Citrus Sinensis ID: 040947

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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
Protein Sequence
MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRTASSSSTSPAEQIENKPDDESGAEDQTEEQS
Secondary Structure (PSIPRED)
cccccccccccccccEEEEEEEEEEcccccccccccccccccccccccccccccEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccHHHHHHHHcccccccccccccccccccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccEEEEEEEEEEcccccccccEEEHHccccccccccccccccEEccccHHHHcccccccccccccccccccccccccccccccHcccccccHccccccEEEEcEEEEEcccccccccEEEHHccccccccccccccccEEccHHHHHHccccccccccccccccccccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
maftgtldkckacdktVYVVDMLslegmpyhkscfkcshckgtlvmsnyssmdgvlyckphfeqlfkesgnfsknfqtgknpsscsnqnrtpsklsslfsgtqdkcaacektvyplekvtmegdcfhktcfrcahggcplthssyaaldGVLYCKHHFAQLFMEKGNYSHVLKAAnhkrtasssstspaeqienkpddesgaedqteeqs
Flexible Loop (DISEMBL)
maftgtldkckacdkTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTgknpsscsnqnRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKrtasssstspaeqienkpddesgaedqteeqs
Low Complexity Region (SEG)
MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRTASSSSTSPAEQIENKPDDESGAEDQTEEQS
Disordered region (IsUnstruct)
****GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK************************************DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVL**************************************
Disordered Region (DISOPRED)
**FTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME**********************************************
Disordered Region (DISEMBL)
MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKN*****************SKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKA************************************
Disordered Region (DISPRO)
******LDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKES**********************************DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKA************************************
Transmembrane Helix (TMHMM)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
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Signal Peptide (SignalP NN Mode)
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Coiled Coils (COILS)
MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRTASSSSTSPAEQIENKPDDESGAEDQTEEQS
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	210	2.2.26 [Sep-21-2011]
P29675	219	Pollen-specific protein S	N/A	no	0.985	0.945	0.440	3e-49
P50462	194	Cysteine and glycine-rich	yes	no	0.780	0.845	0.329	1e-17
P50461	194	Cysteine and glycine-rich	yes	no	0.780	0.845	0.329	2e-17
P50463	194	Cysteine and glycine-rich	yes	no	0.780	0.845	0.329	6e-17
Q4U0T9	194	Cysteine and glycine-rich	no	no	0.780	0.845	0.313	1e-16
P97314	193	Cysteine and glycine-rich	no	no	0.790	0.860	0.301	2e-16
Q16527	193	Cysteine and glycine-rich	no	no	0.790	0.860	0.301	2e-16
Q32LE9	193	Cysteine and glycine-rich	no	no	0.790	0.860	0.301	2e-16
Q62908	193	Cysteine and glycine-rich	no	no	0.790	0.860	0.301	2e-16
Q0VFX8	208	Cysteine-rich protein 2 O	no	no	0.752	0.759	0.331	3e-16

>sp|P29675|SF3_HELAN Pollen-specific protein SF3 OS=Helianthus annuus GN=SF3 PE=2 SV=1

 Score =  194 bits (494), Expect = 3e-49,   Method: Compositional matrix adjust.
 Identities = 93/211 (44%), Positives = 134/211 (63%), Gaps = 4/211 (1%)

Query: 2   AFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPH 61
           +FTGT  KC  C+KTVY+VD L      YHK+CF+C HC  TL +SN++S DGV+YC+ H
Sbjct: 3   SFTGTTQKCTVCEKTVYLVDKLVANQRVYHKACFRCHHCNSTLKLSNFNSFDGVVYCRHH 62

Query: 62  FEQLFKESGNFSKNFQTG---KNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEK 118
           F+QLFK +G+  K+F      K   + S + ++ ++LSS F GT+DKC AC K VYP+E+
Sbjct: 63  FDQLFKRTGSLEKSFDGTPKFKPERTFSQETQSANRLSSFFEGTRDKCNACAKIVYPIER 122

Query: 119 VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHV-LKAANH 177
           V ++G  +H+ CF+C HGGC ++ S+Y A +G LYCKHH  QLF +KGNYS + ++    
Sbjct: 123 VKVDGTAYHRACFKCCHGGCTISPSNYIAHEGRLYCKHHHIQLFKKKGNYSQLEVEETVA 182

Query: 178 KRTASSSSTSPAEQIENKPDDESGAEDQTEE 208
               S +  +  +  E +  D   A+ Q  E
Sbjct: 183 APAESETQNTETQNAETQNADTQNADTQNTE 213

Could possibly involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization.
Helianthus annuus (taxid: 4232)

>sp|P50462|CSRP3_MOUSE Cysteine and glycine-rich protein 3 OS=Mus musculus GN=Csrp3 PE=1 SV=1

 Score = 89.7 bits (221), Expect = 1e-17,   Method: Compositional matrix adjust.
 Identities = 60/182 (32%), Positives = 86/182 (47%), Gaps = 18/182 (9%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M   G   KC AC+KTVY  + +   G  +HK+CF C  C+  L  +  ++ +  +YCK 
Sbjct: 1   MPNWGGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKV 60

Query: 61  HFEQLFKESG----------------NFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQD 104
            + + +   G                +    FQ    P+  +  +  PSK S+ F G  +
Sbjct: 61  CYGRRYGPKGIGFGQGAGCLSTDTGEHLGLQFQQSPKPARAATTS-NPSKFSAKF-GESE 118

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME 164
           KC  C K+VY  EKV   G  +HKTCFRCA  G  L  ++    DG LYCK  +A+ F  
Sbjct: 119 KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGP 178

Query: 165 KG 166
            G
Sbjct: 179 TG 180

Positive regulator of myogenesis. Plays a crucial and specific role in the organization of cytosolic structures in cardiomyocytes. Could play a role in mechanical stretch sensing. May be a scaffold protein that promotes the assembly of interacting proteins at Z-line structures. It is essential for calcineurin anchorage to the Z line. Required for stress-induced calcineurin-NFAT activation.

Mus musculus (taxid: 10090)

>sp|P50461|CSRP3_HUMAN Cysteine and glycine-rich protein 3 OS=Homo sapiens GN=CSRP3 PE=1 SV=1

 Score = 89.0 bits (219), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 60/182 (32%), Positives = 85/182 (46%), Gaps = 18/182 (9%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M   G   KC AC+KTVY  + +   G  +HK+CF C  C+  L  +  ++ +  +YCK 
Sbjct: 1   MPNWGGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKV 60

Query: 61  HFEQLFKESG----------------NFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQD 104
            + + +   G                +    FQ    P+  S     PSK ++ F G  +
Sbjct: 61  CYGRRYGPKGIGYGQGAGCLSTDTGEHLGLQFQQSPKPAR-SVTTSNPSKFTAKF-GESE 118

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME 164
           KC  C K+VY  EKV   G  +HKTCFRCA  G  L  ++    DG LYCK  +A+ F  
Sbjct: 119 KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGP 178

Query: 165 KG 166
            G
Sbjct: 179 TG 180

Positive regulator of myogenesis. Plays a crucial and specific role in the organization of cytosolic structures in cardiomyocytes. Could play a role in mechanical stretch sensing. May be a scaffold protein that promotes the assembly of interacting proteins at Z-line structures. It is essential for calcineurin anchorage to the Z line. Required for stress-induced calcineurin-NFAT activation.

Homo sapiens (taxid: 9606)

>sp|P50463|CSRP3_RAT Cysteine and glycine-rich protein 3 OS=Rattus norvegicus GN=Csrp3 PE=1 SV=1

 Score = 87.4 bits (215), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 60/182 (32%), Positives = 85/182 (46%), Gaps = 18/182 (9%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M   G   KC ACDKTVY  + +   G  +HK+CF C  C+  L  +  ++ +  +YCK 
Sbjct: 1   MPNWGGGAKCGACDKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKV 60

Query: 61  HFEQLFKESG----------------NFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQD 104
            + + +   G                +    FQ    P+  +  +  PSK S+ F G  +
Sbjct: 61  CYGRKYGPKGIGFGQGAGCLSTDTGEHLGLQFQQSPKPARAATTS-NPSKFSAKF-GESE 118

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME 164
           KC  C K+VY  EKV   G  +HKTCF CA  G  L  ++    DG LYCK  +A+ F  
Sbjct: 119 KCPRCGKSVYAAEKVMGGGKPWHKTCFPCAICGKSLESTNVTDKDGELYCKVCYAKNFGP 178

Query: 165 KG 166
            G
Sbjct: 179 TG 180

Positive regulator of myogenesis. Plays a crucial and specific role in the organization of cytosolic structures in cardiomyocytes. Could play a role in mechanical stretch sensing. May be a scaffold protein that promotes the assembly of interacting proteins at Z-line structures. It is essential for calcineurin anchorage to the Z line. Required for stress-induced calcineurin-NFAT activation.

Rattus norvegicus (taxid: 10116)

>sp|Q4U0T9|CSRP3_BOVIN Cysteine and glycine-rich protein 3 OS=Bos taurus GN=CSRP3 PE=2 SV=1

 Score = 86.3 bits (212), Expect = 1e-16,   Method: Compositional matrix adjust.
 Identities = 57/182 (31%), Positives = 83/182 (45%), Gaps = 18/182 (9%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M   G   KC AC+KTVY  + +   G  +HK+CF C  C+  L  +  ++ +  +YCK 
Sbjct: 1   MPNWGGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKV 60

Query: 61  HFEQLFKESG----------------NFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQD 104
            + + +   G                +    FQ     +  +  +  PSK +    G  +
Sbjct: 61  CYGRRYGPKGIGYGQGAGCLSTDTGEHLGLQFQQSPKQARSATTSSNPSKFAKF--GESE 118

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME 164
           KC  C K+VY  EKV   G  +HKTCFRCA  G  L  ++    DG LYCK  +A+ F  
Sbjct: 119 KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGP 178

Query: 165 KG 166
            G
Sbjct: 179 TG 180

Positive regulator of myogenesis. Plays a crucial and specific role in the organization of cytosolic structures in cardiomyocytes. Could play a role in mechanical stretch sensing. May be a scaffold protein that promotes the assembly of interacting proteins at Z-line structures. It is essential for calcineurin anchorage to the Z line. Required for stress-induced calcineurin-NFAT activation.

Bos taurus (taxid: 9913)

>sp|P97314|CSRP2_MOUSE Cysteine and glycine-rich protein 2 OS=Mus musculus GN=Csrp2 PE=1 SV=3

 Score = 85.5 bits (210), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 84/179 (46%), Gaps = 13/179 (7%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M   G  +KC AC +TVY  + +  +G  +H+ CF C  C+  L  +  +  D  +YCK 
Sbjct: 1   MPVWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDEEIYCKS 60

Query: 61  HFEQLFKESG----------NFSKNFQTGKNPSSCSNQNRTPSKLSSLFS---GTQDKCA 107
            + + +   G          N  +  + G  P S      T +  +S F+   G  +KC+
Sbjct: 61  CYGKKYGPKGYGYGQGAGTLNMDRGERLGIKPESAQPHRPTTNPNTSKFAQKYGGAEKCS 120

Query: 108 ACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKG 166
            C  +VY  EK+   G  +HK CFRCA  G  L  ++    +G +YCK  +A+ F  KG
Sbjct: 121 RCGDSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKG 179

Drastically down-regulated in response to PDGF-BB or cell injury, that promote smooth muscle cell proliferation and dedifferentiation. Seems to play a role in the development of the embryonic vascular system.

Mus musculus (taxid: 10090)

>sp|Q16527|CSRP2_HUMAN Cysteine and glycine-rich protein 2 OS=Homo sapiens GN=CSRP2 PE=1 SV=3

 Score = 85.5 bits (210), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 84/179 (46%), Gaps = 13/179 (7%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M   G  +KC AC +TVY  + +  +G  +H+ CF C  C+  L  +  +  D  +YCK 
Sbjct: 1   MPVWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDEEIYCKS 60

Query: 61  HFEQLFKESG----------NFSKNFQTGKNPSSCSNQNRTPSKLSSLFS---GTQDKCA 107
            + + +   G          N  +  + G  P S      T +  +S F+   G  +KC+
Sbjct: 61  CYGKKYGPKGYGYGQGAGTLNMDRGERLGIKPESVQPHRPTTNPNTSKFAQKYGGAEKCS 120

Query: 108 ACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKG 166
            C  +VY  EK+   G  +HK CFRCA  G  L  ++    +G +YCK  +A+ F  KG
Sbjct: 121 RCGDSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKG 179

Drastically down-regulated in response to PDGF-BB or cell injury, that promote smooth muscle cell proliferation and dedifferentiation. Seems to play a role in the development of the embryonic vascular system.

Homo sapiens (taxid: 9606)

>sp|Q32LE9|CSRP2_BOVIN Cysteine and glycine-rich protein 2 OS=Bos taurus GN=CSRP2 PE=2 SV=3

 Score = 85.5 bits (210), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 84/179 (46%), Gaps = 13/179 (7%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M   G  +KC AC +TVY  + +  +G  +H+ CF C  C+  L  +  +  D  +YCK 
Sbjct: 1   MPVWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDEEIYCKS 60

Query: 61  HFEQLFKESG----------NFSKNFQTGKNPSSCSNQNRTPSKLSSLFS---GTQDKCA 107
            + + +   G          N  +  + G  P S      T +  +S F+   G  +KC+
Sbjct: 61  CYGKKYGPKGYGYGQGAGTLNMDRGERLGIKPESVQPHRPTTNPNTSKFAQKYGGAEKCS 120

Query: 108 ACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKG 166
            C  +VY  EK+   G  +HK CFRCA  G  L  ++    +G +YCK  +A+ F  KG
Sbjct: 121 RCGDSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKG 179

Drastically down-regulated in response to PDGF-BB or cell injury, that promote smooth muscle cell proliferation and dedifferentiation. Seems to play a role in the development of the embryonic vascular system.

Bos taurus (taxid: 9913)

>sp|Q62908|CSRP2_RAT Cysteine and glycine-rich protein 2 OS=Rattus norvegicus GN=Csrp2 PE=2 SV=3

 Score = 85.5 bits (210), Expect = 2e-16,   Method: Compositional matrix adjust.
 Identities = 54/179 (30%), Positives = 84/179 (46%), Gaps = 13/179 (7%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M   G  +KC AC +TVY  + +  +G  +H+ CF C  C+  L  +  +  D  +YCK 
Sbjct: 1   MPVWGGGNKCGACGRTVYHAEEVQCDGRTFHRCCFLCMVCRKNLDSTTVAIHDEEIYCKS 60

Query: 61  HFEQLFKESG----------NFSKNFQTGKNPSSCSNQNRTPSKLSSLFS---GTQDKCA 107
            + + +   G          N  +  + G  P S      T +  +S F+   G  +KC+
Sbjct: 61  CYGKKYGPKGYGYGQGAGTLNMDRGERLGIKPESAQPHRPTTNPNTSKFAQKYGGAEKCS 120

Query: 108 ACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKG 166
            C  +VY  EK+   G  +HK CFRCA  G  L  ++    +G +YCK  +A+ F  KG
Sbjct: 121 RCGDSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKG 179

Drastically down-regulated in response to PDGF-BB or cell injury, that promote smooth muscle cell proliferation and dedifferentiation. Seems to play a role in the development of the embryonic vascular system.

Rattus norvegicus (taxid: 10116)

>sp|Q0VFX8|CRIP2_BOVIN Cysteine-rich protein 2 OS=Bos taurus GN=CRIP2 PE=2 SV=1

 Score = 85.1 bits (209), Expect = 3e-16,   Method: Compositional matrix adjust.
 Identities = 61/184 (33%), Positives = 83/184 (45%), Gaps = 26/184 (14%)

Query: 9   KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYC-KPHFEQLFK 67
           KC  CDKTVY  + +S  G  +H+ C +C HC  TL    ++  DG  +C KP +  LF 
Sbjct: 4   KCPKCDKTVYFAEKVSSLGKDWHRFCLRCEHCSKTLTPGGHAEHDGKPFCHKPCYATLFG 63

Query: 68  E-------SGNFSKNFQTGKNPS---------------SCSNQNRTPSKLSSL--FSGTQ 103
                   +G++     + + P                  S   + PSK SS+  F+G  
Sbjct: 64  PKGVNIGGAGSYIYEKPSAEKPQVTGPIEVPVARTEERKASGPPKGPSKASSVTTFTGEP 123

Query: 104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYC-KHHFAQLF 162
           + C  C K VY  EKVT  G  +H+ C RC   G  LT   +A  DG  YC K  +  LF
Sbjct: 124 NMCPRCNKRVYFAEKVTSLGKDWHRPCLRCERCGKTLTPGGHAEHDGQPYCHKPCYGILF 183

Query: 163 MEKG 166
             KG
Sbjct: 184 GPKG 187

Bos taurus (taxid: 9913)

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	210
255541528	210	Pollen-specific protein SF3, putative [R	0.990	0.990	0.787	1e-91
224067870	206	predicted protein [Populus trichocarpa]	0.980	1.0	0.790	8e-91
297848324	205	LIM domain-containing protein [Arabidops	0.952	0.975	0.754	2e-87
8671848	261	Contains similarity to mRNA for transcri	0.961	0.773	0.747	3e-87
15223476	205	LIM domain-containing protein [Arabidops	0.961	0.985	0.747	5e-87
224130224	206	predicted protein [Populus trichocarpa]	0.976	0.995	0.763	6e-87
169908354	216	LIM domain protein 2b [Nicotiana tabacum	0.966	0.939	0.727	3e-86
297828303	225	LIM domain-containing protein [Arabidops	0.995	0.928	0.725	1e-84
356566891	216	PREDICTED: pollen-specific protein SF3-l	0.995	0.967	0.696	1e-84
225454117	220	PREDICTED: pollen-specific protein SF3 [	0.852	0.813	0.827	2e-84

>gi|255541528|ref|XP_002511828.1| Pollen-specific protein SF3, putative [Ricinus communis] gi|223549008|gb|EEF50497.1| Pollen-specific protein SF3, putative [Ricinus communis]

 Score =  341 bits (875), Expect = 1e-91,   Method: Compositional matrix adjust.
 Identities = 167/212 (78%), Positives = 185/212 (87%), Gaps = 4/212 (1%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           MAFTGTLDKCKACDKTVYVVDMLSLEG+PYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 
Sbjct: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGVPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKT 60

Query: 61  HFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVT 120
           HFEQLFKESGNFSKNFQ GK      +    PSK+SSLF GTQDKC+AC KTVYPLEKVT
Sbjct: 61  HFEQLFKESGNFSKNFQAGKTEKQNDSSRAPPSKVSSLFCGTQDKCSACGKTVYPLEKVT 120

Query: 121 MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRT 180
           MEG+CFHK+CFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKG+Y+HVL+AA+HKR 
Sbjct: 121 MEGECFHKSCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGSYTHVLQAASHKR- 179

Query: 181 ASSSSTSPAEQIENKPDDES--GAEDQTEEQS 210
            S+SST+P  ++    +D S   AED +E++S
Sbjct: 180 -STSSTTPPPELAEPTEDASAPAAEDNSEDRS 210

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224067870|ref|XP_002302574.1| predicted protein [Populus trichocarpa] gi|222844300|gb|EEE81847.1| predicted protein [Populus trichocarpa]

 Score =  338 bits (867), Expect = 8e-91,   Method: Compositional matrix adjust.
 Identities = 166/210 (79%), Positives = 180/210 (85%), Gaps = 4/210 (1%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           MAFTGTLDKCKACDKTVYVVDM+SLEG+PYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 
Sbjct: 1   MAFTGTLDKCKACDKTVYVVDMMSLEGVPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKT 60

Query: 61  HFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVT 120
           HFEQLFKE G+FSKNFQ GK P       RTPSKLSS+F GTQDKC+ C KTVYPLEKVT
Sbjct: 61  HFEQLFKEGGDFSKNFQKGK-PERTHELIRTPSKLSSVFCGTQDKCSTCGKTVYPLEKVT 119

Query: 121 MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRT 180
           MEG+C+HKTCFRCAHGGCPLTHSSYAALDGVLYCK HFAQLFMEKG YSHVL  A HKR 
Sbjct: 120 MEGECYHKTCFRCAHGGCPLTHSSYAALDGVLYCKVHFAQLFMEKGTYSHVLAGATHKR- 178

Query: 181 ASSSSTSPAEQIENKPDDESGAEDQTEEQS 210
             S+ST P E  E+  ++ + AED++EEQS
Sbjct: 179 --STSTPPPELAESNTEEAAAAEDKSEEQS 206

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297848324|ref|XP_002892043.1| LIM domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297337885|gb|EFH68302.1| LIM domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  327 bits (837), Expect = 2e-87,   Method: Compositional matrix adjust.
 Identities = 154/204 (75%), Positives = 175/204 (85%), Gaps = 4/204 (1%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M+FTGTLDKC  CDKTVYVVDMLS+EGMPYHKSCF+C+HCKGTLVMSNYSSMDGVLYCK 
Sbjct: 1   MSFTGTLDKCNVCDKTVYVVDMLSIEGMPYHKSCFRCTHCKGTLVMSNYSSMDGVLYCKT 60

Query: 61  HFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVT 120
           HFEQLFKESGNFSKNFQ GK         +TPSK+SS+F GTQDKCAACEKTVYPLEK+ 
Sbjct: 61  HFEQLFKESGNFSKNFQPGKTEKP--ELTKTPSKISSIFCGTQDKCAACEKTVYPLEKIQ 118

Query: 121 MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRT 180
           MEG+CFHKTCFRCAHGGC LTHSSYA+LD VLYC+HHF QLF+EKGNY+HVL+AANH+RT
Sbjct: 119 MEGECFHKTCFRCAHGGCTLTHSSYASLDSVLYCRHHFNQLFLEKGNYAHVLQAANHRRT 178

Query: 181 ASSSSTS--PAEQIENKPDDESGA 202
           AS ++ +  P E I  +  +E+G 
Sbjct: 179 ASGNTLTPEPTEDIAVEAKEENGV 202

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|8671848|gb|AAF78411.1|AC009273_17 Contains similarity to mRNA for transcription factor L2 from Arabidopsis thaliana gb|X91398. It contains LIM domain containing proteins PF|00412. ESTs gb|T13084 and gb|T42925 come from this gene [Arabidopsis thaliana]

 Score =  326 bits (836), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 154/206 (74%), Positives = 174/206 (84%), Gaps = 4/206 (1%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M+FTGTLDKC  CDKTVYVVDMLS+EGMPYHKSCF+C+HCKGTL MSNYSSMDGVLYCK 
Sbjct: 57  MSFTGTLDKCNVCDKTVYVVDMLSIEGMPYHKSCFRCTHCKGTLQMSNYSSMDGVLYCKT 116

Query: 61  HFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVT 120
           HFEQLFKESGNFSKNFQ GK         RTPSK+SS+F GTQDKCAACEKTVYPLEK+ 
Sbjct: 117 HFEQLFKESGNFSKNFQPGKTEKP--ELTRTPSKISSIFCGTQDKCAACEKTVYPLEKIQ 174

Query: 121 MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRT 180
           MEG+CFHKTCFRCAHGGC LTHSSYA+LD VLYC+HHF QLFMEKGNY+HVL+AANH+RT
Sbjct: 175 MEGECFHKTCFRCAHGGCTLTHSSYASLDSVLYCRHHFNQLFMEKGNYAHVLQAANHRRT 234

Query: 181 ASSSST--SPAEQIENKPDDESGAED 204
           AS ++    P E +  +  +E+G  +
Sbjct: 235 ASGNTLPPEPTEDVAVEAKEENGVSE 260

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|15223476|ref|NP_171683.1| LIM domain-containing protein [Arabidopsis thaliana] gi|107738260|gb|ABF83669.1| At1g01780 [Arabidopsis thaliana] gi|222424160|dbj|BAH20039.1| AT1G01780 [Arabidopsis thaliana] gi|332189213|gb|AEE27334.1| LIM domain-containing protein [Arabidopsis thaliana]

 Score =  325 bits (834), Expect = 5e-87,   Method: Compositional matrix adjust.
 Identities = 154/206 (74%), Positives = 174/206 (84%), Gaps = 4/206 (1%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M+FTGTLDKC  CDKTVYVVDMLS+EGMPYHKSCF+C+HCKGTL MSNYSSMDGVLYCK 
Sbjct: 1   MSFTGTLDKCNVCDKTVYVVDMLSIEGMPYHKSCFRCTHCKGTLQMSNYSSMDGVLYCKT 60

Query: 61  HFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVT 120
           HFEQLFKESGNFSKNFQ GK         RTPSK+SS+F GTQDKCAACEKTVYPLEK+ 
Sbjct: 61  HFEQLFKESGNFSKNFQPGKTEKP--ELTRTPSKISSIFCGTQDKCAACEKTVYPLEKIQ 118

Query: 121 MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRT 180
           MEG+CFHKTCFRCAHGGC LTHSSYA+LD VLYC+HHF QLFMEKGNY+HVL+AANH+RT
Sbjct: 119 MEGECFHKTCFRCAHGGCTLTHSSYASLDSVLYCRHHFNQLFMEKGNYAHVLQAANHRRT 178

Query: 181 ASSSST--SPAEQIENKPDDESGAED 204
           AS ++    P E +  +  +E+G  +
Sbjct: 179 ASGNTLPPEPTEDVAVEAKEENGVSE 204

Source: Arabidopsis thaliana

Species: Arabidopsis thaliana

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224130224|ref|XP_002320783.1| predicted protein [Populus trichocarpa] gi|222861556|gb|EEE99098.1| predicted protein [Populus trichocarpa]

 Score =  325 bits (834), Expect = 6e-87,   Method: Compositional matrix adjust.
 Identities = 161/211 (76%), Positives = 180/211 (85%), Gaps = 6/211 (2%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           MAFTGTLDKCKACDKTVY VDM+SLEG+PYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 
Sbjct: 1   MAFTGTLDKCKACDKTVYFVDMMSLEGVPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKT 60

Query: 61  HFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVT 120
           HFEQLFKE G+FSKNFQ GK P    + +R PSKLSS+F GTQDKC+AC KTVYPLEKVT
Sbjct: 61  HFEQLFKEGGDFSKNFQKGK-PERTHDLSRIPSKLSSVFCGTQDKCSACGKTVYPLEKVT 119

Query: 121 MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRT 180
           MEG+C+HKTCFRCAHGGCPLTHSSYAALDGVLYCK HFAQLFMEKG YSHVL +A HKR 
Sbjct: 120 MEGECYHKTCFRCAHGGCPLTHSSYAALDGVLYCKVHFAQLFMEKGTYSHVLASAAHKR- 178

Query: 181 ASSSSTSPAEQIENKPDDESGAEDQT-EEQS 210
              S+++P E   + P++ +  E++  EEQS
Sbjct: 179 ---SNSTPPELAGSNPEEGAAVEEEKPEEQS 206

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|169908354|gb|ACB05475.1| LIM domain protein 2b [Nicotiana tabacum]

 Score =  323 bits (828), Expect = 3e-86,   Method: Compositional matrix adjust.
 Identities = 152/209 (72%), Positives = 177/209 (84%), Gaps = 6/209 (2%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           MAFTGTLDKCKACDKTVY VD+L+ +G+ YHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP
Sbjct: 1   MAFTGTLDKCKACDKTVYFVDLLTADGITYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60

