_Paxillin_like, The fourth LIM domain	2e-04
cd09429	53	cd09429, LIM3_FHL1, The third LIM domain of Four a	3e-04
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	3e-04
cd09343	59	cd09343, LIM1_FHL, The first LIM domain of Four an	3e-04
cd09336	53	cd09336, LIM1_Paxillin_like, The first LIM domain	3e-04
cd09394	55	cd09394, LIM1_Rga, The first LIM domain of Rga GTP	4e-04
pfam07767	387	pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)	4e-04
cd09337	52	cd09337, LIM2_Paxillin_like, The second LIM domain	6e-04
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	6e-04
cd09345	54	cd09345, LIM2_FHL, The second LIM domain of Four a	7e-04
cd09456	52	cd09456, LIM2_Enigma, The second LIM domain of Eni	7e-04
cd09466	56	cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a	8e-04
cd09362	52	cd09362, LIM2_Enigma_like, The second LIM domain o	8e-04
cd09350	54	cd09350, LIM1_TRIP6, The first LIM domain of Thyro	8e-04
cd09467	55	cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b	8e-04
cd09430	52	cd09430, LIM5_LIMPETin, The fifth LIM domain of pr	0.001
cd09412	52	cd09412, LIM4_Leupaxin, The fourth LIM domain of L	0.001
cd09347	56	cd09347, LIM4_FHL, The fourth LIM domain of Four a	0.001
cd09386	55	cd09386, LIM1_LMO4, The first LIM domain of LMO4 (	0.001
cd09455	54	cd09455, LIM1_Enigma_like_1, The first LIM domain	0.001
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	0.001
cd09346	52	cd09346, LIM3_FHL, The third LIM domain of Four an	0.001
cd09433	58	cd09433, LIM4_FHL2, The fourth LIM domain of Four	0.001
cd09368	52	cd09368, LIM1_Lhx3_Lhx4, The first LIM domain of L	0.002
pfam04889	241	pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle cont	0.002
COG0330	291	COG0330, HflC, Membrane protease subunits, stomati	0.002
cd09334	54	cd09334, LIM4_PINCH, The fourth LIM domain of prot	0.002
cd09391	57	cd09391, LIM1_Lrg1p_like, The first LIM domain of	0.002
PRK07353	140	PRK07353, PRK07353, F0F1 ATP synthase subunit B';	0.003
cd09464	55	cd09464, LIM2_LIMK1, The second LIM domain of LIMK	0.004
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	0.004
cd09340	58	cd09340, LIM1_Testin_like, The first LIM domain of	0.004
cd09395	53	cd09395, LIM2_Rga, The second LIM domain of Rga GT	0.004

>gnl|CDD|204878 pfam12315, DUF3633, Protein of unknown function (DUF3633)

 Score =  239 bits (611), Expect = 2e-77
 Identities = 90/111 (81%), Positives = 100/111 (90%)

Query: 311 GLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAG 370
           GLNMK+EQ++P+LLVERQALN+A EGEK GHHH PETRGLCLSEEQ VT+VL+RPRIG G
Sbjct: 1   GLNMKIEQEIPMLLVERQALNKAREGEKIGHHHTPETRGLCLSEEQIVTSVLKRPRIGPG 60

Query: 371 YRLIDMITEPYRLIRRCEVTAILILYGLPRLLTGSILAHEMMHAWLRLKGF 421
            RLI M TEP +L RRCEVTAIL+LYGLPRLLTGSILAHEMMHAWLRL G+
Sbjct: 61  NRLIGMGTEPQKLTRRCEVTAILVLYGLPRLLTGSILAHEMMHAWLRLNGY 111

This domain family is found in bacteria and eukaryotes, and is approximately 210 amino acids in length. The family is found in association with pfam00412. Length = 212

>gnl|CDD|188782 cd09396, LIM_DA1, The Lim domain of DA1

 Score =  104 bits (261), Expect = 7e-28
 Identities = 37/53 (69%), Positives = 43/53 (81%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           CAGC +EIGHGR+LS + A WHPECFRCH+C  PI + EFS+SGN PYHK CY
Sbjct: 1   CAGCKSEIGHGRFLSALGAVWHPECFRCHACRKPIAEHEFSVSGNDPYHKSCY 53

The Lim domain of DA1: DA1 contains one copy of LIM domain and a domain of unknown function. DA1 is predicted as an ubiquitin receptor, which sets final seed and organ size by restricting the period of cell proliferation. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

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

 Score = 60.8 bits (148), Expect = 3e-12
 Identities = 20/53 (37%), Positives = 25/53 (47%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           CAGC   I     L  +   WHPECF+C  C  P+    F     +PY + CY
Sbjct: 1   CAGCGKPIEGRELLRALGKKWHPECFKCSVCGKPLGGDSFYEKDGKPYCEKCY 53

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

>gnl|CDD|188718 cd09332, LIM2_PINCH, The second LIM domain of protein PINCH

 Score = 50.8 bits (122), Expect = 9e-09
 Identities = 19/52 (36%), Positives = 24/52 (46%), Gaps = 1/52 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHC 213
           C  C  E   GR +  M   WHP+CFRC  CN  + D+ F  +  R     C
Sbjct: 1   CGKCG-EFVIGRVIKAMNNNWHPDCFRCEICNKELADIGFVKNAGRALCHPC 51

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

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

 Score = 51.2 bits (123), Expect = 9e-09
 Identities = 22/55 (40%), Positives = 27/55 (49%), Gaps = 3/55 (5%)

Query: 162 CAGCNTEIGHGRYLS--CMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           CAGC   I + R L    +   WHPECFRC  C  P+   +F     + Y KH Y
Sbjct: 1   CAGCGKPI-YDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDY 54

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

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

 Score = 50.5 bits (121), Expect = 1e-08
 Identities = 21/54 (38%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 161 ICAGCNTEI-GHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHC 213
            CAGC   I G  R L  +   WHPECF+C +C  P++   F     + Y K C
Sbjct: 1   KCAGCGKPIYGTERVLRALGKVWHPECFKCATCGKPLSGDTFFEKDGKLYCKDC 54

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

>gnl|CDD|188724 cd09338, LIM3_Paxillin_like, The third LIM domain of the paxillin like protein family

 Score = 46.9 bits (112), Expect = 3e-07
 Identities = 21/54 (38%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPY---HKH 212
           C GCN  I    Y+S +   WHPECF C  C+ P  +  F      PY   H H
Sbjct: 1   CGGCNKPI-LENYISALNTQWHPECFVCRECHKPFINGSFFEHEGLPYCETHYH 53

The third LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

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

 Score = 46.2 bits (110), Expect = 4e-07
 Identities = 19/53 (35%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           CAGC  EI +G+ L  ++  WH  CF+C  C   +T       G +PY +  Y
Sbjct: 1   CAGCGQEIKNGQALLALDKQWHVWCFKCKECGKVLTGEYMGKDG-KPYCERDY 52

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

>gnl|CDD|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like family

 Score = 45.8 bits (109), Expect = 5e-07
 Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           CA CN  I  G +L  +   WHPE F C  C+  + ++ F       Y + CY
Sbjct: 1   CAHCNQVI-RGPFLVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

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

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

 Score = 45.6 bits (108), Expect = 8e-07
 Identities = 20/48 (41%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPY 209
           C+GC   +    YLS     WHPECF C  C  P TD  F     RP 
Sbjct: 1   CSGCGRPVKEN-YLSAANGVWHPECFVCSDCLKPFTDGSFFELDGRPL 47

The third LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein (TLP)

 Score = 44.6 bits (106), Expect = 2e-06
 Identities = 14/53 (26%), Positives = 20/53 (37%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           C  C   +      + +   WH  C RC  C   +T  + S    +PY   CY
Sbjct: 1   CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNKCY 53

The LIM domain of thymus LIM protein (TLP) like proteins: This family includes the LIM domains of TLP and CRIP (Cysteine-Rich Intestinal Protein). TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. CRIP is a short LIM protein with only one LIM domain. CRIP gene is developmentally regulated and can be induced by glucocorticoid hormones during the first three postnatal weeks. The domain shows close sequence homology to LIM domain of thymus LIM protein. However, unlike the TLP proteins which have two LIM domains, the members of this family have only one LIM domain. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188838 cd09454, LIM1_ZASP_Cypher, The first LIM domain of ZASP/Cypher family

 Score = 43.0 bits (101), Expect = 6e-06
 Identities = 21/53 (39%), Positives = 27/53 (50%), Gaps = 1/53 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           C  CN  I  G +L  +   WHPE F CH C+  + DV F    N  Y ++CY
Sbjct: 1   CGHCNNII-RGPFLVALGRSWHPEEFTCHYCHTSLADVSFVEEQNNVYCENCY 52

The first LIM domain of ZASP/Cypher family: ZASP was identified in human heart and skeletal muscle and Cypher is a mice ortholog of ZASP. ZASP/Cyppher contains three LIM domains at the C-terminus and a PDZ domain at N-terminus. 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|188727 cd09341, LIM2_Testin_like, The second LIM domain of Testin-like family

 Score = 41.8 bits (99), Expect = 2e-05
 Identities = 16/53 (30%), Positives = 23/53 (43%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           CA C+  I  G Y       WH + F C  C+ P+    + +   +PY   CY
Sbjct: 3   CAACDELIFSGEYTQAEGKNWHLKHFCCFQCDEPLGGQRYVLREGKPYCLDCY 55

The second LIM domain of Testin-like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

>gnl|CDD|188793 cd09409, LIM3_Paxillin, The third LIM domain of paxillin

 Score = 41.4 bits (97), Expect = 2e-05
 Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 1/48 (2%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPY 209
           C GC   I    Y+S +   WHPECF C  C  P  +  F     +PY
Sbjct: 1   CGGCARAILEN-YISALNTLWHPECFVCRECFTPFVNGSFFEHDGQPY 47

The third LIM domain of paxillin: Paxillin is an adaptor protein, which recruits key components of the signal-transduction machinery to specific sub-cellular locations to respond to environmental changes rapidly. The C-terminal region of paxillin contains four LIM domains which target paxillin to focal adhesions, presumably through a direct association with the cytoplasmic tail of beta-integrin. The N-terminal of paxillin is leucine-rich LD-motifs. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. The binding partners of paxillin are diverse and include protein tyrosine kinases, such as Src and FAK, structural proteins, such as vinculin and actopaxin, and regulators of actin organization. Paxillin recruits these proteins to their function sites to control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

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

 Score = 39.7 bits (93), Expect = 8e-05
 Identities = 16/44 (36%), Positives = 24/44 (54%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSG 205
           CAGC+  I     L+ ++  WH +C +C  C  P+T+  FS  G
Sbjct: 1   CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTEKCFSREG 44

The first LIM domain of Lhx1 (also known as Lim1) and Lhx5. Lhx1 and Lhx5 are closely related members of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx1 is required for regulating the vertebrate head organizer, the nervous system, and female reproductive tract development. During embryogenesis in the mouse, Lhx1 is expressed early in mesodermal tissue, then later during urogenital, kidney, liver, and nervous system development. In the adult, expression is restricted to the kidney and brain. A mouse embryos with Lhx1 gene knockout cannot grow normal anterior head structures, kidneys, and gonads, but with normally developed trunk and tail morphology. In the developing nervous system, Lhx1 is required to direct the trajectories of motor axons in the limb. Lhx1 null female mice lack the oviducts and uterus. Lhx5 protein may play complementary or overlapping roles with Lhx1. The expression of Lhx5 in the anterior portion of the mouse neural tube suggests a role in patterning of the forebrain. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188852 cd09468, LIM1_Lhx4, The first LIM domain of Lhx4

 Score = 39.6 bits (92), Expect = 1e-04
 Identities = 16/45 (35%), Positives = 23/45 (51%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGN 206
           CAGCN  I     L  ++  WH  C +C  C + + +  FS +GN
Sbjct: 1   CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLAERCFSRAGN 45

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

>gnl|CDD|188783 cd09397, LIM1_UF1, LIM domain in proteins of unknown function

 Score = 39.2 bits (92), Expect = 1e-04
 Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)

Query: 182 WHPECFRCHSCNLPITD-VEFSMSGNRPYHKHCY 214
           WH ECF C +C  P    V   +  ++PY +  Y
Sbjct: 24  WHRECFVCTTCGCPFQFSVPCYVLDDKPYCQQHY 57

The first Lim domain of a LIM domain containing protein: The functions of the proteins are unknown. The members of this family contain two copies of LIM domain. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 58

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

 Score = 39.5 bits (92), Expect = 1e-04
 Identities = 18/54 (33%), Positives = 25/54 (46%), Gaps = 1/54 (1%)

Query: 162 CAGCNTEIG-HGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           C  C+  IG   + LS  +  WH  CF C  C + + D  F    +R Y  +CY
Sbjct: 5   CEECSKIIGIDSKDLSYKDKHWHEACFLCSKCKISLVDKPFGSKADRIYCGNCY 58

The third LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 59

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

 Score = 39.0 bits (91), Expect = 2e-04
 Identities = 15/36 (41%), Positives = 21/36 (58%), Gaps = 3/36 (8%)

Query: 162 CAGCNTEI---GHGRYLSCMEAFWHPECFRCHSCNL 194
           CA CN  I   G G+Y+S  +  WH  CF+C  C++
Sbjct: 1   CAACNKPITGFGGGKYVSFEDRQWHQPCFKCSRCSV 36

The fourth LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 56

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

 Score = 39.1 bits (91), Expect = 2e-04
 Identities = 14/32 (43%), Positives = 19/32 (59%)

Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSC 192
           +CA C   I  G+YL  + + WH +CFRC  C
Sbjct: 21  VCASCGQSIYDGQYLQALNSDWHADCFRCCEC 52

The first LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 74

>gnl|CDD|188725 cd09339, LIM4_Paxillin_like, The fourth LIM domain of the Paxillin-like protein family

 Score = 38.5 bits (90), Expect = 2e-04
 Identities = 18/53 (33%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           CAGC   I  GR ++ M   +HPE F C  C   ++   F    ++PY   C+
Sbjct: 1   CAGCGKPI-TGRCITAMGRKFHPEHFVCAFCLKQLSKGTFKEQDDKPYCHPCF 52

The fourth LIM domain of the Paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188813 cd09429, LIM3_FHL1, The third LIM domain of Four and a half LIM domains protein 1 (FHL1)

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYK 215
           C  CN  I  G  ++  +  WH ECF C SC+  +    F+   ++ Y   CYK
Sbjct: 1   CVKCNKPITSGG-VTYQDQPWHSECFVCSSCSKKLAGQRFTAVEDQYYCVDCYK 53

The third LIM domain of Four and a half LIM domains protein 1 (FHL1): FHL1 is heavily expressed in skeletal and cardiac muscles. It plays important roles in muscle growth, differentiation, and sarcomere assembly by acting as a modulator of transcription factors. Defects in FHL1 gene are responsible for a number of Muscular dystrophy-like muscle disorders. It has been detected that FHL1 binds to Myosin-binding protein C, regulating myosin filament formation and sarcomere assembly. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

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

 Score = 38.3 bits (89), Expect = 3e-04
 Identities = 15/51 (29%), Positives = 22/51 (43%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKH 212
           C GC   I    +   ++  WH  CF+C  C   +T+  +   G    HKH
Sbjct: 1   CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLTNWYYEKDGKLYCHKH 51

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|188729 cd09343, LIM1_FHL, The first LIM domain of Four and a half LIM domains protein (FHL)

 Score = 38.6 bits (90), Expect = 3e-04
 Identities = 16/54 (29%), Positives = 22/54 (40%), Gaps = 1/54 (1%)

Query: 162 CAGCNTEIGH-GRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           C  C  +IG   + LS  +  WH  CF+C  C   + D  F+          CY
Sbjct: 5   CEECKKKIGCDSKDLSYKDRHWHEGCFKCFKCQRSLVDKPFAAKDEDLLCTECY 58

The first 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 = 59

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

 Score = 38.1 bits (89), Expect = 3e-04
 Identities = 16/53 (30%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           CA C   I  G+ ++ +   WHPE F C  C   +    F     +PY +  Y
Sbjct: 1   CAACKKPIV-GQVVTALGKTWHPEHFVCAECKTELGTKNFFERDGQPYCEKDY 52

The first LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188780 cd09394, LIM1_Rga, The first LIM domain of Rga GTPase-Activating Proteins

 Score = 38.1 bits (89), Expect = 4e-04
 Identities = 11/36 (30%), Positives = 16/36 (44%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPIT 197
           C GC   I  G         WH  CF+C+ C+  ++
Sbjct: 1   CVGCKESITEGHAYELGGDRWHIHCFKCYKCDKKLS 36

The first LIM domain of Rga GTPase-Activating Proteins: The members of this family contain two tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Rga activates GTPases during polarized morphogenesis. In yeast, a known regulating target of Rga is CDC42p, a small GTPase. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|219563 pfam07767, Nop53, Nop53 (60S ribosomal biogenesis)

 Score = 42.0 bits (99), Expect = 4e-04
 Identities = 23/98 (23%), Positives = 45/98 (45%), Gaps = 4/98 (4%)

Query: 43  EEIDRAIALSLVEVDQKGKKVIENEYDSEDDLQCIKSDDSDEDELDEDEIRAIAQQEEDE 102
           E+    +A     +D+  + ++E   D  +     +SDD    E  E E   I +    +
Sbjct: 221 EKKLEKMAPEASRLDEMSEGLLEESDDDGE----EESDDESAWEGFESEYEPINKPVRPK 276

Query: 103 RRAKAQQEEDERRARARAQLEEDEQLAKAIQDSLRVDS 140
           R+ KAQ+ +++RR     + +E++QL K +    R+  
Sbjct: 277 RKTKAQRNKEKRRKELEREAKEEKQLKKKLAQLARLKE 314

This nucleolar family of proteins are involved in 60S ribosomal biogenesis. They are specifically involved in the processing beyond the 27S stage of 25S rRNA maturation. This family contains sequences that bear similarity to the glioma tumour suppressor candidate region gene 2 protein (p60). This protein has been found to interact with herpes simplex type 1 regulatory proteins. Length = 387

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

 Score = 37.4 bits (87), Expect = 6e-04
 Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           CA CN  I   + ++ ++  WHPE F C  C  P  D  F     +PY +  Y
Sbjct: 1   CAYCNGPILD-KCVTALDKTWHPEHFFCAQCGKPFGDEGFHEKDGKPYCREDY 52

The second LIM domain of the paxillin like protein family: This family consists of paxillin, leupaxin, Hic-5 (ARA55), and other related proteins. There are four LIM domains in the C-terminal of the proteins and leucine-rich LD-motifs in the N-terminal region. Members of this family are adaptor proteins to recruit key components of signal-transduction machinery to specific sub-cellular locations. Paxillin is found at the interface between the plasma membrane and the actin cytoskeleton. Paxillin serves as a platform for the recruitment of numerous regulatory and structural proteins that together control the dynamic changes in cell adhesion, cytoskeletal reorganization and gene expression that are necessary for cell migration and survival. Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. It associates with focal adhesion kinases PYK2 and pp125FAK and identified to be a component of the osteoclast pososomal signaling complex. Hic-5 controls cell proliferation, migration and senescence by functioning as coactivator for steroid receptors such as androgen receptor, glucocorticoid receptor and progesterone receptor. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188831 cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP)

 Score = 37.4 bits (87), Expect = 6e-04
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 5/58 (8%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH 219
           CA C   +     L+C++  WH  CF+C  C + +      M   + Y+K  Y   H+
Sbjct: 1   CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLN-----MKNYKGYNKKPYCNAHY 53

The LIM domain of LIM and SH3 Protein (LASP): LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains ,but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. 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|188731 cd09345, LIM2_FHL, The second LIM domain of Four and a half LIM domains protein (FHL)

 Score = 37.3 bits (87), Expect = 7e-04
 Identities = 17/54 (31%), Positives = 22/54 (40%), Gaps = 1/54 (1%)

Query: 162 CAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           C  C   I  G + +     FWH +CF C  C  PI    F    ++ Y   CY
Sbjct: 1   CKACGKAIMPGSKKMEYKGKFWHEKCFTCSECKKPIGTKSFIPKDDKIYCVPCY 54

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|188840 cd09456, LIM2_Enigma, The second LIM domain of Enigma

 Score = 37.3 bits (86), Expect = 7e-04
 Identities = 18/53 (33%), Positives = 25/53 (47%), Gaps = 1/53 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           CA C  +I  G  +  ++  WH  CF C +C  PI +  F M    PY +  Y
Sbjct: 1   CAKCKKKIT-GEIMHALKMTWHVHCFTCAACKTPIRNRAFYMEEGAPYCERDY 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|188850 cd09466, LIM1_Lhx3a, The first LIM domain of Lhx3a

 Score = 37.1 bits (86), Expect = 8e-04
 Identities = 16/44 (36%), Positives = 21/44 (47%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSG 205
           CAGC+  I     L   +  WH +C +C  C   +TD  FS  G
Sbjct: 4   CAGCDHPIFDRFILKVQDKPWHSKCLKCVDCQAQLTDKCFSRGG 47

The first LIM domain of Lhx3a: Lhx3a is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3a is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 56

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

 Score = 37.1 bits (86), Expect = 8e-04
 Identities = 17/48 (35%), Positives = 24/48 (50%), Gaps = 1/48 (2%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPY 209
           CA C+ +I  G  +  ++  WH  CF C +C  PI +  F M    PY
Sbjct: 1   CARCHKKI-LGEVMHALKQTWHVSCFVCAACKQPIGNSLFHMEDGEPY 47

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

 Score = 37.0 bits (86), Expect = 8e-04
 Identities = 15/54 (27%), Positives = 24/54 (44%), Gaps = 1/54 (1%)

Query: 162 CAGCNTE-IGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           C  C    +G G   + M+  +H +CF C +CN  +    F     + Y + CY
Sbjct: 1   CGRCGENVVGEGTGCTAMDQVFHVDCFTCMTCNGKLRGQPFYAVEKKAYCEPCY 54

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|188851 cd09467, LIM1_Lhx3b, The first LIM domain of Lhx3b

 Score = 37.2 bits (86), Expect = 8e-04
 Identities = 14/42 (33%), Positives = 21/42 (50%)

Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFS 202
           +CAGCN  I     L  ++  WH +C +C  C   + +  FS
Sbjct: 3   LCAGCNQHIVDRFILKVLDRHWHSKCLKCSDCQTQLAEKCFS 44

The first LIM domain of Lhx3b. Lhx3b is a member of LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. Lhx3b is one of the two isoforms of Lhx3. The Lhx3 gene is expressed in the ventral spinal cord, the pons, the medulla oblongata, and the pineal gland of the developing nervous system during mouse embryogenesis, and transcripts are found in the emergent pituitary gland. Lhx3 functions in concert with other transcription factors to specify interneuron and motor neuron fates during development. Lhx3 proteins have been demonstrated to directly bind to the promoters of several pituitary hormone gene promoters. The Lhx3 gene encodes two isoforms, LHX3a and LHX3b that differ in their amino-terminal sequences, where Lhx3a has longer N-terminal. They show differential activation of pituitary hormone genes and distinct DNA binding properties. In human, Lhx3a trans-activated the alpha-glycoprotein subunit promoter and genes containing a high-affinity Lhx3 binding site more effectively than the hLhx3b isoform. In addition, hLhx3a induce transcription of the TSHbeta-subunit gene by acting on pituitary POU domain factor, Pit-1, while hLhx3b does not. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

>gnl|CDD|188814 cd09430, LIM5_LIMPETin, The fifth LIM domain of protein LIMPETin

 Score = 36.7 bits (85), Expect = 0.001
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           C+ CN  I  G      E  WH ECF C +C+  +    F+    +PY   C+
Sbjct: 1   CSKCNKIINSGGVTYKNEP-WHRECFTCTNCSKSLAGQRFTSRDEKPYCADCF 52

The fifth LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188796 cd09412, LIM4_Leupaxin, The fourth LIM domain of Leupaxin

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 18/53 (33%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           C  C   I  GR +S +   +HPE F C  C  P+T   F     +PY   C+
Sbjct: 1   CGSCGLPIT-GRCISALGRKFHPEHFVCAFCLRPLTQGSFKEQSGKPYCSTCF 52

The fourth LIM domain of Leupaxin: Leupaxin is a cytoskeleton adaptor protein, which is preferentially expressed in hematopoietic cells. Leupaxin belongs to the paxillin focal adhesion protein family. Same as other members of the family, it has four leucine-rich LD-motifs in the N-terminus and four LIM domains in the C-terminus. It may function in cell type-specific signaling by associating with interaction partners PYK2, FAK, PEP and p95PKL. When expressed in human leukocytic cells, leupaxin significantly suppressed integrin-mediated cell adhesion to fibronectin and the tyrosine phosphorylation of paxillin. These findings indicate that leupaxin may negatively regulate the functions of paxillin during integrin signaling. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 52

>gnl|CDD|188733 cd09347, LIM4_FHL, The fourth LIM domain of Four and a half LIM domains protein (FHL)

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 14/43 (32%), Positives = 22/43 (51%), Gaps = 3/43 (6%)

Query: 162 CAGCN---TEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEF 201
           CA C    T +G  +++S  E  WH +CF C  C++ +    F
Sbjct: 1   CAACTKPITGLGGAKFISFEERQWHSDCFNCGKCSVSLVGQGF 43

The fourth 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 interacts 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 = 56

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

 Score = 36.6 bits (85), Expect = 0.001
 Identities = 11/38 (28%), Positives = 19/38 (50%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDV 199
           CAGC  +I     L  ++ +WH  C +C  C   + ++
Sbjct: 1   CAGCGGKIVDRFLLHALDRYWHNGCLKCSCCQAQLGEI 38

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

>gnl|CDD|188839 cd09455, LIM1_Enigma_like_1, The first LIM domain of an Enigma subfamily with unknown function

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 16/55 (29%), Positives = 28/55 (50%), Gaps = 3/55 (5%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRC--HSCNLPITDVEFSMSGNRPYHKHCY 214
           C  CN +I  G +++ +   W P+ F C   SC  P+ D+ F     + Y ++C+
Sbjct: 1   CESCNQQI-RGPFITALGKIWCPDHFICANASCRRPLQDIGFVEEKGQLYCEYCF 54

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

 Score = 36.3 bits (84), Expect = 0.001
 Identities = 13/31 (41%), Positives = 18/31 (58%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSC 192
           CAGC  +I   +Y+  +   WH +CFRC  C
Sbjct: 1   CAGCRGKILDSQYVQALNQDWHCDCFRCSVC 31

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|188732 cd09346, LIM3_FHL, The third LIM domain of Four and a half LIM domains protein (FHL)

 Score = 36.2 bits (84), Expect = 0.001
 Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 1/53 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           CA C   I  G  ++  +  WH ECF C  C   +    F+     PY   C+
Sbjct: 1   CAKCKKAITSGG-VTYRDQPWHKECFVCTGCKKQLAGQRFTSRDEYPYCVDCF 52

The third 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 = 52

>gnl|CDD|188817 cd09433, LIM4_FHL2, The fourth LIM domain of Four and a half LIM domains protein 2 (FHL2)

 Score = 36.5 bits (84), Expect = 0.001
 Identities = 16/38 (42%), Positives = 21/38 (55%), Gaps = 3/38 (7%)

Query: 162 CAGCNTEI---GHGRYLSCMEAFWHPECFRCHSCNLPI 196
           CAGC   I   G  +Y+S  E  WH +CF C  C+L +
Sbjct: 1   CAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSL 38

The fourth 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 = 58

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

 Score = 36.2 bits (84), Expect = 0.002
 Identities = 14/45 (31%), Positives = 23/45 (51%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGN 206
           C GC   I     L  ++  WH +C +C+ C   +TD  F+ +G+
Sbjct: 1   CGGCQEHILDRFILKVLDRTWHAKCLKCNDCGAQLTDKCFARNGH 45

The first LIM domain of Lhx3-Lhx4 family: Lhx3 and Lhx4 belong to the LHX protein family, which features two tandem N-terminal LIM domains and a C-terminal DNA binding homeodomain. Members of LHX family are found in the nucleus and act as transcription factors or cofactors. LHX proteins are critical for the development of specialized cells in multiple tissue types, including the nervous system, skeletal muscle, the heart, the kidneys, and endocrine organs, such as the pituitary gland and the pancreas. The LHX3 and LHX4 LIM-homeodomain transcription factors play essential roles in pituitary gland and nervous system development. Although LHX3 and LHX4 share marked sequence homology, the genes have different expression patterns. They play overlapping, but distinct functions during the establishment of the specialized cells of the mammalian pituitary gland and the nervous system. Lhx3 proteins have been demonstrated the ability to directly bind to the promoters/enhancers of several pituitary hormone gene promoters to cause increased transcription. Lhx3a and Lhx3b, whose mRNAs have distinct temporal expression profiles during development, are two isoforms of Lhx3. LHX4 plays essential roles in pituitary gland and nervous system development. In mice, the lhx4 gene is expressed in the developing hindbrain, cerebral cortex, pituitary gland, and spinal cord. LHX4 shows significant sequence similarity to LHX3, particularly to isoforms Lhx3a. In gene regulation experiments, the LHX4 protein exhibits regulation roles towards pituitary genes, acting on their promoters/enhancers. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 52

>gnl|CDD|218312 pfam04889, Cwf_Cwc_15, Cwf15/Cwc15 cell cycle control protein

 Score = 39.3 bits (92), Expect = 0.002
 Identities = 23/118 (19%), Positives = 48/118 (40%), Gaps = 9/118 (7%)

Query: 13  RRHYHARYGDDRTWDERRYSAADDSSGFDNEEIDRAIALSLVEVDQKGKKVIENEYDSED 72
           R H   +       D  + +  D S+  D ++ +          +           D++D
Sbjct: 68  RAHKSKKENKLAIEDADKSTNLDASNEGDEDDDEEDEIKRKRIEED------ARNSDADD 121

Query: 73  DLQCIKSDDSDED---ELDEDEIRAIAQQEEDERRAKAQQEEDERRARARAQLEEDEQ 127
                 SD SD+D   +  EDE  A+ ++ E  ++ +A+++E E   +A  + +  E+
Sbjct: 122 SDSSSDSDSSDDDSDDDDSEDETAALLRELEKIKKERAEEKEREEEEKAAEEEKAREE 179

This family represents Cwf15/Cwc15 (from Schizosaccharomyces pombe and Saccharomyces cerevisiae respectively) and their homologues. The function of these proteins is unknown, but they form part of the spliceosome and are thus thought to be involved in mRNA splicing. Length = 241

>gnl|CDD|223407 COG0330, HflC, Membrane protease subunits, stomatin/prohibitin homologs [Posttranslational modification, protein turnover, chaperones]

 Score = 39.7 bits (93), Expect = 0.002
 Identities = 14/58 (24%), Positives = 27/58 (46%), Gaps = 5/58 (8%)

Query: 86  ELDEDEIRAIAQQ--EEDERRAK---AQQEEDERRARARAQLEEDEQLAKAIQDSLRV 138
           +  E+   A+ +Q   E ++RA+   A+ E      RA  + E    LA+A  ++  +
Sbjct: 170 DPPEEVQAAMEKQMAAERDKRAEILEAEGEAQAAILRAEGEAEAAIILAEAEAEAEVI 227

Length = 291

>gnl|CDD|188720 cd09334, LIM4_PINCH, The fourth LIM domain of protein PINCH

 Score = 35.8 bits (83), Expect = 0.002
 Identities = 20/60 (33%), Positives = 24/60 (40%), Gaps = 10/60 (16%)

Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHK--HCYKEQH 218
           IC  C   I  GR ++ +   WH E F C  C  P         G+R Y K    Y E H
Sbjct: 2   ICGACRRPI-EGRVVTALGKHWHVEHFVCAKCEKP-------FLGHRHYEKKGLAYCETH 53

The fourth LIM domain of protein PINCH: PINCH plays a pivotal role in the assembly of focal adhesions (FAs), regulating diverse functions in cell adhesion, growth, and differentiation through LIM-mediated protein-protein interactions. PINCH comprises an array of five LIM domains that interact with integrin-linked kinase (ILK), Nck2 (also called Nckbeta or Grb4) and other interaction partners. These interactions are essential for triggering the FA assembly and for relaying diverse mechanical and biochemical signals between Cell-extracellular matrix and the actin cytoskeleton. The PINCH LIM4 domain recognizes the third SH3 domain of another adaptor protein, Nck2. This step is an important component of integrin signaling event. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assem bly of multimeric protein complexes. Length = 54

>gnl|CDD|188777 cd09391, LIM1_Lrg1p_like, The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein

 Score = 35.7 bits (83), Expect = 0.002
 Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 1/35 (2%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPI 196
           CA C   I  G+++  +   +H +CF CH C  P+
Sbjct: 1   CAKCGKPIT-GQFVRALGDVYHLDCFTCHDCGKPV 34

The first LIM domain of Lrg1p, a LIM and RhoGap domain containing protein: The members of this family contain three tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Lrg1p is a Rho1 GTPase-activating protein required for efficient cell fusion in yeast. Lrg1p-GAP domain strongly and specifically stimulates the GTPase activity of Rho1p, a regulator of beta (1-3)-glucan synthase in vitro. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 57

>gnl|CDD|235999 PRK07353, PRK07353, F0F1 ATP synthase subunit B'; Validated

 Score = 37.7 bits (88), Expect = 0.003
 Identities = 18/58 (31%), Positives = 33/58 (56%), Gaps = 5/58 (8%)

Query: 84  EDELDEDEIR----AIAQQEEDERRAKAQQEEDERRARARAQLEED-EQLAKAIQDSL 136
           E E + D++     A AQ E    + KA++E ++++  A AQLE+  + L++ I + L
Sbjct: 79  EAEAEADKLAAEALAEAQAEAQASKEKARREIEQQKQAALAQLEQQVDALSRQILEKL 136

Length = 140

>gnl|CDD|188848 cd09464, LIM2_LIMK1, The second LIM domain of LIMK1 (LIM domain Kinase 1)

 Score = 35.2 bits (81), Expect = 0.004
 Identities = 22/59 (37%), Positives = 26/59 (44%), Gaps = 10/59 (16%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITD------VEFSMSGNRPYHKHCY 214
           C GC+  I  G  +   E  +HPECF C  C   I D      VE S    + Y  HCY
Sbjct: 1   CHGCSETITTGLVMVAGEQKYHPECFSCLRCGAFIGDGDTYALVEHS----KLYCGHCY 55

The second LIM domain of LIMK1 (LIM domain Kinase 1): LIMK1 belongs to the LIMK protein family, which comprises LIMK1 and LIMK2. LIMK contains two LIM domains, a PDZ domain, and a kinase domain. LIMK is involved in the regulation of actin polymerization and microtubule disassembly. LIMK influences architecture of the actin cytoskeleton by regulating the activity of the cofilin family proteins cofilin1, cofilin2, and destrin. The mechanism of the activation is to phosphorylates cofilin on serine 3 and inactivates its actin-severing activity, and altering the rate of actin depolymerization. LIMKs can function in both cytoplasm and nucleus. Both LIMK1 and LIMK2 can act in the nucleus to suppress Rac/Cdc42-dependent cyclin D1 expression. LIMK1 is expressed in all tissues and is localized to focal adhesions in the cell. LIMK1 can form homodimers upon binding of HSP90 and is activated by Rho effector Rho kinase and MAPKAPK2. LIMK1 is important for normal central nervous system development, and its deletion has been implicated in the development of the human genetic disorder Williams syndrome. Moreover, LIMK1 up-regulates the promoter activity of urokinase type plasminogen activator and induces its mRNA and protein expression in breast cancer cells. The LIM domains have been shown to play an important role in regulating kinase activity and likely also contribute to LIMK function by acting as sites of protein-to-protein interactions. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 55

>gnl|CDD|188745 cd09359, LIM_LASP_like, The LIM domain of LIM and SH3 Protein (LASP)-like proteins

 Score = 34.9 bits (80), Expect = 0.004
 Identities = 13/52 (25%), Positives = 23/52 (44%), Gaps = 1/52 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPY-HKH 212
           CA C   +     ++C++  WH  CF C  C + +    +     +PY + H
Sbjct: 1   CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAH 52

The LIM domain of LIM and SH3 Protein (LASP) like proteins: This family contains two types of LIM containing proteins; LASP and N-RAP. LASP family contains two highly homologous members, LASP-1 and LASP-2. LASP contains a LIM motif at its amino terminus, a src homology 3 (SH3) domains at its C-terminal part, and a nebulin-like region in the middle. LASP-1 and -2 are highly conserved in their LIM, nebulin-like, and SH3 domains, but differ significantly at their linker regions. Both proteins are ubiquitously expressed and involved in cytoskeletal architecture, especially in the organization of focal adhesions. LASP-1 and LASP-2, are important during early embryo- and fetogenesis and are highly expressed in the central nervous system of the adult. However, only LASP-1 seems to participate significantly in neuronal differentiation and plays an important functional role in migration and proliferation of certain cancer cells while the role of LASP-2 is more structural. The expression of LASP-1 in breast tumors is increased significantly. N-RAP is a muscle-specific protein concentrated at myotendinous junctions in skeletal muscle and intercalated disks in cardiac muscle. LIM domain is found at the N-terminus of N-RAP and the C-terminal of N-RAP contains a region with multiple of nebulin repeats. N-RAP functions as a scaffolding protein that organizes alpha-actinin and actin into symmetrical I-Z-I structures in developing myofibrils. Nebulin repeat is known as actin binding domain. The N-RAP is hypothesized to form antiparallel dimerization via its LIM domain. 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|188726 cd09340, LIM1_Testin_like, The first LIM domain of Testin-like family

 Score = 34.9 bits (81), Expect = 0.004
 Identities = 10/20 (50%), Positives = 13/20 (65%)

Query: 179 EAFWHPECFRCHSCNLPITD 198
           +A WHP CF C +CN  + D
Sbjct: 23  DACWHPGCFVCETCNELLVD 42

The first LIM domain of Testin_like family: This family includes testin, prickle, dyxin and LIMPETin. Structurally, testin and prickle proteins contain three LIM domains at C-terminal; LIMPETin has six LIM domains; and dyxin presents only two LIM domains. However, all members of the family contain a PET protein-protein interaction domain. Testin is a cytoskeleton associated focal adhesion protein that localizes along actin stress fibers, at cell-cell-contact areas, and at focal adhesion plaques. Testin interacts with a variety of cytoskeletal proteins, including zyxin, mena, VASP, talin, and actin and it is involved in cell motility and adhesion events. Prickles have been implicated in roles of regulating tissue polarity or planar cell polarity (PCP). Dyxin involves in lung and heart development by interaction with GATA6 and blocking GATA6 activated target genes. LIMPETin might be the recombinant product of genes coding testin and four and half LIM proteins and its function is not well understood. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 58

>gnl|CDD|188781 cd09395, LIM2_Rga, The second LIM domain of Rga GTPase-Activating Proteins

 Score = 34.8 bits (80), Expect = 0.004
 Identities = 13/53 (24%), Positives = 25/53 (47%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCY 214
           C  C  +I     L   +  +  +CFRC  C+  ITD++++ +    +   C+
Sbjct: 1   CKNCGKKIDDTAILLSSDEAYCSDCFRCRRCSRDITDLKYAKTKRGLFCMSCH 53

The second LIM domain of Rga GTPase-Activating Proteins: The members of this family contain two tandem repeats of LIM domains and a Rho-type GTPase activating protein (RhoGap) domain. Rga activates GTPases during polarized morphogenesis. In yeast, a known regulating target of Rga is CDC42p, a small GTPase. The LIM domain is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	431
PF12315	212	DUF3633: Protein of unknown function (DUF3633); In	100.0
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.94
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.86
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.77
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.76
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	99.76
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.7
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	99.69
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.63
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.62
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.27
KOG1700	200	consensus Regulatory protein MLP and related LIM p	98.66
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	98.44
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.35
KOG4577	383	consensus Transcription factor LIM3, contains LIM	97.76
KOG1702	264	consensus Nebulin repeat protein [Cytoskeleton]	97.38
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	97.12
KOG1700	200	consensus Regulatory protein MLP and related LIM p	97.08
KOG0490	235	consensus Transcription factor, contains HOX domai	96.97
smart00726	26	UIM Ubiquitin-interacting motif. Present in protea	90.1
PF02809	18	UIM: Ubiquitin interaction motif; InterPro: IPR003	86.92
PF14891	174	Peptidase_M91: Effector protein	84.41
PF13699	79	DUF4157: Domain of unknown function (DUF4157)	83.94
PF01431	206	Peptidase_M13: Peptidase family M13 This is family	80.81

>PF12315 DUF3633: Protein of unknown function (DUF3633); InterPro: IPR022087 This domain family is found in bacteria and eukaryotes, and is approximately 210 amino acids in length

Probab=100.00  E-value=8.3e-43  Score=324.20  Aligned_cols=117  Identities=79%  Similarity=1.236  Sum_probs=115.0

Q ss_pred             hccccccccccchhhhHHHHHHHhcCCcCCccCCcccCCcccccccceeeeecccccCCCcceeeeeccceecccceEEE
Q 014080          311 GLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVT  390 (431)
Q Consensus       311 ~l~~~~~~~~pl~lv~~~ALn~~~~~e~~g~~~~~e~rGl~~~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~  390 (431)
                      +|||||++++||+||+++|||+|.++|++|++|.++|||||+||+|+++||.|+|++|+|+++++|.++|++++|+|+||
T Consensus         1 ~lnmki~q~~PllLVe~~aLN~a~~~Ek~~~~~~~~tRGLclseeq~v~sv~~~p~~~~~~~~~~~~~e~~~~~~~~eV~   80 (212)
T PF12315_consen    1 GLNMKIEQEIPLLLVERQALNEAEEGEKIGHHHMPETRGLCLSEEQTVTSVLRRPRMGPGNQLIDMSTEPQRLTRGCEVT   80 (212)
T ss_pred             CCCCcccCCCCeEEecHHHHHHHHhhccCCCCCCeeeeeeeeeeeEEEEEEEecCCcCCCCccceeeecceeeccceeEE
Confidence            58999999999999999999999999999999999999999999999999999999999999999999999999999999


Q ss_pred             EEEEecCCChhhhhhHHHHhhhHhHhhhcCCCCCcee
Q 014080          391 AILILYGLPRLLTGSILAHEMMHAWLRLKGFICFKLI  427 (431)
Q Consensus       391 ~il~l~glprl~~g~ilaHE~~Ha~lrl~g~~~l~~~  427 (431)
                      +|||||||||++||||||||||||||||+||++|++.
T Consensus        81 ~Ilvl~GLPrll~gsiLAHE~mHa~Lrl~g~~~L~~~  117 (212)
T PF12315_consen   81 AILVLYGLPRLLTGSILAHELMHAWLRLNGFPNLSPE  117 (212)
T ss_pred             EEEEECCCCHHHHhhHHHHHHHHHHhcccCCCCCChH
Confidence            9999999999999999999999999999999999974

The family is found in association with PF00412 from PFAM.