Query: 61  HFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVT 120
           HFEQLFKE GNFSKNFQT   P       RTPSKLS++FSGTQDKCAAC KTVYPLEKVT
Sbjct: 61  HFEQLFKECGNFSKNFQTSAKPEREHALTRTPSKLSAMFSGTQDKCAACNKTVYPLEKVT 120

Query: 121 MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRT 180
           MEG+ FHK+CF+CAHGGCPLTH++YA+LDGVLYCKHHFAQLFMEKG Y HVL+AAN+K+ 
Sbjct: 121 MEGESFHKSCFKCAHGGCPLTHATYASLDGVLYCKHHFAQLFMEKGTYQHVLEAANNKKI 180

Query: 181 ASSSSTSPAEQIENKPDDESGAEDQTEEQ 209
            + + T+      N+P+D+  A++  ++Q
Sbjct: 181 NAETPTN------NEPEDDEAAKETIDKQ 203

Source: Nicotiana tabacum

Species: Nicotiana tabacum

Genus: Nicotiana

Family: Solanaceae

Order: Solanales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|297828303|ref|XP_002882034.1| LIM domain-containing protein [Arabidopsis lyrata subsp. lyrata] gi|297327873|gb|EFH58293.1| LIM domain-containing protein [Arabidopsis lyrata subsp. lyrata]

 Score =  318 bits (815), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 153/211 (72%), Positives = 180/211 (85%), Gaps = 2/211 (0%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M+FTGTLDKCKACDKTVYV+D+L+LEG  YHKSCF+CSHCKGTLV+SNYSSMDGVLYCKP
Sbjct: 1   MSFTGTLDKCKACDKTVYVMDLLTLEGNTYHKSCFRCSHCKGTLVISNYSSMDGVLYCKP 60

Query: 61  HFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVT 120
           HFEQLFKESGN+SKNFQTGK      +  RTPSKLSS FSGTQDKCA C+KTVYPLEKVT
Sbjct: 61  HFEQLFKESGNYSKNFQTGKTEKPNDHLTRTPSKLSSFFSGTQDKCATCKKTVYPLEKVT 120

Query: 121 MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLK-AANHKR 179
           MEG+ +HKTCFRC+H GCPLTHSSYA+L+GVLYCK HF QLF+EKG+Y+HV + AANH+R
Sbjct: 121 MEGESYHKTCFRCSHSGCPLTHSSYASLNGVLYCKVHFNQLFLEKGSYNHVHQAAANHRR 180

Query: 180 TASSSSTSPAEQIENKPDDESGAEDQTEEQS 210
           +ASS   SP    ++KP+D +   +  E++S
Sbjct: 181 SASSGGASPPSD-DHKPEDSASIPEGKEDES 210

Source: Arabidopsis lyrata subsp. lyrata

Species: Arabidopsis lyrata

Genus: Arabidopsis

Family: Brassicaceae

Order: Brassicales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|356566891|ref|XP_003551659.1| PREDICTED: pollen-specific protein SF3-like [Glycine max]

 Score =  318 bits (814), Expect = 1e-84,   Method: Compositional matrix adjust.
 Identities = 147/211 (69%), Positives = 176/211 (83%), Gaps = 2/211 (0%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M+FTGT DKCKACDKTVYVVDML+LEG+PYHK+CF+CSHCKG L M+ YSSMDGVLYCKP
Sbjct: 1   MSFTGTTDKCKACDKTVYVVDMLTLEGIPYHKNCFRCSHCKGYLTMNTYSSMDGVLYCKP 60

Query: 61  HFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVT 120
           HFEQLFKESGNFSKNFQT K+    +  N+ P++LSS+FSGT DKC+ C KTVYPLEK+T
Sbjct: 61  HFEQLFKESGNFSKNFQTAKSSDKQNETNKAPNRLSSMFSGTLDKCSVCSKTVYPLEKMT 120

Query: 121 MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRT 180
           +EG+C+HK CFRCAH GC LTHSSYAALDGVLYC+HHF QLFMEKGNY HVL++ANHK+ 
Sbjct: 121 LEGECYHKNCFRCAHAGCHLTHSSYAALDGVLYCRHHFQQLFMEKGNYHHVLQSANHKKN 180

Query: 181 ASSSSTSPAEQIENKP--DDESGAEDQTEEQ 209
            +     PA + + +P   +ES +E+ TEE+
Sbjct: 181 VTPEPAEPAAEGDEEPPKPEESDSEEHTEEK 211

Source: Glycine max

Species: Glycine max

Genus: Glycine

Family: Fabaceae

Order: Fabales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225454117|ref|XP_002269537.1| PREDICTED: pollen-specific protein SF3 [Vitis vinifera] gi|147796476|emb|CAN74803.1| hypothetical protein VITISV_006290 [Vitis vinifera]

 Score =  317 bits (812), Expect = 2e-84,   Method: Compositional matrix adjust.
 Identities = 149/180 (82%), Positives = 166/180 (92%), Gaps = 1/180 (0%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           MAFTGTLDKCKACDKTVYVVD+LS +G  YHK+CFKCSHCKGTLVMSNYSSMDGVLYCKP
Sbjct: 1   MAFTGTLDKCKACDKTVYVVDLLSADGASYHKTCFKCSHCKGTLVMSNYSSMDGVLYCKP 60

Query: 61  HFEQLFKESGNFSKNFQTGKNPSSCSNQ-NRTPSKLSSLFSGTQDKCAACEKTVYPLEKV 119
           HFEQLFKESGNFSKNFQT   P+   N+ +R PSKLSS+FSGTQDKC+AC KTVYPLEKV
Sbjct: 61  HFEQLFKESGNFSKNFQTSAKPADKLNELSRAPSKLSSMFSGTQDKCSACRKTVYPLEKV 120

Query: 120 TMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKR 179
           T+EG+ +HK+CF+CAHGGCPLTHSSYAAL+GVLYCKHHF+QLFMEKGNYSHVL+AA HK+
Sbjct: 121 TLEGESYHKSCFKCAHGGCPLTHSSYAALNGVLYCKHHFSQLFMEKGNYSHVLEAATHKK 180

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

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	210
TAIR|locus:2198210	205	PLIM2b "PLIM2b" [Arabidopsis t	0.961	0.985	0.747	2.6e-86
TAIR|locus:2050735	226	PLIM2a "PLIM2a" [Arabidopsis t	0.995	0.924	0.715	3.4e-84
TAIR|locus:2098871	213	PLIM2c "PLIM2c" [Arabidopsis t	0.980	0.967	0.717	5e-83
TAIR|locus:2061171	200	WLIM2a "WLIM2a" [Arabidopsis t	0.933	0.98	0.62	8.6e-72
TAIR|locus:2012798	190	WLIM1 "AT1G10200" [Arabidopsis	0.814	0.9	0.525	8e-53
MGI|MGI:1330824	194	Csrp3 "cysteine and glycine-ri	0.742	0.804	0.356	6.3e-21
UNIPROTKB|D2SQP3	194	CSRP3 "Cysteine and glycine-ri	0.738	0.798	0.342	1e-20
RGD|71092	194	Csrp3 "cysteine and glycine-ri	0.742	0.804	0.356	1.3e-20
UNIPROTKB|P50463	194	Csrp3 "Cysteine and glycine-ri	0.742	0.804	0.356	1.3e-20
UNIPROTKB|E2R9P5	194	CSRP3 "Uncharacterized protein	0.738	0.798	0.337	2.7e-20

TAIR|locus:2198210 PLIM2b "PLIM2b" [Arabidopsis thaliana (taxid:3702)]

 Score = 863 (308.9 bits), Expect = 2.6e-86, P = 2.6e-86
 Identities = 154/206 (74%), Positives = 174/206 (84%)

Query:     1 MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
             M+FTGTLDKC  CDKTVYVVDMLS+EGMPYHKSCF+C+HCKGTL MSNYSSMDGVLYCK 
Sbjct:     1 MSFTGTLDKCNVCDKTVYVVDMLSIEGMPYHKSCFRCTHCKGTLQMSNYSSMDGVLYCKT 60

Query:    61 HFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVT 120
             HFEQLFKESGNFSKNFQ GK         RTPSK+SS+F GTQDKCAACEKTVYPLEK+ 
Sbjct:    61 HFEQLFKESGNFSKNFQPGKTEKP--ELTRTPSKISSIFCGTQDKCAACEKTVYPLEKIQ 118

Query:   121 MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRT 180
             MEG+CFHKTCFRCAHGGC LTHSSYA+LD VLYC+HHF QLFMEKGNY+HVL+AANH+RT
Sbjct:   119 MEGECFHKTCFRCAHGGCTLTHSSYASLDSVLYCRHHFNQLFMEKGNYAHVLQAANHRRT 178

Query:   181 ASSSST--SPAEQIENKPDDESGAED 204
             AS ++    P E +  +  +E+G  +
Sbjct:   179 ASGNTLPPEPTEDVAVEAKEENGVSE 204

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

GO:0051017 "actin filament bundle assembly" evidence=IDA

GO:0006944 "cellular membrane fusion" evidence=RCA

TAIR|locus:2050735 PLIM2a "PLIM2a" [Arabidopsis thaliana (taxid:3702)]

 Score = 843 (301.8 bits), Expect = 3.4e-84, P = 3.4e-84
 Identities = 151/211 (71%), Positives = 177/211 (83%)

Query:     1 MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
             M+FTGTLDKCKACDKTVYV+D+L+LEG  YHKSCF+C+HCKGTLV+SNYSSMDGVLYCKP
Sbjct:     1 MSFTGTLDKCKACDKTVYVMDLLTLEGNTYHKSCFRCTHCKGTLVISNYSSMDGVLYCKP 60

Query:    61 HFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVT 120
             HFEQLFKESGN+SKNFQ GK      +  RTPSKLSS FSGTQDKCA C+KTVYPLEKVT
Sbjct:    61 HFEQLFKESGNYSKNFQAGKTEKPNDHLTRTPSKLSSFFSGTQDKCATCKKTVYPLEKVT 120

Query:   121 MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAA-NHKR 179
             MEG+ +HKTCFRC H GCPLTHSSYA+L+GVLYCK HF QLF+EKG+Y+HV +AA NH+R
Sbjct:   121 MEGESYHKTCFRCTHSGCPLTHSSYASLNGVLYCKVHFNQLFLEKGSYNHVHQAAANHRR 180

Query:   180 TASSSSTSPAEQIENKPDDESGAEDQTEEQS 210
             +ASS   SP    ++KPDD +   +  E+ +
Sbjct:   181 SASSGGASPPSD-DHKPDDTASIPEAKEDDA 210

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

GO:0051017 "actin filament bundle assembly" evidence=IDA

GO:0006944 "cellular membrane fusion" evidence=RCA

TAIR|locus:2098871 PLIM2c "PLIM2c" [Arabidopsis thaliana (taxid:3702)]

 Score = 832 (297.9 bits), Expect = 5.0e-83, P = 5.0e-83
 Identities = 150/209 (71%), Positives = 173/209 (82%)

Query:     2 AFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPH 61
             AFTGT DKCKACDKTVYV+D+++LEGMPYHKSCF+CSHC GTLV+ NYSSMDGVLYCK H
Sbjct:     3 AFTGTTDKCKACDKTVYVMDLMTLEGMPYHKSCFRCSHCNGTLVICNYSSMDGVLYCKTH 62

Query:    62 FEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTM 121
             FEQLFKESGNFSKNFQT       ++  + P++LSS FSGTQDKCAAC+KTVYPLEK+TM
Sbjct:    63 FEQLFKESGNFSKNFQTAGKTEKSNDATKAPNRLSSFFSGTQDKCAACKKTVYPLEKMTM 122

Query:   122 EGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAA-NHKR- 179
             EG+ +HKTCFRCAH GCPLTHSSYAALDGVLYCK HF+QLF+EKGNY+HVL+AA NH+R 
Sbjct:   123 EGESYHKTCFRCAHSGCPLTHSSYAALDGVLYCKVHFSQLFLEKGNYNHVLQAAANHRRS 182

Query:   180 TASSSSTSPAEQIENKPDDESGAEDQTEE 208
             TA    T P E  E  P +E  ++   EE
Sbjct:   183 TAEEDKTEPKED-EANPTEEETSDAAAEE 210

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

GO:0051017 "actin filament bundle assembly" evidence=IDA

GO:0006944 "cellular membrane fusion" evidence=RCA

TAIR|locus:2061171 WLIM2a "WLIM2a" [Arabidopsis thaliana (taxid:3702)]

 Score = 726 (260.6 bits), Expect = 8.6e-72, P = 8.6e-72
 Identities = 124/200 (62%), Positives = 166/200 (83%)

Query:     1 MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
             M+FTGT  KC+AC+KTVY V++LS +G+ YHK+CFKCSHCK  L +SNYSSM+GV+YC+P
Sbjct:     1 MSFTGTQQKCRACEKTVYPVELLSADGISYHKACFKCSHCKSRLQLSNYSSMEGVVYCRP 60

Query:    61 HFEQLFKESGNFSKNFQTGKNPSS---CSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLE 117
             HFEQLFKESG+FSKNFQ+   P +       NRTPS+L+ +FSGTQDKCA C KTVYP+E
Sbjct:    61 HFEQLFKESGSFSKNFQSPAKPLTDKPTPELNRTPSRLAGMFSGTQDKCATCTKTVYPIE 120

Query:   118 KVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANH 177
             KVT+E  C+HK+CF+C+HGGCP++ S+YAAL+G+LYCKHHFAQLF EKG+Y+H++K+A+ 
Sbjct:   121 KVTVESQCYHKSCFKCSHGGCPISPSNYAALEGILYCKHHFAQLFKEKGSYNHLIKSASI 180

Query:   178 KRTASSSSTSPAEQIENKPD 197
             KR A++++T+ A  +   P+
Sbjct:   181 KR-ATAAATAAAAAVAAVPE 199

GO:0008270 "zinc ion binding" evidence=IEA

GO:0051015 "actin filament binding" evidence=IDA

GO:0051017 "actin filament bundle assembly" evidence=IDA

GO:0000271 "polysaccharide biosynthetic process" evidence=RCA

GO:0006944 "cellular membrane fusion" evidence=RCA

GO:0009825 "multidimensional cell growth" evidence=RCA

GO:0009932 "cell tip growth" evidence=RCA

GO:0010817 "regulation of hormone levels" evidence=RCA

GO:0043481 "anthocyanin accumulation in tissues in response to UV light" evidence=RCA

GO:0048767 "root hair elongation" evidence=RCA

GO:0071555 "cell wall organization" evidence=RCA

TAIR|locus:2012798 WLIM1 "AT1G10200" [Arabidopsis thaliana (taxid:3702)]

 Score = 547 (197.6 bits), Expect = 8.0e-53, P = 8.0e-53
 Identities = 92/175 (52%), Positives = 125/175 (71%)

Query:     1 MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
             MAF GT  KC ACDKTVY+VD L+ +   YHK+CF+C HCKGTL +SNY+S +GVLYC+P
Sbjct:     1 MAFAGTTQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNYNSFEGVLYCRP 60

Query:    61 HFEQLFKESGNFSKNFQ----TGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPL 116
             HF+Q FK +G+  K+F+     GK       +    +K+S++F GT++KC  C+KTVYP+
Sbjct:    61 HFDQNFKRTGSLEKSFEGTPKIGKPDRPLEGERPAGTKVSNMFGGTREKCVGCDKTVYPI 120

Query:   117 EKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHV 171
             EKV++ G  +HK+CF+C HGGC ++ S+Y A +G LYCKHH  QL  EKGN S +
Sbjct:   121 EKVSVNGTLYHKSCFKCTHGGCTISPSNYIAHEGKLYCKHHHIQLIKEKGNLSQL 175

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

GO:0005737 "cytoplasm" evidence=ISM

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005886 "plasma membrane" evidence=IDA

GO:0051015 "actin filament binding" evidence=IDA

GO:0051017 "actin filament bundle assembly" evidence=IDA

GO:0006944 "cellular membrane fusion" evidence=RCA

MGI|MGI:1330824 Csrp3 "cysteine and glycine-rich protein 3" [Mus musculus (taxid:10090)]

 Score = 246 (91.7 bits), Expect = 6.3e-21, P = 6.3e-21
 Identities = 62/174 (35%), Positives = 87/174 (50%)

Query:     9 KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK--------P 60
             KC AC+KTVY  + +   G  +HK+CF C  C+  L  +  ++ +  +YCK        P
Sbjct:     9 KCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCYGRRYGP 68

Query:    61 H---FEQ----LFKESG-NFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKT 112
                 F Q    L  ++G +    FQ    P+  +  +  PSK S+ F G  +KC  C K+
Sbjct:    69 KGIGFGQGAGCLSTDTGEHLGLQFQQSPKPARAATTSN-PSKFSAKF-GESEKCPRCGKS 126

Query:   113 VYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKG 166
             VY  EKV   G  +HKTCFRCA  G  L  ++    DG LYCK  +A+ F   G
Sbjct:   127 VYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGPTG 180

GO:0002026 "regulation of the force of heart contraction" evidence=IGI

GO:0003300 "cardiac muscle hypertrophy" evidence=ISO

GO:0005515 "protein binding" evidence=IPI

GO:0005634 "nucleus" evidence=ISO

GO:0005737 "cytoplasm" evidence=ISO

GO:0005856 "cytoskeleton" evidence=IEA

GO:0006874 "cellular calcium ion homeostasis" evidence=IGI

GO:0007275 "multicellular organismal development" evidence=IEA

GO:0007517 "muscle organ development" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008307 "structural constituent of muscle" evidence=ISO;IMP

GO:0030018 "Z disc" evidence=ISO;IDA

GO:0030154 "cell differentiation" evidence=IEA

GO:0031433 "telethonin binding" evidence=ISO;IPI

GO:0033365 "protein localization to organelle" evidence=ISO;IMP

GO:0035995 "detection of muscle stretch" evidence=ISO;IMP

GO:0042805 "actinin binding" evidence=IDA

GO:0046872 "metal ion binding" evidence=IEA

GO:0048738 "cardiac muscle tissue development" evidence=IGI

GO:0055003 "cardiac myofibril assembly" evidence=IMP

GO:0060048 "cardiac muscle contraction" evidence=ISO;IMP

UNIPROTKB|D2SQP3 CSRP3 "Cysteine and glycine-rich protein 3" [Sus scrofa (taxid:9823)]

 Score = 244 (91.0 bits), Expect = 1.0e-20, P = 1.0e-20
 Identities = 60/175 (34%), Positives = 85/175 (48%)

Query:     9 KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE 68
             KC ACDKTVY  + +   G  +HK+CF C  C+  L  +  ++ +  +YCK  + + +  
Sbjct:     9 KCGACDKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCYGRRYGP 68

Query:    69 SG----------------NFSKNFQTGKNPS-SCSNQNRTPSKLSSLFSGTQDKCAACEK 111
              G                +    FQ    P+ S +  N  PSK ++ F G  +KC  C K
Sbjct:    69 KGIGYGQGAGCLSTDTGEHLGLQFQQSPKPARSATTSN--PSKFTAKF-GESEKCPRCGK 125

Query:   112 TVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKG 166
             +VY  EKV   G  +HKTCFRCA  G  L  ++    DG LYCK  +A+ F   G
Sbjct:   126 SVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGPTG 180

GO:0060048 "cardiac muscle contraction" evidence=IEA

GO:0055003 "cardiac myofibril assembly" evidence=IEA

GO:0042805 "actinin binding" evidence=IEA

GO:0035995 "detection of muscle stretch" evidence=IEA

GO:0033365 "protein localization to organelle" evidence=IEA

GO:0031433 "telethonin binding" evidence=IEA

GO:0030018 "Z disc" evidence=IEA

GO:0008307 "structural constituent of muscle" evidence=IEA

GO:0006874 "cellular calcium ion homeostasis" evidence=IEA

GO:0003300 "cardiac muscle hypertrophy" evidence=IEA

GO:0002026 "regulation of the force of heart contraction" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

RGD|71092 Csrp3 "cysteine and glycine-rich protein 3 (cardiac LIM protein)" [Rattus norvegicus (taxid:10116)]

 Score = 243 (90.6 bits), Expect = 1.3e-20, P = 1.3e-20
 Identities = 62/174 (35%), Positives = 86/174 (49%)

Query:     9 KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK--------P 60
             KC ACDKTVY  + +   G  +HK+CF C  C+  L  +  ++ +  +YCK        P
Sbjct:     9 KCGACDKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCYGRKYGP 68

Query:    61 H---FEQ----LFKESG-NFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKT 112
                 F Q    L  ++G +    FQ    P+  +  +  PSK S+ F G  +KC  C K+
Sbjct:    69 KGIGFGQGAGCLSTDTGEHLGLQFQQSPKPARAATTSN-PSKFSAKF-GESEKCPRCGKS 126

Query:   113 VYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKG 166
             VY  EKV   G  +HKTCF CA  G  L  ++    DG LYCK  +A+ F   G
Sbjct:   127 VYAAEKVMGGGKPWHKTCFPCAICGKSLESTNVTDKDGELYCKVCYAKNFGPTG 180

GO:0001974 "blood vessel remodeling" evidence=IEP

GO:0002026 "regulation of the force of heart contraction" evidence=IEA;ISO

GO:0003300 "cardiac muscle hypertrophy" evidence=IEA;ISO

GO:0005634 "nucleus" evidence=IDA

GO:0005737 "cytoplasm" evidence=IDA

GO:0005856 "cytoskeleton" evidence=IEA

GO:0006874 "cellular calcium ion homeostasis" evidence=IEA;ISO

GO:0007517 "muscle organ development" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

GO:0008307 "structural constituent of muscle" evidence=IEA;ISO

GO:0030018 "Z disc" evidence=IEA;ISO;IDA

GO:0030154 "cell differentiation" evidence=IEA

GO:0031433 "telethonin binding" evidence=IEA;ISO

GO:0033365 "protein localization to organelle" evidence=IEA;ISO

GO:0035995 "detection of muscle stretch" evidence=IEA;ISO

GO:0042805 "actinin binding" evidence=IEA;ISO

GO:0048738 "cardiac muscle tissue development" evidence=ISO

GO:0055003 "cardiac myofibril assembly" evidence=IEA;ISO

GO:0060048 "cardiac muscle contraction" evidence=IEA;ISO

UNIPROTKB|P50463 Csrp3 "Cysteine and glycine-rich protein 3" [Rattus norvegicus (taxid:10116)]

 Score = 243 (90.6 bits), Expect = 1.3e-20, P = 1.3e-20
 Identities = 62/174 (35%), Positives = 86/174 (49%)

Query:     9 KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK--------P 60
             KC ACDKTVY  + +   G  +HK+CF C  C+  L  +  ++ +  +YCK        P
Sbjct:     9 KCGACDKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCYGRKYGP 68

Query:    61 H---FEQ----LFKESG-NFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKT 112
                 F Q    L  ++G +    FQ    P+  +  +  PSK S+ F G  +KC  C K+
Sbjct:    69 KGIGFGQGAGCLSTDTGEHLGLQFQQSPKPARAATTSN-PSKFSAKF-GESEKCPRCGKS 126

Query:   113 VYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKG 166
             VY  EKV   G  +HKTCF CA  G  L  ++    DG LYCK  +A+ F   G
Sbjct:   127 VYAAEKVMGGGKPWHKTCFPCAICGKSLESTNVTDKDGELYCKVCYAKNFGPTG 180

GO:0008270 "zinc ion binding" evidence=IEA

UNIPROTKB|E2R9P5 CSRP3 "Uncharacterized protein" [Canis lupus familiaris (taxid:9615)]

 Score = 240 (89.5 bits), Expect = 2.7e-20, P = 2.7e-20
 Identities = 59/175 (33%), Positives = 85/175 (48%)

Query:     9 KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE 68
             KC AC+KTVY  + +   G  +HK+CF C  C+  L  +  ++ +  +YCK  + + +  
Sbjct:     9 KCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVCYGRRYGP 68

Query:    69 SG----------------NFSKNFQTGKNPS-SCSNQNRTPSKLSSLFSGTQDKCAACEK 111
              G                +    FQ    P+ S +  N  PSK ++ F G  +KC  C K
Sbjct:    69 KGIGYGQGAGCLSTDTGEHLGLQFQQSPKPARSATTSN--PSKFTAKF-GESEKCPRCGK 125

Query:   112 TVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKG 166
             +VY  EKV   G  +HKTCFRCA  G  L  ++    DG LYCK  +A+ F   G
Sbjct:   126 SVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFGPTG 180

GO:0060048 "cardiac muscle contraction" evidence=IEA

GO:0055003 "cardiac myofibril assembly" evidence=IEA

GO:0042805 "actinin binding" evidence=IEA

GO:0035995 "detection of muscle stretch" evidence=IEA

GO:0033365 "protein localization to organelle" evidence=IEA

GO:0031433 "telethonin binding" evidence=IEA

GO:0030018 "Z disc" evidence=IEA

GO:0008307 "structural constituent of muscle" evidence=IEA

GO:0006874 "cellular calcium ion homeostasis" evidence=IEA

GO:0003300 "cardiac muscle hypertrophy" evidence=IEA

GO:0002026 "regulation of the force of heart contraction" evidence=IEA

GO:0008270 "zinc ion binding" evidence=IEA

---

Prediction of Enzyme Commission (EC) Number

EC Number Prediction by Annotation Transfer from SWISS-PROT Entries

Original result of BLAST against SWISS-PROT

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

EC Number Prediction by 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	210
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	2e-37
cd09441	61	cd09441, LIM2_SF3, The second Lim domain of pollen	5e-32
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	2e-22
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	9e-21
cd09441	61	cd09441, LIM2_SF3, The second Lim domain of pollen	1e-20
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	2e-20
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	1e-13
cd09439	55	cd09439, LIM_Mical, The LIM domain of Mical (molec	2e-13
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	1e-12
pfam00412	58	pfam00412, LIM, LIM domain	1e-12
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	6e-12
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	8e-12
cd09445	53	cd09445, LIM_Mical_like_2, This domain belongs to	4e-11
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	5e-11
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	1e-10
pfam00412	58	pfam00412, LIM, LIM domain	3e-10
cd09439	55	cd09439, LIM_Mical, The LIM domain of Mical (molec	4e-10
cd09445	53	cd09445, LIM_Mical_like_2, This domain belongs to	4e-10
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	4e-10
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	1e-09
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	2e-09
cd09443	55	cd09443, LIM_Ltd-1, The LIM domain of LIM and tran	4e-09
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	6e-09
cd09443	55	cd09443, LIM_Ltd-1, The LIM domain of LIM and tran	9e-09
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	1e-08
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	3e-08
cd09403	54	cd09403, LIM2_CRP, The second LIM domain of Cystei	3e-08
cd09482	54	cd09482, LIM2_CRP3, The second LIM domain of Cyste	3e-07
cd09326	53	cd09326, LIM_CRP_like, The LIM domains of Cysteine	4e-07
cd09482	54	cd09482, LIM2_CRP3, The second LIM domain of Cyste	7e-07
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	7e-07
cd09403	54	cd09403, LIM2_CRP, The second LIM domain of Cystei	1e-06
cd09326	53	cd09326, LIM_CRP_like, The LIM domains of Cysteine	1e-06
cd09404	54	cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84	1e-06
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	5e-06
cd09840	54	cd09840, LIM2_CRP2, The second LIM domain of Cyste	5e-06
cd09481	54	cd09481, LIM1_CRP3, The first LIM domain of Cystei	7e-06
cd09444	55	cd09444, LIM_Mical_like_1, This domain belongs to	9e-06
cd09840	54	cd09840, LIM2_CRP2, The second LIM domain of Cyste	1e-05
cd09402	53	cd09402, LIM1_CRP, The first LIM domain of Cystein	1e-05
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	1e-05
cd09400	61	cd09400, LIM_like_1, LIM domain in proteins of unk	3e-05
cd09402	53	cd09402, LIM1_CRP, The first LIM domain of Cystein	8e-05
cd09446	53	cd09446, LIM_N_RAP, The LIM domain of N-RAP	8e-05
cd09479	56	cd09479, LIM1_CRP1, The first LIM domain of Cystei	9e-05
cd09481	54	cd09481, LIM1_CRP3, The first LIM domain of Cystei	1e-04
cd09476	54	cd09476, LIM1_TLP, The first LIM domain of thymus	1e-04
cd09444	55	cd09444, LIM_Mical_like_1, This domain belongs to	2e-04
cd09479	56	cd09479, LIM1_CRP1, The first LIM domain of Cystei	2e-04
cd09478	54	cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich	2e-04
cd09477	54	cd09477, LIM2_TLP, The second LIM domain of thymus	2e-04
cd09404	54	cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84	3e-04
cd09400	61	cd09400, LIM_like_1, LIM domain in proteins of unk	3e-04
cd09480	55	cd09480, LIM1_CRP2, The first LIM domain of Cystei	4e-04
cd09477	54	cd09477, LIM2_TLP, The second LIM domain of thymus	5e-04
cd09480	55	cd09480, LIM1_CRP2, The first LIM domain of Cystei	5e-04
cd09414	58	cd09414, LIM1_LIMPETin, The first LIM domain of pr	7e-04
cd09478	54	cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich	8e-04
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	8e-04
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	8e-04
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	0.002
cd09446	53	cd09446, LIM_N_RAP, The LIM domain of N-RAP	0.002
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	0.002
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	0.002
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	0.002
cd09329	52	cd09329, LIM3_abLIM, The third LIM domain of actin	0.003
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	0.003
cd09371	53	cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b	0.003
cd09476	54	cd09476, LIM1_TLP, The first LIM domain of thymus	0.004