>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]

Probab=99.94  E-value=6.7e-29  Score=234.83  Aligned_cols=178  Identities=26%  Similarity=0.542  Sum_probs=157.5

Q ss_pred             CCCcCCCCCC-CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccc-----cC
Q 014080          146 SGNIFQPFPF-FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQ-----HH  219 (431)
Q Consensus       146 ~g~~~~p~~~-~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~-----f~  219 (431)
                      .|..|+.-++ ...+|.|++|++.| .|++|.+|+.+|||.||+|..|++.|.+..|+...|+.+|..|-.+.     ..
T Consensus        59 EgRkYCEhDF~~LfaPcC~kC~EFi-iGrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~  137 (332)
T KOG2272|consen   59 EGRKYCEHDFHVLFAPCCGKCGEFI-IGRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGR  137 (332)
T ss_pred             cCcccccccchhhhchhhcccccch-hhHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccce
Confidence            5677888887 78999999999999 59999999999999999999999999999999999999999998752     24


Q ss_pred             cccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCCCCC
Q 014080          220 PKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQ  299 (431)
Q Consensus       220 pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~~C~  299 (431)
                      ..|..|+..|...   .+.+++.||          |...|+|..|++.|....+-+   .|.+||+.|+++  |..|+|.
T Consensus       138 YvC~KCh~~iD~~---~l~fr~d~y----------H~yHFkCt~C~keL~sdaRev---k~eLyClrChD~--mgipiCg  199 (332)
T KOG2272|consen  138 YVCQKCHAHIDEQ---PLTFRGDPY----------HPYHFKCTTCGKELTSDAREV---KGELYCLRCHDK--MGIPICG  199 (332)
T ss_pred             eehhhhhhhcccc---cccccCCCC----------Cccceecccccccccchhhhh---ccceeccccccc--cCCcccc
Confidence            5799999999874   588999985          555599999999998887765   579999999999  9999999


Q ss_pred             cccHHHHHHHhhccccccccccchhhhHHHHHHHhcC----------CcCCccCCcccCCcccccccceee
Q 014080          300 PLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEG----------EKNGHHHLPETRGLCLSEEQTVTT  360 (431)
Q Consensus       300 ~C~~~I~~f~~~l~~~~~~~~pl~lv~~~ALn~~~~~----------e~~g~~~~~e~rGl~~~E~~~~~~  360 (431)
                      +|.+||.           .++      +.|||++|+.          ++.||.|| |++||+|||+||+.+
T Consensus       200 aC~rpIe-----------erv------i~amgKhWHveHFvCa~CekPFlGHrHY-EkkGlaYCe~h~~qL  252 (332)
T KOG2272|consen  200 ACRRPIE-----------ERV------IFAMGKHWHVEHFVCAKCEKPFLGHRHY-EKKGLAYCETHYHQL  252 (332)
T ss_pred             cccCchH-----------HHH------HHHhccccchhheeehhcCCcccchhhh-hhcCchhHHHHHHHH
Confidence            9999885           444      7899999965          57899998 999999999999877

>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]

Probab=99.86  E-value=3.7e-24  Score=215.53  Aligned_cols=171  Identities=21%  Similarity=0.419  Sum_probs=144.0

Q ss_pred             CCCCCcCCCCCccccc-CceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCCCccccCCc
Q 014080          156 FSGYRICAGCNTEIGH-GRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSA  234 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~-g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~  234 (431)
                      .....+|.+|+|.|.. +..++||++.||..||+|..|++.|.++.||..++++||+.||.. ...||.+|++.|.+.  
T Consensus       271 ~~~~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~-tlekC~~Cg~~I~d~--  347 (468)
T KOG1701|consen  271 EDYFGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQD-TLEKCNKCGEPIMDR--  347 (468)
T ss_pred             hhhhhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHH-HHHHHhhhhhHHHHH--
Confidence            3445699999999953 255899999999999999999999999999999999999999986 567999999999974  


Q ss_pred             ceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCCCCCcccHHHHHHHhhccc
Q 014080          235 GLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNM  314 (431)
Q Consensus       235 ~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~~C~~C~~~I~~f~~~l~~  314 (431)
                       ++.+.++.          ||.+||+|.+|.+.| .|..|....++++||..||.+  +++++|+.|.++|        |
T Consensus       348 -iLrA~Gka----------yHp~CF~Cv~C~r~l-dgipFtvd~~n~v~Cv~dfh~--kfAPrCs~C~~PI--------~  405 (468)
T KOG1701|consen  348 -ILRALGKA----------YHPGCFTCVVCARCL-DGIPFTVDSQNNVYCVPDFHK--KFAPRCSVCGNPI--------L  405 (468)
T ss_pred             -HHHhcccc----------cCCCceEEEEecccc-CCccccccCCCceeeehhhhh--hcCcchhhccCCc--------c
Confidence             67777775          499999999999999 789999999999999999999  9999999999999        6


Q ss_pred             cccccccchhhhHHHHHHHhcCCcCCccCCcccCCcccc-cccc
Q 014080          315 KVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLS-EEQT  357 (431)
Q Consensus       315 ~~~~~~pl~lv~~~ALn~~~~~e~~g~~~~~e~rGl~~~-E~~~  357 (431)
                      |-+++-.  .|.+.||++.+|...-   + -|..||-|| |+.-
T Consensus       406 P~~G~~e--tvRvvamdr~fHv~CY---~-CEDCg~~LS~e~e~  443 (468)
T KOG1701|consen  406 PRDGKDE--TVRVVAMDRDFHVNCY---K-CEDCGLLLSSEEEG  443 (468)
T ss_pred             CCCCCcc--eEEEEEccccccccce---e-hhhcCccccccCCC
Confidence            7765431  2456688888876542   2 377888888 5543

>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]

Probab=99.77  E-value=6.8e-21  Score=183.45  Aligned_cols=123  Identities=26%  Similarity=0.567  Sum_probs=110.7

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCCCccccCCcce
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGL  236 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~  236 (431)
                      ...++|++|.+.|.+.-+++++++.||..|++|+.|..+|++.+|. ++|.+||+.+|.++|+++|..|+..|++..   
T Consensus        31 ~eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFs-R~~s~yCkedFfKrfGTKCsaC~~GIpPtq---  106 (383)
T KOG4577|consen   31 VEIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFS-REGSVYCKEDFFKRFGTKCSACQEGIPPTQ---  106 (383)
T ss_pred             cccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhh-cCCceeehHHHHHHhCCcchhhcCCCChHH---
Confidence            3678999999999755667999999999999999999999998877 589999999999999999999999999853   


Q ss_pred             EEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcc
Q 014080          237 IEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA  291 (431)
Q Consensus       237 i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~  291 (431)
                      +..+...|        .||..||.|..|+|.|..|+.|+.+.|++++|+..|+++
T Consensus       107 VVRkAqd~--------VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~A  153 (383)
T KOG4577|consen  107 VVRKAQDF--------VYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETA  153 (383)
T ss_pred             HHHHhhcc--------eeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHH
Confidence            44555555        689999999999999999999999999999999999875

>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]

Probab=99.76  E-value=4.8e-20  Score=186.00  Aligned_cols=134  Identities=23%  Similarity=0.474  Sum_probs=117.2

Q ss_pred             CCCcCCCCCCCCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceee-cCCccccccccccccCccccc
Q 014080          146 SGNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSM-SGNRPYHKHCYKEQHHPKCDV  224 (431)
Q Consensus       146 ~g~~~~p~~~~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~-~dg~pyC~~CY~~~f~pkC~~  224 (431)
                      .++.||...+.....+|..|+++|. .+++.|+|+.||+.||+|..|++.|.+..|.+ .++++||..||+++|+|+|+.
T Consensus       321 ~~k~~CE~cyq~tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~  399 (468)
T KOG1701|consen  321 DGKPYCEGCYQDTLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSV  399 (468)
T ss_pred             CCcccchHHHHHHHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhh
Confidence            4566776666777889999999994 89999999999999999999999999999986 788999999999999999999


Q ss_pred             CCCccccCC----cceEEEecccccccccCCCcccCCCCccCCCCCccC---CCCceEEccCCcccCcchhhcc
Q 014080          225 CQNFIPTNS----AGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEP---RDTKYLSLDDGRKLCLECLDSA  291 (431)
Q Consensus       225 C~~~I~~~~----~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~---~g~~f~~l~dG~~yC~~C~~~~  291 (431)
                      |+++|...+    ...|+.+++.|          |.+|++|-.|+.+|+   .|...+.+ ||.++|+.|..+.
T Consensus       400 C~~PI~P~~G~~etvRvvamdr~f----------Hv~CY~CEDCg~~LS~e~e~qgCyPl-d~HllCk~Ch~~R  462 (468)
T KOG1701|consen  400 CGNPILPRDGKDETVRVVAMDRDF----------HVNCYKCEDCGLLLSSEEEGQGCYPL-DGHLLCKTCHLKR  462 (468)
T ss_pred             ccCCccCCCCCcceEEEEEccccc----------cccceehhhcCccccccCCCCcceec-cCceeechhhhhh
Confidence            999999763    33578889986          999999999999987   35567877 8899999998764

>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]

Probab=99.76  E-value=6.7e-19  Score=186.24  Aligned_cols=242  Identities=49%  Similarity=0.831  Sum_probs=212.1

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCcccccccccc-ccCcccccCCCccccCCcc
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE-QHHPKCDVCQNFIPTNSAG  235 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~-~f~pkC~~C~~~I~~~~~~  235 (431)
                      ....+|.+|.-.|..+..+          ||.|..|..++.          .+...||.. ...+.|.+|...|..+..+
T Consensus       132 ~~~~~~~~~~~~~~~~~~~----------~~~~~~~~~p~~----------~~~~~~~~~~~~~~~~~v~~~~~~~~~~~  191 (479)
T KOG1703|consen  132 PLDSICGGCNSAIEHGRSV----------CFQCKRCSEPLS----------GFPKPSYHESGRSKNEDVEEASSPSSRAG  191 (479)
T ss_pred             cccccccCCCcccccccch----------hhhhcccccccC----------Ccccccccccccccccccccccccccccc
Confidence            4567899999999777655          899999988882          223344444 3567899999999988778


Q ss_pred             eEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCCCCCcccHHHHHHHhhcccc
Q 014080          236 LIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMK  315 (431)
Q Consensus       236 ~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~~C~~C~~~I~~f~~~l~~~  315 (431)
                      .+.++.++||.+.||+.|.++.+..|..|.+..+.+..++.+.+++.+|..|....+++.+.|++....+..++....|+
T Consensus       192 ~~~~~~~~~~~~~~~~~~e~~~tp~~~~~~r~e~~~~~~~~l~~~~~~~~~~~~~~~~~~p~~~p~~~~~~~~~~~~~~~  271 (479)
T KOG1703|consen  192 LILSRSHPFWKQKYCPSHENDGTPKCCSCERLEPLDTRYVELADGRALCLECMGSASMDSPECQPLVSAPRPASEGLHMK  271 (479)
T ss_pred             ccccccchhhhhcccccccCCCCCCcccccccccccccceecccchhhhhhccCCcccCCCccCcceecccccccccccc
Confidence            88999999999999999999999999999999877888999999999999999888899999999999999999999999


Q ss_pred             ccccccchhhhHHHHHHHhcCCcCCccCCcccCCcccccccceeeeecccccCCCcceeeeeccceecccceEEEEEEEe
Q 014080          316 VEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAILIL  395 (431)
Q Consensus       316 ~~~~~pl~lv~~~ALn~~~~~e~~g~~~~~e~rGl~~~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~~il~l  395 (431)
                      +++..++++++..+++++-........|. .++++|.++.++++++         ..+++|.++..+....|+|++++++
T Consensus       272 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~p~c~~c~~~i~~~---------~~i~~~~~~~h~~~~~c~~~~~~~~  341 (479)
T KOG1703|consen  272 VEKELPLLLVESEALKKLREEEKPAEYHN-VTRPLCLSCNQKIRSV---------KVIVALGKEWHPEHFSCEVCAIVIL  341 (479)
T ss_pred             cccccchhhcccccccccccccccccccc-cccccccccccCcccc---------eeEeeccccccccceeecccccccc
Confidence            99999999999999999998877665443 7899999999998554         4577888899999999999999999


Q ss_pred             cCCChhhhhhHHHHhhhHhHhhhcCCCCCceee
Q 014080          396 YGLPRLLTGSILAHEMMHAWLRLKGFICFKLIY  428 (431)
Q Consensus       396 ~glprl~~g~ilaHE~~Ha~lrl~g~~~l~~~~  428 (431)
                      +|+|++.+|.|++||+||+|++.++++.+.+|.
T Consensus       342 ~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~  374 (479)
T KOG1703|consen  342 DGGPRELDGKILCHECFHAPFRPNCKRCLLPIL  374 (479)
T ss_pred             CCCccccCCCccHHHHHHHhhCccccccCCchH
Confidence            999999999999999999999999999988874

>KOG2272 consensus Focal adhesion protein PINCH-1, contains LIM domains [Signal transduction mechanisms; Cytoskeleton]

Probab=99.70  E-value=9.7e-19  Score=166.12  Aligned_cols=136  Identities=21%  Similarity=0.472  Sum_probs=121.4

Q ss_pred             CCCCCCCCCcCCCCCC-CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCcccccccccccc
Q 014080          140 SPPRYESGNIFQPFPF-FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH  218 (431)
Q Consensus       140 spp~~~~g~~~~p~~~-~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f  218 (431)
                      +.+|.-++..|++.-. ..+-++|+.|.++| .+++|.+||+.||.++|+|+.|.+|+-+...+.+.|.+||+.+|.++|
T Consensus       175 sdaRevk~eLyClrChD~mgipiCgaC~rpI-eervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLf  253 (332)
T KOG2272|consen  175 SDAREVKGELYCLRCHDKMGIPICGACRRPI-EERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLF  253 (332)
T ss_pred             chhhhhccceeccccccccCCcccccccCch-HHHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHh
Confidence            3445557888998766 78999999999999 599999999999999999999999999999999999999999999999


Q ss_pred             CcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          219 HPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       219 ~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      +..|..|+..|.|.   ++.+.++.|          -+.||.|+.|.+.|...++|+.+ |-+++|+.||++
T Consensus       254 G~~CF~C~~~i~G~---vv~al~Kaw----------Cv~cf~Cs~Cdkkl~~K~Kf~E~-DmkP~CKkCy~r  311 (332)
T KOG2272|consen  254 GNLCFICNRVIGGD---VVSALNKAW----------CVECFSCSTCDKKLTQKNKFYEF-DMKPVCKKCYDR  311 (332)
T ss_pred             hhhheecCCccCcc---HHHHhhhhh----------ccccccccccccccccccceeee-ccchHHHHHHhh
Confidence            99999999999985   677777753          56679999999999988999986 779999999986

>KOG1703 consensus Adaptor protein Enigma and related PDZ-LIM proteins [Signal transduction mechanisms; Cytoskeleton]

Probab=99.69  E-value=1.4e-17  Score=176.16  Aligned_cols=173  Identities=17%  Similarity=0.286  Sum_probs=136.4

Q ss_pred             CCCcCCCCCcccccC-ceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCCCccccCCcce
Q 014080          158 GYRICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGL  236 (431)
Q Consensus       158 ~~~~C~~C~k~I~~g-~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~  236 (431)
                      ..+.|..|+..|. + +++.++++.||+.+|.|..|+..|....|...+|.+||..||.+.+.|+|.+|+.+|.++   .
T Consensus       302 ~~p~c~~c~~~i~-~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~p~C~~C~~~i~~~---~  377 (479)
T KOG1703|consen  302 TRPLCLSCNQKIR-SVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFRPNCKRCLLPILEE---G  377 (479)
T ss_pred             ccccccccccCcc-cceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhCccccccCCchHHh---H
Confidence            4599999999995 6 999999999999999999999999998998899999999999999999999999999987   3


Q ss_pred             EEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCCCCCcccHHHHHH---Hhhcc
Q 014080          237 IEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEIQEF---YEGLN  313 (431)
Q Consensus       237 i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~~C~~C~~~I~~f---~~~l~  313 (431)
                      |.+.++          +||..||.|..|++.+. +..|+. .+|.+||..||..  .+++.|..|.++|..+   -+++|
T Consensus       378 v~a~~~----------~wH~~cf~C~~C~~~~~-~~~~~~-~~~~pyce~~~~~--~~~~~~~~~~~p~~~~~~~ie~~~  443 (479)
T KOG1703|consen  378 VCALGR----------LWHPECFVCADCGKPLK-NSSFFE-SDGEPYCEDHYKK--LFTTKCDYCKKPVEFGSRQIEADG  443 (479)
T ss_pred             hhhccC----------eechhceeeecccCCCC-CCcccc-cCCccchhhhHhh--hccccchhccchhHhhhhHhhccC
Confidence            556555          68999999999999884 445553 6999999999998  7788999999998633   23445


Q ss_pred             ccccccccchhhhHHHHHHHhcCCcCCccCCcccCCcccccccc
Q 014080          314 MKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQT  357 (431)
Q Consensus       314 ~~~~~~~pl~lv~~~ALn~~~~~e~~g~~~~~e~rGl~~~E~~~  357 (431)
                      -++.++...    ....+++     .....+..+.+.+||..+.
T Consensus       444 ~~~h~~~F~----c~~c~~~-----l~~~~~~~~~~~p~c~~~~  478 (479)
T KOG1703|consen  444 SPFHGDCFR----CANCMKK-----LTKKTFFETLDKPLCQKHF  478 (479)
T ss_pred             cccccccee----hhhhhcc-----ccCCceeecCCccccccCC
Confidence            555444311    1111111     2223456788888887653

>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]

Probab=99.63  E-value=2e-16  Score=164.71  Aligned_cols=163  Identities=16%  Similarity=0.318  Sum_probs=135.3

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCCCccccCCcce
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGL  236 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~  236 (431)
                      .....|..|.+.. .|+++.+.++.||..||+|..|+..|+..+|+.+++.        +++++  ..|..+|.+.   +
T Consensus        14 ~~~i~c~~c~~kc-~gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~--------~~ygt--~~c~~~~~ge---v   79 (670)
T KOG1044|consen   14 KQGIKCDKCRKKC-SGEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPEN--------RLYGT--DDCRAFVEGE---V   79 (670)
T ss_pred             ccceehhhhCCcc-ccceeEeeccccceeeeeccccCCCcccccceecccc--------eeecc--cchhhhccce---e
Confidence            3456899999999 5999999999999999999999999999999887665        45555  7889999885   6


Q ss_pred             EEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccC------CCCCCCcccHHHHHHHh
Q 014080          237 IEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIM------DTHECQPLYLEIQEFYE  310 (431)
Q Consensus       237 i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~------~~~~C~~C~~~I~~f~~  310 (431)
                      +...++.|          |.+||.|+.|..+++.|++. .+.....+|..|-..+-.      +...|++|...|.    
T Consensus        80 vsa~gkty----------h~~cf~cs~ck~pf~~g~~v-t~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk----  144 (670)
T KOG1044|consen   80 VSTLGKTY----------HPKCFSCSTCKSPFKSGDKV-TFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELK----  144 (670)
T ss_pred             Eeccccee----------ccccceecccCCCCCCCCee-eecchhhhhhhhcCcccCCcccccCCccccchhhhhh----
Confidence            88888864          99999999999999999884 455667889999765322      4568999999996    


Q ss_pred             hccccccccccchhhhHHHHHHHhcCC--------cCCccCCcccCCcccccccceee
Q 014080          311 GLNMKVEQQVPLLLVERQALNEAMEGE--------KNGHHHLPETRGLCLSEEQTVTT  360 (431)
Q Consensus       311 ~l~~~~~~~~pl~lv~~~ALn~~~~~e--------~~g~~~~~e~rGl~~~E~~~~~~  360 (431)
                            .+|.      .-||.++||..        ...++.|+.++|++|||.+|+.-
T Consensus       145 ------~gq~------llald~qwhv~cfkc~~c~~vL~gey~skdg~pyce~dy~~~  190 (670)
T KOG1044|consen  145 ------NGQA------LLALDKQWHVSCFKCKSCSAVLNGEYMSKDGVPYCEKDYQAK  190 (670)
T ss_pred             ------ccce------eeeeccceeeeeeehhhhcccccceeeccCCCcchhhhhhhh
Confidence                  3676      45999999864        34678899999999999999643

>KOG1044 consensus Actin-binding LIM Zn-finger protein Limatin involved in axon guidance [Signal transduction mechanisms; Cytoskeleton]

Probab=99.62  E-value=1e-16  Score=166.81  Aligned_cols=120  Identities=26%  Similarity=0.628  Sum_probs=108.0

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCCCccccCCcc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAG  235 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~  235 (431)
                      ..++..|++|++.|..|+.+.++++.||..||+|..|...|.+ +|..++|.|||+.||.+.|+.+|..|.++|.+.   
T Consensus       130 ~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisgk---  205 (670)
T KOG1044|consen  130 SYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGK---  205 (670)
T ss_pred             ccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhhh---
Confidence            4578899999999999999999999999999999999999987 778899999999999999999999999999985   


Q ss_pred             eEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          236 LIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       236 ~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      ++.+.++          |||+.|-+|..|+.+|+.|+.-+ |....+|-..|-..
T Consensus       206 vLqag~k----------h~HPtCARCsRCgqmF~eGEEMY-lQGs~iWHP~C~qa  249 (670)
T KOG1044|consen  206 VLQAGDK----------HFHPTCARCSRCGQMFGEGEEMY-LQGSEIWHPDCKQA  249 (670)
T ss_pred             hhhccCc----------ccCcchhhhhhhccccccchhee-eccccccCCccccc
Confidence            6777665          78999999999999999888866 46778998888754

>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=99.27  E-value=2.6e-12  Score=97.04  Aligned_cols=57  Identities=39%  Similarity=0.996  Sum_probs=51.9

Q ss_pred             CCCCCcccccCceE-eecCccccCCCcccCCCCCCCCCcceeecCCcccccccccccc
Q 014080          162 CAGCNTEIGHGRYL-SCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH  218 (431)
Q Consensus       162 C~~C~k~I~~g~~v-~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f  218 (431)
                      |.+|+++|..+..+ .++++.||+.||+|..|+++|.+..|+..+|++||+.||.++|
T Consensus         1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~C~~c~~~~f   58 (58)
T PF00412_consen    1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPLNDGDFYEKDGKPYCKDCYQKRF   58 (58)
T ss_dssp             BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBTTTSSEEEETTEEEEHHHHHHHT
T ss_pred             CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCccCCCeeEeECCEEECHHHHhhhC
Confidence            88999999766555 7999999999999999999999988999999999999998765

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

>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]

Probab=98.66  E-value=3.8e-09  Score=100.10  Aligned_cols=119  Identities=22%  Similarity=0.430  Sum_probs=88.7

Q ss_pred             CCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcc----------------
Q 014080          158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK----------------  221 (431)
Q Consensus       158 ~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pk----------------  221 (431)
                      ....|..|++.++.-+.+...|..||+.||+|..|.+.|....+..+++.+||+.||-..++|+                
T Consensus         6 ~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~   85 (200)
T KOG1700|consen    6 TTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGK   85 (200)
T ss_pred             ccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccCCCCc
Confidence            4568999999998777777899999999999999999999999999999999999876544443                


Q ss_pred             -------------------------cccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEE
Q 014080          222 -------------------------CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLS  276 (431)
Q Consensus       222 -------------------------C~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~  276 (431)
                                               |..|++.+...+  -+...+.          -||..||+|+.|+..|..+ .|..
T Consensus        86 ~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~E--k~~~~~~----------~~hk~cfrc~~~~~~ls~~-~~~~  152 (200)
T KOG1700|consen   86 DGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLE--KVTGNGL----------EFHKSCFRCTHCGKKLSPK-NYAA  152 (200)
T ss_pred             ccccccccccccchhHHhhhccccccccccceeeehH--HHhhhhh----------hhhhhheeecccccccCCc-chhh
Confidence                                     444444444321  1222233          4699999999999999544 4554


Q ss_pred             ccCCcccCcchhhc
Q 014080          277 LDDGRKLCLECLDS  290 (431)
Q Consensus       277 l~dG~~yC~~C~~~  290 (431)
                       ..|.+||...+..
T Consensus       153 -~~g~l~~~~~~~~  165 (200)
T KOG1700|consen  153 -LEGVLYCKHHFAQ  165 (200)
T ss_pred             -cCCccccchhhhe
Confidence             4678888766544

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

Probab=98.44  E-value=1.6e-07  Score=70.64  Aligned_cols=56  Identities=18%  Similarity=0.411  Sum_probs=44.6

Q ss_pred             cccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          222 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       222 C~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      |..|+++|.+.. ..+.+.++.          ||..||+|..|++.|..+. |+. .+|++||..||.+
T Consensus         1 C~~C~~~I~~~~-~~~~~~~~~----------~H~~Cf~C~~C~~~l~~~~-~~~-~~~~~~C~~c~~~   56 (58)
T PF00412_consen    1 CARCGKPIYGTE-IVIKAMGKF----------WHPECFKCSKCGKPLNDGD-FYE-KDGKPYCKDCYQK   56 (58)
T ss_dssp             BTTTSSBESSSS-EEEEETTEE----------EETTTSBETTTTCBTTTSS-EEE-ETTEEEEHHHHHH
T ss_pred             CCCCCCCccCcE-EEEEeCCcE----------EEccccccCCCCCccCCCe-eEe-ECCEEECHHHHhh
Confidence            889999999764 223466664          6999999999999996554 664 5889999999976

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

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

Probab=98.35  E-value=3.2e-07  Score=63.01  Aligned_cols=37  Identities=43%  Similarity=1.115  Sum_probs=33.4

Q ss_pred             cCCCCCcccccC-ceEeecCccccCCCcccCCCCCCCC
Q 014080          161 ICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPIT  197 (431)
Q Consensus       161 ~C~~C~k~I~~g-~~v~algk~wHp~CF~C~~C~~~L~  197 (431)
                      +|.+|+++|..+ ..+.++++.||+.||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            589999999755 7788999999999999999999985

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

>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]

Probab=97.76  E-value=3.2e-06  Score=82.71  Aligned_cols=77  Identities=22%  Similarity=0.471  Sum_probs=65.1

Q ss_pred             CCCcCCCCCC-CCCCCcCCCCCcccccCceE-eecCccccCCCcccCCCCCCCCC-ccee-ecCCccccccccccccCcc
Q 014080          146 SGNIFQPFPF-FSGYRICAGCNTEIGHGRYL-SCMEAFWHPECFRCHSCNLPITD-VEFS-MSGNRPYHKHCYKEQHHPK  221 (431)
Q Consensus       146 ~g~~~~p~~~-~~~~~~C~~C~k~I~~g~~v-~algk~wHp~CF~C~~C~~~L~~-~~F~-~~dg~pyC~~CY~~~f~pk  221 (431)
                      .+++||...+ ..+...|..|...|.+..+| ++.+..||..||.|..|++.|.. .+|+ +.++++.|+.+|...-..-
T Consensus        78 ~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~  157 (383)
T KOG4577|consen   78 EGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAKQKH  157 (383)
T ss_pred             CCceeehHHHHHHhCCcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHHhcc
Confidence            5789998887 88899999999999877776 68999999999999999999974 3555 5789999999998754444


Q ss_pred             c
Q 014080          222 C  222 (431)
Q Consensus       222 C  222 (431)
                      |
T Consensus       158 ~  158 (383)
T KOG4577|consen  158 C  158 (383)
T ss_pred             c
Confidence            4

>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]

Probab=97.38  E-value=2e-05  Score=74.05  Aligned_cols=61  Identities=20%  Similarity=0.578  Sum_probs=54.8

Q ss_pred             CCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccC
Q 014080          159 YRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH  219 (431)
Q Consensus       159 ~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~  219 (431)
                      ...|..|++.+++-+-++++++.||..||+|..|+.+|....|-..+.+|||..+|.+..+
T Consensus         4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a   64 (264)
T KOG1702|consen    4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA   64 (264)
T ss_pred             cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence            3568899999988888999999999999999999999999988888999999999987543

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

Probab=97.12  E-value=0.00036  Score=47.58  Aligned_cols=37  Identities=16%  Similarity=0.268  Sum_probs=29.2

Q ss_pred             ccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCcc
Q 014080          221 KCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERME  268 (431)
Q Consensus       221 kC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l  268 (431)
                      +|..|+++|.+.. ..+.+.+.          .||..||+|..|++.|
T Consensus         1 ~C~~C~~~i~~~~-~~~~~~~~----------~~H~~Cf~C~~C~~~L   37 (39)
T smart00132        1 KCAGCGKPIRGGE-LVLRALGK----------VWHPECFKCSKCGKPL   37 (39)
T ss_pred             CccccCCcccCCc-EEEEeCCc----------cccccCCCCcccCCcC
Confidence            5899999999851 24555555          4699999999999987

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.

>KOG1700 consensus Regulatory protein MLP and related LIM proteins [Signal transduction mechanisms; Cytoskeleton]

Probab=97.08  E-value=0.00013  Score=69.25  Aligned_cols=63  Identities=19%  Similarity=0.408  Sum_probs=55.6

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCcccccccccccc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQH  218 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f  218 (431)
                      ....-.|..|.+.+++-+-+...+..||..||+|+.|+..|+...+....+.+||..++.+++
T Consensus       105 ~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~  167 (200)
T KOG1700|consen  105 AGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLF  167 (200)
T ss_pred             hccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheee
Confidence            445678999999998778888999999999999999999999999999999999987766543

>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]

Probab=96.97  E-value=0.00011  Score=70.08  Aligned_cols=114  Identities=19%  Similarity=0.402  Sum_probs=86.7

Q ss_pred             CCCcccccCceEeecCccccCCCcccCCCCCCCC--CcceeecCCcccccccccc--ccCcccccCCCccccCCcceEEE
Q 014080          164 GCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPIT--DVEFSMSGNRPYHKHCYKE--QHHPKCDVCQNFIPTNSAGLIEY  239 (431)
Q Consensus       164 ~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~--~~~F~~~dg~pyC~~CY~~--~f~pkC~~C~~~I~~~~~~~i~~  239 (431)
                      +|+..|.+...+.+.+..||..|..|..|...+.  ...|.. +|..||..+|..  .+..+|..|...|...+  .+  
T Consensus         1 ~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~~~ql~--~l--   75 (235)
T KOG0490|consen    1 GCGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFTISQLD--EL--   75 (235)
T ss_pred             CCCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCCcCHHH--HH--
Confidence            4777785445567779999999999999999998  667777 999999999998  78899999999996532  12  


Q ss_pred             ecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          240 RAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       240 ~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                       .+-|      ... |.-||.|..|.+.+..+..+.........|...+..
T Consensus        76 -er~f------~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~  118 (235)
T KOG0490|consen   76 -ERAF------EKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKE  118 (235)
T ss_pred             -HHhh------cCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhh
Confidence             1222      112 678999999999887777766544447778777754

>smart00726 UIM Ubiquitin-interacting motif

Probab=90.10  E-value=0.23  Score=31.94  Aligned_cols=21  Identities=29%  Similarity=0.469  Sum_probs=17.1

Q ss_pred             CChhHHHHHHHhhhhhhhccC
Q 014080           40 FDNEEIDRAIALSLVEVDQKG   60 (431)
Q Consensus        40 ~~~~~~~~~~~~~~~~~~~~~   60 (431)
                      .|+|+|.+||++||.|.....
T Consensus         1 ~EDe~Lq~Ai~lSl~e~e~~~   21 (26)
T smart00726        1 DEDEDLQLALELSLQEAEESX   21 (26)
T ss_pred             ChHHHHHHHHHHhHHHhhhcc
Confidence            368999999999998776544

Present in proteasome subunit S5a and other ubiquitin-associated proteins.

>PF02809 UIM: Ubiquitin interaction motif; InterPro: IPR003903 The Ubiquitin Interacting Motif (UIM), or 'LALAL-motif', is a stretch of about 20 amino acid residues, which was first described in the 26S proteasome subunit PSD4/RPN-10 that is known to recognise ubiquitin [,]

Probab=86.92  E-value=0.28  Score=28.85  Aligned_cols=16  Identities=38%  Similarity=0.646  Sum_probs=13.5

Q ss_pred             CChhHHHHHHHhhhhh
Q 014080           40 FDNEEIDRAIALSLVE   55 (431)
Q Consensus        40 ~~~~~~~~~~~~~~~~   55 (431)
                      .|+++|.+||++|+.|
T Consensus         2 ~Ed~~L~~Al~~S~~e   17 (18)
T PF02809_consen    2 DEDEDLQRALEMSLEE   17 (18)
T ss_dssp             HHHHHHHHHHHHHHHH
T ss_pred             chHHHHHHHHHhhhcc
Confidence            4678999999999865

In addition, the UIM is found, often in tandem or triplet arrays, in a variety of proteins either involved in ubiquitination and ubiquitin metabolism, or known to interact with ubiquitin-like modifiers. Among the UIM proteins are two different subgroups of the UBP (ubiquitin carboxy-terminal hydrolase) family of deubiquitinating enzymes, one F-box protein, one family of HECT-containing ubiquitin-ligases (E3s) from plants, and several proteins containing ubiquitin-associated UBA and/or UBX domains []. In most of these proteins, the UIM occurs in multiple copies and in association with other domains such as UBA (IPR015940 from INTERPRO), UBX (IPR001012 from INTERPRO), ENTH, EH (IPR000261 from INTERPRO), VHS (IPR002014 from INTERPRO), SH3 (IPR001452 from INTERPRO), HECT (IPR000569 from INTERPRO), VWFA (IPR002035 from INTERPRO), EF-hand calcium-binding, WD-40 (IPR001680 from INTERPRO), F-box (IPR001810 from INTERPRO), LIM (IPR001781 from INTERPRO), protein kinase (IPR000719 from INTERPRO), ankyrin (IPR002110 from INTERPRO), PX (IPR001683 from INTERPRO), phosphatidylinositol 3- and 4-kinase (IPR000403 from INTERPRO), C2 (IPR000008 from INTERPRO), OTU (IPR003323 from INTERPRO), dnaJ (IPR001623 from INTERPRO), RING-finger (IPR001841 from INTERPRO) or FYVE-finger (IPR017455 from INTERPRO). UIMs have been shown to bind ubiquitin and to serve as a specific targeting signal important for monoubiquitination. Thus, UIMs may have several functions in ubiquitin metabolism each of which may require different numbers of UIMs [, , ]. The UIM is unlikely to form an independent folding domain. Instead, based on the spacing of the conserved residues, the motif probably forms a short alpha-helix that can be embedded into different protein folds []. Some proteins known to contain an UIM are listed below: Eukaryotic PSD4/RPN-10/S5, a multi-ubiquitin binding subunit of the 26S proteasome. Vertebrate Machado-Joseph disease protein 1 (Ataxin-3), which acts as a histone-binding protein that regulates transcription; defects in Ataxin-3 cause the neurodegenerative disorder Machado-Joseph disease (MJD). Vertebrate epsin and epsin2. Vertebrate hepatocyte growth factor-regulated tyrosine kinase substrate (HRS). Mammalian epidermal growth factor receptor substrate 15 (EPS15), which is involved in cell growth regulation. Mammalian epidermal growth factor receptor substrate EPS15R. Drosophila melanogaster (Fruit fly) liquid facets (lqf), an epsin. Yeast VPS27 vacuolar sorting protein, which is required for membrane traffic to the vacuole. ; PDB: 2KDE_A 2KDF_A 1YX6_A 1YX5_A 1YX4_A 1P9C_A 1UEL_B 1P9D_S 2KLZ_A.