>gnl|CDD|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific protein SF3

 Score =  124 bits (312), Expect = 2e-37
 Identities = 51/63 (80%), Positives = 57/63 (90%)

Query: 6  TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQL 65
          T  KCKACDKTVY+VD LS +G+ YHKSCF+CSHCKGTL +SNYSSM+GVLYCKPHFEQL
Sbjct: 1  TTQKCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 60

Query: 66 FKE 68
          FKE
Sbjct: 61 FKE 63

The first Lim domain of pollen specific protein SF3: SF3 is a Lim protein that is found exclusively in mature plant pollen grains. It contains two LIM domains. The exact function of SF3 is unknown. It may be a transcription factor required for the expression of late pollen genes. It is possible that SF3 protein is involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 63

>gnl|CDD|188825 cd09441, LIM2_SF3, The second Lim domain of pollen specific protein SF3

 Score =  110 bits (276), Expect = 5e-32
 Identities = 40/61 (65%), Positives = 51/61 (83%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEK 165
           C AC KTVYP+EKVT+EG  +HK+CF+C+HGGC ++ S+YAA +G LYCKHH +QLF EK
Sbjct: 1   CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60

Query: 166 G 166
           G
Sbjct: 61  G 61

The second Lim domain of pollen specific protein SF3: SF3 is a Lim protein that is found exclusively in mature plant pollen grains. It contains two LIM domains. The exact function of SF3 is unknown. It may be a transcription factor required for the expression of late pollen genes. It is possible that SF3 protein is involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization. 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 = 61

>gnl|CDD|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific protein SF3

 Score = 85.6 bits (212), Expect = 2e-22
 Identities = 32/63 (50%), Positives = 47/63 (74%)

Query: 102 TQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQL 161
           T  KC AC+KTVY +++++ +G  +HK+CFRC+H    L  S+Y++++GVLYCK HF QL
Sbjct: 1   TTQKCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 60

Query: 162 FME 164
           F E
Sbjct: 61  FKE 63

The first Lim domain of pollen specific protein SF3: SF3 is a Lim protein that is found exclusively in mature plant pollen grains. It contains two LIM domains. The exact function of SF3 is unknown. It may be a transcription factor required for the expression of late pollen genes. It is possible that SF3 protein is involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 63

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

 Score = 81.2 bits (201), Expect = 9e-21
 Identities = 30/53 (56%), Positives = 39/53 (73%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
          C  C KTVY ++ L  +G  +HKSCF+CSHC  TL + NY+S++G LYCKPHF
Sbjct: 1  CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPHF 53

The LIM domain of Mical (molecule interacting with CasL) like family: Known members of this family includes LIM domain containing proteins; Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2) and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth and mobility. Eplin has also found to be tumor suppressor. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs.. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188825 cd09441, LIM2_SF3, The second Lim domain of pollen specific protein SF3

 Score = 81.0 bits (200), Expect = 1e-20
 Identities = 35/61 (57%), Positives = 44/61 (72%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKES 69
          C AC KTVY ++ +++EG  YHKSCFKCSH   T+  SNY++ +G LYCK H  QLFKE 
Sbjct: 1  CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60

Query: 70 G 70
          G
Sbjct: 61 G 61

The second Lim domain of pollen specific protein SF3: SF3 is a Lim protein that is found exclusively in mature plant pollen grains. It contains two LIM domains. The exact function of SF3 is unknown. It may be a transcription factor required for the expression of late pollen genes. It is possible that SF3 protein is involved in controlling pollen-specific processes such as male gamete maturation, pollen tube formation, or even fertilization. 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 = 61

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

 Score = 80.4 bits (199), Expect = 2e-20
 Identities = 29/53 (54%), Positives = 38/53 (71%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
           CA C KTVYP+E++  +G  FHK+CFRC+H    L   +YA+L+G LYCK HF
Sbjct: 1   CAVCGKTVYPMERLVADGKLFHKSCFRCSHCNKTLRLGNYASLEGKLYCKPHF 53

The LIM domain of Mical (molecule interacting with CasL) like family: Known members of this family includes LIM domain containing proteins; Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2) and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth and mobility. Eplin has also found to be tumor suppressor. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs.. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188826 cd09442, LIM_Eplin_like, The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins

 Score = 62.5 bits (152), Expect = 1e-13
 Identities = 25/53 (47%), Positives = 34/53 (64%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
          C  C K VY ++ L  +   +HKSCF+C HC   L + NY+S+ G +YCKPHF
Sbjct: 1  CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHGRIYCKPHF 53

The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins: This family contains Epithelial Protein Lost in Neoplasm in Neoplasm (Eplin), xin actin-binding repeat-containing protein 2 (XIRP2) and a group of protein with unknown function. The members of this family all contain a single LIM domain. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. Xirp2 contains a LIM domain and Xin re peats for binding to and stabilising F-actin. Xirp2 is expressed in muscles and is significantly induced in the heart in response to systemic administration of angiotensin II. Xirp2 is an important effector of the Ang II signaling pathway in the heart. The expression of Xirp2 is activated by myocyte enhancer factor (MEF)2A, whose transcriptional activity is stimulated by angiotersin II. Thus, Xirp2 plays important pathological roles in the angiotensin II induced hypertension. 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|188823 cd09439, LIM_Mical, The LIM domain of Mical (molecule interacting with CasL)

 Score = 62.3 bits (152), Expect = 2e-13
 Identities = 29/55 (52%), Positives = 37/55 (67%), Gaps = 2/55 (3%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYS--SMDGVLYCKPHF 62
          C  C K VYV++ LS EG+ +H+SCFKCS+C  TL +  Y+    DG  YCKPHF
Sbjct: 1  CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKPHF 55

The LIM domain of Mical (molecule interacting with CasL): MICAL is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semapho-rin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM domain and calporin homology domain are known for interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein monooxygenase (MO) is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. In addition, MICAL was characterized to interact with Rab13 and Rab8 to coordinate the assembly of tight junctions and adherens junctions in epithelial cells. Thus, MICAL was also named junctional Rab13-binding protein (JRAB). 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|188826 cd09442, LIM_Eplin_like, The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins

 Score = 59.8 bits (145), Expect = 1e-12
 Identities = 25/53 (47%), Positives = 35/53 (66%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
           C  C+K VYP+E++  +   FHK+CFRC H    L+  +YA+L G +YCK HF
Sbjct: 1   CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHGRIYCKPHF 53

The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins: This family contains Epithelial Protein Lost in Neoplasm in Neoplasm (Eplin), xin actin-binding repeat-containing protein 2 (XIRP2) and a group of protein with unknown function. The members of this family all contain a single LIM domain. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. Xirp2 contains a LIM domain and Xin re peats for binding to and stabilising F-actin. Xirp2 is expressed in muscles and is significantly induced in the heart in response to systemic administration of angiotensin II. Xirp2 is an important effector of the Ang II signaling pathway in the heart. The expression of Xirp2 is activated by myocyte enhancer factor (MEF)2A, whose transcriptional activity is stimulated by angiotersin II. Thus, Xirp2 plays important pathological roles in the angiotensin II induced hypertension. 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|215907 pfam00412, LIM, LIM domain

 Score = 60.4 bits (147), Expect = 1e-12
 Identities = 26/58 (44%), Positives = 31/58 (53%), Gaps = 1/58 (1%)

Query: 106 CAACEKTVYPLEKVT-MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162
           CA C K +Y  E V    G  +H  CFRCA  G PL    +   DG LYCKH + +LF
Sbjct: 1   CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58

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

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

 Score = 58.4 bits (141), Expect = 6e-12
 Identities = 24/53 (45%), Positives = 36/53 (67%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
           C +C+KTVYPLE++      +H +CFRC++    L+  +YA+L G +YCK HF
Sbjct: 1   CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPHF 53

The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin): Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

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

 Score = 57.6 bits (139), Expect = 8e-12
 Identities = 25/53 (47%), Positives = 34/53 (64%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
          C +C KTVY ++ L      YH SCF+CS+C   L +  Y+S+ G +YCKPHF
Sbjct: 1  CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPHF 53

The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin): Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Eplin interacts and stabilizes F-actin filaments and stress fibers, which correlates with its ability to suppress anchorage independent growth. In epithelial cells, Eplin is required for formation of the F-actin adhesion belt by binding to the E-cadherin-catenin complex through alpha-catenin. Eplin is expressed in two isoforms, a longer Eplin-beta and a shorter Eplin-alpha. Eplin-alpha mRNA is detected in various tissues and cell lines, but is absent or down regulated in cancer cells. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 53

>gnl|CDD|188829 cd09445, LIM_Mical_like_2, This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins

 Score = 55.9 bits (135), Expect = 4e-11
 Identities = 24/53 (45%), Positives = 33/53 (62%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
          C++C K VY ++ +  E   YHK+CF+C  C   L + NY S +G LYCK HF
Sbjct: 1  CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYCKVHF 53

The LIM domain on proteins of unknown function: This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL)-like proteins. Known members of the Mical-like family includes single LIM domain containing proteins, Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2), and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth, and mobility. 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|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of proteins with unknown function

 Score = 55.7 bits (134), Expect = 5e-11
 Identities = 26/53 (49%), Positives = 35/53 (66%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
           C++C+KTVYP+E++  +   FH +CF C H    L+  SYAAL G  YCK HF
Sbjct: 1   CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPHF 53

This model represents a LIM domain subfamily of Eplin-like family. This family shows highest homology to the LIM domains on Eplin and XIRP2 protein families. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Xirp2 is expressed in muscles and is an important effector of the Ang II signaling pathway in the heart. 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|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 54.3 bits (131), Expect = 1e-10
 Identities = 23/54 (42%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 105 KCAACEKTVYPLEKV-TMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHH 157
           KCA C K +Y  E+V    G  +H  CF+CA  G PL+  ++   DG LYCK  
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|215907 pfam00412, LIM, LIM domain

 Score = 53.5 bits (129), Expect = 3e-10
 Identities = 19/58 (32%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 10 CKACDKTVYVVDMLSL-EGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
          C  C K +Y  +++    G  +H  CF+C+ C   L   ++   DG LYCK  + +LF
Sbjct: 1  CAGCGKPIYDRELVRRALGKVWHPECFRCAVCGKPLGPGDFFEKDGKLYCKHDYFKLF 58

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

>gnl|CDD|188823 cd09439, LIM_Mical, The LIM domain of Mical (molecule interacting with CasL)

 Score = 53.1 bits (128), Expect = 4e-10
 Identities = 24/55 (43%), Positives = 35/55 (63%), Gaps = 2/55 (3%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYA--ALDGVLYCKHHF 158
           C  C+K VY +E+++ EG  FH++CF+C++ G  L   +YA    DG  YCK HF
Sbjct: 1   CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKPHF 55

The LIM domain of Mical (molecule interacting with CasL): MICAL is a large, multidomain, cytosolic protein with a single LIM domain, a calponin homology (CH) domain and a flavoprotein monooxygenase domain. In Drosophila, MICAL is expressed in axons, interacts with the neuronal A (PlexA) receptor and is required for Semapho-rin 1a (Sema-1a)-PlexA-mediated repulsive axon guidance. The LIM domain and calporin homology domain are known for interactions with the cytoskeleton, cytoskeletal adaptor proteins, and other signaling proteins. The flavoprotein monooxygenase (MO) is required for semaphorin-plexin repulsive axon guidance during axonal pathfinding in the Drosophila neuromuscular system. In addition, MICAL was characterized to interact with Rab13 and Rab8 to coordinate the assembly of tight junctions and adherens junctions in epithelial cells. Thus, MICAL was also named junctional Rab13-binding protein (JRAB). 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|188829 cd09445, LIM_Mical_like_2, This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins

 Score = 53.2 bits (128), Expect = 4e-10
 Identities = 22/53 (41%), Positives = 30/53 (56%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
           C +C K VY +E++  E   +HK CFRC      L   +Y + +G LYCK HF
Sbjct: 1   CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYCKVHF 53

The LIM domain on proteins of unknown function: This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL)-like proteins. Known members of the Mical-like family includes single LIM domain containing proteins, Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2), and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth, and mobility. 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|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of proteins with unknown function

 Score = 53.0 bits (127), Expect = 4e-10
 Identities = 23/53 (43%), Positives = 34/53 (64%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
          C +C KTVY ++ L  + + +H SCF C HC   L + +Y+++ G  YCKPHF
Sbjct: 1  CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPHF 53

This model represents a LIM domain subfamily of Eplin-like family. This family shows highest homology to the LIM domains on Eplin and XIRP2 protein families. Epithelial Protein Lost in Neoplasm is a cytoskeleton-associated tumor suppressor whose expression inversely correlates with cell growth, motility, invasion and cancer mortality. Xirp2 is expressed in muscles and is an important effector of the Ang II signaling pathway in the heart. 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|188831 cd09447, LIM_LASP, The LIM domain of LIM and SH3 Protein (LASP)

 Score = 52.4 bits (126), Expect = 1e-09
 Identities = 22/53 (41%), Positives = 27/53 (50%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
          C  C KTVY  + L+     +HK CFKC  C  TL M NY   +   YC  H+
Sbjct: 1  CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 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|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 51.2 bits (123), Expect = 2e-09
 Identities = 20/54 (37%), Positives = 26/54 (48%), Gaps = 1/54 (1%)

Query: 9  KCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPH 61
          KC  C K +Y  + +L   G  +H  CFKC+ C   L    +   DG LYCK  
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|188827 cd09443, LIM_Ltd-1, The LIM domain of LIM and transglutaminase domains protein (Ltd-1)

 Score = 50.5 bits (121), Expect = 4e-09
 Identities = 21/54 (38%), Positives = 28/54 (51%), Gaps = 2/54 (3%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYA--ALDGVLYCKHH 157
           C  C KT YP E V  +G  +HK CF+C   G  L+  ++     DG +YC  H
Sbjct: 1   CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 54

The LIM domain of LIM and transglutaminase domains protein (Ltd-1): This family includes mouse Ky protein and Caenorhabditis elegans Ltd-1 protein. The members of this family consists a N-terminal Lim domain and a C-terminal transglutaminase domain. The mouse Ky protein has putative function in muscle development. The mouse with ky mutant exhibits combined posterior and lateral curvature of the spine. The Ltd-1 gene in C. elegans is expressed in developing hypodermal cells from the twofold stage embryo through adulthood. These data define the ltd-1 gene as a novel marker for C. elegans epithelial cell development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

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

 Score = 50.0 bits (120), Expect = 6e-09
 Identities = 18/53 (33%), Positives = 26/53 (49%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
           CA C K +   E +   G  +H  CF+C+  G PL   S+   DG  YC+  +
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|188827 cd09443, LIM_Ltd-1, The LIM domain of LIM and transglutaminase domains protein (Ltd-1)

 Score = 49.7 bits (119), Expect = 9e-09
 Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 2/54 (3%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYS--SMDGVLYCKPH 61
          C  C KT Y  + +  +G  YHK CFKC  C   L +  ++    DG +YC  H
Sbjct: 1  CPRCGKTAYPAESVDKDGTFYHKGCFKCRECGTRLSLKTFTFVQGDGEVYCARH 54

The LIM domain of LIM and transglutaminase domains protein (Ltd-1): This family includes mouse Ky protein and Caenorhabditis elegans Ltd-1 protein. The members of this family consists a N-terminal Lim domain and a C-terminal transglutaminase domain. The mouse Ky protein has putative function in muscle development. The mouse with ky mutant exhibits combined posterior and lateral curvature of the spine. The Ltd-1 gene in C. elegans is expressed in developing hypodermal cells from the twofold stage embryo through adulthood. These data define the ltd-1 gene as a novel marker for C. elegans epithelial cell development. As in other LIM domains, this domain family is 50-60 amino acids in size and shares two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein. Length = 55

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

 Score = 49.3 bits (118), Expect = 1e-08
 Identities = 21/53 (39%), Positives = 27/53 (50%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
           CA C KTVYP EK+      +HK CF+C   G  L   +Y   +   YC  H+
Sbjct: 1   CARCGKTVYPTEKLNCLDKIWHKGCFKCEVCGMTLNMKNYKGYNKKPYCNAHY 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|188711 cd08368, LIM, LIM is a small protein-protein interaction domain, containing two zinc fingers

 Score = 48.1 bits (115), Expect = 3e-08
 Identities = 17/53 (32%), Positives = 25/53 (47%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
          C  C K +   ++L   G  +H  CFKCS C   L   ++   DG  YC+  +
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|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein (CRP)

 Score = 48.3 bits (115), Expect = 3e-08
 Identities = 24/54 (44%), Positives = 31/54 (57%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFA 159
           C  C K+VY  EK+   G  +HK CFRCA  G  L  ++ A  DG +YCK  +A
Sbjct: 1   CPRCGKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCKGCYA 54

The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, 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|188866 cd09482, LIM2_CRP3, The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 45.8 bits (108), Expect = 3e-07
 Identities = 26/54 (48%), Positives = 31/54 (57%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFA 159
           C  C K+VY  EKV   G  +HKTCFRCA  G  L  ++    DG LYCK  +A
Sbjct: 1   CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYCKVCYA 54

The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. 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|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein (CRP) family

 Score = 44.9 bits (107), Expect = 4e-07
 Identities = 19/50 (38%), Positives = 27/50 (54%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 59
          C  C K+VY  + +   G  +HKSCF C+ C   L  +  +  DG +YCK
Sbjct: 1  CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCK 50

The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188866 cd09482, LIM2_CRP3, The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 44.6 bits (105), Expect = 7e-07
 Identities = 20/50 (40%), Positives = 30/50 (60%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 59
          C  C K+VY  + +   G P+HK+CF+C+ C  +L  +  +  DG LYCK
Sbjct: 1  CPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTTVTDKDGELYCK 50

The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. 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|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein (TLP)

 Score = 44.6 bits (106), Expect = 7e-07
 Identities = 18/51 (35%), Positives = 24/51 (47%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
          C  C K VY  +  +  G  +HK C +C  CK TL    +S  +G  YC  
Sbjct: 1  CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 51

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

>gnl|CDD|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein (CRP)

 Score = 43.7 bits (103), Expect = 1e-06
 Identities = 19/50 (38%), Positives = 30/50 (60%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 59
          C  C K+VY  + +   G P+HK+CF+C+ C  +L  +  +  DG +YCK
Sbjct: 1  CPRCGKSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLADKDGEIYCK 50

The second LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific targets. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residu es, 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|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein (CRP) family

 Score = 43.7 bits (104), Expect = 1e-06
 Identities = 21/50 (42%), Positives = 28/50 (56%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCK 155
           C  C K+VY  E+V   G  +HK+CF CA     L  ++ A  DG +YCK
Sbjct: 1   CPRCGKSVYAAEEVIAAGKSWHKSCFTCAVCNKRLDSTTLAEHDGEIYCK 50

The LIM domains of Cysteine Rich Protein (CRP) family: Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The known CRP family members include CRP1, CRP2, and CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. All LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 53

>gnl|CDD|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A

 Score = 44.0 bits (104), Expect = 1e-06
 Identities = 21/52 (40%), Positives = 27/52 (51%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
          KC  C K+VY  +     G  +HK CFKC  C   L  +N +  +G LYCK 
Sbjct: 1  KCPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEHEGELYCKQ 52

The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A belong to the CRP LIM domain protein family. The Mlp84B protein contains five copies of the LIM domains, each followed by a Glycin Rich Region (GRR). However, only the first LIM domain of Mlp84B is in this family. Mlp60A exhibits only one LIM domain linked to a glycin-rich region. Mlp84B and Mlp60A are muscle specific proteins and have been implicated in muscle differentiation. While Mlp84B transcripts are enriched at the terminal ends of muscle fibers, Mlp60A transcripts are found throughout the muscle fibers. 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 = 54

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

 Score = 42.3 bits (100), Expect = 5e-06
 Identities = 19/51 (37%), Positives = 23/51 (45%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKH 156
           C  C K VY  EK T  G  +HK C RC      LT   ++  +G  YC  
Sbjct: 1   CPKCGKPVYFAEKKTSLGRDWHKPCLRCEKCKKTLTPGQHSEHEGKPYCNK 51

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

>gnl|CDD|188871 cd09840, LIM2_CRP2, The second LIM domain of Cysteine Rich Protein 2 (CRP2)

 Score = 42.0 bits (98), Expect = 5e-06
 Identities = 21/54 (38%), Positives = 30/54 (55%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFA 159
           C+ C  +VY  EK+   G  +HK CFRCA  G  L  ++    +G +YCK  +A
Sbjct: 1   CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYA 54

The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. 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|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 42.0 bits (98), Expect = 7e-06
 Identities = 24/51 (47%), Positives = 30/51 (58%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCK 155
           KC ACEKTVY  E++   G  FHKTCF C      L  ++ AA +  +YCK
Sbjct: 1   KCGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCK 51

The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcriptio n factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. 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|188828 cd09444, LIM_Mical_like_1, This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins

 Score = 41.6 bits (98), Expect = 9e-06
 Identities = 18/55 (32%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMD--GVLYCKPHF 62
          C AC + V++V    ++G  YH++CF+C  C  TL+  +Y +    G   C  H 
Sbjct: 1  CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLPGSYKAGPEPGTFVCTHHH 55

The LIM domain on proteins of unknown function: This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins. Known members of the Mical-like family includes single LIM domain containing proteins, Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2), and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth, and mobility. 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|188871 cd09840, LIM2_CRP2, The second LIM domain of Cysteine Rich Protein 2 (CRP2)

 Score = 40.9 bits (95), Expect = 1e-05
 Identities = 17/50 (34%), Positives = 29/50 (58%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 59
          C  C  +VY  + +   G P+HK+CF+C+ C  +L  +  +  +G +YCK
Sbjct: 1  CSRCGDSVYAAEKIMGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCK 50

The second LIM domain of Cysteine Rich Protein 2 (CRP2): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. The second LIM domain of CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcription factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. 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|188786 cd09402, LIM1_CRP, The first LIM domain of Cysteine Rich Protein (CRP)

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 24/50 (48%), Positives = 30/50 (60%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCK 155
           C ACEKTVY  E+V  EG  FHK+CF C      L  ++ AA +  +YCK
Sbjct: 1   CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVAAHEDEIYCK 50

The first LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific 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 = 53

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

 Score = 41.1 bits (96), Expect = 1e-05
 Identities = 20/53 (37%), Positives = 27/53 (50%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
          C  C K VY  + ++     +HK+CF C  CK TL M+NY       YC  H+
Sbjct: 1  CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

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|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function

 Score = 40.5 bits (95), Expect = 3e-05
 Identities = 16/51 (31%), Positives = 28/51 (54%)

Query: 8  DKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYC 58
          + C +C   V++ + L +EG  YH++CFKC+ C   L   ++   +   YC
Sbjct: 3  EPCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53

LIM domain in proteins of unknown function: 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. The 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 = 61

>gnl|CDD|188786 cd09402, LIM1_CRP, The first LIM domain of Cysteine Rich Protein (CRP)

 Score = 38.8 bits (90), Expect = 8e-05
 Identities = 20/50 (40%), Positives = 30/50 (60%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 59
          C AC+KTVY  + +  EG  +HKSCF C  C+  L  +  ++ +  +YCK
Sbjct: 1  CGACEKTVYHAEEVQCEGRSFHKSCFLCMVCRKNLDSTTVAAHEDEIYCK 50

The first LIM domain of Cysteine Rich Protein (CRP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription control, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. It is evident that CRP1, CRP2, and CRP3/MLP are involved in promoting protein assembly along the actin-based cytoskeleton. Although members of the CRP family share common binding partners, they are also capable of recognizing different and specific 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 = 53

>gnl|CDD|188830 cd09446, LIM_N_RAP, The LIM domain of N-RAP

 Score = 38.7 bits (90), Expect = 8e-05
 Identities = 17/52 (32%), Positives = 26/52 (50%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPH 61
          C  C   VY  + ++     +HK+CF C  CK  L ++N+ S     YC+ H
Sbjct: 1  CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAH 52

The LIM domain of N-RAP: 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|188863 cd09479, LIM1_CRP1, The first LIM domain of Cysteine Rich Protein 1 (CRP1)

 Score = 38.8 bits (90), Expect = 9e-05
 Identities = 21/51 (41%), Positives = 27/51 (52%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 59
          KC  C KTVY  + +  EG  +HKSCF C  CK  L  +  +     +YCK
Sbjct: 2  KCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCK 52

The first LIM domain of Cysteine Rich Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1 can associate with the actin cytoskeleton and are capable of interacting with alpha-actinin and zyxin. CRP1 was shown to regulate actin filament bundling by interaction with alpha-actinin and direct binding to actin filaments. 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|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 38.2 bits (88), Expect = 1e-04
 Identities = 19/51 (37%), Positives = 30/51 (58%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 59
          KC AC+KTVY  + +   G  +HK+CF C  C+  L  +  ++ +  +YCK
Sbjct: 1  KCGACEKTVYHAEEIQCNGRSFHKTCFICMACRKALDSTTVAAHESEIYCK 51

The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLPCRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network.CRP3 also called Muscle LIM Protein (MLP), which is a striated muscle-specific factor that enhances myogenic differentiation. CRP3/MLP interacts with cytoskeletal protein beta-spectrin. CRP3/MLP also interacts with the basic helix-loop-helix myogenic transcriptio n factors MyoD, myogenin, and MRF4 thereby increasing their affinity for specific DNA regulatory elements. 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|188860 cd09476, LIM1_TLP, The first LIM domain of thymus LIM protein (TLP)

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 19/49 (38%), Positives = 25/49 (51%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYC 58
          C  CDKTVY  + +S  G  +H+ C KC  C   L    ++  DG  YC
Sbjct: 1  CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49

The first LIM domain of thymus LIM protein (TLP): TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188828 cd09444, LIM_Mical_like_1, This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins

 Score = 38.2 bits (89), Expect = 2e-04
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALD--GVLYCKHHF 158
           CAAC + V+ +++  ++G  +H+ CFRC      L   SY A    G   C HH 
Sbjct: 1   CAACGQHVHLVQRHLVDGKLYHRNCFRCKECSSTLLPGSYKAGPEPGTFVCTHHH 55

The LIM domain on proteins of unknown function: This domain belongs to the LIM domain family which are found on Mical (molecule interacting with CasL) like proteins. Known members of the Mical-like family includes single LIM domain containing proteins, Mical (molecule interacting with CasL), pollen specific protein SF3, Eplin, xin actin-binding repeat-containing protein 2 (XIRP2), and Ltd-1. The members of this family function mainly at the cytoskeleton and focal adhesions. They interact with transcription factors or other signaling molecules to play roles in muscle development, neuronal differentiation, cell growth, and mobility. 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|188863 cd09479, LIM1_CRP1, The first LIM domain of Cysteine Rich Protein 1 (CRP1)

 Score = 38.1 bits (88), Expect = 2e-04
 Identities = 22/51 (43%), Positives = 28/51 (54%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCK 155
           KC  C+KTVY  E+V  EG  FHK+CF C      L  ++ A     +YCK
Sbjct: 2   KCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCK 52

The first LIM domain of Cysteine Rich Protein 1 (CRP1): Cysteine-rich proteins (CRPs) are characterized by the presence of two LIM domains linked to a short glycine-rich repeats (GRRs). The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP1 can associate with the actin cytoskeleton and are capable of interacting with alpha-actinin and zyxin. CRP1 was shown to regulate actin filament bundling by interaction with alpha-actinin and direct binding to actin filaments. 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|188862 cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich Intestinal Protein (CRIP)

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 22/51 (43%), Positives = 28/51 (54%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKH 156
           C  C+K VY  E+VT  G  +H+ C +C   G  LT  S+A  DG  YC H
Sbjct: 1   CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYCNH 51

The LIM domain of Cysteine-Rich Intestinal Protein (CRIP): CRIP is a short 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 = 54

>gnl|CDD|188861 cd09477, LIM2_TLP, The second LIM domain of thymus LIM protein (TLP)

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 17/49 (34%), Positives = 24/49 (48%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYC 58
          C  C K VY  + +   G  +H+ C +C  CK TL    ++  DG  YC
Sbjct: 1  CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49

The second LIM domain of thymus LIM protein (TLP): TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A

 Score = 37.5 bits (87), Expect = 3e-04
 Identities = 20/51 (39%), Positives = 27/51 (52%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCK 155
           KC  C K+VY  E+    G  +HK CF+C      L  ++ A  +G LYCK
Sbjct: 1   KCPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEHEGELYCK 51

The LIM domain of Mlp84B and Mlp60A: Mlp84B and Mlp60A belong to the CRP LIM domain protein family. The Mlp84B protein contains five copies of the LIM domains, each followed by a Glycin Rich Region (GRR). However, only the first LIM domain of Mlp84B is in this family. Mlp60A exhibits only one LIM domain linked to a glycin-rich region. Mlp84B and Mlp60A are muscle specific proteins and have been implicated in muscle differentiation. While Mlp84B transcripts are enriched at the terminal ends of muscle fibers, Mlp60A transcripts are found throughout the muscle fibers. 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 = 54

>gnl|CDD|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function

 Score = 37.4 bits (87), Expect = 3e-04
 Identities = 19/51 (37%), Positives = 30/51 (58%)

Query: 104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYC 154
           + CA+C   V+  E++ +EG  +H+TCF+CA  G  LT  S+   +   YC
Sbjct: 3   EPCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 53

LIM domain in proteins of unknown function: 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. The 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 = 61

>gnl|CDD|188864 cd09480, LIM1_CRP2, The first LIM domain of Cysteine Rich Protein 2 (CRP2)

 Score = 36.9 bits (85), Expect = 4e-04
 Identities = 19/51 (37%), Positives = 28/51 (54%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 59
          KC AC +TVY  + +  +G  +HK CF C  C+  L  +  +  D  +YCK
Sbjct: 1  KCGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCK 51

The first LIM domain of Cysteine Rich Protein 2 (CRP2): The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP2 specifically binds to protein inhibitor of activated STAT-1 (PIAS1) and a novel human protein designed CRP2BP (for CRP2 binding partner). PIAS1 specifically inhibits the STAT-1 pathway and CRP2BP is homologous to members of the histone acetyltransferase family raising the possibility that CRP2 is a modulator of cytokine-controlled pathways or is functionally active in the transcriptional regulatory network. 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|188861 cd09477, LIM2_TLP, The second LIM domain of thymus LIM protein (TLP)

 Score = 36.9 bits (85), Expect = 5e-04
 Identities = 20/49 (40%), Positives = 23/49 (46%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYC 154
           C  C K VY  EKV   G  +H+ C RC      LT   +A  DG  YC
Sbjct: 1   CPGCGKPVYFAEKVMSLGRNWHRPCLRCQRCKKTLTAGGHAEHDGSPYC 49

The second LIM domain of thymus LIM protein (TLP): TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

>gnl|CDD|188864 cd09480, LIM1_CRP2, The first LIM domain of Cysteine Rich Protein 2 (CRP2)

 Score = 36.9 bits (85), Expect = 5e-04
 Identities = 22/51 (43%), Positives = 28/51 (54%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCK 155
           KC AC +TVY  E+V  +G  FHK CF C      L  ++ A  D  +YCK
Sbjct: 1   KCGACGRTVYHAEEVQCDGRSFHKCCFLCMVCRKNLDSTTVAIHDQEIYCK 51

The first LIM domain of Cysteine Rich Protein 2 (CRP2): The CRP family members include CRP1, CRP2, CRP3/MLP and TLP. CRP1, CRP2 and CRP3 share a conserved nuclear targeting signal (K/R-K/R-Y-G-P-K), which supports the fact that these proteins function not only in the cytoplasm but also in the nucleus. CRPs control regulatory pathways during cellular differentiation, and involve in complex transcription circuits, and the organization as well as the arrangement of the myofibrillar/cytoskeletal network. CRP2 specifically binds to protein inhibitor of activated STAT-1 (PIAS1) and a novel human protein designed CRP2BP (for CRP2 binding partner). PIAS1 specifically inhibits the STAT-1 pathway and CRP2BP is homologous to members of the histone acetyltransferase family raising the possibility that CRP2 is a modulator of cytokine-controlled pathways or is functionally active in the transcriptional regulatory network. 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|188798 cd09414, LIM1_LIMPETin, The first LIM domain of protein LIMPETin

 Score = 36.2 bits (84), Expect = 7e-04
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 5/58 (8%)

Query: 10 CKACDKTV-----YVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
          C  C + +      V      E + +H +CF+CS C+  LV   Y   D  +YC+ H+
Sbjct: 1  CGGCSEPLKYGELAVTAPKFGESLLWHPACFRCSTCEELLVDLTYCVHDDQIYCERHY 58

The first LIM domain of protein LIMPETin: LIMPETin contains 6 LIM domains at the C-terminal and an N-terminal PET domain. Four of the six LIM domains are highly homologous to the four and half LIM domain protein family and two of them show sequence similarity to the LIM domains of the Testin family. Thus, LIMPETin may be the recombinant product of genes coding testin and FHL proteins. In Schistosoma mansoni, where LIMPETin was first identified, LIMPETin is down regulated in sexually mature adult Schistosoma females compared to sexually immature adult females and adult male. Its differential expression indicates that it is a transcription regulator. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 58

>gnl|CDD|188862 cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich Intestinal Protein (CRIP)

 Score = 36.0 bits (83), Expect = 8e-04
 Identities = 18/49 (36%), Positives = 26/49 (53%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYC 58
          C  CDK VY  + ++  G  +H+ C KC  C  TL   +++  DG  YC
Sbjct: 1  CPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTPGSHAEHDGKPYC 49

The LIM domain of Cysteine-Rich Intestinal Protein (CRIP): CRIP is a short 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 = 54

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

 Score = 35.9 bits (83), Expect = 8e-04
 Identities = 15/53 (28%), Positives = 23/53 (43%), Gaps = 1/53 (1%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
          C  C   +     +      +H  CF+CS C  +L  + Y   DG LYC+  +
Sbjct: 1  CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSL-SNWYFEKDGKLYCRKDY 52

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

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

 Score = 36.8 bits (85), Expect = 8e-04
 Identities = 18/53 (33%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
           CA+C +++Y  + +      +H  CFRC   G  L+H  Y   DG L+CK  +
Sbjct: 22  CASCGQSIYDGQYLQALNSDWHADCFRCCECGASLSHWYYEK-DGRLFCKKDY 73

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

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 20/53 (37%), Positives = 24/53 (45%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
           CA C K VYP EKV      +HK CF C      L  ++Y       YC  H+
Sbjct: 1   CARCGKIVYPTEKVNCLDKTWHKACFHCEVCKMTLNMNNYKGYQKKPYCNAHY 53

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|188830 cd09446, LIM_N_RAP, The LIM domain of N-RAP

 Score = 35.3 bits (81), Expect = 0.002
 Identities = 18/52 (34%), Positives = 25/52 (48%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHH 157
           CA C   VYP EK+      +HK CF C      LT +++ +     YC+ H
Sbjct: 1   CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAH 52

The LIM domain of N-RAP: 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|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase )

 Score = 34.8 bits (80), Expect = 0.002
 Identities = 16/53 (30%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
           CA C   +   + V      +H  CFRC+     L++  Y   DG LYC+  +
Sbjct: 1   CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLSN-WYFEKDGKLYCRKDY 52

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

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

 Score = 35.2 bits (81), Expect = 0.002
 Identities = 17/58 (29%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 5  GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
            L  C +C +++Y    L      +H  CF+C  C G  +   Y   DG L+CK  +
Sbjct: 17 NVLPVCASCGQSIYDGQYLQALNSDWHADCFRCCEC-GASLSHWYYEKDGRLFCKKDY 73

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

 Score = 34.7 bits (80), Expect = 0.002
 Identities = 16/53 (30%), Positives = 26/53 (49%), Gaps = 1/53 (1%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
          C  CD+ +    +L++    +H  C +C  CK  L    +S  +G LYC+  F
Sbjct: 1  CAGCDRPILDKFLLNVLDRAWHAKCVQCCDCKCPLTEKCFSR-EGKLYCRNDF 52

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

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

 Score = 34.6 bits (80), Expect = 0.003
 Identities = 12/29 (41%), Positives = 15/29 (51%), Gaps = 1/29 (3%)

Query: 30 YHKSCFKCSHCKGTLVMSNYSSMDGVLYC 58
          +H  CFKC  C G ++   Y   DG  YC
Sbjct: 21 WHVWCFKCKEC-GKVLTGEYMGKDGKPYC 48

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

 Score = 34.5 bits (79), Expect = 0.003
 Identities = 15/53 (28%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
           C  C   +       +  + +H +CF+C+     LT+  Y   DG LYC  H+
Sbjct: 1   CTGCGGRIQDSFHYRVVQEAWHNSCFQCSVCQDLLTNWYYEK-DGKLYCHKHY 52

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

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

 Score = 34.3 bits (79), Expect = 0.003
 Identities = 16/51 (31%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKH 156
           CA C++ +     + +    +H+ C +C+    PLT S Y   D  LYCK 
Sbjct: 1   CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPLTTSCYFR-DRKLYCKQ 50

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

>gnl|CDD|188860 cd09476, LIM1_TLP, The first LIM domain of thymus LIM protein (TLP)

 Score = 34.2 bits (78), Expect = 0.004
 Identities = 19/49 (38%), Positives = 26/49 (53%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYC 154
           C  C+KTVY  EKV+  G  +H+ C +C      L+   +A  DG  YC
Sbjct: 1   CPRCDKTVYFAEKVSSLGKNWHRFCLKCERCSKILSPGGHAEHDGKPYC 49

The first LIM domain of thymus LIM protein (TLP): TLP is the distant member of the CRP family of proteins. TLP has two isomers (TLP-A and TLP-B) and sharing approximately 30% with each of the three other CRPs. Like CRP1, CRP2 and CRP3/MLP, TLP has two LIM domains, connected by a flexible linker region. Unlike the CRPs, TLP lacks the nuclear targeting signal (K/R-K/R-Y-G-P-K) and is localized solely in the cytoplasm. TLP is specifically expressed in the thymus in a subset of cortical epithelial cells. TLP has a role in development of normal thymus and in controlling the development and differentiation of thymic epithelial cells. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 54

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	210
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.95
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.9
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.86
KOG1700	200	consensus Regulatory protein MLP and related LIM p	99.84
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.83
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.83
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.82
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	99.81
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	99.76
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.74
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.59
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.57
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.0
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.75
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.72
KOG1700	200	consensus Regulatory protein MLP and related LIM p	98.42
KOG1702	264	consensus Nebulin repeat protein [Cytoskeleton]	98.02
KOG1702	264	consensus Nebulin repeat protein [Cytoskeleton]	97.89
KOG0490	235	consensus Transcription factor, contains HOX domai	97.76
KOG0490	235	consensus Transcription factor, contains HOX domai	91.28
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	88.18
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	86.72
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	84.97
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	83.63
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	83.58
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	82.24
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	81.89
PF14471	51	DUF4428: Domain of unknown function (DUF4428)	81.49

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

Probab=99.95  E-value=2.6e-29  Score=216.16  Aligned_cols=134  Identities=22%  Similarity=0.518  Sum_probs=122.7

Q ss_pred             CCcccCCcceecce-eEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCCC
Q 040947            8 DKCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCS   86 (210)
Q Consensus         8 ~~C~~C~~~I~~~~-~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~   86 (210)
                      .+|.+|+|.|+... .+.||++.||..||+|..|++.|.++.||.+++++||+.||+..+                    
T Consensus       275 ~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl--------------------  334 (468)
T KOG1701|consen  275 GICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL--------------------  334 (468)
T ss_pred             hhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH--------------------
Confidence            48999999999555 389999999999999999999999999999999999999999876                    


Q ss_pred             CCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeec-CCeeecHhHHHhhhcCC
Q 040947           87 NQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAAL-DGVLYCKHHFAQLFMEK  165 (210)
Q Consensus        87 ~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~-dg~~yC~~c~~~~f~~k  165 (210)
                                       .+|..|+++|+ +.++.++|+.||+.||+|..|++.|++..|++. ++++||..||.++|++|
T Consensus       335 -----------------ekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPr  396 (468)
T KOG1701|consen  335 -----------------EKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPR  396 (468)
T ss_pred             -----------------HHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcc
Confidence                             59999999997 667899999999999999999999999999876 79999999999999999


Q ss_pred             CC-cccccccccccc
Q 040947          166 GN-YSHVLKAANHKR  179 (210)
Q Consensus       166 ~~-~~~~~~~~~~~~  179 (210)
                      |. ++..+.+...+.
T Consensus       397 Cs~C~~PI~P~~G~~  411 (468)
T KOG1701|consen  397 CSVCGNPILPRDGKD  411 (468)
T ss_pred             hhhccCCccCCCCCc
Confidence            96 777777776654

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

Probab=99.90  E-value=1.4e-25  Score=193.18  Aligned_cols=126  Identities=28%  Similarity=0.664  Sum_probs=113.1

Q ss_pred             CCCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeec-cCCeeeccchHHHhhhccCCCCCCccCCCC
Q 040947            3 FTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSS-MDGVLYCKPHFEQLFKESGNFSKNFQTGKN   81 (210)
Q Consensus         3 ~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~-~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~   81 (210)
                      |..++.+|..|++.|+ +.+|.|+|+.||+.||+|..|++.|++..|.+ .++++||.+||+++|+              
T Consensus       330 yq~tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA--------------  394 (468)
T KOG1701|consen  330 YQDTLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA--------------  394 (468)
T ss_pred             HHHHHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC--------------
Confidence            4556789999999997 66799999999999999999999999999985 4899999999999999              


Q ss_pred             CCCCCCCCCCCCCcccccCCCCCccccccceeecCc------eeEecCccccccccccCCCCCcCC----CCCeeecCCe
Q 040947           82 PSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLE------KVTMEGDCFHKTCFRCAHGGCPLT----HSSYAALDGV  151 (210)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e------~v~~~g~~~H~~CF~C~~C~~~l~----~~~f~~~dg~  151 (210)
                                            ++|+.|+++|++.+      +|++|++.||.+|++|+.|+.+|.    +...+-.||.
T Consensus       395 ----------------------PrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~H  452 (468)
T KOG1701|consen  395 ----------------------PRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGH  452 (468)
T ss_pred             ----------------------cchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCc
Confidence                                  89999999999743      378999999999999999999997    3357889999


Q ss_pred             eecHhHHHhhhcCC
Q 040947          152 LYCKHHFAQLFMEK  165 (210)
Q Consensus       152 ~yC~~c~~~~f~~k  165 (210)
                      ++|+.|..+++...
T Consensus       453 llCk~Ch~~Rl~~~  466 (468)
T KOG1701|consen  453 LLCKTCHLKRLQAG  466 (468)
T ss_pred             eeechhhhhhhccc
Confidence            99999999887654

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

Probab=99.86  E-value=1.7e-23  Score=172.38  Aligned_cols=137  Identities=28%  Similarity=0.545  Sum_probs=118.0

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCC
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSC   85 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~   85 (210)
                      ..++|+.|.+.|.+..++.++++.||..|++|+.|...|.. ..+.++|.+||+.+|.++|+                  
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfG------------------   92 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFG------------------   92 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhC------------------
Confidence            57899999999986667899999999999999999999998 56679999999999999998                  


Q ss_pred             CCCCCCCCCcccccCCCCCccccccceeecCcee-EecCccccccccccCCCCCcCC-CCCeee-cCCeeecHhHHHhhh
Q 040947           86 SNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKV-TMEGDCFHKTCFRCAHGGCPLT-HSSYAA-LDGVLYCKHHFAQLF  162 (210)
Q Consensus        86 ~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v-~~~g~~~H~~CF~C~~C~~~l~-~~~f~~-~dg~~yC~~c~~~~f  162 (210)
                                        .+|..|...|.+.++| .+.+.+||.+||.|..|+++|. +..|++ .|+++.|+.+|+..-
T Consensus        93 ------------------TKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak  154 (383)
T KOG4577|consen   93 ------------------TKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYETAK  154 (383)
T ss_pred             ------------------CcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHHHH
Confidence                              7999999999988887 5889999999999999999997 556765 489999999999876


Q ss_pred             cCCCCcccccccccccccC
Q 040947          163 MEKGNYSHVLKAANHKRTA  181 (210)
Q Consensus       163 ~~k~~~~~~~~~~~~~~~~  181 (210)
                      ...++  ...+.+..||+.
T Consensus       155 ~k~~~--~l~gd~~nKRPR  171 (383)
T KOG4577|consen  155 QKHCN--ELEGDASNKRPR  171 (383)
T ss_pred             hcccc--ccccccccCCCc
Confidence            65554  444555555544

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

Probab=99.84  E-value=1.1e-21  Score=158.54  Aligned_cols=180  Identities=50%  Similarity=0.905  Sum_probs=147.7

Q ss_pred             CCCCCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCC-CCCCccCC
Q 040947            1 MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGN-FSKNFQTG   79 (210)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~-~~~~~~~~   79 (210)
                      |++++....|..|++.|+..+.+...|..||+.||+|..|.+.|....+.++++.+||+.||...+++++. +...|+..
T Consensus         1 ~~~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~   80 (200)
T KOG1700|consen    1 SSFTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKA   80 (200)
T ss_pred             CCcccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccccccccccccc
Confidence            78899999999999999988888899999999999999999999999999999999999988888887653 44443321


Q ss_pred             CC-CCCCC-CC--CCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecH
Q 040947           80 KN-PSSCS-NQ--NRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCK  155 (210)
Q Consensus        80 ~~-~~~~~-~~--~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~  155 (210)
                      .. ..+.- ..  ..........+.|+...|.+|.+.+++.+.|...+..||+.||+|+.|+..|....+...+|.+||.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~  160 (200)
T KOG1700|consen   81 GGLGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCK  160 (200)
T ss_pred             CCCCcccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccc
Confidence            11 11111 11  1122245566788889999999999999999999999999999999999999999999999999999


Q ss_pred             hHHHhhhcCCCCccccccccccccc
Q 040947          156 HHFAQLFMEKGNYSHVLKAANHKRT  180 (210)
Q Consensus       156 ~c~~~~f~~k~~~~~~~~~~~~~~~  180 (210)
                      .++-++|-.+..+.++...+..++.
T Consensus       161 ~~~~~~~~~~~~~~~~~~~~~~~~~  185 (200)
T KOG1700|consen  161 HHFAQLFKGKGNYNEGFGARENKEA  185 (200)
T ss_pred             hhhheeecCCCcccccchhhhhhhh
Confidence            9999988888888877666655553

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

Probab=99.83  E-value=3.5e-22  Score=161.99  Aligned_cols=117  Identities=22%  Similarity=0.540  Sum_probs=109.6

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCC
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSC   85 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~   85 (210)
                      +.|+|..|.++|. ..+|.++|+.||.+.|+|+.|-+++-+-..|++.|.+||+.+|.++|+                  
T Consensus       194 gipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~~qLfG------------------  254 (332)
T KOG2272|consen  194 GIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHYHQLFG------------------  254 (332)
T ss_pred             CCcccccccCchH-HHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHHHHHhh------------------
Confidence            5789999999996 667899999999999999999999998899999999999999999998                  


Q ss_pred             CCCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCCC-CCeeecCCeeecHhHHHh
Q 040947           86 SNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTH-SSYAALDGVLYCKHHFAQ  160 (210)
Q Consensus        86 ~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~-~~f~~~dg~~yC~~c~~~  160 (210)
                                        ..|..|+.+|- +++|.++++.|.++||.|+.|.+.|.. ..|++.|-.|.|+.||.+
T Consensus       255 ------------------~~CF~C~~~i~-G~vv~al~KawCv~cf~Cs~Cdkkl~~K~Kf~E~DmkP~CKkCy~r  311 (332)
T KOG2272|consen  255 ------------------NLCFICNRVIG-GDVVSALNKAWCVECFSCSTCDKKLTQKNKFYEFDMKPVCKKCYDR  311 (332)
T ss_pred             ------------------hhheecCCccC-ccHHHHhhhhhccccccccccccccccccceeeeccchHHHHHHhh
Confidence                              79999999996 889999999999999999999999984 478999999999999984

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

Probab=99.83  E-value=2.2e-22  Score=163.17  Aligned_cols=164  Identities=19%  Similarity=0.414  Sum_probs=123.8

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc-cCCCC----C------
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE-SGNFS----K------   74 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~-~~~~~----~------   74 (210)
                      .+|.|+.|++.|. +.+|.+++.+||+.||+|..|++.|.+..|+-..|+.+|..|.++.-+. .|-|.    .      
T Consensus        72 faPcC~kC~EFii-GrVikamnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~  150 (332)
T KOG2272|consen   72 FAPCCGKCGEFII-GRVIKAMNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQ  150 (332)
T ss_pred             hchhhcccccchh-hHHHHhhccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccc
Confidence            4689999999998 9999999999999999999999999999999999999999999874332 12121    0      


Q ss_pred             --CccCCCCCC---CCCCCCCCCCCcc-----ccc------CCCCCccccccceeecCceeEecCccccccccccCCCCC
Q 040947           75 --NFQTGKNPS---SCSNQNRTPSKLS-----SLF------SGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGC  138 (210)
Q Consensus        75 --~~~~~~~~~---~~~~~~~~~~~~~-----~~~------~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~  138 (210)
                        .|++....+   .|.++...-...+     .++      .-+.|+|..|.+||. +..|.++|+.||.+.|+|+.|.+
T Consensus       151 ~l~fr~d~yH~yHFkCt~C~keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe-ervi~amgKhWHveHFvCa~Cek  229 (332)
T KOG2272|consen  151 PLTFRGDPYHPYHFKCTTCGKELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEK  229 (332)
T ss_pred             cccccCCCCCccceecccccccccchhhhhccceeccccccccCCcccccccCchH-HHHHHHhccccchhheeehhcCC
Confidence              112221111   2222211111111     111      124589999999996 66689999999999999999999


Q ss_pred             cCCCCCeeecCCeeecHhHHHhhhcCCCC-cccc
Q 040947          139 PLTHSSYAALDGVLYCKHHFAQLFMEKGN-YSHV  171 (210)
Q Consensus       139 ~l~~~~f~~~dg~~yC~~c~~~~f~~k~~-~~~~  171 (210)
                      ++-+-+.+++.|.+||+.+|.++||--+. ++++
T Consensus       230 PFlGHrHYEkkGlaYCe~h~~qLfG~~CF~C~~~  263 (332)
T KOG2272|consen  230 PFLGHRHYEKKGLAYCETHYHQLFGNLCFICNRV  263 (332)
T ss_pred             cccchhhhhhcCchhHHHHHHHHhhhhheecCCc
Confidence            99998999999999999999999999886 4443

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

Probab=99.82  E-value=2.3e-21  Score=172.35  Aligned_cols=158  Identities=26%  Similarity=0.402  Sum_probs=134.1

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCC
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSC   85 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~   85 (210)
                      +...|++|++.|..+..+.|+++.||..||+|..|...|.+ .|..++|.+||+.||++.|+                  
T Consensus       132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~g-ey~skdg~pyce~dy~~~fg------------------  192 (670)
T KOG1044|consen  132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNG-EYMSKDGVPYCEKDYQAKFG------------------  192 (670)
T ss_pred             CCccccchhhhhhccceeeeeccceeeeeeehhhhcccccc-eeeccCCCcchhhhhhhhcC------------------
Confidence            45789999999998999999999999999999999999987 78899999999999999998                  


Q ss_pred             CCCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCC-CCCeeecCCeeecHhHHHhhhcC
Q 040947           86 SNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLT-HSSYAALDGVLYCKHHFAQLFME  164 (210)
Q Consensus        86 ~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~-~~~f~~~dg~~yC~~c~~~~f~~  164 (210)
                                        .+|..|.+.|. +.++.+.|++||+.|-+|+.|+..+. ++..++....+|-..|-...-.+
T Consensus       193 ------------------vkc~~c~~fis-gkvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~qa~~tE  253 (670)
T KOG1044|consen  193 ------------------VKCEECEKFIS-GKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCKQATKTE  253 (670)
T ss_pred             ------------------eehHHhhhhhh-hhhhhccCcccCcchhhhhhhccccccchheeeccccccCCccccccchh
Confidence                              89999999997 88899999999999999999999997 66788888999988887654444