>PF14891 Peptidase_M91: Effector protein

Probab=84.41  E-value=0.58  Score=43.34  Aligned_cols=18  Identities=33%  Similarity=0.525  Sum_probs=16.1

Q ss_pred             hhHHHHhhhHhHhhhcCC
Q 014080          404 GSILAHEMMHAWLRLKGF  421 (431)
Q Consensus       404 g~ilaHE~~Ha~lrl~g~  421 (431)
                      -.+|||||.|||=.|+|-
T Consensus       104 ~v~L~HEL~HA~~~~~Gt  121 (174)
T PF14891_consen  104 FVVLYHELIHAYDYMNGT  121 (174)
T ss_pred             HHHHHHHHHHHHHHHCCC
Confidence            478999999999999983

>PF13699 DUF4157: Domain of unknown function (DUF4157)

Probab=83.94  E-value=0.59  Score=37.93  Aligned_cols=21  Identities=29%  Similarity=0.400  Sum_probs=16.2

Q ss_pred             hhhhhhHHHHhhhHhHhhhcC
Q 014080          400 RLLTGSILAHEMMHAWLRLKG  420 (431)
Q Consensus       400 rl~~g~ilaHE~~Ha~lrl~g  420 (431)
                      .--.-.+||||++|+++.-.|
T Consensus        58 s~~~~~llaHEl~Hv~Qq~~g   78 (79)
T PF13699_consen   58 SPEGRALLAHELAHVVQQRRG   78 (79)
T ss_pred             CCCcchhHhHHHHHHHhhccC
Confidence            333457999999999987665

>PF01431 Peptidase_M13: Peptidase family M13 This is family M13 in the peptidase classification

Probab=80.81  E-value=0.78  Score=43.05  Aligned_cols=16  Identities=56%  Similarity=0.673  Sum_probs=13.9

Q ss_pred             hhhhHHHHhhhHhHhh
Q 014080          402 LTGSILAHEMMHAWLR  417 (431)
Q Consensus       402 ~~g~ilaHE~~Ha~lr  417 (431)
                      ..|+||||||||++-.
T Consensus        35 ~lG~ilahel~hafd~   50 (206)
T PF01431_consen   35 GLGFILAHELMHAFDP   50 (206)
T ss_dssp             THHHHHHHHHHHCTST
T ss_pred             HHHHHHHHHHHHHHHH
Confidence            4799999999999865

; InterPro: IPR018497 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site []. The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases []. This group of metallopeptidases belong to the MEROPS peptidase family M13 (neprilysin family, clan MA(E)). The protein fold of the peptidase domain for members of this family resembles that of thermolysin, the type example for clan MA and the predicted active site residues for members of this family and thermolysin occur in the motif HEXXH []. M13 peptidases are well-studied proteases found in a wide range of organisms including mammals and bacteria. In mammals they participate in processes such as cardiovascular development, blood-pressure regulation, nervous control of respiration, and regulation of the function of neuropeptides in the central nervous system. In bacteria they may be used for digestion of milk [, ]. The family includes eukaryotic and prokaryotic oligopeptidases, as well as some of the proteins responsible for the molecular basis of the blood group antigens e.g. Kell []. Neprilysin (3.4.24.11 from EC), is another member of this group, it is variously known as common acute lymphoblastic leukemia antigen (CALLA), enkephalinase (gp100) and neutral endopeptidase metalloendopeptidase (NEP). It is a plasma membrane-bound mammalian enzyme that is able to digest biologically-active peptides, including enkephalins []. The zinc ligands of neprilysin are known and are analogous to those in thermolysin, a related peptidase [, ]. Neprilysins, like thermolysin, are inhibited by phosphoramidon, which appears to selectively inhibit this family in mammals. The enzymes are all oligopeptidases, digesting oligo- and polypeptides, but not proteins []. Neprilysin consists of a short cytoplasmic domain, a membrane-spanning region and a large extracellular domain. The cytoplasmic domain contains a conformationally-restrained octapeptide, which is thought to act as a stop transfer sequence that prevents proteolysis and secretion [, ].; GO: 0004222 metalloendopeptidase activity, 0006508 proteolysis; PDB: 2QPJ_A 1R1I_A 1R1J_A 1Y8J_A 1R1H_A 1DMT_A 2YB9_A 3DWB_A 3ZUK_A.

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	431
3mmk_A	169	The Structural Basis For Partial Redundancy In A Cl		8e-07
2jtn_A	182	Nmr Solution Structure Of A Ldb1-Lid:lhx3-Lim Compl		4e-06
2dj7_A	80	Solution Structure Of 3rd Lim Domain Of Actin-Bindi		2e-05
2rgt_A	169	Crystal Structure Of Lhx3 Lim Domains 1 And 2 With		3e-05
1x3h_A	80	Solution Structure Of The Lim Domain Of Human Leupa		2e-04
2cup_A	101	Solution Structure Of The Skeletal Muscle Lim-Prote		3e-04
2d8x_A	70	Solution Structure Of The Second Lim Domain Of Part		8e-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 = 51.6 bits (122), Expect = 8e-07,   Method: Compositional matrix adjust.
 Identities = 36/130 (27%), Positives = 57/130 (43%), Gaps = 12/130 (9%)
Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK 221
           CAGCN  I     L  ++  WH  C +C  C + + D  FS +G+  Y K  + ++   K
Sbjct: 9   CAGCNQHILDKFILKVLDRHWHSSCLKCADCQMQLADRCFSRAGS-VYCKEDFFKRFGTK 67
Query: 222 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGR 281
           C  CQ  IP      +  +A  F    +C +        C  C R      ++  ++DGR
Sbjct: 68  CTACQQGIPPTQ---VVRKAQDFVYHLHCFA--------CIICNRQLATGDEFYLMEDGR 116
Query: 282 KLCLECLDSA 291
            +C E  ++A
Sbjct: 117 LVCKEDYETA 126

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 33/124 (26%), Positives = 55/124 (44%), Gaps = 12/124 (9%)
Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHP 220
           +CAGC+  I     L  ++  WH +C +C  C++P+ +  FS  G   Y K  + ++   
Sbjct: 62  MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFS-RGESVYCKDDFFKRFGT 120
Query: 221 KCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDG 280
           KC  CQ  IP      +  RA  F    +C +        C  C+R      ++  ++D 
Sbjct: 121 KCAACQLGIPPTQ---VVRRAQDFVYHLHCFA--------CVVCKRQLATGDEFYLMEDS 169
Query: 281 RKLC 284
           R +C
Sbjct: 170 RLVC 173

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

Iteration: 1
 Score = 47.4 bits (111), Expect = 2e-05,   Method: Composition-based stats.
 Identities = 22/56 (39%), Positives = 31/56 (55%), Gaps = 1/56 (1%)
Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQ 217
           CAGC  EI HG+ L  ++  WH  CF+C +C++ +T    S  G  PY +  Y  Q
Sbjct: 18  CAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGEYISKDG-VPYCESDYHAQ 72

>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 = 46.6 bits (109), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 33/124 (26%), Positives = 55/124 (44%), Gaps = 12/124 (9%)
Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHP 220
           +CAGC+  I     L  ++  WH +C +C  C++P+ +  FS  G   Y K  + ++   
Sbjct: 8   MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFS-RGESVYCKDDFFKRFGT 66
Query: 221 KCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDG 280
           KC  CQ  IP      +  RA  F    +C +        C  C+R      ++  ++D 
Sbjct: 67  KCAACQLGIPPTQ---VVRRAQDFVYHLHCFA--------CVVCKRQLATGDEFYLMEDS 115
Query: 281 RKLC 284
           R +C
Sbjct: 116 RLVC 119

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

Iteration: 1
 Score = 43.9 bits (102), Expect = 2e-04,   Method: Composition-based stats.
 Identities = 22/58 (37%), Positives = 26/58 (44%), Gaps = 4/58 (6%)
Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH 219
           C GCN  +    YLS M+  WHPECF C  C    +   F     RP+   C    HH
Sbjct: 18  CGGCNRPVLEN-YLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPF---CELHYHH 71

>pdb|2CUP|A Chain A, Solution Structure Of The Skeletal Muscle Lim-Protein 1 Length = 101

Iteration: 1
 Score = 43.1 bits (100), Expect = 3e-04,   Method: Composition-based stats.
 Identities = 22/70 (31%), Positives = 28/70 (40%), Gaps = 1/70 (1%)
Query: 157 SGYRICAGCNTEIG-HGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYK 215
           SG   C  C   IG   + +     FWH  CFRC  C  P+ +  F    N+     C  
Sbjct: 3   SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTT 62
Query: 216 EQHHPKCDVC 225
            +  PKC  C
Sbjct: 63  REDSPKCKGC 72

>pdb|2D8X|A Chain A, Solution Structure Of The Second Lim Domain Of Particularly Interesting New Cys-His Protein (Pinch) Length = 70

Iteration: 1
 Score = 41.6 bits (96), Expect = 8e-04,   Method: Composition-based stats.
 Identities = 21/61 (34%), Positives = 28/61 (45%), Gaps = 1/61 (1%)
Query: 157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE 216
           SG   C  C  E   GR +  M   WHPECFRC  C   + D+ F  +  R   + C+  
Sbjct: 3   SGSSGCHQCG-EFIIGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNR 61
Query: 217 Q 217
           +
Sbjct: 62  E 62

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	431
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	3e-22
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	3e-22
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	7e-22
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	5e-21
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	6e-21
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	9e-20
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	1e-19
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	3e-19
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	2e-18
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-07
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	2e-17
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	3e-17
2cuq_A	80	Four and A half LIM domains 3; structural genomics	6e-17
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	8e-17
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	1e-16
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	2e-16
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	3e-15
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	5e-04
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	2e-16
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	3e-16
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	7e-11
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	5e-16
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	2e-04
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	7e-16
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	9e-16
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	2e-15
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	4e-15
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	5e-15
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	5e-15
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	7e-15
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	2e-14
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	2e-12
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	3e-14
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	3e-14
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	1e-13
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	1e-13
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	4e-13
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	5e-13
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	5e-13
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	6e-10
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	1e-12
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	2e-12
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	3e-12
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	3e-12
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	8e-12
2cor_A	79	Pinch protein; LIM domain, particularly interestin	2e-09
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	1e-08
1vt4_I	1221	APAF-1 related killer DARK; drosophila apoptosome,	5e-06
2co8_A	82	NEDD9 interacting protein with calponin homology a	7e-06
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	1e-04
3lvg_D	190	LCB, clathrin light chain B; SELF assembly, coated	4e-04

>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 = 88.9 bits (221), Expect = 3e-22
 Identities = 16/66 (24%), Positives = 27/66 (40%), Gaps = 1/66 (1%)

Query: 157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE 216
           SG   C  C   I     ++  E  WH ECF C +C   ++   F+   +  Y  +C+ +
Sbjct: 3   SGSSGCVQCKKPIT-TGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCD 61

Query: 217 QHHPKC 222
            +    
Sbjct: 62  LYASGP 67

>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 = 89.0 bits (221), Expect = 3e-22
 Identities = 17/66 (25%), Positives = 27/66 (40%), Gaps = 1/66 (1%)

Query: 157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE 216
           SG   C  CN  I     ++  +  WH +CF C +C+  +    F+   ++ Y   CYK 
Sbjct: 3   SGSSGCVKCNKAIT-SGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKN 61

Query: 217 QHHPKC 222
                 
Sbjct: 62  FVSGPS 67

>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 = 88.0 bits (218), Expect = 7e-22
 Identities = 22/69 (31%), Positives = 29/69 (42%), Gaps = 3/69 (4%)

Query: 157 SGYRICAGCNTEI---GHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHC 213
           SG   CAGC   I   G  +Y+S  E  WH +CF C  C+L +    F    +      C
Sbjct: 3   SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDC 62

Query: 214 YKEQHHPKC 222
            K+   P  
Sbjct: 63  GKDISGPSS 71

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

 Score = 85.9 bits (213), Expect = 5e-21
 Identities = 17/72 (23%), Positives = 27/72 (37%)

Query: 154 PFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHC 213
           P + G   C  C   + H   + C    +H  CF C  C   +     ++     Y K C
Sbjct: 2   PNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSC 61

Query: 214 YKEQHHPKCDVC 225
           Y +++ PK    
Sbjct: 62  YGKKYGPKGYGY 73

>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 = 85.6 bits (212), Expect = 6e-21
 Identities = 22/66 (33%), Positives = 32/66 (48%), Gaps = 1/66 (1%)

Query: 157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE 216
            G   CAGC  EI HG+ L  ++  WH  CF+C +C++ +T  E+      PY +  Y  
Sbjct: 13  RGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHA 71

Query: 217 QHHPKC 222
           Q     
Sbjct: 72  QFGSGP 77

>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 = 82.0 bits (203), Expect = 9e-20
 Identities = 18/67 (26%), Positives = 23/67 (34%), Gaps = 1/67 (1%)

Query: 157 SGYRICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYK 215
           SG   C+ C   +  G R L      WH  CF C  C  P+    F       Y   CY+
Sbjct: 3   SGSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYE 62

Query: 216 EQHHPKC 222
            +     
Sbjct: 63  NKFASGP 69

>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 = 81.7 bits (202), Expect = 1e-19
 Identities = 22/67 (32%), Positives = 28/67 (41%), Gaps = 1/67 (1%)

Query: 157 SGYRICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYK 215
           SG   C  C   I  G R +    + WH  CF CH C  PI    F    N+ +   CY+
Sbjct: 3   SGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYE 62

Query: 216 EQHHPKC 222
           +QH    
Sbjct: 63  KQHASGP 69

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

 Score = 80.2 bits (198), Expect = 3e-19
 Identities = 21/66 (31%), Positives = 28/66 (42%), Gaps = 1/66 (1%)

Query: 157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE 216
           SG   C  C   I  GR +  M   WHPECFRC  C   + D+ F  +  R   + C+  
Sbjct: 3   SGSSGCHQCGEFII-GRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNR 61

Query: 217 QHHPKC 222
           +     
Sbjct: 62  EKASGP 67

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

 Score = 79.8 bits (197), Expect = 2e-18
 Identities = 27/126 (21%), Positives = 40/126 (31%), Gaps = 11/126 (8%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK 221
           CAGC+  I    Y       WH + F C  C+  +    + M  ++P  K CY + H   
Sbjct: 6   CAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVV 65

Query: 222 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGR 281
           C  C N I       + Y    +        H       C  C +      +     +G 
Sbjct: 66  CQGCHNAIDPEVQR-VTYNNFSW--------HASTECFLCSCCSK--CLIGQKFMPVEGM 114

Query: 282 KLCLEC 287
             C   
Sbjct: 115 VFCSVE 120

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

 Score = 49.3 bits (118), Expect = 1e-07
 Identities = 13/60 (21%), Positives = 24/60 (40%), Gaps = 3/60 (5%)

Query: 161 ICAGCNTEI-GHGRYLSCMEAFWHP--ECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQ 217
           +C GC+  I    + ++     WH   ECF C  C+  +   +F       +     K++
Sbjct: 65  VCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKR 124

>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 = 76.0 bits (187), Expect = 2e-17
 Identities = 18/64 (28%), Positives = 23/64 (35%), Gaps = 1/64 (1%)

Query: 161 ICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH 219
            CA C   IGH  R L   +  +H  CFRC  C   + D  F+   +      CY     
Sbjct: 17  TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFS 76

Query: 220 PKCD 223
               
Sbjct: 77  SGPS 80

>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 = 75.6 bits (186), Expect = 3e-17
 Identities = 14/72 (19%), Positives = 24/72 (33%), Gaps = 1/72 (1%)

Query: 151 QPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYH 210
                     +C  C + I  G  +   + + HPECF C  CNL +    +       Y 
Sbjct: 17  GGAGSAQRMPLCDKCGSGI-VGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYC 75

Query: 211 KHCYKEQHHPKC 222
           +   + +     
Sbjct: 76  ETHARARTSGPS 87

>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 = 74.3 bits (183), Expect = 6e-17
 Identities = 15/62 (24%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHP 220
            CA C+  +     ++  +  WH EC  C  C  P+   +F+     PY   C+ E    
Sbjct: 17  RCARCSKTLT-QGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFAS 75

Query: 221 KC 222
             
Sbjct: 76  GP 77

>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 = 73.9 bits (182), Expect = 8e-17
 Identities = 20/62 (32%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHP 220
            C GCN  +    YLS M+  WHPECF C  C    +   F     RP+ +  Y  +   
Sbjct: 17  KCGGCNRPV-LENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGS 75

Query: 221 KC 222
             
Sbjct: 76  GP 77

>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 = 72.9 bits (179), Expect = 1e-16
 Identities = 17/70 (24%), Positives = 26/70 (37%), Gaps = 2/70 (2%)

Query: 157 SGYRICAGCNTEI-GHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYK 215
           SG   C GC  ++ G G  +  ++  +H  CF C +C   +    F     R Y + CY 
Sbjct: 3   SGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYV 62

Query: 216 EQHHPKCDVC 225
                     
Sbjct: 63  ATLE-SGPSS 71

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

 Score = 76.2 bits (187), Expect = 2e-16
 Identities = 23/122 (18%), Positives = 42/122 (34%), Gaps = 9/122 (7%)

Query: 154 PFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHC 213
           P + G + C  C   +     + C  + +H  CF C  C   +     ++ G+  Y K C
Sbjct: 2   PNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSC 61

Query: 214 YKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCP---------SHERDGTPRCCSC 264
           Y +++ PK         T S    E     +   +            + +  G+  C  C
Sbjct: 62  YGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRC 121

Query: 265 ER 266
            +
Sbjct: 122 GQ 123

>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 = 72.7 bits (178), Expect = 3e-15
 Identities = 16/86 (18%), Positives = 22/86 (25%), Gaps = 1/86 (1%)

Query: 141 PPRYESGNIFQPFPFFSGYR-ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDV 199
                +           G    C  C   +     +      WH  CFRC  C   +   
Sbjct: 96  QSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLEST 155

Query: 200 EFSMSGNRPYHKHCYKEQHHPKCDVC 225
             +      Y K CY +   PK    
Sbjct: 156 TLADKDGEIYCKGCYAKNFGPKGFGF 181

>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 = 40.0 bits (93), Expect = 5e-04
 Identities = 16/124 (12%), Positives = 27/124 (21%), Gaps = 14/124 (11%)

Query: 142 PRYESGNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEF 201
                G             I              +   A        C  C   +   E 
Sbjct: 71  KGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAEK 130

Query: 202 SMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSH-ERDGTPR 260
            +   + +HK C+      +C  C       S  L +          YC     ++  P+
Sbjct: 131 VIGAGKSWHKSCF------RCAKCGK--SLESTTLADKDGEI-----YCKGCYAKNFGPK 177

Query: 261 CCSC 264
               
Sbjct: 178 GFGF 181

>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 = 72.9 bits (179), Expect = 2e-16
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHP 220
           +CA CN  I  G +L  +   WHPE F C  C   +  + F       Y + CY++    
Sbjct: 27  MCAHCNQVI-RGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFAS 85

Query: 221 KC 222
             
Sbjct: 86  GP 87

>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 = 75.3 bits (185), Expect = 3e-16
 Identities = 29/127 (22%), Positives = 50/127 (39%), Gaps = 12/127 (9%)

Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHP 220
           +CAGC+  I     L  ++  WH +C +C  C++P+ +  FS      Y K  + ++   
Sbjct: 8   MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFSRGE-SVYCKDDFFKRFGT 66

Query: 221 KCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDG 280
           KC  CQ  IP     +   +        Y           C  C+R      ++  ++D 
Sbjct: 67  KCAACQLGIPPTQV-VRRAQDF-----VYHLHCF-----ACVVCKRQLATGDEFYLMEDS 115

Query: 281 RKLCLEC 287
           R +C   
Sbjct: 116 RLVCKAD 122

>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 = 59.9 bits (145), Expect = 7e-11
 Identities = 13/94 (13%), Positives = 23/94 (24%), Gaps = 6/94 (6%)

Query: 162 CAGCNTEI-GHGRYLSCMEAFWHPECFRCHSCNLPITDVE--FSMSGNRPYHKHCYKEQH 218
           CA C   I          +  +H  CF C  C   +   +  + M  +R   K  Y+   
Sbjct: 68  CAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK 127

Query: 219 HPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPS 252
                             +   +          +
Sbjct: 128 QGGSGGSGGSGGGTP---MVAASPERHDGGLQAN 158

>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 = 72.4 bits (178), Expect = 5e-16
 Identities = 21/73 (28%), Positives = 26/73 (35%), Gaps = 1/73 (1%)

Query: 161 ICAGCNTEIGHGRY-LSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH 219
            C  C   IG     +     FWH  CFRC  C  P+ +  F    N+     C   +  
Sbjct: 7   GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS 66

Query: 220 PKCDVCQNFIPTN 232
           PKC  C   I   
Sbjct: 67  PKCKGCFKAIVAG 79

>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 = 39.3 bits (92), Expect = 2e-04
 Identities = 10/32 (31%), Positives = 13/32 (40%), Gaps = 1/32 (3%)

Query: 162 CAGCNTEIGHG-RYLSCMEAFWHPECFRCHSC 192
           C GC   I  G + +      WH +CF   S 
Sbjct: 69  CKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100

>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 = 71.8 bits (176), Expect = 7e-16
 Identities = 19/85 (22%), Positives = 32/85 (37%), Gaps = 1/85 (1%)

Query: 152 PFPFFSGYR-ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYH 210
              F +  R  C  C   +     L   +  +H  CFRC  CN  ++   ++    R Y 
Sbjct: 7   GMKFQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYC 66

Query: 211 KHCYKEQHHPKCDVCQNFIPTNSAG 235
           K  + +    K +  + F    S+G
Sbjct: 67  KPHFNQLFKSKGNYDEGFGSGPSSG 91

>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 = 74.2 bits (182), Expect = 9e-16
 Identities = 36/171 (21%), Positives = 60/171 (35%), Gaps = 13/171 (7%)

Query: 121 QLEEDEQLAKAIQDSLRVDSPPRYESGNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEA 180
           + E      +  Q            SG             +CAGC+  I     L  ++ 
Sbjct: 23  EDERLITRLENTQFDAANGIDDEGGSGGHMGSGGTPEI-PMCAGCDQHILDRFILKALDR 81

Query: 181 FWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYR 240
            WH +C +C  C++P+ +  FS      Y K  + ++   KC  CQ  IP      +  R
Sbjct: 82  HWHSKCLKCSDCHVPLAERCFSRGE-SVYCKDDFFKRFGTKCAACQLGIP---PTQVVRR 137

Query: 241 AHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA 291
           A       Y           C  C+R      ++  ++D R +C    ++A
Sbjct: 138 AQD---FVYHLHCF-----ACVVCKRQLATGDEFYLMEDSRLVCKADYETA 180

>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 = 69.9 bits (171), Expect = 2e-15
 Identities = 12/58 (20%), Positives = 23/58 (39%), Gaps = 3/58 (5%)

Query: 162 CAGCNTEI---GHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE 216
           C  C+  I      +++   ++ WH ECF C  C++ +    F       + + C   
Sbjct: 8   CVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSG 65

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

 Score = 68.9 bits (169), Expect = 4e-15
 Identities = 18/74 (24%), Positives = 24/74 (32%), Gaps = 9/74 (12%)

Query: 147 GNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGN 206
           G++  P        IC  C   I  GR ++ M   WH E F C  C  P           
Sbjct: 1   GSMGVP--------ICGACRRPI-EGRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKG 51

Query: 207 RPYHKHCYKEQHHP 220
             Y +  Y +    
Sbjct: 52  LAYCETHYNQLFGD 65

>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 = 68.9 bits (169), Expect = 5e-15
 Identities = 16/63 (25%), Positives = 23/63 (36%), Gaps = 1/63 (1%)

Query: 161 ICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH 219
            C GC   I  G + +      WH +CF C +C   I    F   G   Y   C++ +  
Sbjct: 17  KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA 76

Query: 220 PKC 222
              
Sbjct: 77  SGP 79

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

 Score = 68.9 bits (169), Expect = 5e-15
 Identities = 14/62 (22%), Positives = 26/62 (41%), Gaps = 2/62 (3%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMS-GNRPYHKHCYKEQHHP 220
           CA C+  I   R L  M   +HP CF C  C+  +  + F++   ++ +    +  +   
Sbjct: 18  CATCSQPI-LDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFAS 76

Query: 221 KC 222
             
Sbjct: 77  GP 78

>2egq_A FHL1 protein; LIM domain, four and A half LIM domains protein 1, skeletal muscle LIM- protein 1, SLIM 1, structural genomics NPPSFA; NMR {Homo sapiens} Length = 77

 Score = 68.3 bits (167), Expect = 7e-15
 Identities = 18/59 (30%), Positives = 26/59 (44%), Gaps = 4/59 (6%)

Query: 162 CAGCNTEI-GHGRYLSCMEA---FWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE 216
           CAGC   I G G+  S +      WH  CF C  C++ + +  F     + Y   C K+
Sbjct: 18  CAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

>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 = 70.8 bits (173), Expect = 2e-14
 Identities = 30/143 (20%), Positives = 50/143 (34%), Gaps = 16/143 (11%)

Query: 158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFS--MSGNRPYHKHCYK 215
            ++ CAGC  +I     L  M+++WH  C +C SC   + D+  S          ++ Y 
Sbjct: 4   SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

Query: 216 EQH--HPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTK 273
                   C  C   IP   A  +  RA       Y           C +C        +
Sbjct: 64  RLFGNSGACSACGQSIP---ASELVMRAQG---NVYHLKCF-----TCSTCRNRLVPGDR 112

Query: 274 YLSLDDGRKLCLECLDSAIMDTH 296
           +    +G   C     +A+++ H
Sbjct: 113 FH-YINGSLFCEHDRPTALINGH 134

>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 = 64.6 bits (157), Expect = 2e-12
 Identities = 13/108 (12%), Positives = 26/108 (24%), Gaps = 5/108 (4%)

Query: 162 CAGCNTEI-GHGRYLSCMEAFWHPECFRCHSCNLPITDVE-FSMSGNRPYHKHCYKEQHH 219
           C+ C   I      +      +H +CF C +C   +   + F       + +H       
Sbjct: 72  CSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALI 131

Query: 220 PKCDVCQNFIPTNSAGL-IEYRAHPFWLQKYCPSHERDGTPRCCSCER 266
                      +  +G  +     P          + D          
Sbjct: 132 NGHLNSGGSGGSGGSGGDVMVVGEP--TLMGGEFGDEDERLITRLENT 177

>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 = 66.7 bits (163), Expect = 3e-14
 Identities = 14/69 (20%), Positives = 24/69 (34%), Gaps = 1/69 (1%)

Query: 155 FFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPY-HKHC 213
                  C  C+  +     +S +   WH  C +C  C+  +T    +    +P+ HK C
Sbjct: 5   SSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPC 64

Query: 214 YKEQHHPKC 222
           Y        
Sbjct: 65  YATLFGSGP 73

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

 Score = 66.7 bits (163), Expect = 3e-14
 Identities = 13/71 (18%), Positives = 24/71 (33%), Gaps = 1/71 (1%)

Query: 152 PFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHK 211
                    +C  C T I  G ++   +   HPEC+ C  C   +         ++ Y +
Sbjct: 8   SIGNAQKLPMCDKCGTGI-VGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCE 66

Query: 212 HCYKEQHHPKC 222
              +E+     
Sbjct: 67  KHARERVSGPS 77

>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 = 65.1 bits (159), Expect = 1e-13
 Identities = 15/62 (24%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPY-HKHCYKEQHHP 220
           C  C+ E+     ++ +   WH  C +C  C   +T    +    +PY +  CY     P
Sbjct: 3   CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGP 62

Query: 221 KC 222
           K 
Sbjct: 63  KG 64

>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 = 64.7 bits (158), Expect = 1e-13
 Identities = 12/63 (19%), Positives = 21/63 (33%), Gaps = 1/63 (1%)

Query: 161 ICAGCNTEI-GHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH 219
            C  C        + ++     +H +CF C  C     +  F     R Y +H ++    
Sbjct: 13  TCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA 72

Query: 220 PKC 222
           P  
Sbjct: 73  PCW 75

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

 Score = 63.2 bits (153), Expect = 4e-13
 Identities = 18/60 (30%), Positives = 24/60 (40%), Gaps = 2/60 (3%)

Query: 157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDV-EFSMSGNRPYHKHCYK 215
           SG   C  C   I  GR L   E  +HP C  C  C     +  E  + G+  +H  C +
Sbjct: 3   SGSSGCDSCEKYIT-GRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQ 61

>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 = 63.2 bits (154), Expect = 5e-13
 Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 1/58 (1%)

Query: 161 ICAGCNTEI-GHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQ 217
            C  C        + ++     +H +CF C  C     +  F     R Y +H ++  
Sbjct: 13  TCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQML 70

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

 Score = 64.8 bits (158), Expect = 5e-13
 Identities = 26/132 (19%), Positives = 44/132 (33%), Gaps = 16/132 (12%)

Query: 160 RICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFS--MSGNRPYHKHCYKEQ 217
             C GC   IG   +L  ++ +WH +C  C  C   + +V         R   +  Y   
Sbjct: 3   LTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL 62

Query: 218 HHPK--CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYL 275
                 C  C   I    A  +  R      + Y          +C +C++      +YL
Sbjct: 63  FGQDGLCASCDKRIR---AYEMTMRVKD---KVYHLECF-----KCAACQKHFCVGDRYL 111

Query: 276 SLDDGRKLCLEC 287
            L +   +C + 
Sbjct: 112 -LINSDIVCEQD 122

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

 Score = 55.9 bits (135), Expect = 6e-10
 Identities = 12/68 (17%), Positives = 25/68 (36%), Gaps = 2/68 (2%)

Query: 156 FSGYRICAGCNTEI-GHGRYLSCMEAFWHPECFRCHSCNLPITDVE-FSMSGNRPYHKHC 213
           F    +CA C+  I  +   +   +  +H ECF+C +C       + + +  +    +  
Sbjct: 63  FGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQD 122

Query: 214 YKEQHHPK 221
             E     
Sbjct: 123 IYEWTKIN 130

>1m3v_A FLIN4, fusion of the LIM interacting domain of LDB1 and the N-terminal LIM domain of LMO4...; fusion protein, LMO proteins, metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 122

 Score = 63.8 bits (155), Expect = 1e-12
 Identities = 16/78 (20%), Positives = 28/78 (35%), Gaps = 2/78 (2%)

Query: 158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFS--MSGNRPYHKHCYK 215
            ++ CAGC  +I     L  M+++WH  C +C SC   + D+  S          ++ Y 
Sbjct: 4   SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

Query: 216 EQHHPKCDVCQNFIPTNS 233
                           + 
Sbjct: 64  RLFGNSGAGGSGGHMGSG 81

>1j2o_A FLIN2, fusion of rhombotin-2 and LIM domain-binding protein 1; LIM-interaction-domain (LID), metal binding protein; NMR {Mus musculus} SCOP: g.39.1.3 g.39.1.3 Length = 114

 Score = 62.4 bits (151), Expect = 2e-12
 Identities = 14/71 (19%), Positives = 23/71 (32%), Gaps = 2/71 (2%)

Query: 158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFS--MSGNRPYHKHCYK 215
               C GC   IG   +L  ++ +WH +C  C  C   + +V         R   +  Y 
Sbjct: 2   SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 61

Query: 216 EQHHPKCDVCQ 226
                   +  
Sbjct: 62  RLGGSGGHMGS 72

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

 Score = 61.3 bits (149), Expect = 3e-12
 Identities = 18/64 (28%), Positives = 27/64 (42%), Gaps = 3/64 (4%)

Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVE--FSMSGNRPYHKHCYKEQH 218
            C GC+  +  G ++   E  +HPECF C SC + I D +    +     Y   C+ E  
Sbjct: 17  FCHGCSLLM-TGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVV 75

Query: 219 HPKC 222
               
Sbjct: 76  SGPS 79

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

 Score = 61.0 bits (148), Expect = 3e-12
 Identities = 15/56 (26%), Positives = 23/56 (41%), Gaps = 2/56 (3%)

Query: 162 CAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITD-VEFSMSGNRPYHKHCYKE 216
           C  C+  I  G  +S +   +HP+CF C  C LP       + +G     + C   
Sbjct: 18  CFSCDQFI-EGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLP 72

>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 = 61.3 bits (148), Expect = 8e-12
 Identities = 16/62 (25%), Positives = 27/62 (43%), Gaps = 2/62 (3%)

Query: 157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFS--MSGNRPYHKHCY 214
             ++ CAGC  +I     L  M+++WH  C +C SC   + D+  S          ++ Y
Sbjct: 59  LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDY 118

Query: 215 KE 216
             
Sbjct: 119 IR 120

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

 Score = 53.3 bits (128), Expect = 2e-09
 Identities = 15/61 (24%), Positives = 24/61 (39%), Gaps = 2/61 (3%)

Query: 157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE 216
            G  IC  C+  I   + L      +HP+ F C +C   +T     + G   Y   C+ +
Sbjct: 13  LGKYICQKCHAIID-EQPLIFKNDPYHPDHFNCANCGKELTADARELKG-ELYCLPCHDK 70

Query: 217 Q 217
            
Sbjct: 71  M 71

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

 Score = 47.9 bits (113), Expect = 5e-06
 Identities = 66/525 (12%), Positives = 139/525 (26%), Gaps = 185/525 (35%)

Query: 55  EVDQKGKKVIE-NEYDSEDDLQCIKSDDSDEDELDEDEIRAIAQQEEDERRA-------K 106
           E   + K ++   E    D+  C    D  +  L ++EI  I   ++             
Sbjct: 13  EHQYQYKDILSVFEDAFVDNFDCKDVQDMPKSILSKEEIDHIIMSKDAVSGTLRLFWTLL 72

Query: 107 AQQEEDERRARARAQLEED-EQLAKAIQDSLRVDSPPR--YESG-----NIFQPFPFFSG 158
           ++QEE  ++      L  + + L   I+   R  S     Y        N  Q F  ++ 
Sbjct: 73  SKQEEMVQKFVEEV-LRINYKFLMSPIKTEQRQPSMMTRMYIEQRDRLYNDNQVFAKYNV 131

Query: 159 YRI--------CAGCNTEIGHGRYL----------SCMEA----------------FW-- 182
            R+              E+   + +          + +                  FW  
Sbjct: 132 SRLQPYLKLRQAL---LELRPAKNVLIDGVLGSGKTWVALDVCLSYKVQCKMDFKIFWLN 188

Query: 183 ----------------------HPECFRC-HSCNLPITDVEFSMSGNRPYHKHCYKEQHH 219
                                      R  HS N+ +          +   +   K + +
Sbjct: 189 LKNCNSPETVLEMLQKLLYQIDPNWTSRSDHSSNIKLRIHSI-----QAELRRLLKSKPY 243

Query: 220 PKC-----DV------------CQNFIPTNSAGLIEY-----RAHPF------------- 244
             C     +V            C+  + T    + ++       H               
Sbjct: 244 ENCLLVLLNVQNAKAWNAFNLSCKILLTTRFKQVTDFLSAATTTHISLDHHSMTLTPDEV 303

Query: 245 ------WLQKYC---PSHERDGTPRCCSC--ERM-EPRDT----KYLSLD---DGRKLCL 285
                 +L       P       PR  S   E + +   T    K+++ D      +  L
Sbjct: 304 KSLLLKYLDCRPQDLPREVLTTNPRRLSIIAESIRDGLATWDNWKHVNCDKLTTIIESSL 363

Query: 286 ECLDSAIMDTHECQPLYLEIQEFYEGLN--MKV---------EQQVPLLLVERQALNEAM 334
             L+ A     E + ++  +  F    +    +         +  V +++ +    +   
Sbjct: 364 NVLEPA-----EYRKMFDRLSVFPPSAHIPTILLSLIWFDVIKSDVMVVVNKLHKYSLVE 418

Query: 335 EGEKNGHHHLPETRGLCLSEEQTVT--TVLRRPRIGAGYRLIDMITEPYRLIRRCEVTAI 392
           +  K     +P    + L  +  +     L R        ++D     Y + +  +   +
Sbjct: 419 KQPKESTISIP---SIYLELKVKLENEYALHR-------SIVDH----YNIPKTFDSDDL 464

Query: 393 LILYGLPRLLTGSILAHEMMHAWLRLKG------FICFKLIYFVF 431
           +  Y     L     +H   H    LK          F++++  F
Sbjct: 465 IPPY-----LDQYFYSHIGHH----LKNIEHPERMTLFRMVFLDF 500

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

 Score = 43.0 bits (101), Expect = 7e-06
 Identities = 15/69 (21%), Positives = 20/69 (28%), Gaps = 2/69 (2%)