Q ss_pred             CCCc-ccccccccccccCCCCCCCCCccCCCCCCCCCc
Q 040947          165 KGNY-SHVLKAANHKRTASSSSTSPAEQIENKPDDESG  201 (210)
Q Consensus       165 k~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  201 (210)
                      +-.. ..........++.+++..+|...|-+++|+|-.
T Consensus       254 ~i~~~~rtst~Si~~~~~~Ss~Gsp~~ti~akvdneiL  291 (670)
T KOG1044|consen  254 EILKPGRTSTESIYSRPGSSTPGSPGHTIYAKVDNEIL  291 (670)
T ss_pred             hcccCCCCCcccccCCCCCCCCCCCCcEehhhhcchhh
Confidence            4332 223333344556777788999999999888754

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

Probab=99.81  E-value=1.6e-20  Score=170.11  Aligned_cols=128  Identities=30%  Similarity=0.649  Sum_probs=119.3

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCC
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSC   85 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~   85 (210)
                      ..+.|..|++.|....++.++++.||+.+|.|..|...|....|...+|.+||..||.+.+.                  
T Consensus       302 ~~p~c~~c~~~i~~~~~i~~~~~~~h~~~~~c~~~~~~~~~~~~~~~~g~~~c~~~~~~~~~------------------  363 (479)
T KOG1703|consen  302 TRPLCLSCNQKIRSVKVIVALGKEWHPEHFSCEVCAIVILDGGPRELDGKILCHECFHAPFR------------------  363 (479)
T ss_pred             ccccccccccCcccceeEeeccccccccceeeccccccccCCCccccCCCccHHHHHHHhhC------------------
Confidence            45899999999984488999999999999999999999999899999999999999999987                  


Q ss_pred             CCCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCC
Q 040947           86 SNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEK  165 (210)
Q Consensus        86 ~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k  165 (210)
                                        +.|.+|+++|. ++.|.++++.||++||+|..|++.|....|++.+|.+||+.||.++|+++
T Consensus       364 ------------------p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~~~  424 (479)
T KOG1703|consen  364 ------------------PNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFTTK  424 (479)
T ss_pred             ------------------ccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcccc
Confidence                              89999999998 88899999999999999999999999999999999999999999999988


Q ss_pred             CCccc
Q 040947          166 GNYSH  170 (210)
Q Consensus       166 ~~~~~  170 (210)
                      +.++.
T Consensus       425 ~~~~~  429 (479)
T KOG1703|consen  425 CDYCK  429 (479)
T ss_pred             chhcc
Confidence            86553

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

Probab=99.76  E-value=5.4e-20  Score=166.64  Aligned_cols=117  Identities=31%  Similarity=0.631  Sum_probs=108.2

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCC
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSS   84 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~   84 (210)
                      -..+.|.+|+++|. ++.|.++++.||++||.|..|++.|.+..|+.+++.+||+.||.+++.                 
T Consensus       361 ~~~p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~-----------------  422 (479)
T KOG1703|consen  361 PFRPNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFT-----------------  422 (479)
T ss_pred             hhCccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcc-----------------
Confidence            35789999999998 888989999999999999999999999999999999999999999987                 


Q ss_pred             CCCCCCCCCCcccccCCCCCccccccceeecCc-eeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHH
Q 040947           85 CSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLE-KVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF  158 (210)
Q Consensus        85 ~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e-~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~  158 (210)
                                         .+|..|.++|.... .|.+++..||..||+|+.|...|.++.|+...++|+|..|+
T Consensus       423 -------------------~~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~c~~~l~~~~~~~~~~~p~c~~~~  478 (479)
T KOG1703|consen  423 -------------------TKCDYCKKPVEFGSRQIEADGSPFHGDCFRCANCMKKLTKKTFFETLDKPLCQKHF  478 (479)
T ss_pred             -------------------ccchhccchhHhhhhHhhccCccccccceehhhhhccccCCceeecCCccccccCC
Confidence                               68999999986544 48999999999999999999999999999999999999876

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

Probab=99.74  E-value=1.4e-18  Score=154.82  Aligned_cols=161  Identities=21%  Similarity=0.439  Sum_probs=114.2

Q ss_pred             CCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCC-eeeccchHHHhh------------hccCCC--
Q 040947            8 DKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDG-VLYCKPHFEQLF------------KESGNF--   72 (210)
Q Consensus         8 ~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g-~~yC~~cy~~~~------------~~~~~~--   72 (210)
                      -.|.+|.+.-. ++++.+.+++||..||.|..|+..|..+.|+.+++ ++|+.....+..            .+++.+  
T Consensus        17 i~c~~c~~kc~-gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~~~~~gevvsa~gktyh~~cf~cs   95 (670)
T KOG1044|consen   17 IKCDKCRKKCS-GEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCRAFVEGEVVSTLGKTYHPKCFSCS   95 (670)
T ss_pred             eehhhhCCccc-cceeEeeccccceeeeeccccCCCcccccceecccceeecccchhhhccceeEecccceeccccceec
Confidence            57999999998 99999999999999999999999999998887744 677763222111            011100  


Q ss_pred             --CCCccCCCC------CCCCCCC-CCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCCCC
Q 040947           73 --SKNFQTGKN------PSSCSNQ-NRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHS  143 (210)
Q Consensus        73 --~~~~~~~~~------~~~~~~~-~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~  143 (210)
                        ..-|..+..      ...|..+ ..++..  ....-+...|++|++.|..++.+.++++.||..||+|..|...|.++
T Consensus        96 ~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~--p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~ge  173 (670)
T KOG1044|consen   96 TCKSPFKSGDKVTFSGKECLCQTCSQPMPVS--PAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLNGE  173 (670)
T ss_pred             ccCCCCCCCCeeeecchhhhhhhhcCcccCC--cccccCCccccchhhhhhccceeeeeccceeeeeeehhhhcccccce
Confidence              000111000      0011111 011111  11111336899999999989999999999999999999999999874


Q ss_pred             CeeecCCeeecHhHHHhhhcCCCCccccc
Q 040947          144 SYAALDGVLYCKHHFAQLFMEKGNYSHVL  172 (210)
Q Consensus       144 ~f~~~dg~~yC~~c~~~~f~~k~~~~~~~  172 (210)
                       |+..||.|||+.||.+.|+.||..++-+
T Consensus       174 -y~skdg~pyce~dy~~~fgvkc~~c~~f  201 (670)
T KOG1044|consen  174 -YMSKDGVPYCEKDYQAKFGVKCEECEKF  201 (670)
T ss_pred             -eeccCCCcchhhhhhhhcCeehHHhhhh
Confidence             8999999999999999999999755433

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

Probab=99.59  E-value=2.1e-15  Score=98.16  Aligned_cols=57  Identities=37%  Similarity=0.838  Sum_probs=53.0

Q ss_pred             cccccceeecCcee-EecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhh
Q 040947          106 CAACEKTVYPLEKV-TMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF  162 (210)
Q Consensus       106 C~~C~~~I~~~e~v-~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f  162 (210)
                      |.+|+++|.+.+.+ .++|+.||++||+|..|+++|..+.|+..+|++||+.||.++|
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            78999999977775 6999999999999999999999888999999999999999986

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

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

Probab=99.57  E-value=2.4e-15  Score=97.87  Aligned_cols=57  Identities=33%  Similarity=0.805  Sum_probs=53.1

Q ss_pred             cccCCcceecceeE-eeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhh
Q 040947           10 CKACDKTVYVVDML-SLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF   66 (210)
Q Consensus        10 C~~C~~~I~~~~~v-~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~   66 (210)
                      |.+|+++|.+.+.+ .++|+.||++||+|..|+++|.+..|+..+|++||+.||.++|
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            88999999977765 7999999999999999999999988999999999999999876

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 ....

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

Probab=99.00  E-value=1.6e-11  Score=101.96  Aligned_cols=80  Identities=20%  Similarity=0.418  Sum_probs=69.5

Q ss_pred             CCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCC-ccccccccccccc
Q 040947          102 TQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN-YSHVLKAANHKRT  180 (210)
Q Consensus       102 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~-~~~~~~~~~~~~~  180 (210)
                      ..++|+.|.+.|...-++.++++.||..|++|+.|+-+|.. +.+.++|.+||+++|-++||+||. +..++.+...-|.
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVRk  110 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVRK  110 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHHH
Confidence            45899999999985545689999999999999999999976 477899999999999999999995 7788888777665


Q ss_pred             CC
Q 040947          181 AS  182 (210)
Q Consensus       181 ~~  182 (210)
                      +.
T Consensus       111 Aq  112 (383)
T KOG4577|consen  111 AQ  112 (383)
T ss_pred             hh
Confidence            54

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

Probab=98.75  E-value=7.1e-09  Score=61.29  Aligned_cols=37  Identities=38%  Similarity=0.730  Sum_probs=33.6

Q ss_pred             CcccCCcceecc-eeEeeCCccccCCCcccccccCCCC
Q 040947            9 KCKACDKTVYVV-DMLSLEGMPYHKSCFKCSHCKGTLV   45 (210)
Q Consensus         9 ~C~~C~~~I~~~-~~v~~~g~~~H~~CF~C~~C~~~L~   45 (210)
                      +|..|+++|.+. ..+.++++.||+.||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            589999999866 6689999999999999999999986

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

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

Probab=98.72  E-value=7.6e-09  Score=61.18  Aligned_cols=37  Identities=35%  Similarity=0.750  Sum_probs=33.0

Q ss_pred             ccccccceeecC-ceeEecCccccccccccCCCCCcCC
Q 040947          105 KCAACEKTVYPL-EKVTMEGDCFHKTCFRCAHGGCPLT  141 (210)
Q Consensus       105 ~C~~C~~~I~~~-e~v~~~g~~~H~~CF~C~~C~~~l~  141 (210)
                      +|..|+++|.+. ..+.+.++.||+.||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            589999999866 5578999999999999999999885

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=98.42  E-value=5.7e-08  Score=78.70  Aligned_cols=73  Identities=48%  Similarity=1.078  Sum_probs=63.5

Q ss_pred             CCCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCC
Q 040947            3 FTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKN   75 (210)
Q Consensus         3 ~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~   75 (210)
                      +.+....|.+|++.+++.+.+...+..||..||+|+.|+..|+...+....+.+||...+.++|-..+.++..
T Consensus       104 ~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~~~~~~~~~~~~~~~~  176 (200)
T KOG1700|consen  104 FAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKHHFAQLFKGKGNYNEG  176 (200)
T ss_pred             hhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccchhhheeecCCCccccc
Confidence            3466789999999999999999999999999999999999999999999999999988887776655555443

>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]

Probab=98.02  E-value=3.7e-07  Score=72.87  Aligned_cols=61  Identities=33%  Similarity=0.688  Sum_probs=55.4

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcC
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME  164 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~  164 (210)
                      ..|..|++.++|.|.|..+++.||+.||+|..|+-+|.-.++.-.|.++||..+|.+..+.
T Consensus         5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~at   65 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVAT   65 (264)
T ss_pred             chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccceee
Confidence            5788999999999999999999999999999999999888888889999999999776543

>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]

Probab=97.89  E-value=9.3e-07  Score=70.63  Aligned_cols=59  Identities=39%  Similarity=0.745  Sum_probs=54.2

Q ss_pred             CCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhh
Q 040947            8 DKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF   66 (210)
Q Consensus         8 ~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~   66 (210)
                      ..|..|++.+++.|.|..+++.||..||+|..|+-+|.-.+|-..+.++||..+|....
T Consensus         5 ~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~   63 (264)
T KOG1702|consen    5 CNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQV   63 (264)
T ss_pred             chhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCcccccce
Confidence            56889999999999999999999999999999999999888888899999999996554

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

Probab=97.76  E-value=2.7e-06  Score=69.81  Aligned_cols=111  Identities=23%  Similarity=0.488  Sum_probs=87.6

Q ss_pred             CCcceecceeEeeCCccccCCCcccccccCCCC--CCCeeccCCeeeccchHHH--hhhccCCCCCCccCCCCCCCCCCC
Q 040947           13 CDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLV--MSNYSSMDGVLYCKPHFEQ--LFKESGNFSKNFQTGKNPSSCSNQ   88 (210)
Q Consensus        13 C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~--~~~~~~~~~~~~~~~~~~~~~~~~   88 (210)
                      |+..|.+...+.+.+..||..|+.|..|...|.  ...|.. +|..||..+|.+  .+.                     
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~---------------------   59 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS---------------------   59 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc---------------------
Confidence            677787555577789999999999999999998  555555 999999999987  333                     


Q ss_pred             CCCCCCcccccCCCCCccccccceeecCcee-EecCccccccccccCCCCCcCC-CCCeeecCC-eeecHhHHHhh
Q 040947           89 NRTPSKLSSLFSGTQDKCAACEKTVYPLEKV-TMEGDCFHKTCFRCAHGGCPLT-HSSYAALDG-VLYCKHHFAQL  161 (210)
Q Consensus        89 ~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v-~~~g~~~H~~CF~C~~C~~~l~-~~~f~~~dg-~~yC~~c~~~~  161 (210)
                                     .+|.+|...|...+.| .+..+. |.-||.|..|...+. +..+.+.+. +.+|..++.+.
T Consensus        60 ---------------~rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~  119 (235)
T KOG0490|consen   60 ---------------KRCARCKFTISQLDELERAFEKV-HLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE  119 (235)
T ss_pred             ---------------ccccCCCCCcCHHHHHHHhhcCC-CcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence                           6899999998665554 566666 999999999988665 556666654 99999888654

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

Probab=91.28  E-value=0.052  Score=44.28  Aligned_cols=58  Identities=22%  Similarity=0.646  Sum_probs=45.3

Q ss_pred             ccceeecCceeEecCccccccccccCCCCCcCC--CCCeeecCCeeecHhHHHh--hhcCCCC
Q 040947          109 CEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLT--HSSYAALDGVLYCKHHFAQ--LFMEKGN  167 (210)
Q Consensus       109 C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~--~~~f~~~dg~~yC~~c~~~--~f~~k~~  167 (210)
                      |+..|.+...+.+.+..||..|..|..|...|.  ...|.. +|..||...|..  .+..++.
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~   63 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCA   63 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcccccc
Confidence            566676444466779999999999999999997  555566 999999999998  5555543

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=88.18  E-value=0.32  Score=30.93  Aligned_cols=36  Identities=28%  Similarity=0.611  Sum_probs=25.5

Q ss_pred             CccccccceeecCce-eE--ecCcccccccc----ccCC--CCCc
Q 040947          104 DKCAACEKTVYPLEK-VT--MEGDCFHKTCF----RCAH--GGCP  139 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~-v~--~~g~~~H~~CF----~C~~--C~~~  139 (210)
                      .+|..|+++|.+++- |.  .-+..||++|+    .|..  |+..
T Consensus         6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~~g~C~~~~c~~~   50 (54)
T PF14446_consen    6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWEKAGGCINYSCGTG   50 (54)
T ss_pred             ccChhhCCcccCCCCEEECCCCCCcccHHHHhhCCceEeccCCCC
Confidence            689999999975444 43  34788999988    4655  5443

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

Probab=86.72  E-value=0.27  Score=35.28  Aligned_cols=30  Identities=33%  Similarity=0.626  Sum_probs=21.6

Q ss_pred             ccccccceeecCceeEe-cCccccccccccC
Q 040947          105 KCAACEKTVYPLEKVTM-EGDCFHKTCFRCA  134 (210)
Q Consensus       105 ~C~~C~~~I~~~e~v~~-~g~~~H~~CF~C~  134 (210)
                      +|..|+++|+.++.+++ .+..-|..||+=.
T Consensus         4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~   34 (101)
T PF09943_consen    4 KCYICGKPIYEGQLFTFTKKGPVHYECFREK   34 (101)
T ss_pred             EEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence            68888888887777654 3456788887644

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=84.97  E-value=0.61  Score=29.65  Aligned_cols=29  Identities=34%  Similarity=0.718  Sum_probs=21.4

Q ss_pred             CCCcccCCcceecc-eeE--eeCCccccCCCc
Q 040947            7 LDKCKACDKTVYVV-DML--SLEGMPYHKSCF   35 (210)
Q Consensus         7 ~~~C~~C~~~I~~~-~~v--~~~g~~~H~~CF   35 (210)
                      ..+|..|+++|.++ +.|  ..-+..||++|.
T Consensus         5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~   36 (54)
T PF14446_consen    5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW   36 (54)
T ss_pred             CccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence            45699999999644 343  556778999886

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

Probab=83.63  E-value=1  Score=29.69  Aligned_cols=33  Identities=15%  Similarity=0.304  Sum_probs=17.1

Q ss_pred             cccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      ++|+.|...|...-....=..+||..|....++
T Consensus         8 LrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~   40 (65)
T PF14835_consen    8 LRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG   40 (65)
T ss_dssp             TS-SSS-S--SS-B---SSS--B-TTTGGGGTT
T ss_pred             cCCcHHHHHhcCCceeccCccHHHHHHhHHhcC
Confidence            688999888876544445667899999987766

>smart00504 Ubox Modified RING finger domain

Probab=83.58  E-value=1.6  Score=27.79  Aligned_cols=32  Identities=16%  Similarity=0.179  Sum_probs=26.2

Q ss_pred             cccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      |.|..|+..+.. ......|..||+.|..+.+.
T Consensus         2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~   33 (63)
T smart00504        2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLL   33 (63)
T ss_pred             cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHH
Confidence            678899998887 45557899999999988775

Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.

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

Probab=82.24  E-value=1.1  Score=31.83  Aligned_cols=30  Identities=30%  Similarity=0.433  Sum_probs=17.2

Q ss_pred             CCCcccCCcceeccee-EeeCCccccCCCcc
Q 040947            7 LDKCKACDKTVYVVDM-LSLEGMPYHKSCFK   36 (210)
Q Consensus         7 ~~~C~~C~~~I~~~~~-v~~~g~~~H~~CF~   36 (210)
                      ...|..|+++|..... +.-.|..+|..|++
T Consensus        78 ~~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   78 STKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            4557777777764433 33345556766653

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

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

Probab=81.89  E-value=0.94  Score=32.16  Aligned_cols=29  Identities=28%  Similarity=0.495  Sum_probs=20.6

Q ss_pred             CccccccceeecCcee-EecCccccccccc
Q 040947          104 DKCAACEKTVYPLEKV-TMEGDCFHKTCFR  132 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v-~~~g~~~H~~CF~  132 (210)
                      ..|+.|+++|.....+ -..|..+|..|++
T Consensus        79 ~~C~vC~k~l~~~~f~~~p~~~v~H~~C~~  108 (109)
T PF10367_consen   79 TKCSVCGKPLGNSVFVVFPCGHVVHYSCIK  108 (109)
T ss_pred             CCccCcCCcCCCceEEEeCCCeEEeccccc
Confidence            6799999999754333 3456778888863

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

>PF14471 DUF4428: Domain of unknown function (DUF4428)

Probab=81.49  E-value=1.3  Score=27.77  Aligned_cols=29  Identities=28%  Similarity=0.559  Sum_probs=22.8

Q ss_pred             ccCCCCCcCCC-CCeeecCCeeecHhHHHhh
Q 040947          132 RCAHGGCPLTH-SSYAALDGVLYCKHHFAQL  161 (210)
Q Consensus       132 ~C~~C~~~l~~-~~f~~~dg~~yC~~c~~~~  161 (210)
                      .|..|+..+.- ..+.+.|| ..|..|+.++
T Consensus         1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl   30 (51)
T PF14471_consen    1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL   30 (51)
T ss_pred             CCCccccccccccceeccCc-cchHHHHHHh
Confidence            47888888873 33667788 6899999987

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	210
2d8y_A	91	Solution Structure Of The Lim Domain Of Epithelial		2e-14
2d8y_A	91	Solution Structure Of The Lim Domain Of Epithelial		1e-13
1b8t_A	192	Solution Structure Of The Chicken Crp1 Length = 192		2e-14
1cxx_A	113	Mutant R122a Of Quail Cysteine And Glycine-Rich Pro		7e-09
1qli_A	113	Quail Cysteine And Glycine-Rich Protein, Nmr, 15 Mi		3e-08
1ctl_A	85	Structure Of The Carboxy-Terminal Lim Domain From T		8e-08
2o13_A	58	Solution Structure Of The C-Terminal Lim Domain Of		5e-07
2o13_A	58	Solution Structure Of The C-Terminal Lim Domain Of		1e-06
2cu8_A	76	Solution Structure Of The Lim Domain Of Human Cyste		3e-06
2co8_A	82	Solution Structures Of The Lim Domain Of Human Nedd		4e-06
2co8_A	82	Solution Structures Of The Lim Domain Of Human Nedd		4e-04
2o10_A	60	Solution Structure Of The N-Terminal Lim Domain Of		3e-05
1iml_A	76	Cysteine Rich Intestinal Protein, Nmr, 48 Structure		5e-05
1iml_A	76	Cysteine Rich Intestinal Protein, Nmr, 48 Structure		2e-04
1a7i_A	81	Amino-Terminal Lim Domain From Quail Cysteine And G		1e-04

>pdb|2D8Y|A Chain A, Solution Structure Of The Lim Domain Of Epithelial Protein Lost In Neoplasm Length = 91

Iteration: 1
 Score = 75.9 bits (185), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 35/77 (45%), Positives = 48/77 (62%), Gaps = 2/77 (2%)
Query: 8  DKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK 67
          + C  C KTVY ++ L      +H SCF+CS+C   L +  Y+S+ G +YCKPHF QLFK
Sbjct: 16 ETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFK 75
Query: 68 ESGNFSKNFQTGKNPSS 84
            GN+ + F +G  PSS
Sbjct: 76 SKGNYDEGFGSG--PSS 90

>pdb|2D8Y|A Chain A, Solution Structure Of The Lim Domain Of Epithelial Protein Lost In Neoplasm Length = 91

Iteration: 1
 Score = 72.4 bits (176), Expect = 1e-13,   Method: Compositional matrix adjust.
 Identities = 31/67 (46%), Positives = 44/67 (65%)
Query: 102 TQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQL 161
            ++ C  C+KTVYP+E++      FH +CFRC++    L+  +YA+L G +YCK HF QL
Sbjct: 14  ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQL 73
Query: 162 FMEKGNY 168
           F  KGNY
Sbjct: 74  FKSKGNY 80

>pdb|1B8T|A Chain A, Solution Structure Of The Chicken Crp1 Length = 192

Iteration: 1
 Score = 75.1 bits (183), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 56/179 (31%), Positives = 82/179 (45%), Gaps = 24/179 (13%)
Query: 5   GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQ 64
           G   KC  C K VY  + +  EG  +HKSCF C  CK  L  +  +     +YCK  + +
Sbjct: 5   GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGK 64
Query: 65  ---------------LFKESG-NFSKNFQTGKN--PSSCSNQNRTPSKLSSLFSGTQDKC 106
                          L  + G +    ++ G++  P++  N +R   K+     G  D C
Sbjct: 65  KYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTN-PNASRMAQKV-----GGSDGC 118
Query: 107 AACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEK 165
             C + VY  EKV   G  +HK+CFRCA  G  L  ++ A  DG +YCK  +A+ F  K
Sbjct: 119 PRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 177

>pdb|1CXX|A Chain A, Mutant R122a Of Quail Cysteine And Glycine-Rich Protein, Nmr, Minimized Structure Length = 113

Iteration: 1
 Score = 57.0 bits (136), Expect = 7e-09,   Method: Compositional matrix adjust.
 Identities = 32/78 (41%), Positives = 43/78 (55%), Gaps = 1/78 (1%)
Query: 89  NRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAAL 148
           N   SK +  F G  +KC+AC  +VY  EKV   G  +HK CFRCA  G  L  ++    
Sbjct: 23  NPNTSKFAQKFGGA-EKCSACGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEK 81
Query: 149 DGVLYCKHHFAQLFMEKG 166
           +G +YCK  +A+ F  KG
Sbjct: 82  EGEIYCKGCYAKNFGPKG 99

>pdb|1QLI|A Chain A, Quail Cysteine And Glycine-Rich Protein, Nmr, Minimized Average Structure Length = 113

Iteration: 1
 Score = 55.1 bits (131), Expect = 3e-08,   Method: Compositional matrix adjust.
 Identities = 31/78 (39%), Positives = 42/78 (53%), Gaps = 1/78 (1%)
Query: 89  NRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAAL 148
           N   SK +  F G  +KC+ C  +VY  EKV   G  +HK CFRCA  G  L  ++    
Sbjct: 23  NPNTSKFAQKFGGA-EKCSRCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEK 81
Query: 149 DGVLYCKHHFAQLFMEKG 166
           +G +YCK  +A+ F  KG
Sbjct: 82  EGEIYCKGCYAKNFGPKG 99

>pdb|1CTL|A Chain A, Structure Of The Carboxy-Terminal Lim Domain From The Cysteine Rich Protein Crp Length = 85

Iteration: 1
 Score = 53.5 bits (127), Expect = 8e-08,   Method: Compositional matrix adjust.
 Identities = 28/65 (43%), Positives = 36/65 (55%)
Query: 101 GTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQ 160
           G  D C  C + VY  EKV   G  +HK+CFRCA  G  L  ++ A  DG +YCK  +A+
Sbjct: 6   GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAK 65
Query: 161 LFMEK 165
            F  K
Sbjct: 66  NFGPK 70

>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of MlpCRP3 Length = 58

Iteration: 1
 Score = 50.8 bits (120), Expect = 5e-07,   Method: Compositional matrix adjust.
 Identities = 23/58 (39%), Positives = 35/58 (60%)
Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
          KC  C K+VY  + +   G P+HK+CF+C+ C  +L  +N +  DG LYCK  + + F
Sbjct: 1  KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNF 58

>pdb|2O13|A Chain A, Solution Structure Of The C-Terminal Lim Domain Of MlpCRP3 Length = 58

Iteration: 1
 Score = 50.1 bits (118), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 28/58 (48%), Positives = 34/58 (58%)
Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162
           KC  C K+VY  EKV   G  +HKTCFRCA  G  L  ++    DG LYCK  +A+ F
Sbjct: 1   KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNF 58

>pdb|2CU8|A Chain A, Solution Structure Of The Lim Domain Of Human Cysteine-Rich Protein 2 Length = 76

Iteration: 1
 Score = 48.5 bits (114), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 25/59 (42%), Positives = 32/59 (54%), Gaps = 1/59 (1%)
Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYC-KPHFEQLF 66
          KC  CDKTVY  + +S  G  +HK C KC  C  TL    ++  DG  +C KP +  LF
Sbjct: 11 KCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLF 69

>pdb|2CO8|A Chain A, Solution Structures Of The Lim Domain Of Human Nedd9 Interacting Protein With Calponin Homology And Lim Domains Length = 82

Iteration: 1
 Score = 48.1 bits (113), Expect = 4e-06,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 32/63 (50%), Gaps = 2/63 (3%)
Query: 4  TGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSM--DGVLYCKPH 61
           G  D C  C + +YV++ L + G  +H+SCF+C  C+ TL    Y     DG  YC  H
Sbjct: 12 AGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQH 71
Query: 62 FEQ 64
            Q
Sbjct: 72 LPQ 74

>pdb|2CO8|A Chain A, Solution Structures Of The Lim Domain Of Human Nedd9 Interacting Protein With Calponin Homology And Lim Domains Length = 82