Query: 154 PFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCN--LPITDVEFSMSGNRPYHK 211
                  +CA C   +     L     F+H  CFRCH+C   L     E        Y  
Sbjct: 10  QEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCL 69

Query: 212 HCYKEQHHP 220
               +    
Sbjct: 70  QHLPQTDSG 78

>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 = 39.1 bits (91), Expect = 1e-04
 Identities = 14/60 (23%), Positives = 23/60 (38%), Gaps = 4/60 (6%)

Query: 161 ICAGCNTEIGHG-RYLSCMEAFWH--PECFRCHSCNLPITDVEFSMSGNRPY-HKHCYKE 216
           +C GC+  I    + ++     WH   ECF C  C+  +   +F       +    C K 
Sbjct: 4   VCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKR 63

>3lvg_D LCB, clathrin light chain B; SELF assembly, coated PIT, cytoplasmic vesicle, membrane, Ca structural protein; 7.94A {Bos taurus} Length = 190

 Score = 40.5 bits (94), Expect = 4e-04
 Identities = 19/69 (27%), Positives = 31/69 (44%), Gaps = 12/69 (17%)

Query: 82  SDEDELDEDEIRAIAQ-QEE-----DERRAKAQQEEDERRARARAQLEE-----DEQLAK 130
           +  D L + E  +I + +EE      E  A ++  E E R +A+  LEE      EQ+ K
Sbjct: 75  AQADRLTQ-EPESIRKWREEQRKRLQELDAASKVMEQEWREKAKKDLEEWNQRQSEQVEK 133

Query: 131 AIQDSLRVD 139
              ++   D
Sbjct: 134 NKINNRIAD 142

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	431
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.91
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.91
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.9
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.9
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.9
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.88
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.83
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.74
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.68
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.6
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.59
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.58
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.58
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.57
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.56
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.56
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.55
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.55
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.54
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.54
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.53
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.52
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.52
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.52
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.51
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.51
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.5
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.5
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.49
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.49
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.49
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.49
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.46
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.45
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.44
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.44
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.44
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.43
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.43
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.41
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.4
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.4
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.4
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.39
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.38
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.37
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.34
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.34
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.29
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.28
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.26
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.26
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.2
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.19
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.14
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.03
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.02
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.02
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.0
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.0
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	98.99
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	98.99
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	98.99
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	98.99
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	98.98
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	98.97
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	98.95
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	98.95
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	98.93
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	98.93
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	98.88
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	98.87
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	98.86
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	98.84
2cor_A	79	Pinch protein; LIM domain, particularly interestin	98.84
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	98.8
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	98.78
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	98.77
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	98.77
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	98.77
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	98.76
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	98.74
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	98.74
2co8_A	82	NEDD9 interacting protein with calponin homology a	98.72
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	97.17
2d3g_P	26	Ubiquitin interacting motif from hepatocyte growth	94.01
1q0v_A	81	Hydrophilic protein; has cysteine rich putative zi	85.51
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	85.38
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	83.66

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

Probab=99.91  E-value=3.3e-25  Score=204.20  Aligned_cols=124  Identities=23%  Similarity=0.542  Sum_probs=109.0

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCCCccccCCcc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAG  235 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~  235 (431)
                      ....++|.+|+++|....++.++++.||+.||+|..|+++|.+..| .++|++||+.||.++|+++|.+|+++|.+.. .
T Consensus        57 ~~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~~kC~~C~~~I~~~~-~  134 (182)
T 2jtn_A           57 TPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTKCAACQLGIPPTQ-V  134 (182)
T ss_dssp             CCSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCE-EETTEEECHHHHHHTTSCCCTTTCCCCCSSC-C
T ss_pred             CCCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCce-eECCEeeecCccccccccccccCCCccCCCc-e
Confidence            5567999999999976567899999999999999999999998776 6899999999999999999999999999753 2


Q ss_pred             eEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcc
Q 014080          236 LIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA  291 (431)
Q Consensus       236 ~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~  291 (431)
                      ++.+.++          +||..||+|..|++.|..|..|+...+|++||..||.++
T Consensus       135 v~~a~~~----------~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~~  180 (182)
T 2jtn_A          135 VRRAQDF----------VYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETA  180 (182)
T ss_dssp             CCEETTE----------ECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHHH
T ss_pred             EEecCCC----------CEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHHh
Confidence            3456665          469999999999999977888887789999999999864

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

Probab=99.91  E-value=1.3e-24  Score=188.19  Aligned_cols=120  Identities=23%  Similarity=0.485  Sum_probs=107.6

Q ss_pred             CCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCCCccccCCcceE
Q 014080          158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLI  237 (431)
Q Consensus       158 ~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~i  237 (431)
                      ..++|.+|+++|..++++.++++.||++||+|..|+++|.+..|+.++|++||+.||.++|+++|.+|+++|.+.+ .+|
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~-~~~   80 (126)
T 2xqn_T            2 EKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPEV-QRV   80 (126)
T ss_dssp             CCCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCTTTCSBCCTTS-CEE
T ss_pred             cCCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCcccCCcCCcCc-eEE
Confidence            4689999999998788999999999999999999999999989999999999999999999999999999999742 467


Q ss_pred             EEecccccccccCCCccc--CCCCccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          238 EYRAHPFWLQKYCPSHER--DGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       238 ~~~~~pfw~~~yCp~h~H--~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .+.++.          ||  ..||+|..|+++|. +..|+. .+|++||..++.+
T Consensus        81 ~a~~~~----------~H~~~~CF~C~~C~~~l~-~~~f~~-~~~~~yC~~~~~~  123 (126)
T 2xqn_T           81 TYNNFS----------WHASTECFLCSCCSKCLI-GQKFMP-VEGMVFCSVECKK  123 (126)
T ss_dssp             EETTEE----------EESSTTTSBCTTTCCBCT-TSEEEE-ETTEEESSHHHHH
T ss_pred             ECCCCE----------eeCCCCCcCcCCCCCccC-CCeeEe-ECCEEcchHHhhh
Confidence            888875          58  99999999999995 777775 6899999966655

>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=99.90  E-value=1.9e-24  Score=196.78  Aligned_cols=124  Identities=23%  Similarity=0.539  Sum_probs=107.4

Q ss_pred             CCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCCCccccCCcceE
Q 014080          158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLI  237 (431)
Q Consensus       158 ~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~i  237 (431)
                      +.++|.+|+++|....++.++++.||+.||+|..|+++|.+..| .++|++||+.||.++|+++|.+|+++|.+.+ .++
T Consensus         5 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~~~C~~C~~~I~~~~-~v~   82 (169)
T 2rgt_A            5 EIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTKCAACQLGIPPTQ-VVR   82 (169)
T ss_dssp             --CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCCE-ESSSCEECHHHHHHHHSCBCTTTCCBCCTTS-EEE
T ss_pred             CCCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCCc-ccCCeeeecccccccccccccccccccCCCc-EEE
Confidence            56899999999976567899999999999999999999998775 6899999999999999999999999999753 234


Q ss_pred             EEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccC
Q 014080          238 EYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIM  293 (431)
Q Consensus       238 ~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~  293 (431)
                      .+.++          +||..||+|..|++.|..|+.|+...+|++||..||.+...
T Consensus        83 ~a~~~----------~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~~  128 (169)
T 2rgt_A           83 RAQDF----------VYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQ  128 (169)
T ss_dssp             EETTE----------EEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHHH
T ss_pred             EcCCc----------eEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHhh
Confidence            56665          46999999999999997788887778999999999988543

>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=99.90  E-value=2.3e-24  Score=200.18  Aligned_cols=133  Identities=20%  Similarity=0.424  Sum_probs=116.5

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcc---------------
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK---------------  221 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pk---------------  221 (431)
                      .+.++|.+|+++|..++.+.++++.||+.||+|..|+++|.+..|+.++|++||+.||.++|+|+               
T Consensus         5 ~~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~c~~c~~~~g~~~~~~   84 (192)
T 1b8t_A            5 GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGTLSTDK   84 (192)
T ss_dssp             CCCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCCCCCCC
T ss_pred             CCCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCccccccccccccEecCC
Confidence            35689999999998788899999999999999999999999989999999999999999999887               


Q ss_pred             ---------------------------------cccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCcc
Q 014080          222 ---------------------------------CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERME  268 (431)
Q Consensus       222 ---------------------------------C~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l  268 (431)
                                                       |.+|+++|.+..  .+.+.++          +||..||+|..|++.|
T Consensus        85 ~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~~C~~C~~~I~~~~--~v~a~~~----------~~H~~CF~C~~C~~~L  152 (192)
T 1b8t_A           85 GESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRCGQAVYAAE--KVIGAGK----------SWHKSCFRCAKCGKSL  152 (192)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECTTTSCEECSSS--CEEETTE----------EECTTTCBCTTTCCBC
T ss_pred             CcccccccccccccCCCCcCccccccccCCCCcCCCCCCEecCcE--EEecCCC----------ccchhcCCccccCCCC
Confidence                                             678889998643  5667776          4699999999999999


Q ss_pred             CCCCceEEccCCcccCcchhhcccCCCCCCCcccHHH
Q 014080          269 PRDTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEI  305 (431)
Q Consensus       269 ~~g~~f~~l~dG~~yC~~C~~~~v~~~~~C~~C~~~I  305 (431)
                      .. ..|+. .+|++||..||.+  .+.++|.+|.+.|
T Consensus       153 ~~-~~~~~-~~g~~yC~~cy~~--~f~~kc~~C~~~~  185 (192)
T 1b8t_A          153 ES-TTLAD-KDGEIYCKGCYAK--NFGPKGFGFGQGA  185 (192)
T ss_dssp             CS-SSEEE-ETTEEEEHHHHHH--HTCCCCCCCCCCC
T ss_pred             CC-Ccccc-cCCEEeCHHHHHH--hcCCcCCCCCCcc
Confidence            54 46774 6999999999998  8999999999654

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

Probab=99.90  E-value=3.1e-24  Score=186.93  Aligned_cols=120  Identities=18%  Similarity=0.455  Sum_probs=106.5

Q ss_pred             CCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCC--cceeecCCccccccccccccCc--ccccCCCccccCCc
Q 014080          159 YRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITD--VEFSMSGNRPYHKHCYKEQHHP--KCDVCQNFIPTNSA  234 (431)
Q Consensus       159 ~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~--~~F~~~dg~pyC~~CY~~~f~p--kC~~C~~~I~~~~~  234 (431)
                      .++|.+|+++|..+.++.++++.||+.||+|..|+.+|..  ..|+.++|+|||+.||.++|++  +|.+|+++|.+.+ 
T Consensus         2 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~~e-   80 (131)
T 2xjy_A            2 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRAYE-   80 (131)
T ss_dssp             CCBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECTTS-
T ss_pred             cccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCccc-
Confidence            5789999999975557999999999999999999999963  6799999999999999999999  9999999998743 


Q ss_pred             ceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          235 GLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       235 ~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .++.+.++.          ||..||+|..|++.|+.|..|+. .+|++||..||.+
T Consensus        81 ~~~~a~~~~----------~H~~CF~C~~C~~~L~~g~~f~~-~~~~~~C~~c~~~  125 (131)
T 2xjy_A           81 MTMRVKDKV----------YHLECFKCAACQKHFCVGDRYLL-INSDIVCEQDIYE  125 (131)
T ss_dssp             EEEEETTEE----------EEGGGCBCTTTCCBCCTTCEEEE-ETTEEEEGGGHHH
T ss_pred             eeEeeCCce----------ECccCcccCCCCCCCCCCCEEEE-ECCEEEcHHHHHH
Confidence            356777775          59999999999999977888886 5899999999976

>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=99.88  E-value=7.5e-24  Score=196.21  Aligned_cols=129  Identities=18%  Similarity=0.408  Sum_probs=109.1

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCC--cceeecCCccccccccccccCc--ccccCCCccccC
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITD--VEFSMSGNRPYHKHCYKEQHHP--KCDVCQNFIPTN  232 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~--~~F~~~dg~pyC~~CY~~~f~p--kC~~C~~~I~~~  232 (431)
                      ...++|.+|+++|....++.++++.||++||+|..|+++|..  ..|+.++|++||+.||.++|++  +|.+|+++|.+.
T Consensus         3 l~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~~   82 (188)
T 1rut_X            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPAS   82 (188)
T ss_dssp             -CCCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECTT
T ss_pred             CCCCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCccccC
Confidence            356899999999975557899999999999999999999985  6899999999999999999999  799999999974


Q ss_pred             CcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCCCCC
Q 014080          233 SAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQ  299 (431)
Q Consensus       233 ~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~~C~  299 (431)
                      + .++.+.++.          ||..||+|..|++.|..|..|+. .+|++||..||.+  .+.+.|-
T Consensus        83 e-~~i~a~~~~----------~H~~CF~C~~C~~~L~~g~~f~~-~~g~~yC~~c~~~--~~~~~~~  135 (188)
T 1rut_X           83 E-LVMRAQGNV----------YHLKCFTCSTCRNRLVPGDRFHY-INGSLFCEHDRPT--ALINGHL  135 (188)
T ss_dssp             S-EEEEETTEE----------ECGGGCBCTTTCCBCCTTCEEEE-ETTEEEEGGGCCT--TTC----
T ss_pred             c-EEEEcCCCE----------EeCCCCeECCCCCCCCCCCeEEE-ECCeEECHHHHHH--Hhccccc
Confidence            2 356777774          59999999999999977788875 5899999999988  5566553

>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=99.83  E-value=5e-21  Score=159.29  Aligned_cols=98  Identities=27%  Similarity=0.563  Sum_probs=88.4

Q ss_pred             CCCCcCCCCCccccc-CceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCCCccccCCcc
Q 014080          157 SGYRICAGCNTEIGH-GRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAG  235 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~-g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~  235 (431)
                      .+.++|.+|+++|.. +.++.++++.||+.||+|..|+++|.+..|+..+|++||+.||.++|+++|.+|+++|...+ .
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~~-~   81 (101)
T 2cup_A            3 SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVAGD-Q   81 (101)
T ss_dssp             SCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCSSSCCBCCSSS-C
T ss_pred             CCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccccCCCccccCC-e
Confidence            467899999999964 78999999999999999999999999888999999999999999999999999999999532 3


Q ss_pred             eEEEecccccccccCCCcccCCCCccCCCC
Q 014080          236 LIEYRAHPFWLQKYCPSHERDGTPRCCSCE  265 (431)
Q Consensus       236 ~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~  265 (431)
                      +|.+.++.          ||..||+|..|+
T Consensus        82 ~~~a~~~~----------~H~~CF~C~~C~  101 (101)
T 2cup_A           82 NVEYKGTV----------WHKDCFSGPSSG  101 (101)
T ss_dssp             EEESSSCE----------EETTTCCCTTCC
T ss_pred             EEEeCCcc----------hHHhCCCCCCCC
Confidence            67787775          599999999996

>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=99.74  E-value=2.7e-19  Score=154.59  Aligned_cols=106  Identities=16%  Similarity=0.315  Sum_probs=89.4

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCC--cceeecCCccccccccccccCc--ccccCCCccccC
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITD--VEFSMSGNRPYHKHCYKEQHHP--KCDVCQNFIPTN  232 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~--~~F~~~dg~pyC~~CY~~~f~p--kC~~C~~~I~~~  232 (431)
                      ...++|++|+++|..+.++.++++.||+.||+|..|+++|.+  ..|+.++|++||+.||.++|++  +|.+|+++|.+.
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~   82 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGG   82 (122)
T ss_dssp             SCCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCE
T ss_pred             CCCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCch
Confidence            457899999999975567999999999999999999999973  5799999999999999999999  999999999974


Q ss_pred             CcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          233 SAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       233 ~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .   +++.++                       ..| .|++|++ .++++||..|+..
T Consensus        83 ~---~~~~g~-----------------------~~l-~g~~f~~-~~~~~yC~~~~~~  112 (122)
T 1m3v_A           83 D---VMVVGE-----------------------PTL-MGGEFGD-EDERLITRLENTQ  112 (122)
T ss_dssp             E---SSSSSS-----------------------SSC-CSCTTCC-TTCCCCEECTTTT
T ss_pred             h---eEEcCC-----------------------cCC-CCCccEe-cCCEeEccCcchh
Confidence            2   333222                       123 6888875 6899999999986

>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=99.68  E-value=2.6e-17  Score=140.44  Aligned_cols=101  Identities=15%  Similarity=0.372  Sum_probs=84.6

Q ss_pred             CCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCC--cceeecCCccccccccccccCcccccCCCccccCCcc
Q 014080          158 GYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITD--VEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTNSAG  235 (431)
Q Consensus       158 ~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~--~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~  235 (431)
                      +.++|.+|+++|..+.++.++++.||+.||+|..|+++|.+  ..|+.++|+|||+.||.++|+|+|..|..   +.   
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c~~---~~---   75 (114)
T 1j2o_A            2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGSG---GD---   75 (114)
T ss_dssp             CCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSCBS---CS---
T ss_pred             cCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcCCC---Cc---
Confidence            45789999999975568999999999999999999999985  57999999999999999999999998862   21   


Q ss_pred             eEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          236 LIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       236 ~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      +|                      .   |.+.+..|++|++ .++++||..|+..
T Consensus        76 ~~----------------------~---~~~~~~~g~~f~~-~~~~~~C~~~~~~  104 (114)
T 1j2o_A           76 VM----------------------V---VGEPTLMGGEFGD-EDERLITRLENTQ  104 (114)
T ss_dssp             CC----------------------C---SSCSSTTSSBCCC-SSSCCCEEEECTT
T ss_pred             ee----------------------E---cCCccCCCCeeEE-cCCEeecchhhhc
Confidence            11                      1   3455557888874 7899999999976

>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=99.60  E-value=4.3e-16  Score=123.15  Aligned_cols=71  Identities=21%  Similarity=0.506  Sum_probs=66.8

Q ss_pred             CcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccc-cccccccCcccccCCCccc
Q 014080          160 RICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHK-HCYKEQHHPKCDVCQNFIP  230 (431)
Q Consensus       160 ~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~-~CY~~~f~pkC~~C~~~I~  230 (431)
                      |+|.+|+++|..++.+.++++.||+.||+|..|+++|.+..|+..+|.+||+ .||.++|+++|.+|++.+.
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~~C~~~~~   72 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGGAES   72 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSCCCSSS
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCCCcCCcee
Confidence            5899999999778999999999999999999999999998999999999999 6999999999999997665

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

Probab=99.59  E-value=3.7e-16  Score=125.00  Aligned_cols=74  Identities=22%  Similarity=0.480  Sum_probs=58.0

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCCCcc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFI  229 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I  229 (431)
                      ..+.++|.+|+++|..++.+.++++.||+.||+|..|+++|....|+..++++||+.||.++|+|+|.+|++..
T Consensus         4 ~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~gcg~g~   77 (81)
T 1a7i_A            4 WGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGYGYGQGA   77 (81)
T ss_dssp             ----CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC----------
T ss_pred             CCCCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCcccccCCcc
Confidence            34678999999999878899999999999999999999999988899999999999999999999999998764

>2ehe_A Four and A half LIM domains 3; FHL-3, skeletal muscle LIM- protein 2, SLIM 2, FHL3, SLIM2, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=99.58  E-value=1.6e-15  Score=121.50  Aligned_cols=78  Identities=22%  Similarity=0.404  Sum_probs=71.2

Q ss_pred             CCcCCCCCC-CCCCCcCCCCCcccc-cCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCccccc
Q 014080          147 GNIFQPFPF-FSGYRICAGCNTEIG-HGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDV  224 (431)
Q Consensus       147 g~~~~p~~~-~~~~~~C~~C~k~I~-~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~  224 (431)
                      |.+|+...+ ....++|.+|+++|. .+.++.++++.||+.||+|..|+++|.+..|+..++++||+.||.++|+++|++
T Consensus         2 g~~yC~~~y~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C~~   81 (82)
T 2ehe_A            2 SSGSSGPCYDNTFANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGPSS   81 (82)
T ss_dssp             CCCCCCCCCCCCCSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGGGSSCC
T ss_pred             CceechhHhCcccCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCccEeeCCEEECHHHHhhhcCCCCCC
Confidence            567888877 677889999999997 368889999999999999999999999989999999999999999999999974

>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=99.58  E-value=1.6e-15  Score=123.81  Aligned_cols=68  Identities=26%  Similarity=0.568  Sum_probs=64.0

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCccccc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDV  224 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~  224 (431)
                      ....++|.+|+++| .++++.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|+|+|+.
T Consensus        22 ~~~~~~C~~C~~~I-~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c~s   89 (90)
T 2dar_A           22 GKRTPMCAHCNQVI-RGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPSS   89 (90)
T ss_dssp             TTCCCBBSSSCCBC-CSCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCCCC
T ss_pred             CCCCCCCccCCCEe-cceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCCCC
Confidence            56789999999999 589999999999999999999999999889999999999999999999999974

>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=99.57  E-value=2.1e-15  Score=120.64  Aligned_cols=78  Identities=19%  Similarity=0.373  Sum_probs=70.8

Q ss_pred             CCCcCCCCCCCCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeec-CCccccccccccccCccccc
Q 014080          146 SGNIFQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMS-GNRPYHKHCYKEQHHPKCDV  224 (431)
Q Consensus       146 ~g~~~~p~~~~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~-dg~pyC~~CY~~~f~pkC~~  224 (431)
                      .+++|+...+....++|++|+++|. ++++.++++.||+.||+|..|+++|.+..|+.. ++++||+.||.++|+|+|++
T Consensus         2 ~g~~yC~~~y~~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~~~C~~   80 (81)
T 2dlo_A            2 SSGSSGEGCYVATLEKCATCSQPIL-DRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGPSS   80 (81)
T ss_dssp             CCCCCCCCCCCSSCCBCTTTCCBCC-SCCEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTTSSSCC
T ss_pred             cCCEECHHHhhcCCCccccCCCeec-ceeEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhcCcCCC
Confidence            4677888877678899999999996 789999999999999999999999998888875 78999999999999999974

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

Probab=99.56  E-value=2.4e-15  Score=119.72  Aligned_cols=77  Identities=27%  Similarity=0.523  Sum_probs=70.4

Q ss_pred             CCcCCCCCC-CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCccccc
Q 014080          147 GNIFQPFPF-FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDV  224 (431)
Q Consensus       147 g~~~~p~~~-~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~  224 (431)
                      +++|+...+ ....++|.+|+++|. +++|.++++.||+.||+|..|+++|.+..|+..++++||+.||.++|+++|++
T Consensus         2 g~~yC~~~y~~~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C~~   79 (80)
T 1x3h_A            2 SSGSSGKDFLAMFSPKCGGCNRPVL-ENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGPSS   79 (80)
T ss_dssp             CCCCCCCCCCCCCSCBCTTTCCBCC-SSCEEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHHHSSSCCC
T ss_pred             CCccchhHHhhhcCCccccCCCeec-ceeEEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHHcCCCCCC
Confidence            466888777 667899999999996 68899999999999999999999999888999999999999999999999974

>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=99.56  E-value=3.6e-15  Score=119.61  Aligned_cols=68  Identities=32%  Similarity=0.738  Sum_probs=62.9

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCccccc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDV  224 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~  224 (431)
                      ..+.++|.+|+++|..++++.++++.||++||+|..|+++|.+ .|+.++++|||+.||.++|+++|.+
T Consensus        12 ~~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C~~   79 (80)
T 2dj7_A           12 IRGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPSS   79 (80)
T ss_dssp             CSSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCSTT
T ss_pred             CCCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCCCC
Confidence            3467899999999987899999999999999999999999986 6889999999999999999999974

>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=99.55  E-value=3e-15  Score=118.34  Aligned_cols=70  Identities=20%  Similarity=0.569  Sum_probs=64.7

Q ss_pred             CCCCcCCCCCccccc---CceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCC
Q 014080          157 SGYRICAGCNTEIGH---GRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQ  226 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~---g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~  226 (431)
                      ...++|.+|+++|..   .+++.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+++|..+.
T Consensus         3 ~~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C~~~s   75 (76)
T 1x68_A            3 SGSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISGPSS   75 (76)
T ss_dssp             TCCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSSSSSC
T ss_pred             ccCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcCCCCC
Confidence            357899999999962   3899999999999999999999999988999999999999999999999999875

>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=99.55  E-value=3.7e-15  Score=118.64  Aligned_cols=77  Identities=19%  Similarity=0.424  Sum_probs=70.5

Q ss_pred             CCcCCCCCC-CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCccccc
Q 014080          147 GNIFQPFPF-FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDV  224 (431)
Q Consensus       147 g~~~~p~~~-~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~  224 (431)
                      |.+|+...+ ....++|.+|+++|. +++|.++++.||+.||+|..|+++|.+..|+..++++||+.||.++|+|+|+.
T Consensus         2 g~~yC~~cy~~~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~s   79 (80)
T 2cuq_A            2 SSGSSGPCYENKFAPRCARCSKTLT-QGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPSS   79 (80)
T ss_dssp             CCCSCCCCCCCCSSCCCTTTCCCCC-SCCEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCSTTC
T ss_pred             CcEEcHHHHccccCCcCCCCCCEec-CcEEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCCCCC
Confidence            567888877 667899999999995 67899999999999999999999999888999999999999999999999974

>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=99.54  E-value=4.1e-15  Score=117.46  Aligned_cols=69  Identities=17%  Similarity=0.444  Sum_probs=64.1

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccc-cccccccCccccc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHK-HCYKEQHHPKCDV  224 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~-~CY~~~f~pkC~~  224 (431)
                      ....++|.+|+++|..++.|.++++.||+.||+|..|+++|.+..|+..++++||+ .||.++|+|+|.+
T Consensus         6 ~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~kc~g   75 (76)
T 2cu8_A            6 SGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGPSS   75 (76)
T ss_dssp             CCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSSCSC
T ss_pred             CCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccccCC
Confidence            34678999999999778999999999999999999999999988899999999999 7999999999974

>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=99.54  E-value=3.1e-15  Score=115.89  Aligned_cols=67  Identities=25%  Similarity=0.579  Sum_probs=62.6

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCccccc
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDV  224 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~  224 (431)
                      .+.++|.+|+++|. ++.+.++++.||+.||+|..|+++|.+..|+..++++||+.||.++|+++|++
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~g   69 (69)
T 2cur_A            3 SGSSGCVKCNKAIT-SGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSSG   69 (69)
T ss_dssp             CCCCCCSSSCCCCC-TTCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSCCC
T ss_pred             CCcCCCcccCCEeC-cceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCCCC
Confidence            46789999999995 78899999999999999999999999889999999999999999999999974

>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=99.53  E-value=4.6e-15  Score=115.12  Aligned_cols=67  Identities=24%  Similarity=0.534  Sum_probs=62.4

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCccccc
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDV  224 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~  224 (431)
                      .+.++|.+|+++|. ++.+.++++.||+.||+|..|+++|.+..|+..++++||+.||.++|+|+|+.
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~~   69 (70)
T 2d8z_A            3 SGSSGCVQCKKPIT-TGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPSS   69 (70)
T ss_dssp             CCCCBCSSSCCBCC-SSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCTT
T ss_pred             CCCCCCcccCCeec-cceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccCC
Confidence            36789999999995 77899999999999999999999999889999999999999999999999974

>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=99.52  E-value=5.9e-15  Score=115.00  Aligned_cols=68  Identities=26%  Similarity=0.597  Sum_probs=63.0

Q ss_pred             CCCCcCCCCCcccccC-ceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCccccc
Q 014080          157 SGYRICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDV  224 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g-~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~  224 (431)
                      ...++|.+|+++|..+ .++.++++.||+.||+|..|+++|.+..|+..++.+||+.||.++|+|+|+.
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1wyh_A            3 SGSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGPSS   71 (72)
T ss_dssp             CCCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCCCC
T ss_pred             ccCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcCCC
Confidence            3578999999999764 8899999999999999999999999989999999999999999999999974

>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=99.52  E-value=7.8e-15  Score=114.31  Aligned_cols=68  Identities=32%  Similarity=0.679  Sum_probs=62.9

Q ss_pred             CCCCcCCCCCcccccC-ceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCccccc
Q 014080          157 SGYRICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDV  224 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g-~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~  224 (431)
                      ...++|.+|+++|..+ .++.++++.||+.||+|..|+++|.+..|+..++++||+.||.++|+|+|+.
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1x4k_A            3 SGSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGPSS   71 (72)
T ss_dssp             SCCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCCCC
T ss_pred             ccCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCCCC
Confidence            3568999999999765 6899999999999999999999999989999999999999999999999974

>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=99.52  E-value=1.3e-14  Score=118.67  Aligned_cols=75  Identities=20%  Similarity=0.379  Sum_probs=67.4

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCCCccc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIP  230 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~  230 (431)
                      ..+.++|.+|+++|..++.+.++++.||+.||+|..|+++|....|+..++++||+.||.++|+++|..+..+..
T Consensus        12 ~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~g~g~   86 (91)
T 2d8y_A           12 APARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFGS   86 (91)
T ss_dssp             SSSSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCCC
T ss_pred             CCCCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccCCcCC
Confidence            346789999999998778899999999999999999999999888999999999999999999999986555443

>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=99.51  E-value=1.4e-14  Score=115.82  Aligned_cols=77  Identities=21%  Similarity=0.382  Sum_probs=69.9

Q ss_pred             CCcCCCCCC-CCCCCcCCCCCcccccC-ceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccc
Q 014080          147 GNIFQPFPF-FSGYRICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCD  223 (431)
Q Consensus       147 g~~~~p~~~-~~~~~~C~~C~k~I~~g-~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~  223 (431)
                      +++|+...+ ....++|.+|+++|..+ .++.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+|+|.
T Consensus         2 ~~~yC~~cy~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~   80 (82)
T 1x63_A            2 SSGSSGKCTTREDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPS   80 (82)
T ss_dssp             CSCCCCCCCSCCCSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCS
T ss_pred             CCcCchhHHccccCCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCC
Confidence            467888777 66789999999999764 679999999999999999999999998999999999999999999999986

>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=99.51  E-value=1.9e-14  Score=117.15  Aligned_cols=67  Identities=21%  Similarity=0.521  Sum_probs=62.4

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCD  223 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~  223 (431)
                      ....++|.+|+++|. ++++.++++.||++||+|..|+++|.+..|+..++.+||+.||.++|+|+|.
T Consensus        22 ~~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~~   88 (89)
T 1x64_A           22 AQRMPLCDKCGSGIV-GAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSS   88 (89)
T ss_dssp             CCSCCBCTTTCCBCC-SCCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCCC
T ss_pred             CCcCCCcccCCCEec-ccEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            456789999999996 7889999999999999999999999988899999999999999999999986

>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=99.50  E-value=6.4e-15  Score=117.43  Aligned_cols=67  Identities=19%  Similarity=0.463  Sum_probs=62.0

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCD  223 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~  223 (431)
                      ....++|.+|+++|. ++++.++++.||+.||+|..|+++|.+..|+..++++||+.||.++|+|++.
T Consensus        12 ~~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g~   78 (79)
T 1x62_A           12 AQKLPMCDKCGTGIV-GVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSS   78 (79)
T ss_dssp             CCCCCCCSSSCCCCC-SSCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCCC
T ss_pred             CCCCCccccCCCCcc-CcEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            346789999999996 6899999999999999999999999988899999999999999999999875

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

Probab=99.50  E-value=1e-14  Score=115.18  Aligned_cols=68  Identities=18%  Similarity=0.378  Sum_probs=61.0

Q ss_pred             CCCCCcCCCCCccccc-CceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccc
Q 014080          156 FSGYRICAGCNTEIGH-GRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCD  223 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~-g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~  223 (431)
                      ..+.++|.+|+++|.. +.++.++++.||+.||+|..|+++|.+..|+..+|++||+.||.++|+|+|.
T Consensus         8 ~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C~   76 (77)
T 1g47_A            8 ALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCWI   76 (77)
T ss_dssp             CCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC--
T ss_pred             CCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcccC
Confidence            3467899999999974 5678999999999999999999999988899999999999999999999996

>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=99.49  E-value=1.4e-14  Score=113.12  Aligned_cols=66  Identities=32%  Similarity=0.700  Sum_probs=61.0

Q ss_pred             CCCCcCCCCCccccc---CceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCccc
Q 014080          157 SGYRICAGCNTEIGH---GRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKC  222 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~---g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC  222 (431)
                      .+.++|.+|+++|..   ..++.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|+|++
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p~~   71 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPSS   71 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCSSC
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCCCC
Confidence            367899999999973   388999999999999999999999999899999999999999999999986

>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=99.49  E-value=1.7e-14  Score=114.85  Aligned_cols=79  Identities=18%  Similarity=0.462  Sum_probs=68.7

Q ss_pred             CCccccccccccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccC
Q 014080          205 GNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLC  284 (431)
Q Consensus       205 dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC  284 (431)
                      +|+|||+.||.++++++|.+|+++|.+.   .+.+.++          .||..||+|..|++.| .+..|+. .+|++||
T Consensus         1 gg~~yC~~cy~~~~~~~C~~C~~~I~~~---~v~a~~~----------~~H~~CF~C~~C~~~L-~~~~~~~-~~~~~yC   65 (80)
T 2cuq_A            1 GSSGSSGPCYENKFAPRCARCSKTLTQG---GVTYRDQ----------PWHRECLVCTGCQTPL-AGQQFTS-RDEDPYC   65 (80)
T ss_dssp             CCCCSCCCCCCCCSSCCCTTTCCCCCSC---CEESSSS----------EECTTTCBCSSSCCBC-TTCCEEE-CSSSEEE
T ss_pred             CCcEEcHHHHccccCCcCCCCCCEecCc---EEEECCc----------hhhhhhCCcccCCCcC-CCCeeEe-ECCEEEC
Confidence            5899999999999999999999999874   5777776          4699999999999999 4567775 7999999


Q ss_pred             cchhhcccCCCCCCCc
Q 014080          285 LECLDSAIMDTHECQP  300 (431)
Q Consensus       285 ~~C~~~~v~~~~~C~~  300 (431)
                      ..||.+  .+.++|++
T Consensus        66 ~~cy~~--~f~~~c~s   79 (80)
T 2cuq_A           66 VACFGE--LFASGPSS   79 (80)
T ss_dssp             HHHHHH--HTTCSTTC
T ss_pred             HHHHHH--HcCCCCCC
Confidence            999998  78888864

>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=99.49  E-value=8.9e-15  Score=112.34  Aligned_cols=64  Identities=27%  Similarity=0.545  Sum_probs=60.0

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcc
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK  221 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pk  221 (431)
                      ...++|.+|+++|. ++++.++++.||++||+|..|+++|.+..|+..+|.+||+.||.++|+|+
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~k   66 (66)
T 1nyp_A            3 MGVPICGACRRPIE-GRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGDV   66 (66)
T ss_dssp             CCCCEETTTTEECC-SCEECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSCC
T ss_pred             cCCCCCcccCCEec-ceEEEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHhCCC
Confidence            35789999999996 89999999999999999999999999989999999999999999999885

>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=99.49  E-value=1.6e-14  Score=115.65  Aligned_cols=81  Identities=27%  Similarity=0.563  Sum_probs=68.0

Q ss_pred             CCccccccccccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccC
Q 014080          205 GNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLC  284 (431)
Q Consensus       205 dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC  284 (431)
                      +|+|||+.||.++|+++|.+|+++|.+.. .++.+.++          .||..||+|..|++.|. +..|+. .+|++||
T Consensus         1 ~g~~yC~~~y~~~~~~~C~~C~~~I~~~~-~~~~a~~~----------~~H~~CF~C~~C~~~L~-~~~f~~-~~~~~~C   67 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFANTCAECQQLIGHDS-RELFYEDR----------HFHEGCFRCCRCQRSLA-DEPFTC-QDSELLC   67 (82)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSSC-CBCCCSSC----------CCBTTTSBCTTTCCBCS-SCCEEE-ETTEEEE
T ss_pred             CCceechhHhCcccCCcCccCCCccccCc-EEEEeCCc----------cccccCCeecCCCCccC-CCccEe-eCCEEEC
Confidence            58999999999999999999999999421 25566666          46999999999999995 667764 6899999


Q ss_pred             cchhhcccCCCCCCCc
Q 014080          285 LECLDSAIMDTHECQP  300 (431)
Q Consensus       285 ~~C~~~~v~~~~~C~~  300 (431)
                      ..||.+  .+.++|+.
T Consensus        68 ~~c~~~--~~~~~C~~   81 (82)
T 2ehe_A           68 NDCYCS--AFSSGPSS   81 (82)
T ss_dssp             TTTSSC--CGGGSSCC
T ss_pred             HHHHhh--hcCCCCCC
Confidence            999988  78888864

>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=99.46  E-value=3.5e-14  Score=110.24  Aligned_cols=66  Identities=32%  Similarity=0.689  Sum_probs=61.1

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccc
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCD  223 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~  223 (431)
                      .+.++|.+|+++|. ++++.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|++++.
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~   68 (70)
T 2d8x_A            3 SGSSGCHQCGEFII-GRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGPS   68 (70)
T ss_dssp             CCSSBCSSSCCBCC-SCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCCSC
T ss_pred             CCCCcCccCCCEec-ceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCCCC
Confidence            35789999999996 8899999999999999999999999998999999999999999999988764

>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=99.45  E-value=3.6e-14  Score=113.25  Aligned_cols=80  Identities=13%  Similarity=0.237  Sum_probs=67.0

Q ss_pred             CCccccccccccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccC
Q 014080          205 GNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLC  284 (431)
Q Consensus       205 dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC  284 (431)
                      ++.|||+.||.++|+++|.+|+++|.+.   .+.+.++.          ||..||+|..|++.|..|..|+...+|++||
T Consensus         1 g~~~yC~~~y~~~~~~~C~~C~~~I~~~---~~~a~~~~----------~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C   67 (81)
T 1x6a_A            1 GSSGSSGKDYWGKFGEFCHGCSLLMTGP---FMVAGEFK----------YHPECFACMSCKVIIEDGDAYALVQHATLYC   67 (81)
T ss_dssp             CCCCCCCCCSSCCSSCBCTTTCCBCCSC---CBCCTTCC----------BCTTSCBCTTTCCBCCTTSCEEECSSSCEEE
T ss_pred             CCCccchhHHhhhcCCcCccCCCCcCce---EEEECCce----------eccccCCccCCCCccCCCCcEEEeeCCEEEC
Confidence            4689999999999999999999999954   56677764          6999999999999997677776447999999