Iteration: 1
 Score = 41.2 bits (95), Expect = 4e-04,   Method: Compositional matrix adjust.
 Identities = 23/63 (36%), Positives = 31/63 (49%), Gaps = 2/63 (3%)
Query: 100 SGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYA--ALDGVLYCKHH 157
           +G  D CA C + +Y LE++ + G  FH++CFRC      L    Y     DG  YC  H
Sbjct: 12  AGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQH 71
Query: 158 FAQ 160
             Q
Sbjct: 72  LPQ 74

>pdb|2O10|A Chain A, Solution Structure Of The N-Terminal Lim Domain Of MlpCRP3 Length = 60

Iteration: 1
 Score = 45.1 bits (105), Expect = 3e-05,   Method: Compositional matrix adjust.
 Identities = 24/51 (47%), Positives = 30/51 (58%)
Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCK 155
           KC ACEKTVY  E++   G  FHKTCF C      L  ++ AA +  +YCK
Sbjct: 3   KCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCK 53

>pdb|1IML|A Chain A, Cysteine Rich Intestinal Protein, Nmr, 48 Structures Length = 76

Iteration: 1
 Score = 44.3 bits (103), Expect = 5e-05,   Method: Compositional matrix adjust.
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 1/63 (1%)
Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK-PHFEQLFK 67
          KC  CDK VY  + ++  G  +H+ C KC  C  TL    ++  +G  YC  P +  +F 
Sbjct: 2  KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61
Query: 68 ESG 70
            G
Sbjct: 62 PKG 64

>pdb|1IML|A Chain A, Cysteine Rich Intestinal Protein, Nmr, 48 Structures Length = 76

Iteration: 1
 Score = 42.4 bits (98), Expect = 2e-04,   Method: Compositional matrix adjust.
 Identities = 24/63 (38%), Positives = 34/63 (53%), Gaps = 1/63 (1%)
Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHH-FAQLFM 163
           KC  C+K VY  E+VT  G  +H+ C +C   G  LT   +A  +G  YC H  ++ +F 
Sbjct: 2   KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61
Query: 164 EKG 166
            KG
Sbjct: 62  PKG 64

>pdb|1A7I|A Chain A, Amino-Terminal Lim Domain From Quail Cysteine And Glycine- Rich Protein, Nmr, Minimized Average Structure Length = 81

Iteration: 1
 Score = 43.1 bits (100), Expect = 1e-04,   Method: Compositional matrix adjust.
 Identities = 24/66 (36%), Positives = 35/66 (53%)
Query: 101 GTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQ 160
           G  +KC AC +TVY  E+V  +G  FH+ CF C      L  ++ A  D  +YCK  + +
Sbjct: 5   GGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGK 64
Query: 161 LFMEKG 166
            +  KG
Sbjct: 65  KYGPKG 70

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	210
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	3e-45
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	6e-16
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	2e-27
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	9e-26
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	4e-24
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	1e-22
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	8e-24
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	2e-22
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	3e-22
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	7e-20
2co8_A	82	NEDD9 interacting protein with calponin homology a	1e-19
2co8_A	82	NEDD9 interacting protein with calponin homology a	3e-19
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	2e-17
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	1e-14
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	5e-17
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-09
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	9e-16
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	2e-13
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	2e-15
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	5e-07
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	3e-14
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	4e-12
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	6e-06
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	3e-05
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	1e-11
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	2e-10
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	2e-11
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	3e-10
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	2e-11
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	5e-11
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	6e-10
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	7e-11
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	1e-09
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	5e-10
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	2e-09
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	8e-10
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	6e-09
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	2e-09
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	3e-09
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	2e-09
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	1e-08
2cuq_A	80	Four and A half LIM domains 3; structural genomics	2e-09
2cuq_A	80	Four and A half LIM domains 3; structural genomics	4e-08
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	5e-09
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	1e-08
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	8e-09
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	1e-08
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	9e-09
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	1e-07
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	1e-08
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	2e-08
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	1e-08
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	5e-08
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	2e-08
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	2e-07
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	2e-08
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	4e-08
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	3e-08
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	4e-07
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	4e-08
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	1e-06
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	1e-07
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	2e-07
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	2e-07
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	4e-07
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	3e-07
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	4e-07
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	8e-07
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	8e-07
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	2e-06
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	2e-05
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	2e-05
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	4e-05
2cor_A	79	Pinch protein; LIM domain, particularly interestin	1e-04
2cor_A	79	Pinch protein; LIM domain, particularly interestin	4e-04
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	1e-04
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	5e-04

>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 =  148 bits (374), Expect = 3e-45
 Identities = 52/179 (29%), Positives = 71/179 (39%), Gaps = 12/179 (6%)

Query: 1   MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
           M   G   KC  C K VY  + +  EG  +HKSCF C  CK  L  +  +     +YCK 
Sbjct: 1   MPNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKS 60

Query: 61  HFEQLFKESGNFSKNFQTGK------------NPSSCSNQNRTPSKLSSLFSGTQDKCAA 108
            + + +   G                                  +   +   G  D C  
Sbjct: 61  CYGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPR 120

Query: 109 CEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN 167
           C + VY  EKV   G  +HK+CFRCA  G  L  ++ A  DG +YCK  +A+ F  KG 
Sbjct: 121 CGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGF 179

>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 = 72.0 bits (176), Expect = 6e-16
 Identities = 24/80 (30%), Positives = 34/80 (42%)

Query: 99  FSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
             G   KC  C+K VY  E+V  EG  FHK+CF C      L  ++ A     +YCK  +
Sbjct: 3   NWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCY 62

Query: 159 AQLFMEKGNYSHVLKAANHK 178
            + +  KG    +       
Sbjct: 63  GKKYGPKGKGKGMGAGTLST 82

>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 = 98.8 bits (246), Expect = 2e-27
 Identities = 32/79 (40%), Positives = 47/79 (59%)

Query: 91  TPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDG 150
           + S      +  ++ C  C+KTVYP+E++      FH +CFRC++    L+  +YA+L G
Sbjct: 3   SGSSGMKFQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHG 62

Query: 151 VLYCKHHFAQLFMEKGNYS 169
            +YCK HF QLF  KGNY 
Sbjct: 63  RIYCKPHFNQLFKSKGNYD 81

>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 = 94.5 bits (235), Expect = 9e-26
 Identities = 32/78 (41%), Positives = 45/78 (57%)

Query: 3  FTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHF 62
               + C  C KTVY ++ L      +H SCF+CS+C   L +  Y+S+ G +YCKPHF
Sbjct: 11 QAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHF 70

Query: 63 EQLFKESGNFSKNFQTGK 80
           QLFK  GN+ + F +G 
Sbjct: 71 NQLFKSKGNYDEGFGSGP 88

>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 = 89.8 bits (223), Expect = 4e-24
 Identities = 29/73 (39%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 96  SSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYC- 154
           SS  SG   KC  C+KTVY  EKV+  G  +HK C +C      LT   +A  DG  +C 
Sbjct: 2   SSGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCH 61

Query: 155 KHHFAQLFMEKGN 167
           K  +A LF    +
Sbjct: 62  KPCYATLFGSGPS 74

>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 = 86.3 bits (214), Expect = 1e-22
 Identities = 26/71 (36%), Positives = 35/71 (49%), Gaps = 1/71 (1%)

Query: 2  AFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYC-KP 60
            +G   KC  CDKTVY  + +S  G  +HK C KC  C  TL    ++  DG  +C KP
Sbjct: 4  GSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKP 63

Query: 61 HFEQLFKESGN 71
           +  LF    +
Sbjct: 64 CYATLFGSGPS 74

>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 = 89.4 bits (222), Expect = 8e-24
 Identities = 24/69 (34%), Positives = 35/69 (50%)

Query: 99  FSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
             G  +KC AC +TVY  E+V  +G  FH+ CF C      L  ++ A  D  +YCK  +
Sbjct: 3   NWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCY 62

Query: 159 AQLFMEKGN 167
            + +  KG 
Sbjct: 63  GKKYGPKGY 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 = 85.5 bits (212), Expect = 2e-22
 Identities = 22/79 (27%), Positives = 38/79 (48%), Gaps = 1/79 (1%)

Query: 1  MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
          M   G  +KC AC +TVY  + +  +G  +H+ CF C  C+  L  +  +  D  +YCK 
Sbjct: 1  MPNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKS 60

Query: 61 HFEQLFKESG-NFSKNFQT 78
           + + +   G  + +   T
Sbjct: 61 CYGKKYGPKGYGYGQGAGT 79

>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 = 85.1 bits (211), Expect = 3e-22
 Identities = 25/75 (33%), Positives = 37/75 (49%), Gaps = 1/75 (1%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKH-HFAQLFM 163
           KC  C+K VY  E+VT  G  +H+ C +C   G  LT   +A  +G  YC H  ++ +F 
Sbjct: 2   KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61

Query: 164 EKGNYSHVLKAANHK 178
            KG      ++   K
Sbjct: 62  PKGFGRGGAESHTFK 76

>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 = 78.9 bits (195), Expect = 7e-20
 Identities = 21/64 (32%), Positives = 31/64 (48%), Gaps = 1/64 (1%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK-PHFEQLFK 67
          KC  CDK VY  + ++  G  +H+ C KC  C  TL    ++  +G  YC  P +  +F 
Sbjct: 2  KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61

Query: 68 ESGN 71
            G 
Sbjct: 62 PKGF 65

>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 = 78.8 bits (194), Expect = 1e-19
 Identities = 24/73 (32%), Positives = 32/73 (43%), Gaps = 2/73 (2%)

Query: 92  PSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAAL--D 149
            S      +G  D CA C + +Y LE++ + G  FH++CFRC      L    Y     D
Sbjct: 4   GSSGQHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGD 63

Query: 150 GVLYCKHHFAQLF 162
           G  YC  H  Q  
Sbjct: 64  GHFYCLQHLPQTD 76

>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 = 77.7 bits (191), Expect = 3e-19
 Identities = 23/72 (31%), Positives = 33/72 (45%), Gaps = 2/72 (2%)

Query: 2  AFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSM--DGVLYCK 59
             G  D C  C + +YV++ L + G  +H+SCF+C  C+ TL    Y     DG  YC 
Sbjct: 10 QEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCL 69

Query: 60 PHFEQLFKESGN 71
           H  Q      +
Sbjct: 70 QHLPQTDSGPSS 81

>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 = 72.4 bits (178), Expect = 2e-17
 Identities = 19/61 (31%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 103 QDKCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQL 161
              C  C+    P EK V   G+ +H+ CF CA          +   +G  YC+H F  L
Sbjct: 11  SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQML 70

Query: 162 F 162
           F
Sbjct: 71  F 71

>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 = 65.5 bits (160), Expect = 1e-14
 Identities = 15/60 (25%), Positives = 26/60 (43%), Gaps = 1/60 (1%)

Query: 8  DKCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
            C+ C       + +++  G  YH+ CF C+ C        +   +G  YC+  F+ LF
Sbjct: 12 ATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF 71

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

 Score = 72.8 bits (179), Expect = 5e-17
 Identities = 22/157 (14%), Positives = 43/157 (27%), Gaps = 39/157 (24%)

Query: 9   KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE 68
           +C  CD+ ++  +    E   +H   F C  C   L    Y  ++    CKP + +    
Sbjct: 5   RCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAV 64

Query: 69  SGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDC--- 125
                                                C  C   + P  +     +    
Sbjct: 65  ------------------------------------VCQGCHNAIDPEVQRVTYNNFSWH 88

Query: 126 FHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162
               CF C+     L    +  ++G+++C     +  
Sbjct: 89  ASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM 125

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

 Score = 53.6 bits (129), Expect = 1e-09
 Identities = 12/61 (19%), Positives = 22/61 (36%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME 164
           +CA C++ ++  E    E   +H   F C      L    Y  ++    CK  + +    
Sbjct: 5   RCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAV 64

Query: 165 K 165
            
Sbjct: 65  V 65

>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 = 68.2 bits (167), Expect = 9e-16
 Identities = 19/62 (30%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 102 TQDKCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQ 160
               C  C+    P EK V   G+ +H+ CF CA          +   +G  YC+H F  
Sbjct: 10  ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQM 69

Query: 161 LF 162
           LF
Sbjct: 70  LF 71

>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 = 62.4 bits (152), Expect = 2e-13
 Identities = 17/67 (25%), Positives = 28/67 (41%), Gaps = 1/67 (1%)

Query: 1  MAFTGTLDKCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK 59
          MA       C+ C       + +++  G  YH+ CF C+ C        +   +G  YC+
Sbjct: 5  MANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCE 64

Query: 60 PHFEQLF 66
            F+ LF
Sbjct: 65 HDFQMLF 71

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

 Score = 69.4 bits (170), Expect = 2e-15
 Identities = 28/165 (16%), Positives = 46/165 (27%), Gaps = 38/165 (23%)

Query: 6   TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYS--SMDGVLYCKPHFE 63
           +L  C  C + +     L      +H+ C  C  C   L           G   C+  + 
Sbjct: 1   SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYL 60

Query: 64  QLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEG 123
           +LF                                  G    CA+C+K +   E      
Sbjct: 61  RLF----------------------------------GQDGLCASCDKRIRAYEMTMRVK 86

Query: 124 DC-FHKTCFRCAHGGCPL-THSSYAALDGVLYCKHHFAQLFMEKG 166
           D  +H  CF+CA           Y  ++  + C+    +     G
Sbjct: 87  DKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKING 131

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

 Score = 46.3 bits (110), Expect = 5e-07
 Identities = 17/68 (25%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 5   GTLDKCKACDKTVYVVDM-LSLEGMPYHKSCFKCSHCKGTLVM-SNYSSMDGVLYCKPHF 62
           G    C +CDK +   +M + ++   YH  CFKC+ C+    +   Y  ++  + C+   
Sbjct: 64  GQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDI 123

Query: 63  EQLFKESG 70
            +  K +G
Sbjct: 124 YEWTKING 131

>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 = 66.8 bits (163), Expect = 3e-14
 Identities = 35/160 (21%), Positives = 47/160 (29%), Gaps = 40/160 (25%)

Query: 9   KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE 68
            C  CD+ +    +L      +H  C KCS C   L    +S     +YCK  F + F  
Sbjct: 8   MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCFS-RGESVYCKDDFFKRF-- 64

Query: 69  SGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGD-CFH 127
                                               KCAAC+  + P + V    D  +H
Sbjct: 65  ----------------------------------GTKCAACQLGIPPTQVVRRAQDFVYH 90

Query: 128 KTCFRCAHGGCPLTH--SSYAALDGVLYCKHHFAQLFMEK 165
             CF C      L      Y   D  L CK  +       
Sbjct: 91  LHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGG 130

>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 = 61.1 bits (148), Expect = 4e-12
 Identities = 35/153 (22%), Positives = 47/153 (30%), Gaps = 40/153 (26%)

Query: 9   KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE 68
            C  CD+ +    +L      +H  C KCS C   L    + S    +YCK  F + F  
Sbjct: 62  MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRF-- 118

Query: 69  SGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDC-FH 127
                                               KCAAC+  + P + V    D  +H
Sbjct: 119 ----------------------------------GTKCAACQLGIPPTQVVRRAQDFVYH 144

Query: 128 KTCFRCAHGGCPLTH--SSYAALDGVLYCKHHF 158
             CF C      L      Y   D  L CK  +
Sbjct: 145 LHCFACVVCKRQLATGDEFYLMEDSRLVCKADY 177

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

 Score = 44.1 bits (104), Expect = 6e-06
 Identities = 15/83 (18%), Positives = 32/83 (38%), Gaps = 1/83 (1%)

Query: 83  SSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTH 142
           +   ++  +   + S  +     CA C++ +     +      +H  C +C+    PL  
Sbjct: 40  NGIDDEGGSGGHMGSGGTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAE 99

Query: 143 SSYAALDGVLYCKHHFAQLFMEK 165
             ++     +YCK  F + F  K
Sbjct: 100 RCFSR-GESVYCKDDFFKRFGTK 121

>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 = 42.2 bits (99), Expect = 3e-05
 Identities = 18/59 (30%), Positives = 22/59 (37%), Gaps = 3/59 (5%)

Query: 9   KCKACDKTVYVVDM-LSLEGMPYHKSCFKCSHCKGTLVM--SNYSSMDGVLYCKPHFEQ 64
           KC AC   +    +    +   YH  CF C  CK  L      Y   D  L CK  +E 
Sbjct: 121 KCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYET 179

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

 Score = 57.4 bits (139), Expect = 1e-11
 Identities = 20/59 (33%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 9  KCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
           C AC +TV      L   G  +H+ CF CS C+  L   ++    G  YC P +E  F
Sbjct: 7  GCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKF 65

>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 = 54.3 bits (131), Expect = 2e-10
 Identities = 18/59 (30%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 105 KCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162
            C+AC +TV P  + +   G  +H+ CF C+    PL   S+    G  YC   +   F
Sbjct: 7   GCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKF 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 = 57.4 bits (139), Expect = 2e-11
 Identities = 19/59 (32%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 9  KCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
          KCK C K +   D  +  +G  +HK CF CS+CK  +   ++       YC    E  F
Sbjct: 17 KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKF 75

>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 = 53.9 bits (130), Expect = 3e-10
 Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 105 KCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162
           KC  C K +   ++ V  +G  +HK CF C++    +   S+       YC       F
Sbjct: 17  KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKF 75

>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 = 59.6 bits (144), Expect = 2e-11
 Identities = 33/195 (16%), Positives = 64/195 (32%), Gaps = 38/195 (19%)

Query: 9   KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTL--VMSNYSSMDGVLYCKPHFEQLF 66
           +C  C   +    +L      +H  C KCS C+  L  + ++  +  G++ C+  + +LF
Sbjct: 7   RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 66

Query: 67  KESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKV-TMEGDC 125
                                             G    C+AC +++   E V   +G+ 
Sbjct: 67  ----------------------------------GNSGACSACGQSIPASELVMRAQGNV 92

Query: 126 FHKTCFRCAHGGCPLTH-SSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHKRTASSS 184
           +H  CF C+     L     +  ++G L+C+H      +     S     +         
Sbjct: 93  YHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALINGHLNSGGSGGSGGSGGDVMV 152

Query: 185 STSPAEQIENKPDDE 199
              P        D++
Sbjct: 153 VGEPTLMGGEFGDED 167

>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 = 55.5 bits (134), Expect = 5e-11
 Identities = 14/59 (23%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 9  KCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
           C+ C KT+      +  +G  +H++CF C  C+  +   ++   D   +C P +E+  
Sbjct: 7  GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQH 65

>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 = 52.8 bits (127), Expect = 6e-10
 Identities = 15/62 (24%), Positives = 27/62 (43%), Gaps = 1/62 (1%)

Query: 105 KCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFM 163
            C  C+KT+ P  + +  +G  +H+TCF C     P+   S+   D   +C   + +   
Sbjct: 7   GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHA 66

Query: 164 EK 165
             
Sbjct: 67  SG 68

>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 = 55.9 bits (135), Expect = 7e-11
 Identities = 20/129 (15%), Positives = 36/129 (27%), Gaps = 38/129 (29%)

Query: 9   KCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK 67
            C  C K +      +  +   +H +CF+C+ C   L    + + D  + C     +   
Sbjct: 7   GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS 66

Query: 68  ESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTM-EGDCF 126
                                                KC  C K +   ++    +G  +
Sbjct: 67  P------------------------------------KCKGCFKAIVAGDQNVEYKGTVW 90

Query: 127 HKTCFRCAH 135
           HK CF    
Sbjct: 91  HKDCFSGPS 99

>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 = 52.8 bits (127), Expect = 1e-09
 Identities = 18/62 (29%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 105 KCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFM 163
            C  C K +    K V  +   +H TCFRCA    PL + ++ A D  + C     +   
Sbjct: 7   GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS 66

Query: 164 EK 165
            K
Sbjct: 67  PK 68

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

 Score = 52.7 bits (127), Expect = 5e-10
 Identities = 17/61 (27%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME 164
            C  C+K +     VT     +HK CF C      L+   + A D   YC + F  L+  
Sbjct: 7   GCVQCKKPITT-GGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYAS 65

Query: 165 K 165
            
Sbjct: 66  G 66

>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 = 51.6 bits (124), Expect = 2e-09
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
           C  C K +     ++    P+HK CF C+ C+  L    +++ D   YC   F  L+
Sbjct: 7  GCVQCKKPI-TTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLY 63

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

 Score = 52.4 bits (126), Expect = 8e-10
 Identities = 13/66 (19%), Positives = 21/66 (31%), Gaps = 1/66 (1%)

Query: 100 SGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFA 159
           S     C  C K +     +T +   +H  CF C      L    + A++   YC   + 
Sbjct: 2   SSGSSGCVKCNKAITS-GGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYK 60

Query: 160 QLFMEK 165
                 
Sbjct: 61  NFVSGP 66

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

 Score = 50.1 bits (120), Expect = 6e-09
 Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 8  DKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
            C  C+K +     ++ +  P+H  CF C  C   L    +++++   YC   ++   
Sbjct: 6  SGCVKCNKAI-TSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFV 63

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

 Score = 51.1 bits (123), Expect = 2e-09
 Identities = 15/58 (25%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
           C AC + +    +++  G  +H   F C+ C+   +   +    G+ YC+ H+ QLF
Sbjct: 7  ICGACRRPIEG-RVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLF 63

>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 = 50.7 bits (122), Expect = 3e-09
 Identities = 17/58 (29%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162
            C AC + +     V   G  +H   F CA    P     +    G+ YC+ H+ QLF
Sbjct: 7   ICGACRRPIEG-RVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLF 63

>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 = 51.2 bits (123), Expect = 2e-09
 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
          +C  C KT+     ++    P+H+ C  C+ C+  L    ++S D   YC   F +LF
Sbjct: 17 RCARCSKTLTQ-GGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELF 73

>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 = 48.1 bits (115), Expect = 4e-08
 Identities = 18/61 (29%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME 164
           +CA C KT+     VT     +H+ C  C     PL    + + D   YC   F +LF  
Sbjct: 17  RCARCSKTLTQ-GGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFAS 75

Query: 165 K 165
            
Sbjct: 76  G 76

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

 Score = 50.5 bits (121), Expect = 5e-09
 Identities = 19/58 (32%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
           C  C + +     L      +H SCFKC  C   L    Y S DGV YC+  +   F
Sbjct: 17 HCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTGE-YISKDGVPYCESDYHAQF 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 = 49.4 bits (118), Expect = 1e-08
 Identities = 16/61 (26%), Positives = 27/61 (44%), Gaps = 1/61 (1%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME 164
            CA C++ +   + +      +H +CF+C      LT   Y + DGV YC+  +   F  
Sbjct: 17  HCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGS 75

Query: 165 K 165
            
Sbjct: 76  G 76

>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 = 49.7 bits (119), Expect = 8e-09
 Identities = 12/62 (19%), Positives = 23/62 (37%), Gaps = 1/62 (1%)

Query: 6  TLDKCKACDKTVYVVDM-LSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQ 64
              C  C + V      +      +H  CF CS C+  L   ++ +++   YC+  +  
Sbjct: 4  GSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVA 63

Query: 65 LF 66
            
Sbjct: 64 TL 65

>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 = 49.0 bits (117), Expect = 1e-08
 Identities = 14/64 (21%), Positives = 21/64 (32%), Gaps = 1/64 (1%)

Query: 100 SGTQDKCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHF 158
           S     C  C + V      V      FH  CF C+     L    + A++   YC+  +
Sbjct: 2   SSGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCY 61

Query: 159 AQLF 162
               
Sbjct: 62  VATL 65

>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 = 49.8 bits (119), Expect = 9e-09
 Identities = 12/59 (20%), Positives = 22/59 (37%), Gaps = 1/59 (1%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK 67
           C  C   +  V  + L     H  C+ C+ C   L    +  ++  +YC+ H  +   
Sbjct: 17 MCDKCGTGIVGV-FVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVS 74

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

 Score = 47.1 bits (112), Expect = 1e-07
 Identities = 11/58 (18%), Positives = 20/58 (34%), Gaps = 1/58 (1%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162
            C  C   +     V +     H  C+ C   G  L    +  ++  +YC+ H  +  
Sbjct: 17  MCDKCGTGIVG-VFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERV 73

>2ehe_A Four and A half LIM domains 3; FHL-3, skeletal muscle LIM- protein 2, SLIM 2, FHL3, SLIM2, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 82

 Score = 49.4 bits (118), Expect = 1e-08
 Identities = 15/62 (24%), Positives = 23/62 (37%), Gaps = 1/62 (1%)

Query: 105 KCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFM 163
            CA C++ +    + +  E   FH+ CFRC      L    +   D  L C   +   F 
Sbjct: 17  TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFS 76

Query: 164 EK 165
             
Sbjct: 77  SG 78

>2ehe_A Four and A half LIM domains 3; FHL-3, skeletal muscle LIM- protein 2, SLIM 2, FHL3, SLIM2, structural genomics, NPPSFA; NMR {Homo sapiens} Length = 82

 Score = 49.0 bits (117), Expect = 2e-08
 Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 9  KCKACDKTVYV-VDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
           C  C + +      L  E   +H+ CF+C  C+ +L    ++  D  L C   +   F
Sbjct: 17 TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAF 75

>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 = 49.3 bits (118), Expect = 1e-08
 Identities = 15/58 (25%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
          KC  C++ V + + LS     +H  CF C  C  +    ++  +DG  +C+ H+    
Sbjct: 17 KCGGCNRPV-LENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRR 73

>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 = 47.7 bits (114), Expect = 5e-08
 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162
           KC  C + V     ++     +H  CF C       +  S+  LDG  +C+ H+    
Sbjct: 17  KCGGCNRPVLE-NYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRR 73

>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 = 50.1 bits (119), Expect = 2e-08
 Identities = 14/85 (16%), Positives = 29/85 (34%), Gaps = 2/85 (2%)

Query: 80  KNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCP 139
           K+ S                  +  +CA C   +     +      +H  C +C+     
Sbjct: 38  KDGSQSKLGGGGSGGHMGSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQ 97

Query: 140 LTH--SSYAALDGVLYCKHHFAQLF 162
           L    +S     G++ C++ + +LF
Sbjct: 98  LGDIGTSSYTKSGMILCRNDYIRLF 122

>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 = 47.4 bits (112), Expect = 2e-07
 Identities = 16/65 (24%), Positives = 27/65 (41%), Gaps = 2/65 (3%)

Query: 4   TGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSM--DGVLYCKPH 61
             +  +C  C   +    +L      +H  C KCS C+  L     SS    G++ C+  
Sbjct: 58  GLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRND 117

Query: 62  FEQLF 66
           + +LF
Sbjct: 118 YIRLF 122

>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 = 49.0 bits (117), Expect = 2e-08
 Identities = 16/72 (22%), Positives = 22/72 (30%), Gaps = 1/72 (1%)

Query: 91  TPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDG 150
           T     +  +     C  C   +     V       H  CF CA     L    Y  ++G
Sbjct: 13  TKVHGGAGSAQRMPLCDKCGSGIVG-AVVKARDKYRHPECFVCADCNLNLKQKGYFFVEG 71

Query: 151 VLYCKHHFAQLF 162
            LYC+ H     
Sbjct: 72  ELYCETHARART 83

>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 = 48.3 bits (115), Expect = 4e-08
 Identities = 15/66 (22%), Positives = 23/66 (34%), Gaps = 1/66 (1%)