Q ss_pred             cchhhcccCCCCCCC
Q 014080          285 LECLDSAIMDTHECQ  299 (431)
Q Consensus       285 ~~C~~~~v~~~~~C~  299 (431)
                      ..||.+  .+++.|.
T Consensus        68 ~~c~~~--~~~~~~s   80 (81)
T 1x6a_A           68 GKCHNE--VVSGPSS   80 (81)
T ss_dssp             HHHHHH--HHCTTSC
T ss_pred             HHHHHH--HhcCCCC
Confidence            999988  5555554

>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=99.44  E-value=5.4e-14  Score=111.87  Aligned_cols=79  Identities=15%  Similarity=0.210  Sum_probs=68.4

Q ss_pred             CCccccccccccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccC
Q 014080          205 GNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLC  284 (431)
Q Consensus       205 dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC  284 (431)
                      +|++||+.||.++|+++|.+|+++|.+.   .|.+.++.          ||..||+|..|++.|.. ..|+. .+|++||
T Consensus         1 gg~~yC~~~y~~~~~~~C~~C~~~I~~~---~v~a~~~~----------~H~~CF~C~~C~~~L~~-~~~~~-~~~~~yC   65 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFSPKCGGCNRPVLEN---YLSAMDTV----------WHPECFVCGDCFTSFST-GSFFE-LDGRPFC   65 (80)
T ss_dssp             CCCCCCCCCCCCCCSCBCTTTCCBCCSS---CEEETTEE----------ECTTTCBCSSSCCBSCS-SCCEE-SSSCEEC
T ss_pred             CCCccchhHHhhhcCCccccCCCeecce---eEEECCCe----------EecCcCChhhCCCCCCC-CcEEe-ECCEEEC
Confidence            5789999999999999999999999974   57777774          69999999999999954 46775 6899999


Q ss_pred             cchhhcccCCCCCCCc
Q 014080          285 LECLDSAIMDTHECQP  300 (431)
Q Consensus       285 ~~C~~~~v~~~~~C~~  300 (431)
                      ..||.+  .+.++|++
T Consensus        66 ~~~y~~--~f~~~C~~   79 (80)
T 1x3h_A           66 ELHYHH--RRGSGPSS   79 (80)
T ss_dssp             HHHHHH--HHSSSCCC
T ss_pred             HHHHHH--HcCCCCCC
Confidence            999998  78888874

>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=99.44  E-value=5.2e-14  Score=112.31  Aligned_cols=77  Identities=23%  Similarity=0.430  Sum_probs=67.9

Q ss_pred             CCcCCCCCC-CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCC-ccee-ecCCccccccccccccCcccc
Q 014080          147 GNIFQPFPF-FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITD-VEFS-MSGNRPYHKHCYKEQHHPKCD  223 (431)
Q Consensus       147 g~~~~p~~~-~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~-~~F~-~~dg~pyC~~CY~~~f~pkC~  223 (431)
                      ++.|+...+ ....++|.+|+++|. ++++.++++.||++||+|..|+++|.. ..|. ..+++|||+.||.++|++.|.
T Consensus         2 ~~~yC~~~y~~~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~~s   80 (81)
T 1x6a_A            2 SSGSSGKDYWGKFGEFCHGCSLLMT-GPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSGPSS   80 (81)
T ss_dssp             CCCCCCCCSSCCSSCBCTTTCCBCC-SCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCTTSC
T ss_pred             CCccchhHHhhhcCCcCccCCCCcC-ceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcCCCC
Confidence            456888777 668899999999996 889999999999999999999999974 5677 489999999999999999886


Q ss_pred             c
Q 014080          224 V  224 (431)
Q Consensus       224 ~  224 (431)
                      +
T Consensus        81 g   81 (81)
T 1x6a_A           81 G   81 (81)
T ss_dssp             C
T ss_pred             C
Confidence            3

>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=99.44  E-value=6.7e-14  Score=111.80  Aligned_cols=79  Identities=15%  Similarity=0.268  Sum_probs=68.0

Q ss_pred             CCccccccccccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccC
Q 014080          205 GNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLC  284 (431)
Q Consensus       205 dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC  284 (431)
                      +|+|||+.||. ++.++|.+|+++|.+.   ++.+.++.          ||..||+|..|++.|. +..|+...+|++||
T Consensus         2 ~g~~yC~~~y~-~~~~~C~~C~~~I~~~---~~~a~~~~----------~H~~CF~C~~C~~~L~-~~~f~~~~~g~~yC   66 (81)
T 2dlo_A            2 SSGSSGEGCYV-ATLEKCATCSQPILDR---ILRAMGKA----------YHPGCFTCVVCHRGLD-GIPFTVDATSQIHC   66 (81)
T ss_dssp             CCCCCCCCCCC-SSCCBCTTTCCBCCSC---CEEETTEE----------ECTTTCBCSSSCCBCT-TSCEECCTTCCCEE
T ss_pred             cCCEECHHHhh-cCCCccccCCCeecce---eEEECCcc----------ccHHhcCcccCCCccC-CCeeEECCCCEEEC
Confidence            68999999999 7999999999999963   67777774          6999999999999994 66776534789999


Q ss_pred             cchhhcccCCCCCCCc
Q 014080          285 LECLDSAIMDTHECQP  300 (431)
Q Consensus       285 ~~C~~~~v~~~~~C~~  300 (431)
                      ..||.+  .+.++|++
T Consensus        67 ~~cy~~--~f~~~C~~   80 (81)
T 2dlo_A           67 IEDFHR--KFASGPSS   80 (81)
T ss_dssp             HHHHHH--HTTSSSCC
T ss_pred             HHHHHH--HhcCcCCC
Confidence            999998  78899874

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

Probab=99.43  E-value=1.5e-13  Score=110.53  Aligned_cols=68  Identities=19%  Similarity=0.386  Sum_probs=61.0

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCccee--ecCCccccccccccccCcccc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFS--MSGNRPYHKHCYKEQHHPKCD  223 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~--~~dg~pyC~~CY~~~f~pkC~  223 (431)
                      ..+.++|.+|+++|..++.+.++++.||+.||+|..|+++|....|+  ..++++||+.||.++|++.+.
T Consensus        12 ~~~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~   81 (82)
T 2co8_A           12 AGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSGPSS   81 (82)
T ss_dssp             CCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCCCCC
T ss_pred             CCCCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcCCCC
Confidence            44678999999999878889999999999999999999999998887  479999999999999887654

>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=99.43  E-value=6.1e-14  Score=111.99  Aligned_cols=66  Identities=21%  Similarity=0.329  Sum_probs=60.4

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCD  223 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~  223 (431)
                      ..+.++|.+|+++|. +++|.++++.||+.||+|..|+++|.+..| .+++++||+.||.++|+|++.
T Consensus        12 ~~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f-~~~g~~yC~~cy~~~f~p~~s   77 (79)
T 2cor_A           12 GLGKYICQKCHAIID-EQPLIFKNDPYHPDHFNCANCGKELTADAR-ELKGELYCLPCHDKMGVSGPS   77 (79)
T ss_dssp             CCCCCBCTTTCCBCC-SCCCCCSSSCCCTTTSBCSSSCCBCCTTCE-EETTEEECHHHHHTTSCCSSC
T ss_pred             ccCCCCCccCCCEec-ceEEEECcceeCCCCCEeCCCCCccCCCCE-eECCEEeCHHHHHHhCCCCCC
Confidence            456789999999996 889999999999999999999999998755 889999999999999999775

>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=99.41  E-value=1e-13  Score=108.00  Aligned_cols=68  Identities=24%  Similarity=0.575  Sum_probs=59.9

Q ss_pred             CCCCcCCCCCccccc-CceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccC
Q 014080          157 SGYRICAGCNTEIGH-GRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVC  225 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~-g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C  225 (431)
                      .+.++|.+|+++|.. +.++.++++.||+.||+|..|+++|.+..|+..++++||+.||.++|. +|..+
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~~-~~~~~   71 (72)
T 1x61_A            3 SGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLE-SGPSS   71 (72)
T ss_dssp             SCCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHHH-TCSSC
T ss_pred             CCCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHHc-cCCCC
Confidence            467899999999975 368999999999999999999999998889999999999999998873 55543

>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=99.40  E-value=1.4e-13  Score=108.15  Aligned_cols=64  Identities=28%  Similarity=0.594  Sum_probs=57.8

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCC-CcceeecCCccccccccccccCcc
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPIT-DVEFSMSGNRPYHKHCYKEQHHPK  221 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~-~~~F~~~dg~pyC~~CY~~~f~pk  221 (431)
                      .+.++|++|+++|. +++|.++++.||++||+|..|+++|. +..|+..++++||..||.+++...
T Consensus         3 ~~~~~C~~C~~~I~-~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~~   67 (73)
T 1wig_A            3 SGSSGCDSCEKYIT-GRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTED   67 (73)
T ss_dssp             CSCCSCSSSCCCCS-SCCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSSS
T ss_pred             cCcCCcccCCCEec-CeeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhccc
Confidence            36789999999995 78999999999999999999999998 778999999999999999877653

>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=99.40  E-value=2e-13  Score=107.73  Aligned_cols=70  Identities=21%  Similarity=0.487  Sum_probs=62.7

Q ss_pred             CCcCCCCCC-CCCCCcCCCCCccccc----CceEeecCccccCCCcccCCCCCCCCCcceeecCCcccccccccc
Q 014080          147 GNIFQPFPF-FSGYRICAGCNTEIGH----GRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKE  216 (431)
Q Consensus       147 g~~~~p~~~-~~~~~~C~~C~k~I~~----g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~  216 (431)
                      +++|+...+ ....++|++|+++|..    ..++.++++.||+.||+|..|+++|.+..|+.++++|||+.||.+
T Consensus         2 ~~~yC~~cy~~~~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~   76 (77)
T 2egq_A            2 SSGSSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK   76 (77)
T ss_dssp             CSSCCTTCCCSCCCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHH
T ss_pred             CCeEchhHhchhhCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCccEeECCEEEChHHhcc
Confidence            456888777 6778999999999973    388999999999999999999999999889999999999999975

>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=99.40  E-value=1.5e-13  Score=108.53  Aligned_cols=74  Identities=20%  Similarity=0.452  Sum_probs=62.1

Q ss_pred             CCccccccccccccCcccccCCCccccC--CcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcc
Q 014080          205 GNRPYHKHCYKEQHHPKCDVCQNFIPTN--SAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRK  282 (431)
Q Consensus       205 dg~pyC~~CY~~~f~pkC~~C~~~I~~~--~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~  282 (431)
                      +++|||+.||.++|+++|.+|+++|.+.  ....+.+.++          +||..||+|..|++.|. +..|+. .+|++
T Consensus         1 g~~~yC~~cy~~~~~~~C~~C~~~I~~~g~~~~~~~a~~~----------~~H~~CF~C~~C~~~L~-~~~f~~-~~~~~   68 (77)
T 2egq_A            1 GSSGSSGDCYKNFVAKKCAGCKNPITGFGKGSSVVAYEGQ----------SWHDYCFHCKKCSVNLA-NKRFVF-HQEQV   68 (77)
T ss_dssp             CCSSCCTTCCCSCCCCCCSSSCCCCCCCSSCCCEEEETTE----------EEETTTCBCSSSCCBCT-TSCCCE-ETTEE
T ss_pred             CCCeEchhHhchhhCccCcccCCcccCCCCCceeEEECcc----------eeCcccCEehhcCCCCC-CCccEe-ECCEE
Confidence            4789999999999999999999999961  1236777777          46999999999999994 566764 68999


Q ss_pred             cCcchhhc
Q 014080          283 LCLECLDS  290 (431)
Q Consensus       283 yC~~C~~~  290 (431)
                      ||..||.+
T Consensus        69 yC~~cy~~   76 (77)
T 2egq_A           69 YCPDCAKK   76 (77)
T ss_dssp             CCHHHHHH
T ss_pred             EChHHhcc
Confidence            99999965

>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=99.39  E-value=2.1e-13  Score=108.97  Aligned_cols=80  Identities=16%  Similarity=0.392  Sum_probs=66.7

Q ss_pred             CCccccccccccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccC
Q 014080          205 GNRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLC  284 (431)
Q Consensus       205 dg~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC  284 (431)
                      ++.|||+.||.++++++|.+|+++|...+ .++.+.++          .||..||+|..|++.|.. ..|+. .+|++||
T Consensus         1 ~~~~yC~~cy~~~~~~~C~~C~~~I~~~~-~~~~a~~~----------~~H~~CF~C~~C~~~L~~-~~~~~-~~~~~yC   67 (82)
T 1x63_A            1 GSSGSSGKCTTREDSPKCKGCFKAIVAGD-QNVEYKGT----------VWHKDCFTCSNCKQVIGT-GSFFP-KGEDFYC   67 (82)
T ss_dssp             CCSCCCCCCCSCCCSCBCSSSCCBCCSSS-CEEECSSC----------EEETTTCCCSSSCCCCTT-SCEEE-ETTEEEE
T ss_pred             CCCcCchhHHccccCCcCccCCcccccCc-eEEEECcc----------ccccccCchhhCCCccCC-CccEe-eCCEEEC
Confidence            46899999999999999999999999542 25677776          469999999999999954 46765 6899999


Q ss_pred             cchhhcccCCCCCCC
Q 014080          285 LECLDSAIMDTHECQ  299 (431)
Q Consensus       285 ~~C~~~~v~~~~~C~  299 (431)
                      ..||.+  .+.++|.
T Consensus        68 ~~cy~~--~f~~~~~   80 (82)
T 1x63_A           68 VTCHET--KFASGPS   80 (82)
T ss_dssp             HHHHHH--HTSCCCS
T ss_pred             HHHHHH--HhCCCCC
Confidence            999988  6777765

>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=99.38  E-value=1.4e-13  Score=127.33  Aligned_cols=74  Identities=22%  Similarity=0.447  Sum_probs=69.1

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccCcccccCCCccc
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIP  230 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~  230 (431)
                      .+.++|.+|+++|..++.|.++++.||+.||+|..|+++|.+..|+..++++||+.||.++|+++|.+|+++|-
T Consensus       113 ~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~kc~~C~~~~g  186 (192)
T 1b8t_A          113 GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQGAG  186 (192)
T ss_dssp             CCCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCCCC
T ss_pred             CCCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccccCCEEeCHHHHHHhcCCcCCCCCCccc
Confidence            35678999999997778899999999999999999999999888999999999999999999999999999864

>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=99.37  E-value=3.8e-13  Score=116.51  Aligned_cols=64  Identities=22%  Similarity=0.541  Sum_probs=57.5

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCC--CcceeecCCccccccccccccC
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPIT--DVEFSMSGNRPYHKHCYKEQHH  219 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~--~~~F~~~dg~pyC~~CY~~~f~  219 (431)
                      ....++|.+|+++|....++.++++.||+.||+|..|+++|.  +..|+.++|++||+.||.++|+
T Consensus        58 ~~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           58 GLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             CSSCSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             CccCCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            556799999999997555799999999999999999999997  4679999999999999998875

>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=99.34  E-value=4.3e-13  Score=103.86  Aligned_cols=63  Identities=19%  Similarity=0.438  Sum_probs=56.9

Q ss_pred             CCCCcCCCCCcccccCc-eEeecCccccCCCcccCCCCCCCCCcceeecCCccccccccccccC
Q 014080          157 SGYRICAGCNTEIGHGR-YLSCMEAFWHPECFRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH  219 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~-~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~  219 (431)
                      ...++|.+|+++|..++ ++.++++.||+.||+|..|+++|.+..|+..+|++||+.||.++|+
T Consensus         9 ~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B            9 SASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             CTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHTC
T ss_pred             cCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhhC
Confidence            46789999999997554 5789999999999999999999998889999999999999998874

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

Probab=99.29  E-value=1.1e-12  Score=100.61  Aligned_cols=59  Identities=24%  Similarity=0.562  Sum_probs=54.3

Q ss_pred             CCcCCCCCccccc-CceEeecCcccc--CCCcccCCCCCCCCCcceeecCCcccc-ccccccc
Q 014080          159 YRICAGCNTEIGH-GRYLSCMEAFWH--PECFRCHSCNLPITDVEFSMSGNRPYH-KHCYKEQ  217 (431)
Q Consensus       159 ~~~C~~C~k~I~~-g~~v~algk~wH--p~CF~C~~C~~~L~~~~F~~~dg~pyC-~~CY~~~  217 (431)
                      .++|.+|+++|.. ++.+.++++.||  +.||+|..|+++|.+..|+.++|+||| ..||.++
T Consensus         2 a~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L~~~~f~~~~g~~yC~~~C~~k~   64 (65)
T 2iyb_E            2 AVVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             CEECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCTTSCCEEETTEEESSHHHHHTT
T ss_pred             cCCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCCCCceEEECCEEecCHHHhhhh
Confidence            5689999999976 489999999999  999999999999999999999999999 8998764

>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=99.28  E-value=3.2e-12  Score=101.96  Aligned_cols=72  Identities=14%  Similarity=0.291  Sum_probs=59.8

Q ss_pred             CccccccccccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCc
Q 014080          206 NRPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCL  285 (431)
Q Consensus       206 g~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~  285 (431)
                      +.+||+.||.++|+++|..|+++|.+.   ++.+.++.          ||..||+|..|+++|..+..|. +.++.+||.
T Consensus         2 ~~~yC~~dy~~~~~~~C~~C~~~I~~~---~v~a~~~~----------wH~~CF~C~~C~~~L~~~~~~~-~~~~~~~C~   67 (81)
T 1v6g_A            2 SSGSSGLDYQRLYGTRCFSCDQFIEGE---VVSALGKT----------YHPDCFVCAVCRLPFPPGDRVT-FNGKECMCQ   67 (81)
T ss_dssp             CCCCCCSCGGGSCCCBCTTTCCBCCSC---CEEETTEE----------ECTTTSSCSSSCCCCCSSSCEE-EETTEEEEH
T ss_pred             CCCcchHHHHhHhCCcCccccCEeccc---eEEECCce----------eCccCCccccCCCCCCCCCEEE-eCCCCEECh
Confidence            578999999999999999999999964   67787774          6999999999999996555554 445457999


Q ss_pred             chhhcc
Q 014080          286 ECLDSA  291 (431)
Q Consensus       286 ~C~~~~  291 (431)
                      .|+.+.
T Consensus        68 ~C~~~~   73 (81)
T 1v6g_A           68 KCSLPV   73 (81)
T ss_dssp             HHHSCC
T ss_pred             hhhccc
Confidence            999763

>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=99.26  E-value=3.5e-12  Score=101.72  Aligned_cols=72  Identities=19%  Similarity=0.370  Sum_probs=60.7

Q ss_pred             CCcCCCCCC-CCCCCcCCCCCcccccCceEeecCccccCCCcccCCCCCCCCCcceeecCC-ccccccccccccC
Q 014080          147 GNIFQPFPF-FSGYRICAGCNTEIGHGRYLSCMEAFWHPECFRCHSCNLPITDVEFSMSGN-RPYHKHCYKEQHH  219 (431)
Q Consensus       147 g~~~~p~~~-~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF~C~~C~~~L~~~~F~~~dg-~pyC~~CY~~~f~  219 (431)
                      +++|+...+ ....++|.+|+++|. ++++.++++.||+.||+|..|+++|....|+..++ .+||..||.+++.
T Consensus         2 ~~~yC~~dy~~~~~~~C~~C~~~I~-~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~   75 (81)
T 1v6g_A            2 SSGSSGLDYQRLYGTRCFSCDQFIE-GEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSV   75 (81)
T ss_dssp             CCCCCCSCGGGSCCCBCTTTCCBCC-SCCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSS
T ss_pred             CCCcchHHHHhHhCCcCccccCEec-cceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCC
Confidence            357888877 778899999999996 88999999999999999999999998666655555 4699999976543

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

Probab=99.26  E-value=8.2e-13  Score=121.24  Aligned_cols=122  Identities=13%  Similarity=0.144  Sum_probs=88.9

Q ss_pred             CCccccccccc---cccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCc
Q 014080          205 GNRPYHKHCYK---EQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGR  281 (431)
Q Consensus       205 dg~pyC~~CY~---~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~  281 (431)
                      ++..||..++.   ....++|.+|+++|.+..  ++.+.++          .||..||+|..|++.|. +..|.  .+|+
T Consensus        43 ~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~~--~~~a~~~----------~wH~~CF~C~~C~~~L~-~~~f~--~~g~  107 (182)
T 2jtn_A           43 DDEGGSGGHMGSGGTPEIPMCAGCDQHILDRF--ILKALDR----------HWHSKCLKCSDCHVPLA-ERCFS--RGES  107 (182)
T ss_dssp             SSSCSSSSSCCCCCCCSCCBCBTSSSBCCCSE--EEEETTE----------EECSSTTSCTTTCCCCS-SCCEE--ETTE
T ss_pred             ccccccccccccCCCCCCCcCccCCCCccCce--eEEecCC----------eEccccCccCCCCCccC-CCcee--ECCE
Confidence            45567777765   456789999999999742  4667776          46999999999999995 44453  5999


Q ss_pred             ccCcchhhcccCCCCCCCcccHHHHHHHhhccccccccccchhhhHHHHHHHhcCCc---------C--CccCCcccCCc
Q 014080          282 KLCLECLDSAIMDTHECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEK---------N--GHHHLPETRGL  350 (431)
Q Consensus       282 ~yC~~C~~~~v~~~~~C~~C~~~I~~f~~~l~~~~~~~~pl~lv~~~ALn~~~~~e~---------~--g~~~~~e~rGl  350 (431)
                      +||..||.+  .+.++|..|.++|..          .+.-     ..|+++.||...         .  |...+...+|.
T Consensus       108 ~yC~~~y~~--~f~~kC~~C~~~I~~----------~~~v-----~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~  170 (182)
T 2jtn_A          108 VYCKDDFFK--RFGTKCAACQLGIPP----------TQVV-----RRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSR  170 (182)
T ss_dssp             EECHHHHHH--TTSCCCTTTCCCCCS----------SCCC-----CEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSC
T ss_pred             eeecCcccc--ccccccccCCCccCC----------CceE-----EecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCE
Confidence            999999998  899999999987731          1110     236788888752         1  22223456788


Q ss_pred             ccccccce
Q 014080          351 CLSEEQTV  358 (431)
Q Consensus       351 ~~~E~~~~  358 (431)
                      .||..+|.
T Consensus       171 ~yC~~cy~  178 (182)
T 2jtn_A          171 LVCKADYE  178 (182)
T ss_dssp             EECHHHHH
T ss_pred             EECHHHHH
Confidence            88887774

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

Probab=99.20  E-value=1.2e-12  Score=112.90  Aligned_cols=112  Identities=16%  Similarity=0.238  Sum_probs=84.1

Q ss_pred             ccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCC
Q 014080          217 QHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTH  296 (431)
Q Consensus       217 ~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~  296 (431)
                      +++++|.+|+++|.+..  ++.+.++.          ||..||+|..|++.|. +..|+. .+|++||..||.+  .+.+
T Consensus         1 ~~~~~C~~C~~~I~~~~--~~~a~~~~----------~H~~CF~C~~C~~~L~-~~~f~~-~~g~~yC~~cy~~--~~~~   64 (126)
T 2xqn_T            1 SEKPRCAGCDELIFSNE--YTQAENQN----------WHLKHFCCFDCDSILA-GEIYVM-VNDKPVCKPCYVK--NHAV   64 (126)
T ss_dssp             -CCCBBTTTSSBCCSSC--EEEETTEE----------ECGGGSBCTTTCCBCT-TSEEEE-ETTEEEEHHHHHH--HSCC
T ss_pred             CcCCCCccCCCEeCCce--EEeeCCCC----------ccCCCCCcCCCCCCCC-cCEEEe-ECCEEechHHhCc--CcCc
Confidence            36789999999999643  67787774          6999999999999994 667775 6999999999998  7899


Q ss_pred             CCCcccHHHHHHHhhccccccccccchhhhHHHHHHHhc--CCc---------CCccCCcccCCccccccccee
Q 014080          297 ECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAME--GEK---------NGHHHLPETRGLCLSEEQTVT  359 (431)
Q Consensus       297 ~C~~C~~~I~~f~~~l~~~~~~~~pl~lv~~~ALn~~~~--~e~---------~g~~~~~e~rGl~~~E~~~~~  359 (431)
                      +|..|.++|..         ....      +.|+++.||  .+.         .....+...+|.+||..++..
T Consensus        65 ~C~~C~~~I~~---------~~~~------~~a~~~~~H~~~~CF~C~~C~~~l~~~~f~~~~~~~yC~~~~~~  123 (126)
T 2xqn_T           65 VCQGCHNAIDP---------EVQR------VTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKK  123 (126)
T ss_dssp             BCTTTCSBCCT---------TSCE------EEETTEEEESSTTTSBCTTTCCBCTTSEEEEETTEEESSHHHHH
T ss_pred             cCcccCCcCCc---------CceE------EECCCCEeeCCCCCcCcCCCCCccCCCeeEeECCEEcchHHhhh
Confidence            99999988841         0111      246788888  531         122334567888888877753

>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=99.19  E-value=8.5e-13  Score=113.69  Aligned_cols=109  Identities=11%  Similarity=0.036  Sum_probs=81.4

Q ss_pred             ccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccC-CCCceEEccCCcccCcchhhcccCCC
Q 014080          217 QHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEP-RDTKYLSLDDGRKLCLECLDSAIMDT  295 (431)
Q Consensus       217 ~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~-~g~~f~~l~dG~~yC~~C~~~~v~~~  295 (431)
                      ++.++|.+|+++|.+..  ++.+.++.          ||..||+|..|++.|. .+..|+. .+|++||..||.+  .+.
T Consensus         3 ~~~~~C~~C~~~I~~~~--~~~a~~~~----------wH~~CF~C~~C~~~L~~~~~~~~~-~~g~~yC~~cy~~--~f~   67 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADRF--LLYAMDSY----------WHSRCLKCSSCQAQLGDIGTSSYT-KSGMILCRNDYIR--LFG   67 (122)
T ss_dssp             SCCCCBSSSSSCCCSSC--CEEETTEE----------ECHHHHCCSSSCCCTTTSEECCEE-ETTEEECHHHHHH--HHC
T ss_pred             CCCCCCcccCCEeCCcE--EEEECCce----------eHhhCCCcCCCCCcccccCCeEEE-ECCeeecHHHHHH--HcC
Confidence            56789999999999753  57777774          6999999999999995 2456775 6999999999998  677


Q ss_pred             C--CCCcccHHHHHHHhhccccccccccchhhhHHHHHHHhcCCcCCccCCcccCCcccccccceeee
Q 014080          296 H--ECQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVTTV  361 (431)
Q Consensus       296 ~--~C~~C~~~I~~f~~~l~~~~~~~~pl~lv~~~ALn~~~~~e~~g~~~~~e~rGl~~~E~~~~~~~  361 (431)
                      +  +|+.|.++|..          ..+       .+++    ........|...+|.+||..++....
T Consensus        68 ~~~~C~~C~~~I~~----------~~~-------~~~g----~~~l~g~~f~~~~~~~yC~~~~~~~~  114 (122)
T 1m3v_A           68 NSGAGGSGGHMGSG----------GDV-------MVVG----EPTLMGGEFGDEDERLITRLENTQFD  114 (122)
T ss_dssp             CCCSSSCSSCCSCC----------EES-------SSSS----SSSCCSCTTCCTTCCCCEECTTTTTT
T ss_pred             CCCccccCCCCcCc----------hhe-------EEcC----CcCCCCCccEecCCEeEccCcchhch
Confidence            7  99999988841          111       1122    12233345678899999999986443

>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=99.14  E-value=2.8e-11  Score=95.35  Aligned_cols=73  Identities=19%  Similarity=0.349  Sum_probs=60.6

Q ss_pred             cccCcccccCCCccccC-CcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCC
Q 014080          216 EQHHPKCDVCQNFIPTN-SAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMD  294 (431)
Q Consensus       216 ~~f~pkC~~C~~~I~~~-~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~  294 (431)
                      ++|+++|..|+++|.+. ...++.+.++          +||..||+|..|++.|. +..|+. .+|++||..||.+  .+
T Consensus         2 ~~~~~~C~~C~~~I~~~g~~~~~~a~~~----------~wH~~CF~C~~C~~~L~-~~~f~~-~~g~~yC~~cy~~--~f   67 (76)
T 1x68_A            2 SSGSSGCVACSKPISGLTGAKFICFQDS----------QWHSECFNCGKCSVSLV-GKGFLT-QNKEIFCQKCGSG--MD   67 (76)
T ss_dssp             TTCCCCCTTTCCCCCTTTTCCEEEETTE----------EEEGGGCBCTTTCCBCS-SSCEEE-ETTEEEETTTTCC--CC
T ss_pred             CccCCCCccCCCcccCCCCceeEEECCc----------ccCcccCChhhCCCcCC-CCceEe-ECCEEECHHHhhh--hh
Confidence            46889999999999961 1236777777          46999999999999995 667775 6999999999998  89


Q ss_pred             CCCCCccc
Q 014080          295 THECQPLY  302 (431)
Q Consensus       295 ~~~C~~C~  302 (431)
                      .++|+++.
T Consensus        68 ~~~C~~~s   75 (76)
T 1x68_A           68 TDISGPSS   75 (76)
T ss_dssp             CCSSSSSC
T ss_pred             CCcCCCCC
Confidence            99999874

>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=99.03  E-value=1.2e-10  Score=96.28  Aligned_cols=75  Identities=20%  Similarity=0.460  Sum_probs=62.7

Q ss_pred             ccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCC
Q 014080          217 QHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTH  296 (431)
Q Consensus       217 ~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~  296 (431)
                      ++.++|.+|+++|... ..++.+.++.          ||..||+|..|++.| .+..|+. .+|++||..||.+  .+.+
T Consensus         3 ~~~~~C~~C~~~I~~~-~~~~~a~~~~----------~H~~CF~C~~C~~~L-~~~~~~~-~~g~~yC~~cy~~--~~~~   67 (101)
T 2cup_A            3 SGSSGCVECRKPIGAD-SKEVHYKNRF----------WHDTCFRCAKCLHPL-ANETFVA-KDNKILCNKCTTR--EDSP   67 (101)
T ss_dssp             SCCCBCSSSCCBCCSS-SCEEEETTEE----------EETTTCCCSSSCCCT-TSSCCEE-ETTEEECHHHHTT--CCCC
T ss_pred             CCCCcCcccCCcccCC-ceEEEECccC----------hhhcCCcccccCCCC-CcCeeEC-cCCEEEChhHhhh--hcCC
Confidence            4678999999999742 1367777774          699999999999999 4666775 6999999999998  8999


Q ss_pred             CCCcccHHHH
Q 014080          297 ECQPLYLEIQ  306 (431)
Q Consensus       297 ~C~~C~~~I~  306 (431)
                      +|..|.++|.
T Consensus        68 ~C~~C~~~I~   77 (101)
T 2cup_A           68 KCKGCFKAIV   77 (101)
T ss_dssp             BCSSSCCBCC
T ss_pred             ccccCCCccc
Confidence            9999998873

>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=99.02  E-value=2.4e-10  Score=92.96  Aligned_cols=77  Identities=13%  Similarity=0.288  Sum_probs=63.0

Q ss_pred             ccccccccccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcc
Q 014080          207 RPYHKHCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLE  286 (431)
Q Consensus       207 ~pyC~~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~  286 (431)
                      .+.+...+...+.++|..|+++|.+.   .+.+.++.          ||..||+|..|++.|. +..|+. .+|++||..
T Consensus        13 ~~~~~~~~~~~~~~~C~~C~~~I~~~---~v~a~~~~----------~H~~CF~C~~C~~~L~-~~~f~~-~~g~~yC~~   77 (90)
T 2dar_A           13 VQRAEHIPAGKRTPMCAHCNQVIRGP---FLVALGKS----------WHPEEFNCAHCKNTMA-YIGFVE-EKGALYCEL   77 (90)
T ss_dssp             CBCCEEECTTTCCCBBSSSCCBCCSC---EEEETTEE----------ECTTTCBCSSSCCBCS-SSCBEE-SSSCEECHH
T ss_pred             hhhcccCCCCCCCCCCccCCCEecce---EEEECCcc----------ccccCCccCCCCCCCC-CCEeEe-ECCEEECHH
Confidence            34455556778899999999999754   67777774          6999999999999995 566774 799999999


Q ss_pred             hhhcccCCCCCCCc
Q 014080          287 CLDSAIMDTHECQP  300 (431)
Q Consensus       287 C~~~~v~~~~~C~~  300 (431)
                      ||.+  .+.++|+.
T Consensus        78 cy~~--~f~~~c~s   89 (90)
T 2dar_A           78 CYEK--FFASGPSS   89 (90)
T ss_dssp             HHHH--HTSCCCCC
T ss_pred             HHHH--HcCCCCCC
Confidence            9998  78898864

>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=99.02  E-value=1.8e-10  Score=89.39  Aligned_cols=70  Identities=14%  Similarity=0.423  Sum_probs=57.4

Q ss_pred             cccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCC
Q 014080          216 EQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDT  295 (431)
Q Consensus       216 ~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~  295 (431)
                      ++|+++|..|+++|.+.+ .++.+.++          .||..||+|..|++.|. +..|+. .+|++||..||.+  .+.
T Consensus         2 ~~~~~~C~~C~~~I~~~~-~~~~a~~~----------~~H~~CF~C~~C~~~L~-~~~~~~-~~~~~yC~~cy~~--~f~   66 (72)
T 1x4k_A            2 SSGSSGCQECKKTIMPGT-RKMEYKGS----------SWHETCFICHRCQQPIG-TKSFIP-KDNQNFCVPCYEK--QHA   66 (72)
T ss_dssp             CSCCCCBSSSCCCCCSSS-CEEEETTE----------EEETTTTCCSSSCCCCC-SSSEEE-ETTEEEEHHHHHH--HTS
T ss_pred             CccCCCCccCCCcccCCc-eEEEECcC----------eecccCCcccccCCccC-CCccCc-cCCeEECHHHHhH--HhC
Confidence            468899999999999642 25777776          46999999999999995 446775 6899999999998  788


Q ss_pred             CCCCc
Q 014080          296 HECQP  300 (431)
Q Consensus       296 ~~C~~  300 (431)
                      ++|+.
T Consensus        67 ~~C~~   71 (72)
T 1x4k_A           67 SGPSS   71 (72)
T ss_dssp             SCCCC
T ss_pred             CCCCC
Confidence            88864

>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=99.00  E-value=4.6e-11  Score=110.13  Aligned_cols=81  Identities=15%  Similarity=0.252  Sum_probs=61.2

Q ss_pred             CCcCCCCCC-CCCCC--cCCCCCcccccC-ceEeecCccccCCCcccCCCCCCCC-CcceeecCCccccccccccccCcc
Q 014080          147 GNIFQPFPF-FSGYR--ICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPIT-DVEFSMSGNRPYHKHCYKEQHHPK  221 (431)
Q Consensus       147 g~~~~p~~~-~~~~~--~C~~C~k~I~~g-~~v~algk~wHp~CF~C~~C~~~L~-~~~F~~~dg~pyC~~CY~~~f~pk  221 (431)
                      +.+|+...+ ....+  +|.+|+++|... .++.++++.||+.||+|..|+++|. +..|+..++++||+.||.+++.++
T Consensus        54 g~~yC~~cy~~~~~~~~~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~~~~~~~  133 (188)
T 1rut_X           54 GMILCRNDYIRLFGNSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALING  133 (188)
T ss_dssp             TEEECHHHHHHHHSCCEECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCCTTTC--
T ss_pred             CccccccccccccccCCccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHHHHhccc
Confidence            455666555 33344  799999999654 5789999999999999999999996 567999999999999999999999


Q ss_pred             cccCCC
Q 014080          222 CDVCQN  227 (431)
Q Consensus       222 C~~C~~  227 (431)
                      |...+.
T Consensus       134 ~~~~g~  139 (188)
T 1rut_X          134 HLNSGG  139 (188)
T ss_dssp             ------
T ss_pred             ccccCC
Confidence            987765

>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=99.00  E-value=1.8e-10  Score=89.35  Aligned_cols=70  Identities=17%  Similarity=0.410  Sum_probs=56.7

Q ss_pred             cccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCC
Q 014080          216 EQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDT  295 (431)
Q Consensus       216 ~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~  295 (431)
                      ++++++|..|+++|.... .++.+.++          .||..||+|..|++.|. +..|+. .+|++||..||.+  .+.
T Consensus         2 ~~~~~~C~~C~~~I~~~~-~~~~a~~~----------~~H~~CF~C~~C~~~L~-~~~~~~-~~~~~yC~~cy~~--~f~   66 (72)
T 1wyh_A            2 SSGSSGCSACGETVMPGS-RKLEYGGQ----------TWHEHCFLCSGCEQPLG-SRSFVP-DKGAHYCVPCYEN--KFA   66 (72)
T ss_dssp             CCCCCBCSSSCCBCCSSS-CEECSTTC----------CEETTTCBCTTTCCBTT-TSCEEE-ETTEEEEHHHHHH--HTS
T ss_pred             CccCCCCccCCCccccCc-cEEEECcc----------ccCcccCeECCCCCcCC-CCccCC-cCCeEECHHHHHH--Hcc
Confidence            467899999999999631 25666666          46999999999999995 446764 6999999999998  788


Q ss_pred             CCCCc
Q 014080          296 HECQP  300 (431)
Q Consensus       296 ~~C~~  300 (431)
                      ++|++
T Consensus        67 ~~C~~   71 (72)
T 1wyh_A           67 SGPSS   71 (72)
T ss_dssp             CCCCC
T ss_pred             CcCCC
Confidence            98874

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

Probab=98.99  E-value=3e-10  Score=89.04  Aligned_cols=61  Identities=16%  Similarity=0.395  Sum_probs=51.8

Q ss_pred             cccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          216 EQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       216 ~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .+|+++|.+|+++|.+.   +|.+.++          +||..||+|..|++.|..+..|+. .+|++||..||..
T Consensus         2 s~~~~~C~~C~~~I~~~---~v~a~~~----------~wH~~CF~C~~C~~~L~~~~~f~~-~~~~~yC~~C~~~   62 (73)
T 1wig_A            2 SSGSSGCDSCEKYITGR---VLEAGEK----------HYHPSCALCVRCGQMFAEGEEMYL-QGSSIWHPACRQA   62 (73)
T ss_dssp             CCSCCSCSSSCCCCSSC---CBCCSSC----------CBCTTTSCCSSSCCCCCSSCCCEE-ETTEEECTTHHHH
T ss_pred             CcCcCCcccCCCEecCe---eEEeCCC----------CCCCCcCEeCCCCCCCCCCCeeEe-eCCEEEChHHChH
Confidence            36889999999999974   5667776          469999999999999965777775 6899999999987

>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=98.99  E-value=2.8e-10  Score=87.86  Aligned_cols=68  Identities=18%  Similarity=0.387  Sum_probs=56.6

Q ss_pred             cccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCC
Q 014080          216 EQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDT  295 (431)
Q Consensus       216 ~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~  295 (431)
                      .+++++|..|+++|.+.   .+.+.++          .||..||+|..|++.| .+..|+. .+|++||..||.+  .+.
T Consensus         2 ~~~~~~C~~C~~~I~~~---~~~a~~~----------~~H~~CF~C~~C~~~L-~~~~~~~-~~~~~yC~~cy~~--~f~   64 (70)
T 2d8z_A            2 SSGSSGCVQCKKPITTG---GVTYREQ----------PWHKECFVCTACRKQL-SGQRFTA-RDDFAYCLNCFCD--LYA   64 (70)
T ss_dssp             CCCCCBCSSSCCBCCSS---EEESSSS----------EEETTTSBCSSSCCBC-TTSCCEE-SSSSEECHHHHHH--HTC
T ss_pred             CCCCCCCcccCCeeccc---eEEECcc----------ccCCCCCccCCCCCcC-CcCceEe-eCCeEECHHHHHH--Hhc
Confidence            35789999999999864   4677776          4699999999999999 4667775 6899999999998  788


Q ss_pred             CCCCc
Q 014080          296 HECQP  300 (431)
Q Consensus       296 ~~C~~  300 (431)
                      ++|++
T Consensus        65 ~~c~~   69 (70)
T 2d8z_A           65 SGPSS   69 (70)
T ss_dssp             CCCTT
T ss_pred             cccCC
Confidence            88864

>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=98.99  E-value=2.4e-10  Score=88.11  Aligned_cols=67  Identities=15%  Similarity=0.424  Sum_probs=56.6

Q ss_pred             ccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCC
Q 014080          217 QHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTH  296 (431)
Q Consensus       217 ~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~  296 (431)
                      +++++|..|+++|.++   .+.+.++.          ||..||+|..|++.|. +..|+. .+|++||..||.+  .+.+
T Consensus         3 ~~~~~C~~C~~~I~~~---~~~a~~~~----------~H~~CF~C~~C~~~L~-~~~~~~-~~~~~yC~~cy~~--~f~~   65 (69)
T 2cur_A            3 SGSSGCVKCNKAITSG---GITYQDQP----------WHADCFVCVTCSKKLA-GQRFTA-VEDQYYCVDCYKN--FVSG   65 (69)
T ss_dssp             CCCCCCSSSCCCCCTT---CEEETTEE----------ECTTTTBCTTTCCBCT-TSCEEE-CSSCEEEHHHHHH--HHTC
T ss_pred             CCcCCCcccCCEeCcc---eEEECccc----------cccCcCEECCCCCCCC-CCccEe-ECCEEECHHHhHH--HhcC
Confidence            5678999999999864   57777774          6999999999999994 667775 6899999999998  7888


Q ss_pred             CCCc
Q 014080          297 ECQP  300 (431)
Q Consensus       297 ~C~~  300 (431)
                      +|++
T Consensus        66 ~C~g   69 (69)
T 2cur_A           66 PSSG   69 (69)
T ss_dssp             SCCC
T ss_pred             CCCC
Confidence            8874

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

Probab=98.99  E-value=1.4e-11  Score=111.69  Aligned_cols=111  Identities=16%  Similarity=0.210  Sum_probs=81.5

Q ss_pred             CcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCCCC
Q 014080          219 HPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHEC  298 (431)
Q Consensus       219 ~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~~C  298 (431)
                      .++|.+|+++|.+..  ++.+.++          .||..||+|..|++.|. +..| . .+|++||..||.+  .++++|
T Consensus         6 ~~~C~~C~~~I~~~~--~~~a~~~----------~wH~~CF~C~~C~~~L~-~~~f-~-~~g~~yC~~~y~~--~f~~~C   68 (169)
T 2rgt_A            6 IPMCAGCDQHILDRF--ILKALDR----------HWHSKCLKCSDCHVPLA-ERCF-S-RGESVYCKDDFFK--RFGTKC   68 (169)
T ss_dssp             -CBBSSSSSBCCSSS--CEECSSC----------EECTTTSBCTTTCCBCC-SCCE-E-SSSCEECHHHHHH--HHSCBC
T ss_pred             CCccccCCCccCCcE--EEEECCc----------EEccccCccCCCCCcCC-CCCc-c-cCCeeeecccccc--cccccc
Confidence            578999999999753  5667776          46999999999999994 3445 3 6999999999998  789999


Q ss_pred             CcccHHHHHHHhhccccccccccchhhhHHHHHHHhcCCc---------C--CccCCcccCCcccccccceeee
Q 014080          299 QPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEK---------N--GHHHLPETRGLCLSEEQTVTTV  361 (431)
Q Consensus       299 ~~C~~~I~~f~~~l~~~~~~~~pl~lv~~~ALn~~~~~e~---------~--g~~~~~e~rGl~~~E~~~~~~~  361 (431)
                      ..|.++|..          .+. +    ..|+++.||.+.         .  |...+...+|..||..+|...+
T Consensus        69 ~~C~~~I~~----------~~~-v----~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~~  127 (169)
T 2rgt_A           69 AACQLGIPP----------TQV-V----RRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAK  127 (169)
T ss_dssp             TTTCCBCCT----------TSE-E----EEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHHH
T ss_pred             cccccccCC----------CcE-E----EEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHHh
Confidence            999987731          111 0    236778887652         1  3333456789999999986544

>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=98.98  E-value=4.6e-10  Score=87.24  Aligned_cols=68  Identities=16%  Similarity=0.347  Sum_probs=54.8

Q ss_pred             ccCcccccCCCccccC-CcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCC
Q 014080          217 QHHPKCDVCQNFIPTN-SAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDT  295 (431)
Q Consensus       217 ~f~pkC~~C~~~I~~~-~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~  295 (431)
                      .+.++|..|+++|.+. ...++.+.++          +||..||+|..|++.|. +..|+. .+|++||..||.+  .+.
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~----------~wH~~CF~C~~C~~~L~-~~~f~~-~~g~~yC~~c~~~--~~~   68 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEER----------QWHNDCFNCKKCSLSLV-GRGFLT-ERDDILCPDCGKD--ISG   68 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSC----------EECTTTCBCSSSCCBCT-TSCCEE-CSSSEECHHHHHT--CCC
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCc----------ccCcccCEeccCCCcCC-CCccEe-ECCEEEChhHcCc--ccC
Confidence            4678999999999961 1235777776          46999999999999994 667774 6999999999988  677


Q ss_pred             CCC
Q 014080          296 HEC  298 (431)
Q Consensus       296 ~~C  298 (431)
                      |++
T Consensus        69 p~~   71 (72)
T 1x4l_A           69 PSS   71 (72)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            765

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

Probab=98.97  E-value=3.3e-11  Score=104.27  Aligned_cols=74  Identities=16%  Similarity=0.306  Sum_probs=60.5

Q ss_pred             CCcCCCCCC-CCCCC--cCCCCCcccccC-ceEeecCccccCCCcccCCCCCCCC-CcceeecCCccccccccccccCc
Q 014080          147 GNIFQPFPF-FSGYR--ICAGCNTEIGHG-RYLSCMEAFWHPECFRCHSCNLPIT-DVEFSMSGNRPYHKHCYKEQHHP  220 (431)
Q Consensus       147 g~~~~p~~~-~~~~~--~C~~C~k~I~~g-~~v~algk~wHp~CF~C~~C~~~L~-~~~F~~~dg~pyC~~CY~~~f~p  220 (431)
                      +.+|+...+ ....+  +|.+|+++|... .++.++++.||+.||+|..|+++|. +..|+..++++||..||.+++++
T Consensus        51 g~~yC~~~y~~~~~~~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~~~~~  129 (131)
T 2xjy_A           51 GRKLCRRDYLRLFGQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKI  129 (131)
T ss_dssp             TEEECHHHHHHHHCCCEECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHHHHHH
T ss_pred             CEEeecCchhhhCCCccChhhcCCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHHHhhc
Confidence            445555444 33445  999999999643 5789999999999999999999995 66799999999999999988764

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

Probab=98.95  E-value=3.9e-10  Score=88.64  Aligned_cols=69  Identities=14%  Similarity=0.231  Sum_probs=57.1

Q ss_pred             cccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCc-chhhcccCCCCCC
Q 014080          220 PKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCL-ECLDSAIMDTHEC  298 (431)
Q Consensus       220 pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~-~C~~~~v~~~~~C  298 (431)
                      |+|.+|+++|....  .+.+.++          .||..||+|..|++.|.. ..|+. .+|++||. .||.+  .+.++|
T Consensus         1 p~C~~C~~~I~~~~--~v~a~~~----------~~H~~CF~C~~C~~~L~~-~~~~~-~~g~~yC~~~cy~~--~f~~~C   64 (76)
T 1iml_A            1 PKCPKCDKEVYFAE--RVTSLGK----------DWHRPCLKCEKCGKTLTS-GGHAE-HEGKPYCNHPCYSA--MFGPKG   64 (76)
T ss_dssp             CBCTTTSSBCCGGG--EEEETTE----------EEETTTCBCTTTCCBCCT-TTEEE-ETTEEEETTTHHHH--HSSCCC
T ss_pred             CcCCCCCCEEECce--EEEECCc----------cccCCCCCccccCccCCC-CceEC-cCCeEeeCHHHHHH--HhCccC
Confidence            68999999998533  5777776          469999999999999954 46775 69999999 69998  889999


Q ss_pred             CcccHH
Q 014080          299 QPLYLE  304 (431)
Q Consensus       299 ~~C~~~  304 (431)
                      .+|...
T Consensus        65 ~~C~~~   70 (76)
T 1iml_A           65 FGRGGA   70 (76)
T ss_dssp             SSCCCS
T ss_pred             CCcCCc
Confidence            999843

>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=98.95  E-value=5.9e-10  Score=87.65  Aligned_cols=69  Identities=13%  Similarity=0.253  Sum_probs=56.7

Q ss_pred             cccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCc-chhhcccCC
Q 014080          216 EQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCL-ECLDSAIMD  294 (431)
Q Consensus       216 ~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~-~C~~~~v~~  294 (431)
                      ..+.++|.+|+++|....  .+.+.++.          ||..||+|..|++.|. +..|+. .+|++||. .||.+  .+
T Consensus         6 ~~~~~~C~~C~~~I~~~~--~v~a~~~~----------~H~~CF~C~~C~~~L~-~~~~~~-~~g~~yC~~~cy~~--~f   69 (76)
T 2cu8_A            6 SGMASKCPKCDKTVYFAE--KVSSLGKD----------WHKFCLKCERCSKTLT-PGGHAE-HDGKPFCHKPCYAT--LF   69 (76)
T ss_dssp             CCCCCBCTTTCCBCCTTT--EEEETTEE----------EETTTCBCSSSCCBCC-TTSCEE-ETTEEECTTTHHHH--HS
T ss_pred             CCCCCCCcCCCCEeECCe--EEEECCeE----------eeCCCCCCCCCCCccC-CCceEe-ECCEEecchHHHHH--hc
Confidence            357889999999999543  57777764          6999999999999995 556775 68999999 79988  78


Q ss_pred             CCCCCc
Q 014080          295 THECQP  300 (431)
Q Consensus       295 ~~~C~~  300 (431)
                      .++|.+
T Consensus        70 ~~kc~g   75 (76)
T 2cu8_A           70 GSGPSS   75 (76)
T ss_dssp             CSSCSC
T ss_pred             ccccCC
Confidence            888864

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

Probab=98.93  E-value=3.3e-10  Score=90.16  Aligned_cols=70  Identities=13%  Similarity=0.172  Sum_probs=50.2

Q ss_pred             cCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCCC
Q 014080          218 HHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHE  297 (431)
Q Consensus       218 f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~~  297 (431)
                      ..++|..|+++|....  .+.+.++          .||..||+|..|++.|.. ..|+. .+|++||..||.+  .+.++
T Consensus         6 ~~~~C~~C~~~I~~~~--~~~a~~~----------~~H~~CF~C~~C~~~L~~-~~~~~-~~~~~yC~~cy~~--~f~~~   69 (81)
T 1a7i_A            6 GGNKCGACGRTVYHAE--EVQCDGR----------SFHRCCFLCMVCRKNLDS-TTVAI-HDAEVYCKSCYGK--KYGPK   69 (81)
T ss_dssp             --CBCSSSCCBCSSTT--EEEETTE----------EEESSSEECSSSCCEECS-SCCEE-ETTEEECSHHHHH--HCC--
T ss_pred             CCCcCcCcCccccCce--eEEeCCc----------ccccccCccCCCCCCCCC-CCeEe-eCCEEECHHHHHH--HhCCc
Confidence            4689999999997543  5777776          469999999999999954 45765 5999999999998  89999


Q ss_pred             CCcccH
Q 014080          298 CQPLYL  303 (431)
Q Consensus       298 C~~C~~  303 (431)
                      |.+|..
T Consensus        70 c~gcg~   75 (81)
T 1a7i_A           70 GYGYGQ   75 (81)
T ss_dssp             ------
T ss_pred             ccccCC
Confidence            999985

>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=98.88  E-value=5.6e-10  Score=85.31  Aligned_cols=60  Identities=15%  Similarity=0.288  Sum_probs=49.8

Q ss_pred             cccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          216 EQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       216 ~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      +++.++|.+|+++|.+.   .+.+.++          .||..||+|..|++.|. +..|+. .+|++||..||.+
T Consensus         2 ~~~~~~C~~C~~~I~~~---~~~a~~~----------~~H~~CF~C~~C~~~L~-~~~~~~-~~g~~yC~~~y~~   61 (66)
T 1nyp_A            2 SMGVPICGACRRPIEGR---VVNAMGK----------QWHVEHFVCAKCEKPFL-GHRHYE-RKGLAYCETHYNQ   61 (66)
T ss_dssp             CCCCCEETTTTEECCSC---EECCTTS----------BEETTTCBCTTTCCBCS-SSCCEE-ETTEEECHHHHHH
T ss_pred             CcCCCCCcccCCEecce---EEEECcc----------ccccCcCEECCCCCCCC-CCceEe-ECCcEECHHHHHH
Confidence            35789999999999953   5667666          46999999999999994 566774 6999999999987

>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=98.87  E-value=1.6e-09  Score=86.50  Aligned_cols=66  Identities=15%  Similarity=0.243  Sum_probs=54.3

Q ss_pred             cCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCCC
Q 014080          218 HHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHE  297 (431)
Q Consensus       218 f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~~  297 (431)
                      ..++|..|+++|....  .+.+.++          .||..||+|..|++.|. + .|+. .+|++||..||.+  .+.++
T Consensus        14 ~~~~C~~C~~~I~~~~--~v~a~~~----------~wH~~CF~C~~C~~~L~-~-~~~~-~~g~~yC~~~y~~--~fg~~   76 (80)
T 2dj7_A           14 GPSHCAGCKEEIKHGQ--SLLALDK----------QWHVSCFKCQTCSVILT-G-EYIS-KDGVPYCESDYHA--QFGSG   76 (80)
T ss_dssp             SCSCCTTTCCCCSSSC--CEEETTE----------EECTTTCBCSSSCCBCS-S-CCEE-ETTEEECTTHHHH--HTTCC
T ss_pred             CCCCCcCcCCeeCCCe--EEEECCc----------ccccccCCcCcCCCCcC-C-CeEE-ECCEEECHHHHHH--HcCCC
Confidence            3578999999998543  5777777          46999999999999995 4 5764 6999999999998  78888


Q ss_pred             CCc
Q 014080          298 CQP  300 (431)
Q Consensus       298 C~~  300 (431)
                      |.+
T Consensus        77 C~~   79 (80)
T 2dj7_A           77 PSS   79 (80)
T ss_dssp             STT
T ss_pred             CCC
Confidence            874

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

Probab=98.86  E-value=1.1e-09  Score=86.07  Aligned_cols=68  Identities=13%  Similarity=0.272  Sum_probs=53.7

Q ss_pred             ccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCC
Q 014080          217 QHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTH  296 (431)
Q Consensus       217 ~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~  296 (431)
                      .+.++|.+|+++|.+.+ .++.+.++.          ||..||+|..|++.|..+ .|+. .+|++||..||.+  .+.+
T Consensus         9 ~~~~~C~~C~~~I~~~~-~~~~a~~~~----------~H~~CF~C~~C~~~L~~~-~~~~-~~g~~yC~~~y~~--~f~~   73 (77)
T 1g47_A            9 LASATCERCKGGFAPAE-KIVNSNGEL----------YHEQCFVCAQCFQQFPEG-LFYE-FEGRKYCEHDFQM--LFAP   73 (77)
T ss_dssp             CCCCBCSSSCCBCCSTT-TCEEETTEE----------ECTTTCCCTTTCCCCGGG-CSEE-ETTEEECHHHHHH--HCCC
T ss_pred             CCCCCchhcCCccCCCc-eEEEeCccE----------eccccCeECCCCCCCCCC-CeEe-ECCeEeCHHHHHH--Hhhc
Confidence            46789999999998532 356677774          699999999999999654 5664 6999999999988  7888


Q ss_pred             CCC
Q 014080          297 ECQ  299 (431)
Q Consensus       297 ~C~  299 (431)
                      +|.
T Consensus        74 ~C~   76 (77)
T 1g47_A           74 CWI   76 (77)
T ss_dssp             C--
T ss_pred             ccC
Confidence            885

>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=98.84  E-value=1.1e-09  Score=93.05  Aligned_cols=101  Identities=13%  Similarity=0.073  Sum_probs=74.0

Q ss_pred             CcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCC-CCceEEccCCcccCcchhhcccCCCCC
Q 014080          219 HPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPR-DTKYLSLDDGRKLCLECLDSAIMDTHE  297 (431)
Q Consensus       219 ~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~-g~~f~~l~dG~~yC~~C~~~~v~~~~~  297 (431)
                      .++|.+|+++|.+..  ++.+.++          .||..||+|..|+++|.. |..|+. .+|++||..||.+  .+.++
T Consensus         3 ~~~C~~C~~~I~~~~--~~~a~~~----------~wH~~CF~C~~C~~~L~~~g~~~~~-~~g~~yC~~~y~~--~f~~~   67 (114)
T 1j2o_A            3 LLTCGGCQQNIGDRY--FLKAIDQ----------YWHEDCLSCDLCGCRLGEVGRRLYY-KLGRKLCRRDYLR--LGGSG   67 (114)
T ss_dssp             CBCBSSSCSCBCSSE--EEECSSS----------EECTTTCCCSSSCSCCCCSSSCCCC-BTTBCCCHHHHHH--HHTSC
T ss_pred             CCCCcCCCCeeCCcE--EEEECch----------hHHHhcCcccccCCchhcCCCeeEE-ECCeeechHHHHH--HhCcc
Confidence            478999999999642  5677776          469999999999999963 457774 6999999999998  88999


Q ss_pred             CCcccHHHHHHHhhccccccccccchhhhHHHHHHHhcCCcCCccCCcccCCccccccccee
Q 014080          298 CQPLYLEIQEFYEGLNMKVEQQVPLLLVERQALNEAMEGEKNGHHHLPETRGLCLSEEQTVT  359 (431)
Q Consensus       298 C~~C~~~I~~f~~~l~~~~~~~~pl~lv~~~ALn~~~~~e~~g~~~~~e~rGl~~~E~~~~~  359 (431)
                      |..|..       +.-|.             +     .........|...+|.+||..++..
T Consensus        68 c~~c~~-------~~~~~-------------~-----~~~~~~g~~f~~~~~~~~C~~~~~~  104 (114)
T 1j2o_A           68 GHMGSG-------GDVMV-------------V-----GEPTLMGGEFGDEDERLITRLENTQ  104 (114)
T ss_dssp             CSSCBS-------CSCCC-------------S-----SCSSTTSSBCCCSSSCCCEEEECTT
T ss_pred             cCcCCC-------CceeE-------------c-----CCccCCCCeeEEcCCEeecchhhhc
Confidence            988862       10010             0     1111222356788999999888763

>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=98.84  E-value=2.6e-09  Score=84.87  Aligned_cols=65  Identities=17%  Similarity=0.339  Sum_probs=52.8

Q ss_pred             ccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCC
Q 014080          217 QHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTH  296 (431)
Q Consensus       217 ~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~  296 (431)
                      .+.++|..|+++|.+.   .+.+.++          .||..||+|..|++.|.. ..|  ..+|++||..||.+  .++|
T Consensus        13 ~~~~~C~~C~~~I~~~---~v~a~~~----------~~H~~CF~C~~C~~~L~~-~~f--~~~g~~yC~~cy~~--~f~p   74 (79)
T 2cor_A           13 LGKYICQKCHAIIDEQ---PLIFKND----------PYHPDHFNCANCGKELTA-DAR--ELKGELYCLPCHDK--MGVS   74 (79)
T ss_dssp             CCCCBCTTTCCBCCSC---CCCCSSS----------CCCTTTSBCSSSCCBCCT-TCE--EETTEEECHHHHHT--TSCC
T ss_pred             cCCCCCccCCCEecce---EEEECcc----------eeCCCCCEeCCCCCccCC-CCE--eECCEEeCHHHHHH--hCCC
Confidence            4678999999999954   4667776          469999999999999953 344  35999999999998  7887


Q ss_pred             CCC
Q 014080          297 ECQ  299 (431)
Q Consensus       297 ~C~  299 (431)
                      .+.
T Consensus        75 ~~s   77 (79)
T 2cor_A           75 GPS   77 (79)
T ss_dssp             SSC
T ss_pred             CCC
Confidence            765

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

Probab=98.80  E-value=2.7e-09  Score=86.90  Aligned_cols=70  Identities=16%  Similarity=0.177  Sum_probs=56.3

Q ss_pred             ccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCC
Q 014080          217 QHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTH  296 (431)
Q Consensus       217 ~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~  296 (431)
                      ...++|..|+++|.+..  .+.+.++          .||..||+|..|++.|..+ .|+. .+|++||..||..  .+.+
T Consensus        13 ~~~~~C~~C~~~I~~~~--~v~a~~~----------~~H~~CF~C~~C~~~L~~~-~~~~-~~g~~yC~~~y~~--~f~~   76 (91)
T 2d8y_A           13 PARETCVECQKTVYPME--RLLANQQ----------VFHISCFRCSYCNNKLSLG-TYAS-LHGRIYCKPHFNQ--LFKS   76 (91)
T ss_dssp             SSSCBCTTTCCBCCTTS--EEECSSS----------EEETTTCBCTTTCCBCCTT-TCCC-SSSCCCCHHHHHH--HSCC
T ss_pred             CCCCcCccCCCccCCce--eEEECCC----------EECCCCCeeCCCCCCCCCC-CcEe-ECCEEECHHHHHH--HhCC
Confidence            35789999999998743  5666666          4699999999999999544 4664 6999999999998  7889


Q ss_pred             CCCccc
Q 014080          297 ECQPLY  302 (431)
Q Consensus       297 ~C~~C~  302 (431)
                      +|..+.
T Consensus        77 kc~~~~   82 (91)
T 2d8y_A           77 KGNYDE   82 (91)
T ss_dssp             CSCCCS
T ss_pred             CcCccC
Confidence            997443

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

Probab=98.78  E-value=2.6e-09  Score=82.35  Aligned_cols=64  Identities=14%  Similarity=0.373  Sum_probs=51.4

Q ss_pred             cccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          214 YKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       214 Y~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      |..++.++|..|+++|.+.+ .++.+.++          .||..||+|..|++.|..+ .|+. .+|++||..||.+
T Consensus         6 y~~~~~~~C~~C~~~i~~~e-~~~~~~~~----------~~H~~CF~C~~C~~~L~~~-~~~~-~~g~~yC~~~y~~   69 (72)
T 3f6q_B            6 FQGSASATCERCKGGFAPAE-KIVNSNGE----------LYHEQCFVCAQCFQQFPEG-LFYE-FEGRKYCEHDFQM   69 (72)
T ss_dssp             CCCCTTCBCTTTCCBCCTTC-EEEEETTE----------EEETTTSSCTTTCCCCGGG-CCEE-ETTEEECHHHHHH
T ss_pred             ccCcCCccchhcCccccCCc-eEEEeCcC----------eeCcCCCcccCCCCCCCCC-CeEe-ECCeEeCHHHHHH
Confidence            45578899999999999753 24556666          4699999999999999655 6664 5899999999976

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

Probab=98.77  E-value=3.5e-09  Score=85.79  Aligned_cols=65  Identities=17%  Similarity=0.309  Sum_probs=52.7

Q ss_pred             cCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCCC
Q 014080          218 HHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHE  297 (431)
Q Consensus       218 f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~~  297 (431)
                      ..++|..|+++|.+.   ++.+.++          .||..||+|..|++.|. +..|+. .+|++||..||.+  .+.++
T Consensus        24 ~~~~C~~C~~~I~~~---~~~a~~~----------~~H~~CF~C~~C~~~L~-~~~~~~-~~g~~yC~~~y~~--~f~p~   86 (89)
T 1x64_A           24 RMPLCDKCGSGIVGA---VVKARDK----------YRHPECFVCADCNLNLK-QKGYFF-VEGELYCETHARA--RTSGP   86 (89)
T ss_dssp             SCCBCTTTCCBCCSC---CEESSSC----------EECTTTCCCSSSCCCTT-TSCCEE-ETTEEECHHHHHH--HSSSC
T ss_pred             cCCCcccCCCEeccc---EEEECCc----------eECccCCEecCCCCCCC-CCCeEe-ECCEEECHHHHHH--HhCCC
Confidence            457899999999974   5667666          46999999999999995 445665 4899999999988  67777


Q ss_pred             CC
Q 014080          298 CQ  299 (431)
Q Consensus       298 C~  299 (431)
                      |.
T Consensus        87 ~~   88 (89)
T 1x64_A           87 SS   88 (89)
T ss_dssp             CC
T ss_pred             CC
Confidence            65

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

Probab=98.77  E-value=3.2e-09  Score=81.12  Aligned_cols=60  Identities=22%  Similarity=0.492  Sum_probs=48.9

Q ss_pred             cCcccccCCCccccCCcceEEEecccccccccCCCccc--CCCCccCCCCCccCCCCceEEccCCcccC-cchhhc
Q 014080          218 HHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHER--DGTPRCCSCERMEPRDTKYLSLDDGRKLC-LECLDS  290 (431)
Q Consensus       218 f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H--~~CF~C~~C~r~l~~g~~f~~l~dG~~yC-~~C~~~  290 (431)
                      |+++|.+|+++|.+.. ..+.+.++.          ||  ..||+|..|+++| .+..|+. .+|++|| ..|+.+
T Consensus         1 fa~~C~~C~~~I~~~~-~~v~a~~~~----------wH~~~~CF~C~~C~~~L-~~~~f~~-~~g~~yC~~~C~~k   63 (65)
T 2iyb_E            1 HAVVCQGCHNAIDPEV-QRVTYNNFS----------WHASTECFLCSCCSKCL-IGQKFMP-VEGMVFCSVECKKR   63 (65)
T ss_dssp             -CEECTTTSSEECTTS-CEEEETTEE----------EETTTTTSBCTTTCCBC-TTSCCEE-ETTEEESSHHHHHT
T ss_pred             CcCCCcCCCCeeccCc-eEEEECCCc----------cCCCCCCEECCCCCCcC-CCCceEE-ECCEEecCHHHhhh
Confidence            5789999999999531 267888874          68  9999999999999 4667775 6899999 899876

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

Probab=98.77  E-value=5.5e-09  Score=80.99  Aligned_cols=62  Identities=15%  Similarity=0.296  Sum_probs=51.0

Q ss_pred             ccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcc
Q 014080          217 QHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSA  291 (431)
Q Consensus       217 ~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~  291 (431)
                      +++++|.+|+++|.+.. .++.+.++          .||..||+|..|++.| .+..|+. .+|++||..||.+.
T Consensus         3 ~~~~~C~~C~~~I~~~~-~~~~a~~~----------~~H~~CF~C~~C~~~L-~~~~~~~-~~~~~yC~~cy~~~   64 (72)
T 1x61_A            3 SGSSGCGGCGEDVVGDG-AGVVALDR----------VFHVGCFVCSTCRAQL-RGQHFYA-VERRAYCEGCYVAT   64 (72)
T ss_dssp             SCCCCCSSSCSCCCSSS-CCEECSSS----------EECTTTCBCSSSCCBC-TTSCEEE-SSSCEEEHHHHHHH
T ss_pred             CCCCCCccCCCccCCCc-eEEEECCC----------eEcccCCcccccCCcC-CcCcCEe-eCCeEECHHHHHHH
Confidence            46889999999999632 25677776          4699999999999999 5677875 68999999999874

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

Probab=98.76  E-value=4e-09  Score=81.43  Aligned_cols=63  Identities=21%  Similarity=0.444  Sum_probs=50.9

Q ss_pred             cCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCCC
Q 014080          218 HHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHE  297 (431)
Q Consensus       218 f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~~  297 (431)
                      +.++|..|+++|.+.   ++.+.++.          ||..||+|..|++.|..+ .|+. .+|++||..||.+  .+.+.
T Consensus         4 ~~~~C~~C~~~I~~~---~~~a~~~~----------~H~~CF~C~~C~~~L~~~-~f~~-~~g~~yC~~c~~~--~~~~~   66 (70)
T 2d8x_A            4 GSSGCHQCGEFIIGR---VIKAMNNS----------WHPECFRCDLCQEVLADI-GFVK-NAGRHLCRPCHNR--EKASG   66 (70)
T ss_dssp             CSSBCSSSCCBCCSC---CEEETTEE----------ECTTTSBCSSSCCBCSSS-CCEE-ETTEEECHHHHHH--HHCCC
T ss_pred             CCCcCccCCCEecce---EEEECccc----------ccccCCEeCCCCCcCCCC-ccEe-ECCeEECHHHhhh--hcCCC
Confidence            568999999999964   57787774          699999999999999544 5664 6999999999987  44443

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

Probab=98.74  E-value=1.9e-09  Score=85.49  Aligned_cols=65  Identities=15%  Similarity=0.261  Sum_probs=52.4

Q ss_pred             cCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEEccCCcccCcchhhcccCCCCC
Q 014080          218 HHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHE  297 (431)
Q Consensus       218 f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~~  297 (431)
                      ..++|..|+++|.+.   ++.+.++          .||..||+|..|++.|. +..|+. .++++||..||.+  .+.++
T Consensus        14 ~~~~C~~C~~~I~~~---~~~a~~~----------~~H~~CF~C~~C~~~L~-~~~~~~-~~g~~yC~~cy~~--~~~p~   76 (79)
T 1x62_A           14 KLPMCDKCGTGIVGV---FVKLRDR----------HRHPECYVCTDCGTNLK-QKGHFF-VEDQIYCEKHARE--RVSGP   76 (79)
T ss_dssp             CCCCCSSSCCCCCSS---CEECSSC----------EECTTTTSCSSSCCCHH-HHCCEE-SSSCEECHHHHHH--HHSSC
T ss_pred             CCCccccCCCCccCc---EEEECcc----------eeCcCcCeeCCCCCCCC-CCCeEe-ECCEEECHHHHHH--HhCCC
Confidence            367999999999974   5777776          46999999999999994 455775 6899999999987  55665


Q ss_pred             CC
Q 014080          298 CQ  299 (431)
Q Consensus       298 C~  299 (431)
                      +.
T Consensus        77 g~   78 (79)
T 1x62_A           77 SS   78 (79)
T ss_dssp             CC
T ss_pred             CC
Confidence            54

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

Probab=98.74  E-value=4.6e-09  Score=90.72  Aligned_cols=62  Identities=18%  Similarity=0.222  Sum_probs=51.3

Q ss_pred             cccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccC-CCCceEEccCCcccCcchhhc
Q 014080          216 EQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEP-RDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       216 ~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~-~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      ..+.++|.+|+++|.+..  ++.+.++          .||..||+|..|++.|. .|..|+. .+|++||..||.+
T Consensus        58 ~~~~~~C~~C~~~I~~~~--~v~a~~~----------~wH~~CF~C~~C~~~L~~~g~~f~~-~dg~~yC~~cy~~  120 (123)
T 2l4z_A           58 GLSWKRCAGCGGKIADRF--LLYAMDS----------YWHSRCLKCSSCQAQLGDIGTSSYT-KSGMILCRNDYIR  120 (123)
T ss_dssp             CSSCSBBSSSSSBCCSSS--EEEETTE----------EEETTTSBCTTTCCBGGGTTCCCBC-SSSCCBCHHHHHH
T ss_pred             CccCCcCcCCCCCcCCcE--EEEeCCc----------EEcccccCcCcCCCcccccCCceEE-ECCEEeCHHHhhh
Confidence            356789999999999753  5777777          46999999999999996 3567774 7999999999986

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

Probab=98.72  E-value=1e-08  Score=81.98  Aligned_cols=63  Identities=22%  Similarity=0.358  Sum_probs=48.8

Q ss_pred             CcccccCCCccccCCcceEEEecccccccccCCCcccCCCCccCCCCCccCCCCceEE-ccCCcccCcchhhcccCCCC
Q 014080          219 HPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTPRCCSCERMEPRDTKYLS-LDDGRKLCLECLDSAIMDTH  296 (431)
Q Consensus       219 ~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF~C~~C~r~l~~g~~f~~-l~dG~~yC~~C~~~~v~~~~  296 (431)
                      .++|..|+++|...+  .+.+.++          .||..||+|..|++.|. +..|+. ..+|++||..||.+  ++.+
T Consensus        15 ~~~C~~C~~~I~~~e--~v~a~~~----------~wH~~CF~C~~C~~~L~-~~~~~~~~~~g~~yC~~~y~~--~~~~   78 (82)
T 2co8_A           15 GDLCALCGEHLYVLE--RLCVNGH----------FFHRSCFRCHTCEATLW-PGGYEQHPGDGHFYCLQHLPQ--TDSG   78 (82)
T ss_dssp             SCBCSSSCCBCCTTT--BCCBTTB----------CCBTTTCBCSSSCCBCC-TTSEECCTTTCCCEETTTCCC--CCCC
T ss_pred             CCCCcccCCCcccce--EEEECCC----------eeCCCcCEEcCCCCCcC-CCceeEeCcCCEEEChHHHHh--hhcC
Confidence            568999999997543  4556666          46999999999999994 445553 36899999999987  4444

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

Probab=97.17  E-value=9.8e-05  Score=48.39  Aligned_cols=29  Identities=31%  Similarity=0.881  Sum_probs=27.0

Q ss_pred             CCcCCCCCcccccCceEeecCccccCCCc
Q 014080          159 YRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       159 ~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      .+.|..|++.|+..+.+.+.|+.||..||
T Consensus         3 ~~~C~~C~k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            3 NPNCARCGKIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             CCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCcCCccCCEEecceeEEECCeEecccCC
Confidence            46899999999989999999999999998

>1q0v_A Hydrophilic protein; has cysteine rich putative zinc finger esential for function;...; stable, non-interacting alpha-helices; NMR {Saccharomyces cerevisiae} SCOP: j.105.1.1 PDB: 1q0w_A

Probab=85.51  E-value=0.98  Score=35.80  Aligned_cols=18  Identities=44%  Similarity=0.427  Sum_probs=15.4

Q ss_pred             CCChhHHHHHHHhhhhhh
Q 014080           39 GFDNEEIDRAIALSLVEV   56 (431)
Q Consensus        39 ~~~~~~~~~~~~~~~~~~   56 (431)
                      +.+.|||.|||+|||-|.
T Consensus         9 ~~eDeDLkrAieLSL~Es   26 (81)
T 1q0v_A            9 EDEEELIRKAIELSLKES   26 (81)
T ss_dssp             SSHHHHHHHHHHHHHHCC
T ss_pred             cCchHHHHHHHHHhHHHH
Confidence            567899999999999664

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

Probab=85.38  E-value=0.21  Score=32.26  Aligned_cols=29  Identities=10%  Similarity=0.239  Sum_probs=21.4

Q ss_pred             CcccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          219 HPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       219 ~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      .++|..|++.+...+  .+.+.++.          ||..||
T Consensus         3 ~~~C~~C~k~Vy~~E--k~~~~g~~----------~Hk~CF   31 (31)
T 1zfo_A            3 NPNCARCGKIVYPTE--KVNCLDKF----------WHKACF   31 (31)
T ss_dssp             CCBCSSSCSBCCGGG--CCCSSSSC----------CCGGGC
T ss_pred             CCcCCccCCEEecce--eEEECCeE----------ecccCC
Confidence            468999999998753  45667765          477776

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=83.66  E-value=0.14  Score=42.80  Aligned_cols=104  Identities=17%  Similarity=0.377  Sum_probs=65.2

Q ss_pred             cccCCCCCCCCCc------ceeecCCccccccccccc--cCcccccCCCccccCCcceEEEecccccccccCCCcccCCC
Q 014080          187 FRCHSCNLPITDV------EFSMSGNRPYHKHCYKEQ--HHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGT  258 (431)
Q Consensus       187 F~C~~C~~~L~~~------~F~~~dg~pyC~~CY~~~--f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~C  258 (431)
                      +.|..|...+...      .....=|..||..|..+.  ....|..|.+.+....  +. ...            ....-
T Consensus         8 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~--l~-~l~------------i~~~~   72 (133)
T 4ap4_A            8 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKR--YH-PIY------------IGSGT   72 (133)
T ss_dssp             CBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTCSBCTTTCCBCTTTC--EE-ECB------------CSSSS
T ss_pred             CCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhCCCCCCCCCcCcccc--cc-ccc------------cCCCC
Confidence            5666666555321      133345678888887654  3458999999998753  21 111            12234