Query: 1  MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKP 60
                +  C  C   + V  ++       H  CF C+ C   L    Y  ++G LYC+ 
Sbjct: 19 AGSAQRMPLCDKCGSGI-VGAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCET 77

Query: 61 HFEQLF 66
          H     
Sbjct: 78 HARART 83

>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 = 48.5 bits (116), Expect = 3e-08
 Identities = 17/65 (26%), Positives = 28/65 (43%), Gaps = 2/65 (3%)

Query: 3  FTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYS-SMDGVLYCKPH 61
          +  TL+KC  C + + +  +L   G  YH  CF C  C   L    ++      ++C   
Sbjct: 11 YVATLEKCATCSQPI-LDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIED 69

Query: 62 FEQLF 66
          F + F
Sbjct: 70 FHRKF 74

>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 = 45.4 bits (108), Expect = 4e-07
 Identities = 14/68 (20%), Positives = 24/68 (35%), Gaps = 2/68 (2%)

Query: 99  FSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYA-ALDGVLYCKHH 157
           +  T +KCA C + +     +   G  +H  CF C      L    +       ++C   
Sbjct: 11  YVATLEKCATCSQPILD-RILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIED 69

Query: 158 FAQLFMEK 165
           F + F   
Sbjct: 70  FHRKFASG 77

>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 = 47.9 bits (114), Expect = 4e-08
 Identities = 12/61 (19%), Positives = 22/61 (36%), Gaps = 3/61 (4%)

Query: 9  KCKACDKTVYVVD---MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQL 65
           C  C   +  +     +S E   +H  CF C  C  +LV   + +    + C    + +
Sbjct: 7  GCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDI 66

Query: 66 F 66
           
Sbjct: 67 S 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 = 44.0 bits (104), Expect = 1e-06
 Identities = 11/61 (18%), Positives = 18/61 (29%), Gaps = 3/61 (4%)

Query: 105 KCAACEKTVYPLEK---VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQL 161
            CA C   +  L     ++ E   +H  CF C      L    +      + C      +
Sbjct: 7   GCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDI 66

Query: 162 F 162
            
Sbjct: 67  S 67

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

 Score = 47.0 bits (112), Expect = 1e-07
 Identities = 17/87 (19%), Positives = 28/87 (32%), Gaps = 1/87 (1%)

Query: 79  GKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGC 138
           G + SS                     CA C + +     +   G  +H   F CAH   
Sbjct: 1   GSSGSSGDQDTLVQRAEHIPAGKRTPMCAHCNQVIRG-PFLVALGKSWHPEEFNCAHCKN 59

Query: 139 PLTHSSYAALDGVLYCKHHFAQLFMEK 165
            + +  +    G LYC+  + + F   
Sbjct: 60  TMAYIGFVEEKGALYCELCYEKFFASG 86

>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 = 46.3 bits (110), Expect = 2e-07
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
           C  C++ +     L   G  +H   F C+HCK T+    +    G LYC+  +E+ F
Sbjct: 27 MCAHCNQVI-RGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFF 83

>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 = 45.9 bits (109), Expect = 2e-07
 Identities = 11/66 (16%), Positives = 19/66 (28%), Gaps = 1/66 (1%)

Query: 100 SGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFA 159
           S     C  C + +     +    + +H  CFRC      L    +    G   C+    
Sbjct: 2   SSGSSGCHQCGEFIIG-RVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHN 60

Query: 160 QLFMEK 165
           +     
Sbjct: 61  REKASG 66

>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 = 45.1 bits (107), Expect = 4e-07
 Identities = 11/58 (18%), Positives = 22/58 (37%), Gaps = 1/58 (1%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
           C  C + + +  ++      +H  CF+C  C+  L    +    G   C+P   +  
Sbjct: 7  GCHQCGEFI-IGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREK 63

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

 Score = 45.6 bits (108), Expect = 3e-07
 Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 4/61 (6%)

Query: 9  KCKACDKTVYVVD----MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQ 64
          KC  C   +        +++ EG  +H  CF C  C   L    +      +YC    ++
Sbjct: 17 KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

Query: 65 L 65
          L
Sbjct: 77 L 77

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

 Score = 45.2 bits (107), Expect = 4e-07
 Identities = 16/61 (26%), Positives = 23/61 (37%), Gaps = 4/61 (6%)

Query: 105 KCAACEKTVYPLEK----VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQ 160
           KCA C+  +    K    V  EG  +H  CF C      L +  +      +YC     +
Sbjct: 17  KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

Query: 161 L 161
           L
Sbjct: 77  L 77

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

 Score = 45.7 bits (108), Expect = 8e-07
 Identities = 13/68 (19%), Positives = 26/68 (38%), Gaps = 2/68 (2%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTH--SSYAALDGVLYCKHHFAQLF 162
           +CA C   +     +      +H  C +C+     L    +S     G++ C++ + +LF
Sbjct: 7   RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 66

Query: 163 MEKGNYSH 170
              G    
Sbjct: 67  GNSGAGGS 74

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

 Score = 45.4 bits (107), Expect = 8e-07
 Identities = 16/64 (25%), Positives = 30/64 (46%), Gaps = 2/64 (3%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTL--VMSNYSSMDGVLYCKPHFEQLF 66
          +C  C   +    +L      +H  C KCS C+  L  + ++  +  G++ C+  + +LF
Sbjct: 7  RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 66

Query: 67 KESG 70
            SG
Sbjct: 67 GNSG 70

>1x68_A FHL5 protein; four-and-A-half LIM protein 5, zinc finger domain, AN actin- interacting protein, structural genomics, NPPSFA; NMR {Homo sapiens} SCOP: g.39.1.3 g.39.1.3 Length = 76

 Score = 43.3 bits (102), Expect = 2e-06
 Identities = 13/68 (19%), Positives = 27/68 (39%), Gaps = 3/68 (4%)

Query: 9  KCKACDKTVYVVD---MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQL 65
           C AC K +  +     +  +   +H  CF C  C  +LV   + + +  ++C+     +
Sbjct: 7  GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGM 66

Query: 66 FKESGNFS 73
            +    S
Sbjct: 67 DTDISGPS 74

>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 = 40.2 bits (94), Expect = 2e-05
 Identities = 11/61 (18%), Positives = 23/61 (37%), Gaps = 3/61 (4%)

Query: 105 KCAACEKTVYPL---EKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQL 161
            C AC K +  L   + +  +   +H  CF C      L    +   +  ++C+   + +
Sbjct: 7   GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGM 66

Query: 162 F 162
            
Sbjct: 67  D 67

>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 = 41.6 bits (97), Expect = 2e-05
 Identities = 13/72 (18%), Positives = 24/72 (33%), Gaps = 2/72 (2%)

Query: 101 GTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTH--SSYAALDGVLYCKHHF 158
           G+   C  C++ +     +      +H+ C  C   GC L           G   C+  +
Sbjct: 1   GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 60

Query: 159 AQLFMEKGNYSH 170
            +L    G+   
Sbjct: 61  LRLGGSGGHMGS 72

>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 = 40.4 bits (94), Expect = 4e-05
 Identities = 14/69 (20%), Positives = 23/69 (33%), Gaps = 2/69 (2%)

Query: 5  GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYS--SMDGVLYCKPHF 62
          G+L  C  C + +     L      +H+ C  C  C   L           G   C+  +
Sbjct: 1  GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 60

Query: 63 EQLFKESGN 71
           +L    G+
Sbjct: 61 LRLGGSGGH 69

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

 Score = 38.6 bits (90), Expect = 1e-04
 Identities = 15/57 (26%), Positives = 26/57 (45%), Gaps = 2/57 (3%)

Query: 10 CKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF 66
          C+ C   +     L  +  PYH   F C++C   L  ++   + G LYC P  +++ 
Sbjct: 18 CQKC-HAIIDEQPLIFKNDPYHPDHFNCANCGKELT-ADARELKGELYCLPCHDKMG 72

>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 = 36.7 bits (85), Expect = 4e-04
 Identities = 15/57 (26%), Positives = 24/57 (42%), Gaps = 2/57 (3%)

Query: 106 CAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162
           C  C   +   + +  + D +H   F CA+ G  LT  +   L G LYC     ++ 
Sbjct: 18  CQKCHAIIDE-QPLIFKNDPYHPDHFNCANCGKELTADAR-ELKGELYCLPCHDKMG 72

>1zfo_A LAsp-1; LIM domain, zinc-finger, metal-binding protein; NMR {Sus scrofa} SCOP: g.39.1.4 Length = 31

 Score = 37.3 bits (86), Expect = 1e-04
 Identities = 14/27 (51%), Positives = 15/27 (55%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCF 131
            CA C K VYP EKV      +HK CF
Sbjct: 5   NCARCGKIVYPTEKVNCLDKFWHKACF 31

>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 = 36.7 bits (85), Expect = 5e-04
 Identities = 13/60 (21%), Positives = 20/60 (33%), Gaps = 3/60 (5%)

Query: 9  KCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVM--SNYSSMDGVLYCKPHFEQLF 66
           C  C   +    M++     YH  CF C  CK  +    +        LYC     ++ 
Sbjct: 17 FCHGCSLLMTGPFMVAG-EFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVV 75

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	210
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	100.0
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.98
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.97
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.97
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.96
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.96
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.93
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.9
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.86
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.83
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.83
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.83
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.82
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.81
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.79
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.78
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.78
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.77
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.74
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.74
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.73
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.71
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.71
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.71
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.7
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.7
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.69
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.69
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.69
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.69
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.68
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.68
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.68
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.68
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.68
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.68
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.67
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.67
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.67
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.67
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.66
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.66
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.66
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.66
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.66
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.66
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.66
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.66
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.65
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.64
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.64
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.64
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.64
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.63
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.62
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.62
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.62
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.62
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.62
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.61
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.61
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.61
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.61
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.61
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.6
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.6
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.6
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.59
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.59
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.59
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.59
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.59
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.58
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.57
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.57
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.56
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.55
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.54
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.53
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.5
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.5
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.5
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.44
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.38
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.42
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.36
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	88.73
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	85.45
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	84.98
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	83.74
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	83.18
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	82.65
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	82.46
1jjd_A	55	Metallothionein, SMTA; zinc finger, zinc cluster,	81.71

>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

Probab=100.00  E-value=1.2e-33  Score=226.35  Aligned_cols=170  Identities=33%  Similarity=0.614  Sum_probs=134.8

Q ss_pred             CCCCCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCC-CCCccCC
Q 040947            1 MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNF-SKNFQTG   79 (210)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~-~~~~~~~   79 (210)
                      |+..++.++|..|+++|+.++.|.++|+.||++||+|..|+++|....|++++|++||+.||.++|++++.. ....+..
T Consensus         1 m~~~~~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~c~~c~~~~g~~   80 (192)
T 1b8t_A            1 MPNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGTL   80 (192)
T ss_dssp             CCCCCCCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCCC
T ss_pred             CCCCCCCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCccccccccccccE
Confidence            888889999999999998888899999999999999999999999999999999999999999999987642 1111110


Q ss_pred             CCC-------CCCCCCCCCC-----CCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeee
Q 040947           80 KNP-------SSCSNQNRTP-----SKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAA  147 (210)
Q Consensus        80 ~~~-------~~~~~~~~~~-----~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~  147 (210)
                      ..+       ..+......|     +...+ ..++.++|++|+++|.+++.|.++++.||++||+|..|+++|..+.|+.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~-~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~  159 (192)
T 1b8t_A           81 STDKGESLGIKYEEGQSHRPTNPNASRMAQ-KVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLAD  159 (192)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEE
T ss_pred             ecCCCcccccccccccccCCCCcCcccccc-ccCCCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccc
Confidence            000       0000000000     11111 1234578999999999888899999999999999999999999888999


Q ss_pred             cCCeeecHhHHHhhhcCCCC-cccc
Q 040947          148 LDGVLYCKHHFAQLFMEKGN-YSHV  171 (210)
Q Consensus       148 ~dg~~yC~~c~~~~f~~k~~-~~~~  171 (210)
                      .||++||+.||.++|++++. ++.+
T Consensus       160 ~~g~~yC~~cy~~~f~~kc~~C~~~  184 (192)
T 1b8t_A          160 KDGEIYCKGCYAKNFGPKGFGFGQG  184 (192)
T ss_dssp             ETTEEEEHHHHHHHTCCCCCCCCCC
T ss_pred             cCCEEeCHHHHHHhcCCcCCCCCCc
Confidence            99999999999999999997 4444

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

Probab=99.98  E-value=1.1e-32  Score=207.68  Aligned_cols=124  Identities=21%  Similarity=0.486  Sum_probs=113.8

Q ss_pred             CCCcccCCcceecceeEeeCCccccCCCcccccccCCCCC--CCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCC
Q 040947            7 LDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVM--SNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSS   84 (210)
Q Consensus         7 ~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~--~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~   84 (210)
                      .++|..|+++|.+.++|.++|+.||++||+|..|+++|..  ..|+.++|++||+.||.++|+                 
T Consensus         2 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~-----------------   64 (131)
T 2xjy_A            2 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFG-----------------   64 (131)
T ss_dssp             CCBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHC-----------------
T ss_pred             cccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCC-----------------
Confidence            5789999999996667999999999999999999999973  689999999999999999998                 


Q ss_pred             CCCCCCCCCCcccccCCCCC--ccccccceeecCc-eeEecCccccccccccCCCCCcCC-CCCeeecCCeeecHhHHHh
Q 040947           85 CSNQNRTPSKLSSLFSGTQD--KCAACEKTVYPLE-KVTMEGDCFHKTCFRCAHGGCPLT-HSSYAALDGVLYCKHHFAQ  160 (210)
Q Consensus        85 ~~~~~~~~~~~~~~~~g~~~--~C~~C~~~I~~~e-~v~~~g~~~H~~CF~C~~C~~~l~-~~~f~~~dg~~yC~~c~~~  160 (210)
                                         +  +|.+|+++|.+.+ .|.++++.||++||+|..|+++|. +..|++.+|++||..||.+
T Consensus        65 -------------------~~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~~~  125 (131)
T 2xjy_A           65 -------------------QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYE  125 (131)
T ss_dssp             -------------------CCEECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGHHH
T ss_pred             -------------------CccChhhcCCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHHHH
Confidence                               5  8999999998755 578999999999999999999995 6679999999999999999


Q ss_pred             hhcCCC
Q 040947          161 LFMEKG  166 (210)
Q Consensus       161 ~f~~k~  166 (210)
                      +|+++|
T Consensus       126 ~~~~~~  131 (131)
T 2xjy_A          126 WTKING  131 (131)
T ss_dssp             HHHHHC
T ss_pred             HhhccC
Confidence            998764

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

Probab=99.97  E-value=6.4e-32  Score=202.29  Aligned_cols=122  Identities=20%  Similarity=0.505  Sum_probs=113.7

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCC
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSC   85 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~   85 (210)
                      .+++|.+|+++|+.+++|.++|+.||++||+|..|+++|.+..|++++|++||+.||.++|+                  
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~------------------   63 (126)
T 2xqn_T            2 EKPRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHA------------------   63 (126)
T ss_dssp             CCCBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSC------------------
T ss_pred             cCCCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcC------------------
Confidence            35899999999997788999999999999999999999999899999999999999999998                  


Q ss_pred             CCCCCCCCCcccccCCCCCccccccceeecCc-eeEecCcccc--ccccccCCCCCcCCCCCeeecCCeeecHhHHHhhh
Q 040947           86 SNQNRTPSKLSSLFSGTQDKCAACEKTVYPLE-KVTMEGDCFH--KTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF  162 (210)
Q Consensus        86 ~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e-~v~~~g~~~H--~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f  162 (210)
                                        ++|++|+++|.+++ .|.++++.||  ++||+|..|+++|.+..|++.+|++||..+|.++|
T Consensus        64 ------------------~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l~~~~f~~~~~~~yC~~~~~~~f  125 (126)
T 2xqn_T           64 ------------------VVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM  125 (126)
T ss_dssp             ------------------CBCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBCTTSEEEEETTEEESSHHHHHSC
T ss_pred             ------------------ccCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCCCCccCCCeeEeECCEEcchHHhhhhc
Confidence                              89999999999744 5899999999  99999999999999888999999999998888876


Q ss_pred             c
Q 040947          163 M  163 (210)
Q Consensus       163 ~  163 (210)
                      .
T Consensus       126 ~  126 (126)
T 2xqn_T          126 S  126 (126)
T ss_dssp             C
T ss_pred             C
Confidence            3

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B

Probab=99.97  E-value=1.8e-31  Score=213.07  Aligned_cols=127  Identities=22%  Similarity=0.572  Sum_probs=112.8

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCC--CCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCC
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVM--SNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPS   83 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~--~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~   83 (210)
                      ..++|..|+++|...++|.++++.||++||+|..|+++|..  ..|++++|++||+.||.++|+                
T Consensus         4 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~----------------   67 (188)
T 1rut_X            4 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG----------------   67 (188)
T ss_dssp             CCCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHS----------------
T ss_pred             CCCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccc----------------
Confidence            46899999999996667999999999999999999999985  689999999999999999998                


Q ss_pred             CCCCCCCCCCCcccccCCCCC--ccccccceeecCce-eEecCccccccccccCCCCCcCC-CCCeeecCCeeecHhHHH
Q 040947           84 SCSNQNRTPSKLSSLFSGTQD--KCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLT-HSSYAALDGVLYCKHHFA  159 (210)
Q Consensus        84 ~~~~~~~~~~~~~~~~~g~~~--~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~l~-~~~f~~~dg~~yC~~c~~  159 (210)
                                          +  +|.+|+++|.+.+. |.++++.||++||+|..|+++|. +..|+..++++||+.||.
T Consensus        68 --------------------~~~~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~c~~  127 (188)
T 1rut_X           68 --------------------NSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRP  127 (188)
T ss_dssp             --------------------CCEECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGCC
T ss_pred             --------------------cCCccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHHHHH
Confidence                                5  79999999997664 78999999999999999999996 567999999999999999


Q ss_pred             hhhcCCCCc
Q 040947          160 QLFMEKGNY  168 (210)
Q Consensus       160 ~~f~~k~~~  168 (210)
                      ++|++++..
T Consensus       128 ~~~~~~~~~  136 (188)
T 1rut_X          128 TALINGHLN  136 (188)
T ss_dssp             TTTC-----
T ss_pred             HHhcccccc
Confidence            999999964

>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=99.96  E-value=1.1e-29  Score=199.54  Aligned_cols=125  Identities=26%  Similarity=0.509  Sum_probs=109.8

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCC
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSS   84 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~   84 (210)
                      .+.++|..|+++|+..++|.++|+.||++||+|..|+++|.+..| +++|++||+.||.++|+                 
T Consensus         4 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~-----------------   65 (169)
T 2rgt_A            4 PEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFG-----------------   65 (169)
T ss_dssp             ---CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCCE-ESSSCEECHHHHHHHHS-----------------
T ss_pred             CCCCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCCc-ccCCeeeeccccccccc-----------------
Confidence            356899999999997667899999999999999999999998764 79999999999999998                 


Q ss_pred             CCCCCCCCCCcccccCCCCCccccccceeecCce-eEecCccccccccccCCCCCcCC-CCCee-ecCCeeecHhHHHhh
Q 040947           85 CSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLT-HSSYA-ALDGVLYCKHHFAQL  161 (210)
Q Consensus        85 ~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~l~-~~~f~-~~dg~~yC~~c~~~~  161 (210)
                                         ++|.+|+++|.+.+. +.++++.||++||+|..|+++|. +..|+ ..||++||+.||.++
T Consensus        66 -------------------~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~~~  126 (169)
T 2rgt_A           66 -------------------TKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETA  126 (169)
T ss_dssp             -------------------CBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHHHH
T ss_pred             -------------------ccccccccccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHHHH
Confidence                               899999999997665 58999999999999999999997 55565 468999999999999


Q ss_pred             hcCCC
Q 040947          162 FMEKG  166 (210)
Q Consensus       162 f~~k~  166 (210)
                      ++...
T Consensus       127 ~~~~~  131 (169)
T 2rgt_A          127 KQGGS  131 (169)
T ss_dssp             HHCC-
T ss_pred             hhccC
Confidence            87643

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

Probab=99.96  E-value=3.5e-29  Score=198.79  Aligned_cols=122  Identities=27%  Similarity=0.535  Sum_probs=108.7

Q ss_pred             CCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCC
Q 040947            4 TGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPS   83 (210)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~   83 (210)
                      ....++|..|+++|+..+++.++|+.||+.||+|..|+++|.+..| .++|++||+.||.++|+                
T Consensus        57 ~~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~----------------  119 (182)
T 2jtn_A           57 TPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFG----------------  119 (182)
T ss_dssp             CCSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCE-EETTEEECHHHHHHTTS----------------
T ss_pred             CCCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCce-eECCEeeecCccccccc----------------
Confidence            3456899999999997677899999999999999999999998765 79999999999999998                


Q ss_pred             CCCCCCCCCCCcccccCCCCCccccccceeecCce-eEecCccccccccccCCCCCcCC-CCCee-ecCCeeecHhHHHh
Q 040947           84 SCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLT-HSSYA-ALDGVLYCKHHFAQ  160 (210)
Q Consensus        84 ~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~l~-~~~f~-~~dg~~yC~~c~~~  160 (210)
                                          ++|..|+++|.+.+. +.+.++.||+.||+|..|+++|. +..|+ ..+|++||+.||.+
T Consensus       120 --------------------~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC~~cy~~  179 (182)
T 2jtn_A          120 --------------------TKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYET  179 (182)
T ss_dssp             --------------------CCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEECHHHHHH
T ss_pred             --------------------cccccCCCccCCCceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEECHHHHHH
Confidence                                899999999997665 58999999999999999999997 45565 46899999999987


Q ss_pred             hh
Q 040947          161 LF  162 (210)
Q Consensus       161 ~f  162 (210)
                      +.
T Consensus       180 ~~  181 (182)
T 2jtn_A          180 AK  181 (182)
T ss_dssp             HT
T ss_pred             hh
Confidence            53

>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=99.93  E-value=6.8e-27  Score=168.33  Aligned_cols=97  Identities=23%  Similarity=0.547  Sum_probs=89.9

Q ss_pred             CCCCCcccCCcceec-ceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCC
Q 040947            5 GTLDKCKACDKTVYV-VDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPS   83 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~-~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~   83 (210)
                      ...++|.+|+++|+. +++|.++|+.||+.||+|..|+++|.+..|++++|++||+.||.++|+                
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~----------------   66 (101)
T 2cup_A            3 SGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS----------------   66 (101)
T ss_dssp             SCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCC----------------
T ss_pred             CCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcC----------------
Confidence            457899999999985 678999999999999999999999998899999999999999999987                


Q ss_pred             CCCCCCCCCCCcccccCCCCCccccccceeecCc-eeEecCccccccccccCCCC
Q 040947           84 SCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLE-KVTMEGDCFHKTCFRCAHGG  137 (210)
Q Consensus        84 ~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e-~v~~~g~~~H~~CF~C~~C~  137 (210)
                                          ++|.+|+++|.+++ .|.++++.||++||+|..|+
T Consensus        67 --------------------~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~  101 (101)
T 2cup_A           67 --------------------PKCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSSG  101 (101)
T ss_dssp             --------------------CBCSSSCCBCCSSSCEEESSSCEEETTTCCCTTCC
T ss_pred             --------------------CccccCCCccccCCeEEEeCCcchHHhCCCCCCCC
Confidence                                89999999998765 58999999999999999986

>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=99.90  E-value=7.6e-25  Score=163.13  Aligned_cols=114  Identities=18%  Similarity=0.321  Sum_probs=99.5

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCC--CCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCC
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLV--MSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNP   82 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~   82 (210)
                      ...++|..|+++|...++|.++++.||++||+|..|+++|.  +..|+.++|++||+.||.++|+               
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~---------------   67 (122)
T 1m3v_A            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG---------------   67 (122)
T ss_dssp             SCCCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHC---------------
T ss_pred             CCCCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcC---------------
Confidence            35789999999999776799999999999999999999997  3579999999999999999998               


Q ss_pred             CCCCCCCCCCCCcccccCCCCC--ccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHh
Q 040947           83 SSCSNQNRTPSKLSSLFSGTQD--KCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQ  160 (210)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~g~~~--~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~  160 (210)
                                           +  +|++|+++|.+ ..|.+.++             ..|.+..|++++++|||..||.+
T Consensus        68 ---------------------~~~~C~~C~~~I~~-~~~~~~g~-------------~~l~g~~f~~~~~~~yC~~~~~~  112 (122)
T 1m3v_A           68 ---------------------NSGAGGSGGHMGSG-GDVMVVGE-------------PTLMGGEFGDEDERLITRLENTQ  112 (122)
T ss_dssp             ---------------------CCCSSSCSSCCSCC-EESSSSSS-------------SSCCSCTTCCTTCCCCEECTTTT
T ss_pred             ---------------------CCCccccCCCCcCc-hheEEcCC-------------cCCCCCccEecCCEeEccCcchh
Confidence                                 5  99999999984 34455553             35778899999999999999999


Q ss_pred             hhcCCCCc
Q 040947          161 LFMEKGNY  168 (210)
Q Consensus       161 ~f~~k~~~  168 (210)
                      ++.+++.-
T Consensus       113 ~~~~~g~~  120 (122)
T 1m3v_A          113 FDAANGID  120 (122)
T ss_dssp             TTCCSCCC
T ss_pred             chhhcCCC
Confidence            99888753

>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=99.86  E-value=2e-22  Score=148.32  Aligned_cols=109  Identities=18%  Similarity=0.254  Sum_probs=91.7

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCC--CCeeccCCeeeccchHHHhhhccCCCCCCccCCCCC
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVM--SNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNP   82 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~--~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~   82 (210)
                      |+.++|.+|+++|+..++|.++++.||+.||+|..|+++|..  ..|+.++|++||+.||.++|+               
T Consensus         1 g~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~---------------   65 (114)
T 1j2o_A            1 GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGG---------------   65 (114)
T ss_dssp             CCCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHT---------------
T ss_pred             CcCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhC---------------
Confidence            567999999999997778999999999999999999999985  589999999999999999998               


Q ss_pred             CCCCCCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccccCCCCCc-CCCCCeeecCCeeecHhHHHhh
Q 040947           83 SSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCP-LTHSSYAALDGVLYCKHHFAQL  161 (210)
Q Consensus        83 ~~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~-l~~~~f~~~dg~~yC~~c~~~~  161 (210)
                                           ++|..|..    ++.|.               |+.+ |.++.|++.+++|||..||.++
T Consensus        66 ---------------------~~c~~c~~----~~~~~---------------~~~~~~~g~~f~~~~~~~~C~~~~~~~  105 (114)
T 1j2o_A           66 ---------------------SGGHMGSG----GDVMV---------------VGEPTLMGGEFGDEDERLITRLENTQF  105 (114)
T ss_dssp             ---------------------SCCSSCBS----CSCCC---------------SSCSSTTSSBCCCSSSCCCEEEECTTC
T ss_pred             ---------------------cccCcCCC----CceeE---------------cCCccCCCCeeEEcCCEeecchhhhcc
Confidence                                 67776642    22221               3344 5677899999999999999999