Q ss_pred             CccCCCCCccCC----CCceEEccCCcccCcchhhcccCCCCCCCcccHHH
Q 014080          259 PRCCSCERMEPR----DTKYLSLDDGRKLCLECLDSAIMDTHECQPLYLEI  305 (431)
Q Consensus       259 F~C~~C~r~l~~----g~~f~~l~dG~~yC~~C~~~~v~~~~~C~~C~~~I  305 (431)
                      ..|..|...+..    +...+...=|..+|..|..+-+.....|--|..+|
T Consensus        73 ~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~  123 (133)
T 4ap4_A           73 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKI  123 (133)
T ss_dssp             CBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBC
T ss_pred             CCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcC
Confidence            679999876532    22234556789999999977555566788787655

---

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	431
d2dara2	45	g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, En	7e-04
d1x3ha1	35	g.39.1.3 (A:8-42) Leupaxin {Human (Homo sapiens) [	0.002

>d2dara2 g.39.1.3 (A:8-52) PDZ and LIM domain protein 5, Enigma {Human (Homo sapiens) [TaxId: 9606]} Length = 45

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

 Score = 35.1 bits (81), Expect = 7e-04
 Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 1/27 (3%)

Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECF 187
           +CA CN  I  G +L  +   WHPE F
Sbjct: 20  MCAHCNQVI-RGPFLVALGKSWHPEEF 45

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

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

 Score = 33.8 bits (78), Expect = 0.002
 Identities = 14/27 (51%), Positives = 16/27 (59%), Gaps = 1/27 (3%)

Query: 161 ICAGCNTEIGHGRYLSCMEAFWHPECF 187
            C GCN  +    YLS M+  WHPECF
Sbjct: 10  KCGGCNRPVL-ENYLSAMDTVWHPECF 35

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	431
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.5
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.38
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.34
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.29
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.26
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.07
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.99
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.95
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	97.94
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	97.77
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.75
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	97.7
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	97.67
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	97.59
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	97.57
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.55
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	97.53
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	97.5
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	97.5
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.48
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	97.47
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.28
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.25
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	97.24
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.22
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.18
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	97.16
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.16
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	97.15
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.12
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	97.04
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.0
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.97
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	96.94
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	96.88
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	96.86
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	96.86
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	96.85
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	96.82
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	96.8
d2co8a2	36	Nedd9 interacting protein with calponin homology,	96.69
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.59
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	96.59
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	96.58
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	96.53
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.49
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.47
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.47
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.44
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	96.24
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	96.14
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	96.1
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	96.1
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	96.01
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	95.98
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	95.85
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.82
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	95.82
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	95.72
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.68
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	95.58
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	95.54
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	95.45
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	95.22
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	95.03
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	94.96
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	94.9
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	94.88
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	94.87
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	94.83
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	94.69
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	94.69
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	94.41
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	94.37
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	94.31
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	94.06
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	94.02
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	93.7
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	93.52
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	93.4
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	93.39
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	93.17
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	93.03
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	93.03
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	92.65
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	92.19
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	92.0
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	91.91
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	91.57
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	89.91
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	89.67
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	89.61
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	89.57
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	89.4
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	88.96
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	87.65
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	87.62
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	87.5
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	87.41
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	87.04
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	86.69
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	86.44
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	86.42
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	86.24
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	86.04
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	85.17
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	84.51
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	83.29
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	83.06
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	82.88
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	82.7
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	82.68
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	82.29
d2co8a2	36	Nedd9 interacting protein with calponin homology,	81.58
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	80.86

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

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

Probab=98.50  E-value=3e-08  Score=65.57  Aligned_cols=31  Identities=45%  Similarity=0.990  Sum_probs=28.8

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      ....++|++|+++| .|++|+|+|+.|||+||
T Consensus         5 ~~fapkC~~C~~~I-~g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           5 AMFSPKCGGCNRPV-LENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CCCSCBCTTTCCBC-CSSCEEETTEEECTTTC
T ss_pred             HHhChhhhhcCCcc-cchheeecCCccCcccC
Confidence            45789999999999 59999999999999998

>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=98.38  E-value=2.9e-08  Score=65.64  Aligned_cols=34  Identities=24%  Similarity=0.436  Sum_probs=33.0

Q ss_pred             cccCCCCCCCCCcceeecCCccccccccccccCc
Q 014080          187 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHP  220 (431)
Q Consensus       187 F~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~p  220 (431)
                      |+|+.|+++|.+..|+.++|+|||+.||+++|+|
T Consensus         1 F~C~~C~~~f~~~~F~e~~G~pYCe~~Y~~lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP   34 (35)
T ss_dssp             CCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCC
T ss_pred             CCCCCCcCCCCCCCeEEECCEecChHhHHhhcCC
Confidence            7999999999999999999999999999999987

>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=98.34  E-value=1.5e-07  Score=64.85  Aligned_cols=31  Identities=39%  Similarity=0.780  Sum_probs=28.2

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      ....++|+.|+++| .|++|.|||+.|||+||
T Consensus        15 ~~r~P~C~~C~~pI-~g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          15 GKRTPMCAHCNQVI-RGPFLVALGKSWHPEEF   45 (45)
T ss_dssp             TTCCCBBSSSCCBC-CSCEEEETTEEECTTTC
T ss_pred             CCCCeeccccCCcc-cCceeeecCCccCcCCC
Confidence            34568999999999 69999999999999998

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

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

Probab=98.26  E-value=2e-07  Score=61.53  Aligned_cols=35  Identities=14%  Similarity=0.179  Sum_probs=30.9

Q ss_pred             cccccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          212 HCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       212 ~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      .+|.++|+|+|.+|+++|.++   +|++.++.          ||+.||
T Consensus         1 ~DY~~~fapkC~~C~~~I~g~---~v~Al~~~----------wHpeCF   35 (35)
T d1x3ha1           1 KDFLAMFSPKCGGCNRPVLEN---YLSAMDTV----------WHPECF   35 (35)
T ss_dssp             CCCCCCCSCBCTTTCCBCCSS---CEEETTEE----------ECTTTC
T ss_pred             CcHHHHhChhhhhcCCcccch---heeecCCc----------cCcccC
Confidence            479999999999999999986   68899885          699888

>d1u5sb1 g.39.1.3 (B:72-102) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.07  E-value=5.8e-07  Score=56.76  Aligned_cols=29  Identities=38%  Similarity=0.802  Sum_probs=26.5

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCC
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPEC  186 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~C  186 (431)
                      .+.++|+.|++|| .++++++|++.|||++
T Consensus         3 mg~p~C~~C~~PI-~~~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           3 MGVPICGACRRPI-EGRVVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCCEETTTTEEC-CSCEECCTTSBEETTT
T ss_pred             cCCcchhhcCCch-hhhHhhhhccccCCCC
Confidence            5789999999999 5999999999999975

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

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

Probab=97.99  E-value=1.3e-06  Score=56.52  Aligned_cols=35  Identities=23%  Similarity=0.704  Sum_probs=31.4

Q ss_pred             cccccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          212 HCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       212 ~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      +||.++|+++|..|+++|+..   .|.|++.||          |..||
T Consensus         1 PCyE~kfa~~C~~Ckk~It~G---GvtY~dqpW----------HkeCF   35 (35)
T d2cuqa2           1 PCYENKFAPRCARCSKTLTQG---GVTYRDQPW----------HRECL   35 (35)
T ss_dssp             CCCCCCSSCCCTTTCCCCCSC---CEESSSSEE----------CTTTC
T ss_pred             CchHHHHHHHHhhcCCccccC---ceeecCCcc----------hhhhC
Confidence            589999999999999999964   599999994          88887

>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=97.95  E-value=1.3e-06  Score=61.48  Aligned_cols=41  Identities=22%  Similarity=0.404  Sum_probs=37.9

Q ss_pred             ccCCCCCCCCCcceeecCCccccccccccccCcccccCCCc
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNF  228 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~  228 (431)
                      +|..|++.|.+.....++++|||+.||.++|+|++...+..
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~g~G~g   41 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQG   41 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCccCcccC
Confidence            69999999999899999999999999999999999988754

>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=97.94  E-value=2.7e-06  Score=54.93  Aligned_cols=32  Identities=44%  Similarity=0.992  Sum_probs=29.7

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      ..++..|++|++.|..|+.+.++++.||.+||
T Consensus         5 ~~g~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           5 IRGPSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CSSCSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             ccCCccccccchhhhCCceeeeeecceeeeeC
Confidence            35778999999999999999999999999998

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

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

Probab=97.77  E-value=5.9e-06  Score=54.76  Aligned_cols=37  Identities=22%  Similarity=0.419  Sum_probs=32.0

Q ss_pred             cccccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          212 HCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       212 ~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      .||.+.|+++|..|+++|... +..++|+++          |||..||
T Consensus         1 kCy~~~~a~~C~~C~k~I~~G-~k~veykg~----------~WHe~CF   37 (37)
T d1x63a1           1 KCTTREDSPKCKGCFKAIVAG-DQNVEYKGT----------VWHKDCF   37 (37)
T ss_dssp             CCCSCCCSCBCSSSCCBCCSS-SCEEECSSC----------EEETTTC
T ss_pred             CccccccCcccccCCCccCCC-CeEeEeCCc----------cchhccC
Confidence            489999999999999999875 356888887          6899998

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.75  E-value=1.1e-05  Score=52.39  Aligned_cols=31  Identities=35%  Similarity=0.750  Sum_probs=28.0

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      ......|..|+++| ..+++.|+|+.|||.||
T Consensus         5 ~~tlEkC~~C~~~I-~driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           5 VATLEKCATCSQPI-LDRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CSSCCBCTTTCCBC-CSCCEEETTEEECTTTC
T ss_pred             HHHHHHHHHhchHH-HHHHHHHhCCCCCCCCC
Confidence            44678999999999 48999999999999998

>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=97.70  E-value=4.3e-06  Score=53.25  Aligned_cols=32  Identities=16%  Similarity=0.497  Sum_probs=29.7

Q ss_pred             ccCCCCCCCCCcceeecCCccccccccccccC
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH  219 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~  219 (431)
                      .|..|+++|+++.|..++++|||..||..+|+
T Consensus         1 ~C~~C~~~L~GQry~~rd~~PyC~~Cf~~lfA   32 (32)
T d2d8za2           1 VCTACRKQLSGQRFTARDDFAYCLNCFCDLYA   32 (32)
T ss_dssp             BCSSSCCBCTTSCCEESSSSEECHHHHHHHTC
T ss_pred             CcccCCccccCceeeecCCCeehHHhhHhhcC
Confidence            48899999999999999999999999998774

>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=97.67  E-value=4.4e-06  Score=56.84  Aligned_cols=34  Identities=24%  Similarity=0.431  Sum_probs=32.1

Q ss_pred             ccCCCCCCCCCcceeecCCccccccccccccCcc
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPK  221 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pk  221 (431)
                      +|..|++.|+...|...+|.+||++||.++|.++
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~k   34 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSK   34 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhh
Confidence            6999999999999999999999999999999876

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

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

Probab=97.59  E-value=1.9e-05  Score=52.20  Aligned_cols=32  Identities=28%  Similarity=0.686  Sum_probs=28.8

Q ss_pred             CCCCCcCCCCCcccccC-ceEeecCccccCCCc
Q 014080          156 FSGYRICAGCNTEIGHG-RYLSCMEAFWHPECF  187 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g-~~v~algk~wHp~CF  187 (431)
                      ...++.|.+|+++|..| +.|.+.|+.||..||
T Consensus         5 ~~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           5 REDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             cccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            34678999999999887 789999999999998

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LASP-1
domain: LASP-1
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=97.57  E-value=8.3e-06  Score=50.51  Aligned_cols=29  Identities=31%  Similarity=0.881  Sum_probs=27.1

Q ss_pred             CCcCCCCCcccccCceEeecCccccCCCc
Q 014080          159 YRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       159 ~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      .+.|++|++.+++.+.++++++.||..||
T Consensus         2 n~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           2 NPNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CCBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CCcccccCCccccHHHhhhhHHHHhhccC
Confidence            36799999999999999999999999998

>d2cuqa1 g.39.1.3 (A:43-74) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.55  E-value=9.6e-06  Score=51.02  Aligned_cols=32  Identities=25%  Similarity=0.704  Sum_probs=29.6

Q ss_pred             ccCCCCCCCCCcceeecCCccccccccccccC
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH  219 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~  219 (431)
                      .|..|+++|+++.|..++..|||..||.++|+
T Consensus         1 vCt~Ck~~LaGqrFTSrde~pYC~~Cfg~LfA   32 (32)
T d2cuqa1           1 VCTGCQTPLAGQQFTSRDEDPYCVACFGELFA   32 (32)
T ss_dssp             BCSSSCCBCTTCCEEECSSSEEEHHHHHHHTT
T ss_pred             CccccCccccCCccccCCCCccHHHHhHhhcC
Confidence            48999999999999999999999999988774

>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=97.53  E-value=1.3e-05  Score=55.60  Aligned_cols=36  Identities=25%  Similarity=0.576  Sum_probs=33.0

Q ss_pred             ccCCCCCCCCCcceeecCCcccc-ccccccccCcccc
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYH-KHCYKEQHHPKCD  223 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC-~~CY~~~f~pkC~  223 (431)
                      +|..|++.|.+.....++++||| +.||..+|+|+=.
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FGPkG~   37 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGF   37 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCS
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccCCCcc
Confidence            68999999999999999999999 8899999999743

>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=97.50  E-value=1.1e-05  Score=51.56  Aligned_cols=31  Identities=19%  Similarity=0.443  Sum_probs=28.6

Q ss_pred             ccCCCCCCCCCcceeecCCcccccccccccc
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQH  218 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f  218 (431)
                      +|..|.+|+.+..|+..+|+|||+.+|+++.
T Consensus         1 VC~~C~~PF~~~~Fy~~~g~PyCe~HyH~~~   31 (32)
T d1x3ha2           1 VCGDCFTSFSTGSFFELDGRPFCELHYHHRR   31 (32)
T ss_dssp             BCSSSCCBSCSSCCEESSSCEECHHHHHHHH
T ss_pred             CcCccCCcCCCCCeEeECCccchHHhhhhhc
Confidence            5899999999999999999999999998764

>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=97.50  E-value=2.8e-05  Score=48.66  Aligned_cols=29  Identities=21%  Similarity=0.553  Sum_probs=27.0

Q ss_pred             CCcCCCCCcccccCceEeecCccccCCCc
Q 014080          159 YRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       159 ~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      .+.|++|+++++..+.+.++|+.||..|+
T Consensus         2 ~~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           2 ASKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CCBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CCcCCCCCCceeeHHhhccCCcccccccC
Confidence            46899999999999999999999999985

>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=97.48  E-value=6.7e-05  Score=50.85  Aligned_cols=37  Identities=24%  Similarity=0.550  Sum_probs=32.0

Q ss_pred             CCCCCCCCCCCcCCCCCcccccCceEeecCccccCCCc
Q 014080          150 FQPFPFFSGYRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       150 ~~p~~~~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      ..+....+..+.|.+|+..| .|.++++.++.+||+||
T Consensus         9 ~~~~~~~QkLP~CdkCg~GI-VG~~VK~rDK~rHPeCf   45 (45)
T d1x64a1           9 HGGAGSAQRMPLCDKCGSGI-VGAVVKARDKYRHPECF   45 (45)
T ss_dssp             CCCCSCCCSCCBCTTTCCBC-CSCCEESSSCEECTTTC
T ss_pred             CCCCCccccCccccccCCCc-EEEEEEeccccCCCCCC
Confidence            34444577889999999999 59999999999999998

>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=97.47  E-value=1.6e-05  Score=49.90  Aligned_cols=31  Identities=26%  Similarity=0.640  Sum_probs=27.7

Q ss_pred             ccCCCCCCCCCcceeecCCccccccccccccC
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH  219 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~  219 (431)
                      +|..|++.|.+ +|..++|.|||+.+|+.+|+
T Consensus         1 kC~~C~~vL~g-EYm~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVILTG-EYISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBCSS-CCEEETTEEECTTHHHHHTT
T ss_pred             CccccCccccc-eeecCCCCcccHHHHHHhcC
Confidence            58999999987 78889999999999998875

>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=97.28  E-value=9.6e-05  Score=50.48  Aligned_cols=31  Identities=23%  Similarity=0.557  Sum_probs=28.8

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCc
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      .+...|..|++.++..+.+.+.|+.||..||
T Consensus        13 g~~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          13 GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCCEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             CCCCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            4668999999999999999999999999998

>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=97.25  E-value=2.3e-05  Score=48.31  Aligned_cols=30  Identities=27%  Similarity=0.702  Sum_probs=28.0

Q ss_pred             cccCCCCCCCCCcceeecCCcccccccccc
Q 014080          187 FRCHSCNLPITDVEFSMSGNRPYHKHCYKE  216 (431)
Q Consensus       187 F~C~~C~~~L~~~~F~~~dg~pyC~~CY~~  216 (431)
                      |+|+.|++.|.+.....++|.+||+.||.+
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeeeec
Confidence            899999999999999999999999999964

>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=97.24  E-value=3.6e-05  Score=48.50  Aligned_cols=32  Identities=19%  Similarity=0.495  Sum_probs=29.1

Q ss_pred             ccCCCCCCCCCcceeecCCccccccccccccC
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH  219 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~  219 (431)
                      .|+.|+.+|.+.+|....|.+||+.||.+.|+
T Consensus         1 nCa~C~~sL~d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           1 NCAHCKNTMAYIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             BCSSSCCBCSSSCBEESSSCEECHHHHHHHTS
T ss_pred             CcccccccHhhcceeeecCcEeHHHHHHHhcC
Confidence            38999999999999999999999999988653

>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=97.22  E-value=0.0001  Score=46.12  Aligned_cols=28  Identities=32%  Similarity=1.080  Sum_probs=24.4

Q ss_pred             CCcCCCCCcccccCceEeecCccccCCC
Q 014080          159 YRICAGCNTEIGHGRYLSCMEAFWHPEC  186 (431)
Q Consensus       159 ~~~C~~C~k~I~~g~~v~algk~wHp~C  186 (431)
                      ...|++|+++|.+.-+++++++.||..|
T Consensus         3 ~~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           3 LLTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             CcccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            4579999999976667899999999987

>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=97.18  E-value=8.1e-05  Score=46.71  Aligned_cols=28  Identities=36%  Similarity=0.997  Sum_probs=24.6

Q ss_pred             CcCCCCCcccccCceEeecCccccCCCc
Q 014080          160 RICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       160 ~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      ..|++|+++|.+.-+++++++.||..|+
T Consensus         3 ~~CaGC~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           3 KRCAGCGGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CBBTTTCCBCCCSEEEEETTEEECGGGC
T ss_pred             cccCCCCCccchhhhhccchhhhhhhhC
Confidence            5799999999766678999999999884

>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=97.16  E-value=5.1e-05  Score=48.32  Aligned_cols=34  Identities=18%  Similarity=0.371  Sum_probs=31.8

Q ss_pred             cccCCCCCCCCCcceeecCCccccccccccccCc
Q 014080          187 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHP  220 (431)
Q Consensus       187 F~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~p  220 (431)
                      |+|+.|.+|+-+...+.+.|..||+.+|+++|+.
T Consensus         1 FvCA~CekPF~G~rhyE~~g~ayCe~Hy~qLfg~   34 (35)
T d1u5sb2           1 FVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGD   34 (35)
T ss_dssp             CBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSC
T ss_pred             CcccccCCccCCchhhhhcCchHHHHHHHHHhcc
Confidence            7899999999999999999999999999999874

>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=97.16  E-value=4.4e-05  Score=56.39  Aligned_cols=38  Identities=24%  Similarity=0.516  Sum_probs=34.2

Q ss_pred             ccCCCCCCCCCcceeecCCccccccccccccCcccccC
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVC  225 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C  225 (431)
                      .|..|++.|.+..+..+++.|||+.||.++|+|+=..=
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG~G~   38 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGK   38 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCcccc
Confidence            48899999999999999999999999999999986543

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.15  E-value=4.1e-05  Score=50.10  Aligned_cols=34  Identities=21%  Similarity=0.402  Sum_probs=28.5

Q ss_pred             CccCCCCCccCCCCceEEccCCcccCcchhhcccCCCC
Q 014080          259 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTH  296 (431)
Q Consensus       259 F~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~  296 (431)
                      |+|+.|+++|. +..|++ .+|++||..||..  +++|
T Consensus         1 F~C~~C~~~f~-~~~F~e-~~G~pYCe~~Y~~--lFAP   34 (35)
T d1g47a2           1 FVCAQCFQQFP-EGLFYE-FEGRKYCEHDFQM--LFAP   34 (35)
T ss_dssp             CCCTTTCCCCG-GGCSEE-ETTEEECHHHHHH--HCCC
T ss_pred             CCCCCCcCCCC-CCCeEE-ECCEecChHhHHh--hcCC
Confidence            78999999995 566775 6999999999998  6665

>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=97.12  E-value=0.00014  Score=46.26  Aligned_cols=31  Identities=29%  Similarity=0.717  Sum_probs=28.3

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      .+..+.|.+|+..| .|.++++.++.+||+||
T Consensus         5 ~qklp~CdkCg~GI-VG~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           5 AQKLPMCDKCGTGI-VGVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCCCCSSSCCCC-CSSCEECSSCEECTTTT
T ss_pred             cccCccccccCCCc-EeEEEEeccccCCCCCC
Confidence            35678999999999 59999999999999998

>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=97.04  E-value=0.00011  Score=46.56  Aligned_cols=29  Identities=21%  Similarity=0.650  Sum_probs=25.9

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .|..|+++| .|++|++ .|+++||..||.+
T Consensus         1 ~C~~C~~~L-~GQry~~-rd~~PyC~~Cf~~   29 (32)
T d2d8za2           1 VCTACRKQL-SGQRFTA-RDDFAYCLNCFCD   29 (32)
T ss_dssp             BCSSSCCBC-TTSCCEE-SSSSEECHHHHHH
T ss_pred             CcccCCccc-cCceeee-cCCCeehHHhhHh
Confidence            488999999 7899885 8999999999987

>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=97.00  E-value=0.00016  Score=44.42  Aligned_cols=26  Identities=46%  Similarity=1.127  Sum_probs=22.8

Q ss_pred             CCCCCccccc---CceEeecCccccCCCc
Q 014080          162 CAGCNTEIGH---GRYLSCMEAFWHPECF  187 (431)
Q Consensus       162 C~~C~k~I~~---g~~v~algk~wHp~CF  187 (431)
                      |++|.+||.-   +.+|+..++.||..||
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            8999999942   2889999999999998

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.97  E-value=0.00019  Score=48.11  Aligned_cols=30  Identities=17%  Similarity=0.430  Sum_probs=26.3

Q ss_pred             cccccccCcccccCCCccccCCcceEEEecccc
Q 014080          212 HCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPF  244 (431)
Q Consensus       212 ~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pf  244 (431)
                      .+|+++|+.+|..|+++|++.   ++.+.++.|
T Consensus         8 ~DYq~~fG~~C~~C~~~ItG~---V~~Ag~~~y   37 (41)
T d1v6ga1           8 LDYQRLYGTRCFSCDQFIEGE---VVSALGKTY   37 (41)
T ss_dssp             SCGGGSCCCBCTTTCCBCCSC---CEEETTEEE
T ss_pred             ccHHHHhCcccccccCEeeee---eeEecCccc
Confidence            579999999999999999986   688888854

>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=96.94  E-value=0.00012  Score=46.19  Aligned_cols=32  Identities=34%  Similarity=0.755  Sum_probs=29.5

Q ss_pred             ccCCCCCCCCCcceeecCCccccccccccccC
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH  219 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~  219 (431)
                      .|..|..||+.+.|..+++..||-.||.++|+
T Consensus         1 ~C~~C~qPIGtksfipk~~~~yCvpCyE~kfA   32 (32)
T d1x4ka1           1 ICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA   32 (32)
T ss_dssp             CCSSSCCCCCSSSEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCcccccccccCCCCceEeecchhhcC
Confidence            38899999999999999999999999998774

>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=96.88  E-value=0.00013  Score=45.95  Aligned_cols=32  Identities=22%  Similarity=0.581  Sum_probs=29.4

Q ss_pred             ccCCCCCCCCCcceeecCCccccccccccccC
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQHH  219 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~  219 (431)
                      .|..|..||+.+.|..+++..||-.||..+|+
T Consensus         1 ~C~~C~qPIGtkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           1 LCSGCEQPLGSRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             BCTTTCCBTTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcccccCcccccccccCCCcEEEEeccccccC
Confidence            48899999999999999999999999998774

>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=96.86  E-value=0.00033  Score=45.56  Aligned_cols=30  Identities=20%  Similarity=0.469  Sum_probs=28.2

Q ss_pred             CCCcCCCCCcccccCceEeecCccccCCCc
Q 014080          158 GYRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       158 ~~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      ....|..|++.++.-+.+.+.|+.||..||
T Consensus         6 ~~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           6 ARETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CCcccccCCCEEeeeeeEecCCeehhhccC
Confidence            567999999999989999999999999998

>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=96.86  E-value=0.00041  Score=44.63  Aligned_cols=31  Identities=23%  Similarity=0.492  Sum_probs=26.6

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      ..++..|..|+++|.. .-|...++.||.+||
T Consensus         5 ~kfa~~C~~Ckk~It~-GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           5 NKFAPRCARCSKTLTQ-GGVTYRDQPWHRECL   35 (35)
T ss_dssp             CCSSCCCTTTCCCCCS-CCEESSSSEECTTTC
T ss_pred             HHHHHHHhhcCCcccc-CceeecCCcchhhhC
Confidence            4578899999999964 457888999999998

>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=96.85  E-value=0.0003  Score=42.23  Aligned_cols=26  Identities=35%  Similarity=0.873  Sum_probs=24.3

Q ss_pred             CCCCCcccccC-ceEeecCccccCCCc
Q 014080          162 CAGCNTEIGHG-RYLSCMEAFWHPECF  187 (431)
Q Consensus       162 C~~C~k~I~~g-~~v~algk~wHp~CF  187 (431)
                      |..|.+.|.+| +.+...|..||..||
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            88999999998 779999999999998

>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=96.82  E-value=0.00018  Score=45.38  Aligned_cols=32  Identities=19%  Similarity=0.562  Sum_probs=28.7

Q ss_pred             ccCCCCCCCCCcceeecCCccccc-cccccccC
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHK-HCYKEQHH  219 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~-~CY~~~f~  219 (431)
                      +|..|++.|....+..++|+|||. +||..+|+
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCCCCccccCCCcCcCcchHHhhcC
Confidence            589999999999999999999996 59988774

>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=96.69  E-value=0.00045  Score=45.12  Aligned_cols=31  Identities=26%  Similarity=0.504  Sum_probs=28.6

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCc
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      .+...|..|++.++.-+.+.+.|+.||..||
T Consensus         6 g~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           6 GAGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CSSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CCCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            3568999999999988999999999999998

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.59  E-value=0.00062  Score=45.57  Aligned_cols=30  Identities=27%  Similarity=0.552  Sum_probs=28.0

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCC
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPEC  186 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~C  186 (431)
                      ..+...|..|++.| .|+++.|.++.|||.|
T Consensus        12 ~~fG~~C~~C~~~I-tG~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          12 RLYGTRCFSCDQFI-EGEVVSALGKTYHPDC   41 (41)
T ss_dssp             GSCCCBCTTTCCBC-CSCCEEETTEEECTTT
T ss_pred             HHhCcccccccCEe-eeeeeEecCcccCCCC
Confidence            56889999999999 6999999999999998

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

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

Probab=96.58  E-value=0.00037  Score=42.64  Aligned_cols=26  Identities=31%  Similarity=1.030  Sum_probs=22.5

Q ss_pred             CCCCCccccc---CceEeecCccccCCCc
Q 014080          162 CAGCNTEIGH---GRYLSCMEAFWHPECF  187 (431)
Q Consensus       162 C~~C~k~I~~---g~~v~algk~wHp~CF  187 (431)
                      |..|.+||.-   ..+|+..++.||.+||
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            8899999942   2789999999999998

>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=96.53  E-value=0.00058  Score=40.87  Aligned_cols=26  Identities=35%  Similarity=0.873  Sum_probs=24.0

Q ss_pred             CCCCCcccccC-ceEeecCccccCCCc
Q 014080          162 CAGCNTEIGHG-RYLSCMEAFWHPECF  187 (431)
Q Consensus       162 C~~C~k~I~~g-~~v~algk~wHp~CF  187 (431)
                      |..|.+.|.+| +.+...|..||..||
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            88999999998 778999999999998

>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=96.49  E-value=0.00076  Score=43.49  Aligned_cols=34  Identities=21%  Similarity=0.484  Sum_probs=27.8

Q ss_pred             cccccccCcccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          212 HCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       212 ~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      .||.. ...+|.+|+++|...   ++.+.+++|          |++||
T Consensus         2 ~Cy~~-tlEkC~~C~~~I~dr---iLrA~Gk~y----------HP~CF   35 (35)
T d2dloa1           2 GCYVA-TLEKCATCSQPILDR---ILRAMGKAY----------HPGCF   35 (35)
T ss_dssp             CCCCS-SCCBCTTTCCBCCSC---CEEETTEEE----------CTTTC
T ss_pred             hhHHH-HHHHHHHhchHHHHH---HHHHhCCCC----------CCCCC
Confidence            56654 467999999999975   789999985          88888

>d1x6aa2 g.39.1.3 (A:42-75) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.47  E-value=0.00054  Score=43.47  Aligned_cols=32  Identities=19%  Similarity=0.458  Sum_probs=30.0

Q ss_pred             CccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          259 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       259 F~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      |.|.+|+.++..|+.|..++..++||..||..
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy~~   32 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCHNE   32 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecchhc
Confidence            78999999999999999999999999999975

>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=96.47  E-value=0.00024  Score=43.70  Aligned_cols=30  Identities=23%  Similarity=0.561  Sum_probs=24.2

Q ss_pred             CccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          259 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       259 F~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      |+|+.|++.|..  .-+..+||.+||..||.+
T Consensus         1 frca~cgk~les--tt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLES--TTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEECS--SCSEEETTEEECHHHHHH
T ss_pred             CccccccCcccc--ceeeccCCcEEEeeeeec
Confidence            789999998833  235568999999999975

>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=96.44  E-value=0.00044  Score=42.85  Aligned_cols=29  Identities=24%  Similarity=0.647  Sum_probs=27.1

Q ss_pred             ccCCCCCCCCCcceeecCCcccccccccc
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKE  216 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~  216 (431)
                      .|..|+++|++..|...+++.||-.||+.
T Consensus         1 vC~~C~K~Lag~rFTa~eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKLAGQRFTAVEDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBCTTSCEEECSSCEEEHHHHHH
T ss_pred             CcccccchhcCceeEEecceEEEeeeecc
Confidence            48999999999999999999999999974

>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=96.24  E-value=0.00025  Score=45.08  Aligned_cols=26  Identities=31%  Similarity=0.406  Sum_probs=22.9

Q ss_pred             cCCcCCccCCcccCCcccccccceeee
Q 014080          335 EGEKNGHHHLPETRGLCLSEEQTVTTV  361 (431)
Q Consensus       335 ~~e~~g~~~~~e~rGl~~~E~~~~~~~  361 (431)
                      +++|.|+.|| |+.|++|||.||+..+
T Consensus         7 ekPF~G~rhy-E~~g~ayCe~Hy~qLf   32 (35)
T d1u5sb2           7 EKPFLGHRHY-ERKGLAYCETHYNQLF   32 (35)
T ss_dssp             CCBCSSSCCE-EETTEEECHHHHHHHC
T ss_pred             CCccCCchhh-hhcCchHHHHHHHHHh
Confidence            6788999998 9999999999998654

>d1a7ia2 g.39.1.3 (A:36-67) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=96.14  E-value=0.00056  Score=42.59  Aligned_cols=31  Identities=19%  Similarity=0.537  Sum_probs=28.0

Q ss_pred             cCCCCCCCCCcceeecCCccccccccccccC
Q 014080          189 CHSCNLPITDVEFSMSGNRPYHKHCYKEQHH  219 (431)
Q Consensus       189 C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~  219 (431)
                      |-.|++.|.+.....+++.+||+.||.+.|+
T Consensus         2 C~~C~K~LdStTva~h~~eiYCKsCygkkyg   32 (32)
T d1a7ia2           2 CMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG   32 (32)
T ss_dssp             CSSSCCEECSSCCEEETTEEECSHHHHHHCC
T ss_pred             chhhhhccCcceeeeecceEEehhhccccCC
Confidence            7889999999999999999999999987664

>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=96.10  E-value=0.0012  Score=41.58  Aligned_cols=31  Identities=23%  Similarity=0.629  Sum_probs=28.6

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCCc
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      .+...|+.|.+.++..+-+.+.|+.||..||
T Consensus         5 ggg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           5 GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CCCceeccccceEeeeeeeeecCcccccccC
Confidence            3678999999999999999999999999998

>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=96.10  E-value=0.0014  Score=44.55  Aligned_cols=23  Identities=17%  Similarity=0.433  Sum_probs=20.1

Q ss_pred             cCcccccCCCccccCCcceEEEeccc
Q 014080          218 HHPKCDVCQNFIPTNSAGLIEYRAHP  243 (431)
Q Consensus       218 f~pkC~~C~~~I~~~~~~~i~~~~~p  243 (431)
                      ..|+|..|+++|.+.   +|++.++.
T Consensus        17 r~P~C~~C~~pI~g~---~vtAlgk~   39 (45)
T d2dara2          17 RTPMCAHCNQVIRGP---FLVALGKS   39 (45)
T ss_dssp             CCCBBSSSCCBCCSC---EEEETTEE
T ss_pred             CCeeccccCCcccCc---eeeecCCc
Confidence            468999999999986   79999985

>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=95.98  E-value=0.0022  Score=38.44  Aligned_cols=28  Identities=25%  Similarity=0.668  Sum_probs=26.1

Q ss_pred             CcCCCCCcccccCceEeecCccccCCCc
Q 014080          160 RICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       160 ~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      ..|+.|.+.++..+-+.+.|+.||..||
T Consensus         1 nkcg~c~ktvy~aeevqc~grsfhk~cf   28 (28)
T d1a7ia1           1 NKCGACGRTVYHAEEVQCDGRSFHRCCF   28 (28)
T ss_dssp             CBCSSSCCBCSSTTEEEETTEEEESSSE
T ss_pred             CccccccceEeeeeeeeecCceeccccC
Confidence            3699999999999999999999999998

>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=95.85  E-value=0.002  Score=40.23  Aligned_cols=29  Identities=21%  Similarity=0.621  Sum_probs=25.6

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .|..|+++| .|++|.. .|..+||..||..
T Consensus         1 vCt~Ck~~L-aGqrFTS-rde~pYC~~Cfg~   29 (32)
T d2cuqa1           1 VCTGCQTPL-AGQQFTS-RDEDPYCVACFGE   29 (32)
T ss_dssp             BCSSSCCBC-TTCCEEE-CSSSEEEHHHHHH
T ss_pred             CccccCccc-cCCcccc-CCCCccHHHHhHh
Confidence            489999999 7999886 7889999999975

>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=95.82  E-value=0.0014  Score=41.13  Aligned_cols=29  Identities=21%  Similarity=0.604  Sum_probs=24.8

Q ss_pred             CCcCCCCCcccccCce-EeecCccccCCCc
Q 014080          159 YRICAGCNTEIGHGRY-LSCMEAFWHPECF  187 (431)
Q Consensus       159 ~~~C~~C~k~I~~g~~-v~algk~wHp~CF  187 (431)
                      ...|++|++.|...+. ..+.+..||..||
T Consensus         2 ~g~Ca~C~~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3           2 SGACSACGQSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             CEECTTTCCEECTTSEEEEETTEEECGGGC
T ss_pred             CcccccccCcCChhHhheecccceeeeccC
Confidence            4579999999976655 5899999999998

>d2dloa2 g.39.1.3 (A:43-75) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.82  E-value=0.0012  Score=41.92  Aligned_cols=32  Identities=9%  Similarity=0.323  Sum_probs=28.4

Q ss_pred             ccCCCCCCCCCcceee-cCCccccccccccccC
Q 014080          188 RCHSCNLPITDVEFSM-SGNRPYHKHCYKEQHH  219 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~-~dg~pyC~~CY~~~f~  219 (431)
                      +|..|++.|.+..|.. ..+++||..+|+++|+
T Consensus         1 tCvvC~~~LDGvPFtvD~~n~i~Cv~DyHrkfA   33 (33)
T d2dloa2           1 TCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFA   33 (33)
T ss_dssp             BCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             CeeEcCcccCCCcEEEcCCCCEeehhhhhhhcC
Confidence            5889999999999986 6889999999998774

>d2cupa3 g.39.1.3 (A:8-34) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.72  E-value=0.0032  Score=37.50  Aligned_cols=26  Identities=35%  Similarity=0.986  Sum_probs=22.4

Q ss_pred             CCCCCcccccC-ceEeecCccccCCCc
Q 014080          162 CAGCNTEIGHG-RYLSCMEAFWHPECF  187 (431)
Q Consensus       162 C~~C~k~I~~g-~~v~algk~wHp~CF  187 (431)
                      |..|.+||..+ .-+...++.||..||
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            78999999654 558889999999998

>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=95.68  E-value=0.0032  Score=38.89  Aligned_cols=29  Identities=41%  Similarity=0.818  Sum_probs=26.0

Q ss_pred             CCCCcCCCCCcccccCceEeecCccccCCC
Q 014080          157 SGYRICAGCNTEIGHGRYLSCMEAFWHPEC  186 (431)
Q Consensus       157 ~~~~~C~~C~k~I~~g~~v~algk~wHp~C  186 (431)
                      .+..-|..|.+.| .|+++.+-++.|||.|
T Consensus         3 sgssgC~~C~~~I-tGkVLEAG~khYHP~C   31 (32)
T d1wiga1           3 SGSSGCDSCEKYI-TGRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCCSCSSSCCCC-SSCCBCCSSCCBCTTT
T ss_pred             Cccchhhhhhhhh-hhhhhhccccccCCCC
Confidence            3567799999999 6999999999999988

>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=95.54  E-value=0.0032  Score=38.46  Aligned_cols=28  Identities=18%  Similarity=0.304  Sum_probs=22.4

Q ss_pred             cccCCCccccCC-cceEEEecccccccccCCCcccCCCC
Q 014080          222 CDVCQNFIPTNS-AGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       222 C~~C~~~I~~~~-~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      |..|.+||++-. ..+|.+..+          |||..||
T Consensus         1 C~~C~kPItg~gg~kyisFE~R----------~WH~~CF   29 (29)
T d1x4la1           1 CAGCTNPISGLGGTKYISFEER----------QWHNDCF   29 (29)
T ss_dssp             BTTTTBCCCCSSSCSCEECSSC----------EECTTTC
T ss_pred             CCccCCcccccCCceEEEeecc----------cccccCC
Confidence            889999999853 347888777          6899998

>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=95.45  E-value=0.003  Score=38.18  Aligned_cols=27  Identities=19%  Similarity=0.537  Sum_probs=24.4

Q ss_pred             CcCCCCCcccccCceEeecCccccCCC
Q 014080          160 RICAGCNTEIGHGRYLSCMEAFWHPEC  186 (431)
Q Consensus       160 ~~C~~C~k~I~~g~~v~algk~wHp~C  186 (431)
                      .+|.+|++.++..+.|.-.|+.||..|
T Consensus         2 d~CpRC~~~VyaAEkviGaG~~WHk~C   28 (28)
T d1ibia1           2 EKCSRCGDSVYAAEKVIGAGKPWHKNC   28 (28)
T ss_dssp             EECTTTSSEESSSSCEESSSSEECSSC
T ss_pred             CcCcccchhHHHHHHHhcCCCccccCC
Confidence            479999999998888888999999987

>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=95.22  E-value=0.0032  Score=38.99  Aligned_cols=29  Identities=24%  Similarity=0.628  Sum_probs=26.4

Q ss_pred             ccCCCCCCCCCcceeecCCcccccccccc
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKE  216 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~  216 (431)
                      .|..|+..|.++.|+-.+.+.||+.||-.
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi~   29 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYVA   29 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceeee
Confidence            48899999999999999999999999953

>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=95.03  E-value=0.0041  Score=38.39  Aligned_cols=29  Identities=14%  Similarity=0.704  Sum_probs=24.7

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .|.+|.+.| .|.+|..+ +.+.||.+||..
T Consensus         1 vC~~C~K~L-ag~rFTa~-eDq~yCVdCYK~   29 (31)
T d2cura1           1 VCVTCSKKL-AGQRFTAV-EDQYYCVDCYKN   29 (31)
T ss_dssp             BCTTTCCBC-TTSCEEEC-SSCEEEHHHHHH
T ss_pred             Ccccccchh-cCceeEEe-cceEEEeeeecc
Confidence            489999999 78999876 559999999975

>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=94.96  E-value=0.004  Score=37.95  Aligned_cols=28  Identities=18%  Similarity=0.270  Sum_probs=22.2

Q ss_pred             cccCCCccccCC-cceEEEecccccccccCCCcccCCCC
Q 014080          222 CDVCQNFIPTNS-AGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       222 C~~C~~~I~~~~-~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      |..|.+||++-. ..+|.+..+          |||..||
T Consensus         1 C~~C~kPItg~gG~k~isFedR----------~WH~~CF   29 (29)
T d1x68a1           1 CVACSKPISGLTGAKFICFQDS----------QWHSECF   29 (29)
T ss_dssp             CTTTCCCCCTTTTCCEEEETTE----------EEEGGGC
T ss_pred             CccccccccccCCceEEEeehh----------hcccccC
Confidence            788999999853 447888777          6898887

>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=94.90  E-value=0.0069  Score=35.99  Aligned_cols=27  Identities=19%  Similarity=0.358  Sum_probs=21.1

Q ss_pred             cccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          222 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       222 C~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      |..|.+||... +.-+.++++          +||++||
T Consensus         1 c~ecrkpigad-~ke~h~knr----------~wh~~cf   27 (27)
T d2cupa3           1 CVECRKPIGAD-SKEVHYKNR----------FWHDTCF   27 (27)
T ss_dssp             CSSSCCBCCSS-SCEEEETTE----------EEETTTC
T ss_pred             CccccCCcCcc-hHHhhcccc----------ccccccC
Confidence            78899999865 345777776          6899998

>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=94.88  E-value=0.0059  Score=37.99  Aligned_cols=28  Identities=25%  Similarity=0.619  Sum_probs=23.5

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      +|..|+++|  ...|+. +||.+||..+|..
T Consensus         1 kC~~C~~vL--~gEYm~-kdG~PyCe~DY~~   28 (31)
T d2dj7a1           1 KCQTCSVIL--TGEYIS-KDGVPYCESDYHA   28 (31)
T ss_dssp             BCSSSCCBC--SSCCEE-ETTEEECTTHHHH
T ss_pred             CccccCccc--cceeec-CCCCcccHHHHHH
Confidence            599999988  446765 7999999999976

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

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

Probab=94.87  E-value=0.0054  Score=42.56  Aligned_cols=38  Identities=21%  Similarity=0.358  Sum_probs=30.0

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhcccCCCCCCCcc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDSAIMDTHECQPL  301 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~~v~~~~~C~~C  301 (431)
                      +|..|++.|.... .. ..||++||..||.+  .+.|+..+.
T Consensus         1 KC~~C~k~Lds~t-~~-ehdg~~YCk~CY~k--~fGPKG~g~   38 (49)
T d1b8ta4           1 RCAKCGKSLESTT-LA-DKDGEIYCKGCYAK--NFGPKGFGF   38 (49)
T ss_dssp             BCTTTCCBCCSSS-EE-EETTEEEEHHHHHH--HTCCCCCCC
T ss_pred             ChhhcCCccCCCc-cc-ccCCcccchhhhhh--ccCCCccCc
Confidence            6999999996543 33 47999999999998  777776554

>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=94.83  E-value=0.0041  Score=38.40  Aligned_cols=29  Identities=17%  Similarity=0.416  Sum_probs=25.6

Q ss_pred             ccCCCCCCCCCcceeecCCcccccccccc
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKE  216 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~  216 (431)
                      .|+.|+..|.+.++|..++++||+.+...
T Consensus         1 vC~dCg~NLKqrG~Ffv~~~lyCE~HAr~   29 (31)
T d1x64a2           1 VCADCNLNLKQKGYFFVEGELYCETHARA   29 (31)
T ss_dssp             CCSSSCCCTTTSCCEEETTEEECHHHHHH
T ss_pred             CccccccChhhcceEEeccEEeehhhhhc
Confidence            48999999999998888999999988653

>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=94.69  E-value=0.0073  Score=38.13  Aligned_cols=29  Identities=24%  Similarity=0.495  Sum_probs=23.2

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .|..|.++++ +..|+.+ ||++||..+|..
T Consensus         1 VC~~C~~PF~-~~~Fy~~-~g~PyCe~HyH~   29 (32)
T d1x3ha2           1 VCGDCFTSFS-TGSFFEL-DGRPFCELHYHH   29 (32)
T ss_dssp             BCSSSCCBSC-SSCCEES-SSCEECHHHHHH
T ss_pred             CcCccCCcCC-CCCeEeE-CCccchHHhhhh
Confidence            4899999995 5566654 899999999865

>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=94.69  E-value=0.0075  Score=37.30  Aligned_cols=29  Identities=21%  Similarity=0.639  Sum_probs=25.3

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .|..|+..| +|++|+.+ +.+.||..||-.
T Consensus         1 vC~tC~~kL-RGqpFYAv-ekkayCE~CYi~   29 (32)
T d1x61a2           1 VCSTCRAQL-RGQHFYAV-ERRAYCEGCYVA   29 (32)
T ss_dssp             BCSSSCCBC-TTSCEEES-SSCEEEHHHHHH
T ss_pred             CeeEeCcee-cCCcceEe-eccccccceeee
Confidence            488999998 89999987 679999999964

>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=94.41  E-value=0.0069  Score=37.08  Aligned_cols=31  Identities=23%  Similarity=0.456  Sum_probs=27.8

Q ss_pred             ccCCCCCCCCCcceeecCCcccccccccccc
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKEQH  218 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f  218 (431)
                      +|+.|+..|+...|+.++...||-.|....|
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtche~kf   31 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKF   31 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHT
T ss_pred             CcchhhhhcccccccCCCCcEEEEEeecccc
Confidence            5899999999999999999999999987665

>d2cora1 g.39.1.3 (A:43-73) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.37  E-value=0.01  Score=36.38  Aligned_cols=28  Identities=32%  Similarity=0.778  Sum_probs=23.9

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .|..|++.++...+-.   .|.+||..|+++
T Consensus         1 nC~~CgkeltadArEl---~geLyCLpChdK   28 (31)
T d2cora1           1 NCANCGKELTADAREL---KGELYCLPCHDK   28 (31)
T ss_dssp             BCSSSCCBCCTTCEEE---TTEEECHHHHHT
T ss_pred             CccccccccchhHHHh---cCCEEEEecccc
Confidence            4899999998777654   789999999998

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.31  E-value=0.0099  Score=37.58  Aligned_cols=30  Identities=10%  Similarity=0.233  Sum_probs=23.7

Q ss_pred             cccccccCcccccCCCccccCCcceEEEecccc
Q 014080          212 HCYKEQHHPKCDVCQNFIPTNSAGLIEYRAHPF  244 (431)
Q Consensus       212 ~CY~~~f~pkC~~C~~~I~~~~~~~i~~~~~pf  244 (431)
                      .+|+.+|+..|..|...|++.   ++.+..+.|
T Consensus         1 kdYw~kfge~C~~C~~~itGp---vMvAG~~K~   30 (34)
T d1x6aa1           1 KDYWGKFGEFCHGCSLLMTGP---FMVAGEFKY   30 (34)
T ss_dssp             CCSSCCSSCBCTTTCCBCCSC---CBCCTTCCB
T ss_pred             CcHHHHHHHHhhhhHhhcccc---eeeeccccc
Confidence            368999999999999999874   455666654

>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=94.06  E-value=0.0062  Score=37.97  Aligned_cols=26  Identities=15%  Similarity=0.406  Sum_probs=21.8

Q ss_pred             cccCcccccCCCccccCCcceEEEecccc
Q 014080          216 EQHHPKCDVCQNFIPTNSAGLIEYRAHPF  244 (431)
Q Consensus       216 ~~f~pkC~~C~~~I~~~~~~~i~~~~~pf  244 (431)
                      +.+.|+|..|++||.+.   ++.+.++.|
T Consensus         2 kmg~p~C~~C~~PI~~~---~vtAlgk~W   27 (31)
T d1u5sb1           2 SMGVPICGACRRPIEGR---VVNAMGKQW   27 (31)
T ss_dssp             CCCCCEETTTTEECCSC---EECCTTSBE
T ss_pred             CcCCcchhhcCCchhhh---Hhhhhcccc
Confidence            35789999999999986   688888864

>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=94.02  E-value=0.0092  Score=37.76  Aligned_cols=30  Identities=17%  Similarity=0.362  Sum_probs=27.3

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      +|..|++.| .|.+|....++++||.++|.+
T Consensus         1 tCvvC~~~L-DGvPFtvD~~n~i~Cv~DyHr   30 (33)
T d2dloa2           1 TCVVCHRGL-DGIPFTVDATSQIHCIEDFHR   30 (33)
T ss_dssp             BCSSSCCBC-TTSCEECCTTCCCEEHHHHHH
T ss_pred             CeeEcCccc-CCCcEEEcCCCCEeehhhhhh
Confidence            589999998 799999999999999999987

>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=93.70  E-value=0.016  Score=36.14  Aligned_cols=29  Identities=17%  Similarity=0.596  Sum_probs=24.7

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .|+.|.+.| ..-.|+. ..|.+||..||.+
T Consensus         1 nCa~C~~sL-~d~gFVE-E~g~lYCe~Cye~   29 (32)
T d2dara1           1 NCAHCKNTM-AYIGFVE-EKGALYCELCYEK   29 (32)
T ss_dssp             BCSSSCCBC-SSSCBEE-SSSCEECHHHHHH
T ss_pred             CcccccccH-hhcceee-ecCcEeHHHHHHH
Confidence            388999988 6677887 7899999999986

>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=93.52  E-value=0.0096  Score=37.20  Aligned_cols=28  Identities=25%  Similarity=0.831  Sum_probs=22.0

Q ss_pred             cCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          261 CCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       261 C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      |.+|++++ ....|+. +++..||..||+.
T Consensus         2 C~~C~qPI-GtkSFip-~~~~~yCvpCYE~   29 (32)
T d1wyha1           2 CSGCEQPL-GSRSFVP-DKGAHYCVPCYEN   29 (32)
T ss_dssp             CTTTCCBT-TTSCEEE-ETTEEEEHHHHHH
T ss_pred             cccccCcc-ccccccc-CCCcEEEEecccc
Confidence            88999976 2345554 7889999999987

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=93.40  E-value=0.022  Score=35.93  Aligned_cols=30  Identities=30%  Similarity=0.615  Sum_probs=26.6

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCC
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPEC  186 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~C  186 (431)
                      ..+...|.+|...| .|.++.+-...|||+|
T Consensus         5 ~kfge~C~~C~~~i-tGpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           5 GKFGEFCHGCSLLM-TGPFMVAGEFKYHPEC   34 (34)
T ss_dssp             CCSSCBCTTTCCBC-CSCCBCCTTCCBCTTS
T ss_pred             HHHHHHhhhhHhhc-ccceeeecccccCCCC
Confidence            45778999999988 5999999999999998

>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=93.39  E-value=0.011  Score=37.02  Aligned_cols=29  Identities=17%  Similarity=0.709  Sum_probs=22.5

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .|..|++++ ....|+. +++..||..||++
T Consensus         1 ~C~~C~qPI-Gtksfip-k~~~~yCvpCyE~   29 (32)
T d1x4ka1           1 ICHRCQQPI-GTKSFIP-KDNQNFCVPCYEK   29 (32)
T ss_dssp             CCSSSCCCC-CSSSEEE-ETTEEEEHHHHHH
T ss_pred             CcccccCcc-ccccccc-CCCCceEeecchh
Confidence            388999976 2345554 7899999999987

>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=93.17  E-value=0.029  Score=32.75  Aligned_cols=26  Identities=31%  Similarity=0.986  Sum_probs=22.2

Q ss_pred             CCCCCccc-ccCceEeecCccccCCCc
Q 014080          162 CAGCNTEI-GHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       162 C~~C~k~I-~~g~~v~algk~wHp~CF  187 (431)
                      |++|++.+ .+|.-+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            88999976 345778999999999998

>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=93.03  E-value=0.0047  Score=38.17  Aligned_cols=29  Identities=14%  Similarity=0.344  Sum_probs=25.4

Q ss_pred             ccCCCCCCCCCcceeecCCcccccccccc
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKE  216 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~  216 (431)
                      .|+.|+..|.+.++|..++++||+.+.+.
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr~   29 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHARE   29 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhhh
Confidence            48999999999988888999999988653

>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=93.03  E-value=0.014  Score=39.06  Aligned_cols=29  Identities=28%  Similarity=0.549  Sum_probs=24.3

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      ||..|++.|..+ .|.. .+|.+||..||..
T Consensus         1 rC~~C~~~Ls~~-~yas-~~G~lYCkpHf~q   29 (42)
T d2d8ya2           1 RCSYCNNKLSLG-TYAS-LHGRIYCKPHFNQ   29 (42)
T ss_dssp             BCTTTCCBCCTT-TCCC-SSSCCCCHHHHHH
T ss_pred             CcCcCCCCccCC-cchh-hCCEeccHHHHHH
Confidence            699999999655 5665 4899999999987

>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=92.19  E-value=0.037  Score=35.23  Aligned_cols=28  Identities=11%  Similarity=0.087  Sum_probs=22.6

Q ss_pred             cccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          220 PKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       220 pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      ..|++|++.|....  .+.+.++          |||.+||
T Consensus         9 ~~CagCg~eik~gQ--aL~ALdk----------qWH~~CF   36 (36)
T d2dj7a2           9 SHCAGCKEEIKHGQ--SLLALDK----------QWHVSCF   36 (36)
T ss_dssp             SCCTTTCCCCSSSC--CEEETTE----------EECTTTC
T ss_pred             ccccccchhhhCCc--eeeeeec----------ceeeeeC
Confidence            47999999998753  5667776          7899998

>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=92.00  E-value=0.029  Score=34.51  Aligned_cols=26  Identities=23%  Similarity=0.585  Sum_probs=20.0

Q ss_pred             cccccCCCccccCCcceEEEecccccccccCCCcccCCC
Q 014080          220 PKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGT  258 (431)
Q Consensus       220 pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~C  258 (431)
                      .-|..|.++|++.   ++++..+          |||+.|
T Consensus         6 sgC~~C~~~ItGk---VLEAG~k----------hYHP~C   31 (32)
T d1wiga1           6 SGCDSCEKYITGR---VLEAGEK----------HYHPSC   31 (32)
T ss_dssp             CSCSSSCCCCSSC---CBCCSSC----------CBCTTT
T ss_pred             chhhhhhhhhhhh---hhhcccc----------ccCCCC
Confidence            4699999999986   5666655          778766

>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=91.91  E-value=0.031  Score=36.27  Aligned_cols=31  Identities=16%  Similarity=0.420  Sum_probs=25.7

Q ss_pred             CccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          259 PRCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       259 F~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      |.|+.|.+++|.|++. ++.....+|..|...
T Consensus         1 FvC~vCr~pFP~GDRV-TFnGKeC~CQ~Cs~p   31 (40)
T d1v6ga2           1 FVCAVCRLPFPPGDRV-TFNGKECMCQKCSLP   31 (40)
T ss_dssp             SSCSSSCCCCCSSSCE-EEETTEEEEHHHHSC
T ss_pred             CcccccCCCCCCCCeE-EEcCceeehhhcCCC
Confidence            7899999999999984 456667889998764

>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=91.57  E-value=0.04  Score=37.72  Aligned_cols=34  Identities=18%  Similarity=0.460  Sum_probs=26.0

Q ss_pred             ccCCCCCccCCCCceEEccCCcccC-cchhhcccCCCCC
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLC-LECLDSAIMDTHE  297 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC-~~C~~~~v~~~~~  297 (431)
                      +|..|++.|..+. .. ..||++|| ..||..  +|.|+
T Consensus         1 kC~~C~K~L~sg~-~a-eHdg~pYC~k~CY~~--~FGPk   35 (48)
T d1imla2           1 KCEKCGKTLTSGG-HA-EHEGKPYCNHPCYSA--MFGPK   35 (48)
T ss_dssp             BCTTTCCBCCTTT-EE-EETTEEEETTTHHHH--HSSCC
T ss_pred             CchhcCcCcCCCC-hh-hcCCcccccccchhh--ccCCC
Confidence            6999999996554 33 47999999 779987  55553

>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=89.91  E-value=0.089  Score=31.21  Aligned_cols=27  Identities=19%  Similarity=0.415  Sum_probs=21.3

Q ss_pred             cccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          222 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       222 C~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      |..|.+.|.+.. .-++|.+..          ||..||
T Consensus         1 C~~C~ktiMPGs-rKme~kG~~----------WHEtCF   27 (27)
T d1x4ka2           1 CQECKKTIMPGT-RKMEYKGSS----------WHETCF   27 (27)
T ss_dssp             BSSSCCCCCSSS-CEEEETTEE----------EETTTT
T ss_pred             CccccccccCCc-eeecccCCc----------cccccC
Confidence            788999998753 467888875          588887

>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=89.67  E-value=0.075  Score=34.76  Aligned_cols=28  Identities=25%  Similarity=0.761  Sum_probs=21.0

Q ss_pred             cCCCCCcccccCc-eEeecCccccCCCcc
Q 014080          161 ICAGCNTEIGHGR-YLSCMEAFWHPECFR  188 (431)
Q Consensus       161 ~C~~C~k~I~~g~-~v~algk~wHp~CF~  188 (431)
                      .|.+|+.....|+ ....-+..|||.|-.
T Consensus         1 ~C~rC~~mF~EGEEMYLQGs~IWHP~C~~   29 (41)
T d1wiga2           1 LCVRCGQMFAEGEEMYLQGSSIWHPACRQ   29 (41)
T ss_dssp             CCSSSCCCCCSSCCCEEETTEEECTTHHH
T ss_pred             CcchhhccccccceeeecCCceeCCcccc
Confidence            4899999988774 344566789998854

>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=89.61  E-value=0.15  Score=32.18  Aligned_cols=29  Identities=14%  Similarity=0.527  Sum_probs=24.4

Q ss_pred             CCCcCCCCCcccccC-ceEeecCccccCCC
Q 014080          158 GYRICAGCNTEIGHG-RYLSCMEAFWHPEC  186 (431)
Q Consensus       158 ~~~~C~~C~k~I~~g-~~v~algk~wHp~C  186 (431)
                      ..-.|.+|+....+. ++|+..|..||++|
T Consensus         6 ~~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           6 ASATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHHHccCCCchHHhhcCCCccccccC
Confidence            456899999988665 67899999999988

>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=89.57  E-value=0.089  Score=33.09  Aligned_cols=29  Identities=21%  Similarity=0.348  Sum_probs=22.4

Q ss_pred             cCcccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          218 HHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       218 f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      -.|.|..|+..|.+.   ++..+.+.          +|+.||
T Consensus         7 klp~CdkCg~GIVG~---~VK~rDk~----------rHPeCf   35 (35)
T d1x62a2           7 KLPMCDKCGTGIVGV---FVKLRDRH----------RHPECY   35 (35)
T ss_dssp             CCCCCSSSCCCCCSS---CEECSSCE----------ECTTTT
T ss_pred             cCccccccCCCcEeE---EEEecccc----------CCCCCC
Confidence            357899999999985   56666663          588887

>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=89.40  E-value=0.1  Score=32.97  Aligned_cols=31  Identities=29%  Similarity=0.486  Sum_probs=26.7

Q ss_pred             CCCCCcCCCCCcccccCceEeecCccccCCCc
Q 014080          156 FSGYRICAGCNTEIGHGRYLSCMEAFWHPECF  187 (431)
Q Consensus       156 ~~~~~~C~~C~k~I~~g~~v~algk~wHp~CF  187 (431)
                      ..+..+|.+|...| +.+-+.+.+..|||.+|
T Consensus         5 glGk~vC~KCh~iI-dd~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           5 GLGKYICQKCHAII-DEQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCCBCTTTCCBC-CSCCCCCSSSCCCTTTS
T ss_pred             chhhHHHHHHHhhh-hcCcceecCCCCCCCCC
Confidence            34778999999999 57888999999999887

>d2d8xa1 g.39.1.3 (A:33-64) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=88.96  E-value=0.076  Score=32.72  Aligned_cols=29  Identities=24%  Similarity=0.613  Sum_probs=26.2

Q ss_pred             ccCCCCCCCCCcceeecCCcccccccccc
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCYKE  216 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY~~  216 (431)
                      +|..|...|.+.+|....|+.+|.+|..+
T Consensus         1 rC~~C~~~LAD~GFvKnagR~LCrpch~r   29 (32)
T d2d8xa1           1 RCDLCQEVLADIGFVKNAGRHLCRPCHNR   29 (32)
T ss_dssp             BCSSSCCBCSSSCCEEETTEEECHHHHHH
T ss_pred             CchHHHhHHHHhhhhhcccccccchhhhh
Confidence            58999999999999999999999998653

>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=87.65  E-value=0.078  Score=32.98  Aligned_cols=28  Identities=14%  Similarity=0.256  Sum_probs=21.1

Q ss_pred             ccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          221 KCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       221 kC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      .|++|++.|..++ .++.++++-          ||..||
T Consensus         4 ~Ca~C~~~I~~~e-~VmRA~~~V----------yHl~CF   31 (31)
T d1rutx3           4 ACSACGQSIPASE-LVMRAQGNV----------YHLKCF   31 (31)
T ss_dssp             ECTTTCCEECTTS-EEEEETTEE----------ECGGGC
T ss_pred             ccccccCcCChhH-hheecccce----------eeeccC
Confidence            6999999999875 455555654          588887

>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=87.62  E-value=0.13  Score=31.68  Aligned_cols=22  Identities=18%  Similarity=0.273  Sum_probs=16.0

Q ss_pred             cccccCCCccccCCcceEEEeccc
Q 014080          220 PKCDVCQNFIPTNSAGLIEYRAHP  243 (431)
Q Consensus       220 pkC~~C~~~I~~~~~~~i~~~~~p  243 (431)
                      ..|++|+++|.+.-  ++.+..+.
T Consensus         4 ~~CaGC~~~I~DRf--lL~a~Dr~   25 (30)
T d1j2oa1           4 LTCGGCQQNIGDRY--FLKAIDQY   25 (30)
T ss_dssp             BCBSSSCSCBCSSE--EEECSSSE
T ss_pred             cccCCCCCcchHHH--HHHHHHHH
Confidence            46999999999863  45555553

>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=87.50  E-value=0.19  Score=31.31  Aligned_cols=29  Identities=21%  Similarity=0.645  Sum_probs=22.7

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcc-hhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLE-CLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~-C~~~  290 (431)
                      +|..|++.|..|.. . -.+|++||.. ||..
T Consensus         1 kCekC~ktL~~G~H-a-EH~gkPYC~~PCY~a   30 (33)
T d2cu8a2           1 KCERCSKTLTPGGH-A-EHDGKPFCHKPCYAT   30 (33)
T ss_dssp             BCSSSCCBCCTTSC-E-EETTEEECTTTHHHH
T ss_pred             CchhcccccCCCCc-c-ccCCCcCcCcchHHh
Confidence            58899999977765 3 3699999975 8864

>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=87.41  E-value=0.061  Score=39.13  Aligned_cols=29  Identities=14%  Similarity=0.482  Sum_probs=23.0

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      .|..|++.|..+ . +...++.+||+.||.+
T Consensus         1 ~C~~C~K~LdS~-~-~~eh~~e~YCk~CY~k   29 (65)
T d1b8ta2           1 LCMVCKKNLDST-T-VAVHGDEIYCKSCYGK   29 (65)
T ss_dssp             BCTTTCCBCCSS-S-EEEETTEEEEHHHHHH
T ss_pred             CchhcCCccCCC-c-cccCCCcccchhhhcc
Confidence            389999999544 3 3457899999999987

>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=87.04  E-value=0.053  Score=34.06  Aligned_cols=32  Identities=16%  Similarity=0.286  Sum_probs=26.0

Q ss_pred             ccCCCCCCCCC--cceeecCCccccccccccccC
Q 014080          188 RCHSCNLPITD--VEFSMSGNRPYHKHCYKEQHH  219 (431)
Q Consensus       188 ~C~~C~~~L~~--~~F~~~dg~pyC~~CY~~~f~  219 (431)
                      +|+-|+..|++  ...+.+.|.+.|+.+|.++|+
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            58888888873  456778999999999998874

>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=86.69  E-value=0.14  Score=31.23  Aligned_cols=27  Identities=26%  Similarity=0.647  Sum_probs=24.3

Q ss_pred             ccCCCCCCCCCcceeecCCcccccccc
Q 014080          188 RCHSCNLPITDVEFSMSGNRPYHKHCY  214 (431)
Q Consensus       188 ~C~~C~~~L~~~~F~~~dg~pyC~~CY  214 (431)
                      +|..|-.||....|..++++++|..|-
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~   27 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCT   27 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHH
T ss_pred             CchhhccccccCcccccCCeEeecccc
Confidence            588899999999999999999998874

>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=86.44  E-value=0.15  Score=31.05  Aligned_cols=29  Identities=24%  Similarity=0.694  Sum_probs=23.8

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      +|..|-.+| .+..|+. +|++++|..|-.+
T Consensus         1 RCaKC~hpL-A~E~F~a-Kd~kI~C~Kc~sr   29 (31)
T d2cupa2           1 RCAKCLHPL-ANETFVA-KDNKILCNKCTTR   29 (31)
T ss_dssp             CCSSSCCCT-TSSCCEE-ETTEEECHHHHTT
T ss_pred             Cchhhcccc-ccCcccc-cCCeEeecccccc
Confidence            588888988 6778886 7999999999654

>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=86.42  E-value=0.16  Score=33.90  Aligned_cols=29  Identities=21%  Similarity=0.315  Sum_probs=22.9

Q ss_pred             cCcccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          218 HHPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       218 f~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      -.|.|..|+..|.+.   ++..+++.          +|+.||
T Consensus        17 kLP~CdkCg~GIVG~---~VK~rDK~----------rHPeCf   45 (45)
T d1x64a1          17 RMPLCDKCGSGIVGA---VVKARDKY----------RHPECF   45 (45)
T ss_dssp             SCCBCTTTCCBCCSC---CEESSSCE----------ECTTTC
T ss_pred             cCccccccCCCcEEE---EEEecccc----------CCCCCC
Confidence            457899999999985   56777764          588887

>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=86.24  E-value=0.13  Score=31.25  Aligned_cols=29  Identities=14%  Similarity=0.627  Sum_probs=22.6

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      +|+.|++.+..| .|+. +....||..|++.
T Consensus         1 tcs~ckq~igsg-sffp-kg~d~ycvtche~   29 (32)
T d1x63a2           1 TCSNCKQVIGTG-SFFP-KGEDFYCVTCHET   29 (32)
T ss_dssp             CCSSSCCCCTTS-CEEE-ETTEEEEHHHHHH
T ss_pred             Ccchhhhhcccc-cccC-CCCcEEEEEeecc
Confidence            499999998655 4665 5668999999875

>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=86.04  E-value=0.12  Score=31.86  Aligned_cols=22  Identities=18%  Similarity=0.244  Sum_probs=16.1

Q ss_pred             cccccCCCccccCCcceEEEeccc
Q 014080          220 PKCDVCQNFIPTNSAGLIEYRAHP  243 (431)
Q Consensus       220 pkC~~C~~~I~~~~~~~i~~~~~p  243 (431)
                      ..|++|+++|.+..  ++...++.
T Consensus         3 ~~CaGC~~~I~DRf--lL~v~dr~   24 (30)
T d1rutx1           3 KRCAGCGGKIADRF--LLYAMDSY   24 (30)
T ss_dssp             CBBTTTCCBCCCSE--EEEETTEE
T ss_pred             cccCCCCCccchhh--hhccchhh
Confidence            36999999999863  55555654

>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=85.17  E-value=0.13  Score=31.62  Aligned_cols=28  Identities=18%  Similarity=0.568  Sum_probs=21.8

Q ss_pred             cCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          261 CCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       261 C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      |-.|.+.|...  -+...++.+||+.||.+
T Consensus         2 C~~C~K~LdSt--Tva~h~~eiYCKsCygk   29 (32)
T d1a7ia2           2 CMVCRKNLDST--TVAIHDAEVYCKSCYGK   29 (32)
T ss_dssp             CSSSCCEECSS--CCEEETTEEECSHHHHH
T ss_pred             chhhhhccCcc--eeeeecceEEehhhccc
Confidence            78899988433  34457899999999976

>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=84.51  E-value=0.2  Score=33.39  Aligned_cols=29  Identities=7%  Similarity=0.052  Sum_probs=22.9

Q ss_pred             CcccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          219 HPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       219 ~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      .++|..|++.+...+  .+...++.          ||..||
T Consensus        15 ~~kC~~C~k~VY~~E--~~~~~g~~----------~Hk~CF   43 (43)
T d1b8ta3          15 SDGCPRCGQAVYAAE--KVIGAGKS----------WHKSCF   43 (43)
T ss_dssp             CEECTTTSCEECSSS--CEEETTEE----------ECTTTC
T ss_pred             CCcCccCCCEeeHHH--HhhcCCCc----------cccCCC
Confidence            468999999998765  56777876          488888

>d1jm7b_ g.44.1.1 (B:) bard1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: bard1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=83.29  E-value=0.52  Score=36.03  Aligned_cols=46  Identities=15%  Similarity=0.313  Sum_probs=31.6

Q ss_pred             cccCCCCCCCCCcceeecCCccccccccccccCcccccCCCccccC
Q 014080          187 FRCHSCNLPITDVEFSMSGNRPYHKHCYKEQHHPKCDVCQNFIPTN  232 (431)
Q Consensus       187 F~C~~C~~~L~~~~F~~~dg~pyC~~CY~~~f~pkC~~C~~~I~~~  232 (431)
                      ++|..|...+........=|..||..|..+.+..+|..|+.++...
T Consensus        23 l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~~~CP~Cr~~~~~~   68 (97)
T d1jm7b_          23 LRCSRCTNILREPVCLGGCEHIFCSNCVSDCIGTGCPVCYTPAWIQ   68 (97)
T ss_dssp             TSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTTTBCSSSCCBCSCS
T ss_pred             CCCccCCchhhcCceeCCCCCchhHHHHHHHHhccccccCCcCchh
Confidence            5677777666543323334778888888777777899998877653

>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=83.06  E-value=0.37  Score=29.62  Aligned_cols=28  Identities=14%  Similarity=0.363  Sum_probs=23.3

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchh
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECL  288 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~  288 (431)
                      .|+.|...|-.|++|.- -+|.+||....
T Consensus         1 tC~tC~n~LVPGDRFHy-vNG~lfCE~D~   28 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHY-INGSLFCEHDR   28 (33)
T ss_dssp             BCTTTCCBCCTTCEEEE-ETTEEEEGGGC
T ss_pred             CcccccccccCCceeEE-ecCEEEEecCC
Confidence            48999999989999875 48999998654

>d2d8xa1 g.39.1.3 (A:33-64) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=82.88  E-value=0.27  Score=30.16  Aligned_cols=29  Identities=31%  Similarity=0.815  Sum_probs=23.9

Q ss_pred             ccCCCCCccCCCCceEEccCCcccCcchhhc
Q 014080          260 RCCSCERMEPRDTKYLSLDDGRKLCLECLDS  290 (431)
Q Consensus       260 ~C~~C~r~l~~g~~f~~l~dG~~yC~~C~~~  290 (431)
                      +|..|...| .+..|+. ..|+.+|.+|..+
T Consensus         1 rC~~C~~~L-AD~GFvK-nagR~LCrpch~r   29 (32)
T d2d8xa1           1 RCDLCQEVL-ADIGFVK-NAGRHLCRPCHNR   29 (32)
T ss_dssp             BCSSSCCBC-SSSCCEE-ETTEEECHHHHHH
T ss_pred             CchHHHhHH-HHhhhhh-cccccccchhhhh
Confidence            588999988 5677875 6899999999864

>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=82.70  E-value=0.38  Score=30.62  Aligned_cols=29  Identities=10%  Similarity=0.024  Sum_probs=23.0

Q ss_pred             CcccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          219 HPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       219 ~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      ..+|..|++.+...+  .+.+.++.          ||.+||
T Consensus         7 ~~kC~~C~K~VY~~E--~~~a~g~~----------~Hk~CF   35 (35)
T d2d8ya1           7 RETCVECQKTVYPME--RLLANQQV----------FHISCF   35 (35)
T ss_dssp             SCBCTTTCCBCCTTS--EEECSSSE----------EETTTC
T ss_pred             CcccccCCCEEeeee--eEecCCee----------hhhccC
Confidence            468999999988754  67777775          488888

>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=82.68  E-value=0.15  Score=31.03  Aligned_cols=29  Identities=10%  Similarity=0.281  Sum_probs=20.2

Q ss_pred             CcccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          219 HPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       219 ~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      .|.|+.|++.+.+.+  -+.-.++          .||.+||
T Consensus         2 n~~CaRC~k~VYp~E--kl~ClDk----------~WHK~CF   30 (30)
T d1zfoa_           2 NPNCARCGKIVYPTE--KVNCLDK----------FWHKACF   30 (30)
T ss_dssp             CCBCSSSCSBCCGGG--CCCSSSS----------CCCGGGC
T ss_pred             CCcccccCCccccHH--HhhhhHH----------HHhhccC
Confidence            468999999888743  3444444          4688887

>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=82.29  E-value=0.28  Score=28.91  Aligned_cols=27  Identities=19%  Similarity=0.370  Sum_probs=20.6

Q ss_pred             cccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          222 CDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       222 C~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      |..|.+.|.+.. .-++|.+..          ||..||
T Consensus         1 C~~C~ktiMPGs-rKmey~G~s----------WHE~CF   27 (27)
T d1wyha2           1 CSACGETVMPGS-RKLEYGGQT----------WHEHCF   27 (27)
T ss_dssp             CSSSCCBCCSSS-CEECSTTCC----------EETTTC
T ss_pred             CccccceecCCc-ccccccCcc----------cccccC
Confidence            788999998753 457787775          588887

>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=81.58  E-value=0.37  Score=30.88  Aligned_cols=29  Identities=10%  Similarity=0.106  Sum_probs=22.2

Q ss_pred             CcccccCCCccccCCcceEEEecccccccccCCCcccCCCC
Q 014080          219 HPKCDVCQNFIPTNSAGLIEYRAHPFWLQKYCPSHERDGTP  259 (431)
Q Consensus       219 ~pkC~~C~~~I~~~~~~~i~~~~~pfw~~~yCp~h~H~~CF  259 (431)
                      ..+|..|++.+...+  .+.+.++.          ||.+||
T Consensus         8 ~~~C~~C~K~VY~~E--rl~a~g~~----------yHk~CF   36 (36)
T d2co8a2           8 GDLCALCGEHLYVLE--RLCVNGHF----------FHRSCF   36 (36)
T ss_dssp             SCBCSSSCCBCCTTT--BCCBTTBC----------CBTTTC
T ss_pred             CCcccccCCEEeeee--EEEecCcE----------eccccC
Confidence            468999999888754  56677775          488888

>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=80.86  E-value=0.42  Score=29.38  Aligned_cols=26  Identities=15%  Similarity=0.540  Sum_probs=22.9

Q ss_pred             cCCCCCCCCCcceeecCCcccccccc
Q 014080          189 CHSCNLPITDVEFSMSGNRPYHKHCY  214 (431)
Q Consensus       189 C~~C~~~L~~~~F~~~dg~pyC~~CY  214 (431)
                      |..|+.+|.+..|......++|..|-
T Consensus         2 cgkcsvslvg~gfltq~~~i~c~~cg   27 (34)
T d1x68a2           2 CGKCSVSLVGKGFLTQNKEIFCQKCG   27 (34)
T ss_dssp             CTTTCCBCSSSCEEEETTEEEETTTT
T ss_pred             CccceEEEEeeeeeeccCcEEehhcC
Confidence            78899999999999988999998874