Q ss_pred             hcCCCCc
Q 040947          162 FMEKGNY  168 (210)
Q Consensus       162 f~~k~~~  168 (210)
                      .++.+..
T Consensus       106 ~~~~g~~  112 (114)
T 1j2o_A          106 DAANGID  112 (114)
T ss_dssp             CCTTSSC
T ss_pred             ccccCCC
Confidence            8887754

>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=99.83  E-value=2.5e-21  Score=133.38  Aligned_cols=79  Identities=20%  Similarity=0.428  Sum_probs=73.7

Q ss_pred             CCeeeccchHHHhhhccCCCCCCccCCCCCCCCCCCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccc
Q 040947           53 DGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFR  132 (210)
Q Consensus        53 ~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~  132 (210)
                      +|++||++||.++|+                                    ++|++|+++|. ++.|.++++.||++||+
T Consensus         1 gg~~yC~~~y~~~~~------------------------------------~~C~~C~~~I~-~~~v~a~~~~~H~~CF~   43 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFS------------------------------------PKCGGCNRPVL-ENYLSAMDTVWHPECFV   43 (80)
T ss_dssp             CCCCCCCCCCCCCCS------------------------------------CBCTTTCCBCC-SSCEEETTEEECTTTCB
T ss_pred             CCCccchhHHhhhcC------------------------------------CccccCCCeec-ceeEEECCCeEecCcCC
Confidence            478999999999887                                    79999999998 57899999999999999


Q ss_pred             cCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCc
Q 040947          133 CAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNY  168 (210)
Q Consensus       133 C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~  168 (210)
                      |..|+++|..+.|+..++++||+.||.++|++++..
T Consensus        44 C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C~~   79 (80)
T 1x3h_A           44 CGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGPSS   79 (80)
T ss_dssp             CSSSCCBSCSSCCEESSSCEECHHHHHHHHSSSCCC
T ss_pred             hhhCCCCCCCCcEEeECCEEECHHHHHHHcCCCCCC
Confidence            999999999888999999999999999999999853

>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=99.83  E-value=2e-21  Score=133.86  Aligned_cols=78  Identities=27%  Similarity=0.532  Sum_probs=73.3

Q ss_pred             CCeeeccchHHHhhhccCCCCCCccCCCCCCCCCCCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccc
Q 040947           53 DGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFR  132 (210)
Q Consensus        53 ~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~  132 (210)
                      +|++||++||.++|+                                    ++|++|+++|. ++.|.++++.||++||+
T Consensus         1 gg~~yC~~cy~~~~~------------------------------------~~C~~C~~~I~-~~~v~a~~~~~H~~CF~   43 (80)
T 2cuq_A            1 GSSGSSGPCYENKFA------------------------------------PRCARCSKTLT-QGGVTYRDQPWHRECLV   43 (80)
T ss_dssp             CCCCSCCCCCCCCSS------------------------------------CCCTTTCCCCC-SCCEESSSSEECTTTCB
T ss_pred             CCcEEcHHHHccccC------------------------------------CcCCCCCCEec-CcEEEECCchhhhhhCC
Confidence            588999999999887                                    79999999998 56899999999999999


Q ss_pred             cCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCC
Q 040947          133 CAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN  167 (210)
Q Consensus       133 C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~  167 (210)
                      |..|+++|.+..|+..++++||+.||.++|++++.
T Consensus        44 C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~   78 (80)
T 2cuq_A           44 CTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPS   78 (80)
T ss_dssp             CSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCSTT
T ss_pred             cccCCCcCCCCeeEeECCEEECHHHHHHHcCCCCC
Confidence            99999999988899999999999999999999985

>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=99.83  E-value=3.2e-21  Score=133.43  Aligned_cols=80  Identities=19%  Similarity=0.328  Sum_probs=73.9

Q ss_pred             CCeeeccchHHHhhhccCCCCCCccCCCCCCCCCCCCCCCCCcccccCCCCCccccccceeecCce-eEecCcccccccc
Q 040947           53 DGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEK-VTMEGDCFHKTCF  131 (210)
Q Consensus        53 ~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~-v~~~g~~~H~~CF  131 (210)
                      ++.+||++||.++|+                                    ++|++|+++|.+++. |.++++.||++||
T Consensus         1 ~~~~yC~~cy~~~~~------------------------------------~~C~~C~~~I~~~~~~~~a~~~~~H~~CF   44 (82)
T 1x63_A            1 GSSGSSGKCTTREDS------------------------------------PKCKGCFKAIVAGDQNVEYKGTVWHKDCF   44 (82)
T ss_dssp             CCSCCCCCCCSCCCS------------------------------------CBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             CCCcCchhHHccccC------------------------------------CcCccCCcccccCceEEEECccccccccC
Confidence            468999999999887                                    799999999997665 8899999999999


Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNY  168 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~  168 (210)
                      +|..|+++|..+.|+..++++||+.||.++|++|+..
T Consensus        45 ~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~~   81 (82)
T 1x63_A           45 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPSS   81 (82)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCSC
T ss_pred             chhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCCC
Confidence            9999999999888999999999999999999999864

>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=99.82  E-value=1.4e-21  Score=135.26  Aligned_cols=80  Identities=21%  Similarity=0.503  Sum_probs=73.7

Q ss_pred             CCeeeccchHHHhhhccCCCCCCccCCCCCCCCCCCCCCCCCcccccCCCCCccccccceeec-CceeEecCcccccccc
Q 040947           53 DGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYP-LEKVTMEGDCFHKTCF  131 (210)
Q Consensus        53 ~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~-~e~v~~~g~~~H~~CF  131 (210)
                      +|++||+.||.++|+                                    ++|++|+++|.+ +..|.++++.||++||
T Consensus         1 ~g~~yC~~~y~~~~~------------------------------------~~C~~C~~~I~~~~~~~~a~~~~~H~~CF   44 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFA------------------------------------NTCAECQQLIGHDSRELFYEDRHFHEGCF   44 (82)
T ss_dssp             CCCCCCCCCCCCCCS------------------------------------CBCTTTCCBCCSSCCBCCCSSCCCBTTTS
T ss_pred             CCceechhHhCcccC------------------------------------CcCccCCCccccCcEEEEeCCccccccCC
Confidence            589999999999987                                    799999999985 4457889999999999


Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNY  168 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~  168 (210)
                      +|+.|+++|.+..|+..++++||+.||.++|++++..
T Consensus        45 ~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C~~   81 (82)
T 2ehe_A           45 RCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGPSS   81 (82)
T ss_dssp             BCTTTCCBCSSCCEEEETTEEEETTTSSCCGGGSSCC
T ss_pred             eecCCCCccCCCccEeeCCEEECHHHHhhhcCCCCCC
Confidence            9999999999889999999999999999999999863

>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=99.81  E-value=1.5e-20  Score=129.93  Aligned_cols=78  Identities=17%  Similarity=0.328  Sum_probs=71.0

Q ss_pred             CCeeeccchHHHhhhccCCCCCCccCCCCCCCCCCCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccc
Q 040947           53 DGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFR  132 (210)
Q Consensus        53 ~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~  132 (210)
                      +|++||++||. +++                                    ++|++|+++|. ++.|.++++.||++||+
T Consensus         2 ~g~~yC~~~y~-~~~------------------------------------~~C~~C~~~I~-~~~~~a~~~~~H~~CF~   43 (81)
T 2dlo_A            2 SSGSSGEGCYV-ATL------------------------------------EKCATCSQPIL-DRILRAMGKAYHPGCFT   43 (81)
T ss_dssp             CCCCCCCCCCC-SSC------------------------------------CBCTTTCCBCC-SCCEEETTEEECTTTCB
T ss_pred             cCCEECHHHhh-cCC------------------------------------CccccCCCeec-ceeEEECCccccHHhcC
Confidence            68999999998 554                                    79999999998 67899999999999999


Q ss_pred             cCCCCCcCCCCCeeec-CCeeecHhHHHhhhcCCCCc
Q 040947          133 CAHGGCPLTHSSYAAL-DGVLYCKHHFAQLFMEKGNY  168 (210)
Q Consensus       133 C~~C~~~l~~~~f~~~-dg~~yC~~c~~~~f~~k~~~  168 (210)
                      |..|+++|.+..|... +|++||+.||.++|++|+..
T Consensus        44 C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~~~C~~   80 (81)
T 2dlo_A           44 CVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGPSS   80 (81)
T ss_dssp             CSSSCCBCTTSCEECCTTCCCEEHHHHHHHTTSSSCC
T ss_pred             cccCCCccCCCeeEECCCCEEECHHHHHHHhcCcCCC
Confidence            9999999998888876 79999999999999999853

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

Probab=99.79  E-value=3.6e-20  Score=127.93  Aligned_cols=67  Identities=30%  Similarity=0.685  Sum_probs=58.3

Q ss_pred             CCCCCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947            1 MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      |+|.++.++|..|+++|+.++.|.++++.||++||+|..|+++|....|+++++++||+.||.++|+
T Consensus         1 m~~~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~   67 (81)
T 1a7i_A            1 MPNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG   67 (81)
T ss_dssp             -------CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC
T ss_pred             CCCCCCCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhC
Confidence            8999999999999999988889999999999999999999999999899999999999999999998

>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=99.78  E-value=7.1e-20  Score=125.15  Aligned_cols=73  Identities=21%  Similarity=0.484  Sum_probs=67.0

Q ss_pred             CCeeeccchHHHhhhccCCCCCCccCCCCCCCCCCCCCCCCCcccccCCCCCccccccceeec----CceeEecCccccc
Q 040947           53 DGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYP----LEKVTMEGDCFHK  128 (210)
Q Consensus        53 ~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~----~e~v~~~g~~~H~  128 (210)
                      ++++||++||.++|+                                    ++|++|+++|.+    .+.|.++++.||+
T Consensus         1 g~~~yC~~cy~~~~~------------------------------------~~C~~C~~~I~~~g~~~~~~~a~~~~~H~   44 (77)
T 2egq_A            1 GSSGSSGDCYKNFVA------------------------------------KKCAGCKNPITGFGKGSSVVAYEGQSWHD   44 (77)
T ss_dssp             CCSSCCTTCCCSCCC------------------------------------CCCSSSCCCCCCCSSCCCEEEETTEEEET
T ss_pred             CCCeEchhHhchhhC------------------------------------ccCcccCCcccCCCCCceeEEECcceeCc
Confidence            478999999999987                                    899999999994    3678999999999


Q ss_pred             cccccCCCCCcCCCCCeeecCCeeecHhHHHhh
Q 040947          129 TCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQL  161 (210)
Q Consensus       129 ~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~  161 (210)
                      +||+|..|+++|.+..|+..+|+|||+.||.++
T Consensus        45 ~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~l   77 (77)
T 2egq_A           45 YCFHCKKCSVNLANKRFVFHQEQVYCPDCAKKL   77 (77)
T ss_dssp             TTCBCSSSCCBCTTSCCCEETTEECCHHHHHHC
T ss_pred             ccCEehhcCCCCCCCccEeECCEEEChHHhccC
Confidence            999999999999988899999999999999763

>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=99.78  E-value=1e-19  Score=125.56  Aligned_cols=78  Identities=15%  Similarity=0.287  Sum_probs=70.5

Q ss_pred             CCeeeccchHHHhhhccCCCCCCccCCCCCCCCCCCCCCCCCcccccCCCCCccccccceeecCceeEecCccccccccc
Q 040947           53 DGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFR  132 (210)
Q Consensus        53 ~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~  132 (210)
                      .+.+||+.||.++|+                                    ++|++|+++|. ++.|.++++.||++||+
T Consensus         1 g~~~yC~~~y~~~~~------------------------------------~~C~~C~~~I~-~~~~~a~~~~~H~~CF~   43 (81)
T 1x6a_A            1 GSSGSSGKDYWGKFG------------------------------------EFCHGCSLLMT-GPFMVAGEFKYHPECFA   43 (81)
T ss_dssp             CCCCCCCCCSSCCSS------------------------------------CBCTTTCCBCC-SCCBCCTTCCBCTTSCB
T ss_pred             CCCccchhHHhhhcC------------------------------------CcCccCCCCcC-ceEEEECCceeccccCC
Confidence            367999999999988                                    89999999999 78899999999999999


Q ss_pred             cCCCCCcCC-CCCee-ecCCeeecHhHHHhhhcCCCC
Q 040947          133 CAHGGCPLT-HSSYA-ALDGVLYCKHHFAQLFMEKGN  167 (210)
Q Consensus       133 C~~C~~~l~-~~~f~-~~dg~~yC~~c~~~~f~~k~~  167 (210)
                      |..|+++|. +..|. ..+++|||+.||.++|+++..
T Consensus        44 C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~~s   80 (81)
T 1x6a_A           44 CMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSGPSS   80 (81)
T ss_dssp             CTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCTTSC
T ss_pred             ccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcCCCC
Confidence            999999996 46677 489999999999999998753

>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=99.77  E-value=7.4e-19  Score=124.01  Aligned_cols=76  Identities=41%  Similarity=0.881  Sum_probs=70.9

Q ss_pred             CCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCccccccccccc
Q 040947          103 QDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLKAANHK  178 (210)
Q Consensus       103 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~~~~~~~~~~~  178 (210)
                      .++|.+|+++|.+.+.|.++++.||++||+|..|+++|....|+..+|++||+.||.++|++|+.+..+++..+++
T Consensus        15 ~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~g~g~~~~~   90 (91)
T 2d8y_A           15 RETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFGSGPSS   90 (91)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCCCCCCC
T ss_pred             CCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccCCcCCCCCC
Confidence            4799999999998788999999999999999999999998889999999999999999999999999998877664

>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=99.74  E-value=1.7e-18  Score=118.00  Aligned_cols=69  Identities=36%  Similarity=0.744  Sum_probs=64.9

Q ss_pred             CCCCCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeecc-chHHHhhhcc
Q 040947            1 MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK-PHFEQLFKES   69 (210)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~-~cy~~~~~~~   69 (210)
                      |+|++..++|..|+++|+.++.|.++++.||++||+|..|+++|.+..|+++++++||. .||.++|+++
T Consensus         3 ~~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~k   72 (76)
T 2cu8_A            3 SGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSG   72 (76)
T ss_dssp             CSCCCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSS
T ss_pred             cccCCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccc
Confidence            67889999999999999988899999999999999999999999998999999999999 7999999843

>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=99.74  E-value=3e-18  Score=116.81  Aligned_cols=70  Identities=37%  Similarity=0.622  Sum_probs=64.0

Q ss_pred             cCCCCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecH-hHHHhhhcCCCCc
Q 040947           99 FSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCK-HHFAQLFMEKGNY  168 (210)
Q Consensus        99 ~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~-~c~~~~f~~k~~~  168 (210)
                      +.+..++|++|+++|.+++.|.++++.||++||+|..|+++|....|+..|+++||+ .||.++|++|+..
T Consensus         5 ~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~kc~g   75 (76)
T 2cu8_A            5 SSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGPSS   75 (76)
T ss_dssp             CCCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSSCSC
T ss_pred             cCCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccccCC
Confidence            334458999999999988899999999999999999999999988899999999999 7999999999863

>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=99.73  E-value=3e-18  Score=116.79  Aligned_cols=60  Identities=33%  Similarity=0.824  Sum_probs=57.3

Q ss_pred             CCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeecc-chHHHhhh
Q 040947            8 DKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCK-PHFEQLFK   67 (210)
Q Consensus         8 ~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~-~cy~~~~~   67 (210)
                      |+|..|+++|..++.|.++|+.||++||+|..|+++|.+..|++++|++||. .||.++|+
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~   61 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG   61 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSS
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhC
Confidence            6899999999988899999999999999999999999998999999999999 69999998

>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=99.71  E-value=3.7e-18  Score=117.76  Aligned_cols=76  Identities=18%  Similarity=0.418  Sum_probs=66.5

Q ss_pred             CeeeccchHHHhhhccCCCCCCccCCCCCCCCCCCCCCCCCcccccCCCCCccccccceeecCceeEecCcccccccccc
Q 040947           54 GVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRC  133 (210)
Q Consensus        54 g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C  133 (210)
                      ..+||+.||.++|+                                    ++|+.|+++|. ++.|.++++.||++||+|
T Consensus         2 ~~~yC~~dy~~~~~------------------------------------~~C~~C~~~I~-~~~v~a~~~~wH~~CF~C   44 (81)
T 1v6g_A            2 SSGSSGLDYQRLYG------------------------------------TRCFSCDQFIE-GEVVSALGKTYHPDCFVC   44 (81)
T ss_dssp             CCCCCCSCGGGSCC------------------------------------CBCTTTCCBCC-SCCEEETTEEECTTTSSC
T ss_pred             CCCcchHHHHhHhC------------------------------------CcCccccCEec-cceEEECCceeCccCCcc
Confidence            46899999999998                                    89999999998 778999999999999999


Q ss_pred             CCCCCcCCCCCeeecCC-eeecHhHHHhhhcCCC
Q 040947          134 AHGGCPLTHSSYAALDG-VLYCKHHFAQLFMEKG  166 (210)
Q Consensus       134 ~~C~~~l~~~~f~~~dg-~~yC~~c~~~~f~~k~  166 (210)
                      ..|+++|..+.++..++ .+||..||.+++...+
T Consensus        45 ~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~~~~   78 (81)
T 1v6g_A           45 AVCRLPFPPGDRVTFNGKECMCQKCSLPVSVSGP   78 (81)
T ss_dssp             SSSCCCCCSSSCEEEETTEEEEHHHHSCCSSCCC
T ss_pred             ccCCCCCCCCCEEEeCCCCEEChhhhcccCCCCC
Confidence            99999998665655554 5799999998877664

>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=99.71  E-value=9.9e-18  Score=115.55  Aligned_cols=65  Identities=25%  Similarity=0.548  Sum_probs=60.7

Q ss_pred             CCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCC
Q 040947          102 TQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN  167 (210)
Q Consensus       102 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~  167 (210)
                      +.++|.+|+++|.+++.|.++++.||++||+|..|+++|.+ .|+..||+|||+.||.++|++++.
T Consensus        14 ~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C~   78 (80)
T 2dj7_A           14 GPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPS   78 (80)
T ss_dssp             SCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCST
T ss_pred             CCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCCC
Confidence            34799999999998889999999999999999999999985 699999999999999999999985

>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=99.71  E-value=4.7e-18  Score=117.20  Aligned_cols=66  Identities=35%  Similarity=0.700  Sum_probs=58.0

Q ss_pred             CCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCC
Q 040947          102 TQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN  167 (210)
Q Consensus       102 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~  167 (210)
                      +.++|.+|+++|.+++.|.++++.||++||+|..|+++|....|+..++++||+.||.++|++++.
T Consensus         6 ~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~   71 (81)
T 1a7i_A            6 GGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGY   71 (81)
T ss_dssp             --CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC----
T ss_pred             CCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCccc
Confidence            348999999999888899999999999999999999999988899999999999999999999997

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

Probab=99.70  E-value=1.8e-17  Score=116.89  Aligned_cols=73  Identities=42%  Similarity=0.959  Sum_probs=67.2

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccC
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQT   78 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~   78 (210)
                      +.++|..|+++|+..+.|.++++.||++||+|..|+++|....|+++++++||+.||.++|++++.+...|+.
T Consensus        14 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~g~g~   86 (91)
T 2d8y_A           14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFGS   86 (91)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCCC
T ss_pred             CCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccCCcCC
Confidence            4689999999999778999999999999999999999999988999999999999999999988877766654

>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=99.70  E-value=1.3e-17  Score=110.58  Aligned_cols=61  Identities=28%  Similarity=0.531  Sum_probs=58.6

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCC
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEK  165 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k  165 (210)
                      ++|++|+++|. ++.|.++++.||++||+|..|+++|.+..|+..+|++||+.||.++|++|
T Consensus         6 ~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~k   66 (66)
T 1nyp_A            6 PICGACRRPIE-GRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGDV   66 (66)
T ss_dssp             CEETTTTEECC-SCEECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSCC
T ss_pred             CCCcccCCEec-ceEEEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHhCCC
Confidence            79999999999 88899999999999999999999999888999999999999999999986

>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=99.69  E-value=4.1e-17  Score=114.75  Aligned_cols=65  Identities=22%  Similarity=0.482  Sum_probs=61.0

Q ss_pred             CCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCc
Q 040947          103 QDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNY  168 (210)
Q Consensus       103 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~  168 (210)
                      .++|+.|+++|. ++.|.++++.||++||+|..|+++|.+..|++.+|++||+.||.++|++|+..
T Consensus        25 ~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c~s   89 (90)
T 2dar_A           25 TPMCAHCNQVIR-GPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGPSS   89 (90)
T ss_dssp             CCBBSSSCCBCC-SCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCCCC
T ss_pred             CCCCccCCCEec-ceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCCCC
Confidence            379999999997 88899999999999999999999999888999999999999999999999853

>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=99.69  E-value=3e-17  Score=109.71  Aligned_cols=63  Identities=19%  Similarity=0.520  Sum_probs=59.9

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCC
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN  167 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~  167 (210)
                      ++|..|+++|. ++.|.++++.||++||+|..|+++|.+..|++.++++||+.||.++|++++.
T Consensus         6 ~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~   68 (69)
T 2cur_A            6 SGCVKCNKAIT-SGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSS   68 (69)
T ss_dssp             CCCSSSCCCCC-TTCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSCC
T ss_pred             CCCcccCCEeC-cceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCCC
Confidence            79999999998 6789999999999999999999999988899999999999999999999985

>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=99.69  E-value=3.6e-17  Score=109.55  Aligned_cols=64  Identities=27%  Similarity=0.555  Sum_probs=60.3

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNY  168 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~  168 (210)
                      ++|.+|+++|. ++.|.++++.||++||+|..|+++|.+..|++.++++||+.||.++|++++..
T Consensus         6 ~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~~   69 (70)
T 2d8z_A            6 SGCVQCKKPIT-TGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPSS   69 (70)
T ss_dssp             CBCSSSCCBCC-SSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCTT
T ss_pred             CCCcccCCeec-cceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccCC
Confidence            79999999998 67799999999999999999999999888999999999999999999999863

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

Probab=99.69  E-value=2.5e-17  Score=113.50  Aligned_cols=63  Identities=30%  Similarity=0.615  Sum_probs=58.8

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE   68 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   68 (210)
                      ++.++|..|+++|+.+++|.++++.||++||+|..|+++|.+ .|+++++++||+.||.++|++
T Consensus        13 ~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~   75 (80)
T 2dj7_A           13 RGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGS   75 (80)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTC
T ss_pred             CCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCC
Confidence            457899999999998889999999999999999999999986 699999999999999999984

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

Probab=99.68  E-value=3e-17  Score=111.78  Aligned_cols=67  Identities=34%  Similarity=0.663  Sum_probs=62.3

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecH-hHHHhhhcCCCCccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCK-HHFAQLFMEKGNYSH  170 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~-~c~~~~f~~k~~~~~  170 (210)
                      |+|++|+++|.+++.|.++++.||++||+|..|+++|..+.|+..+|++||. .||.++|++++....
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~~C~   68 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRG   68 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSCC
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCCCcC
Confidence            4799999999988899999999999999999999999988899999999999 699999999997543

>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=99.68  E-value=1.5e-17  Score=113.35  Aligned_cols=67  Identities=16%  Similarity=0.433  Sum_probs=61.9

Q ss_pred             Cccccccceeec---CceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCccc
Q 040947          104 DKCAACEKTVYP---LEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSH  170 (210)
Q Consensus       104 ~~C~~C~~~I~~---~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~~~  170 (210)
                      ++|+.|+++|.+   .+.|.++++.||++||+|..|+++|.+..|+..+|+|||+.||.++|++++..+.
T Consensus         6 ~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C~~~s   75 (76)
T 1x68_A            6 SGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISGPSS   75 (76)
T ss_dssp             CCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSSSSSC
T ss_pred             CCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcCCCCC
Confidence            799999999983   3779999999999999999999999988899999999999999999999997553

>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=99.68  E-value=3.7e-17  Score=110.00  Aligned_cols=65  Identities=29%  Similarity=0.616  Sum_probs=60.8

Q ss_pred             CccccccceeecC-ceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCc
Q 040947          104 DKCAACEKTVYPL-EKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNY  168 (210)
Q Consensus       104 ~~C~~C~~~I~~~-e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~  168 (210)
                      ++|.+|+++|.++ +.|.++++.||++||+|..|+++|....|+..+|.+||+.||.++|++++..
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1wyh_A            6 SGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGPSS   71 (72)
T ss_dssp             CBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCCCC
T ss_pred             CCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcCCC
Confidence            7999999999975 6788999999999999999999999888999999999999999999999863

>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=99.68  E-value=3.8e-17  Score=109.98  Aligned_cols=65  Identities=25%  Similarity=0.569  Sum_probs=60.6

Q ss_pred             CccccccceeecCc-eeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCc
Q 040947          104 DKCAACEKTVYPLE-KVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNY  168 (210)
Q Consensus       104 ~~C~~C~~~I~~~e-~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~  168 (210)
                      ++|++|+++|.+.+ .|.++++.||++||+|..|+++|....|+..+|++||+.||.++|++++..
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~~   71 (72)
T 1x4k_A            6 SGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGPSS   71 (72)
T ss_dssp             CCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCCCC
T ss_pred             CCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCCCC
Confidence            79999999999764 689999999999999999999999889999999999999999999999853

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

Probab=99.68  E-value=6.8e-17  Score=108.26  Aligned_cols=63  Identities=16%  Similarity=0.344  Sum_probs=59.2

Q ss_pred             CCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCC
Q 040947          103 QDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKG  166 (210)
Q Consensus       103 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~  166 (210)
                      .++|..|+++|. ++.|.++++.||++||+|..|+++|....|+..+|++||+.||.++|+++.
T Consensus         5 ~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   67 (70)
T 2d8x_A            5 SSGCHQCGEFII-GRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGP   67 (70)
T ss_dssp             SSBCSSSCCBCC-SCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCCS
T ss_pred             CCcCccCCCEec-ceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCCC
Confidence            379999999998 678999999999999999999999998889999999999999999999875

>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=99.68  E-value=3.6e-17  Score=109.29  Aligned_cols=62  Identities=19%  Similarity=0.631  Sum_probs=58.3

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      ..+++|..|+++|. ++.|.++++.||++||+|..|+++|.+..|+++++++||+.||.++|+
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~   64 (69)
T 2cur_A            3 SGSSGCVKCNKAIT-SGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVS   64 (69)
T ss_dssp             CCCCCCSSSCCCCC-TTCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHT
T ss_pred             CCcCCCcccCCEeC-cceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhc
Confidence            35689999999998 678999999999999999999999998899999999999999999998

>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=99.67  E-value=4.3e-17  Score=109.16  Aligned_cols=63  Identities=25%  Similarity=0.651  Sum_probs=58.6

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE   68 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   68 (210)
                      ...++|..|+++|. ++.|.++++.||++||+|..|+++|.+..|+++++++||+.||.++|++
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~   65 (70)
T 2d8z_A            3 SGSSGCVQCKKPIT-TGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYAS   65 (70)
T ss_dssp             CCCCBCSSSCCBCC-SSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCC
T ss_pred             CCCCCCcccCCeec-cceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhcc
Confidence            35689999999998 6779999999999999999999999998999999999999999999984

>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=99.67  E-value=1.2e-16  Score=112.19  Aligned_cols=65  Identities=23%  Similarity=0.432  Sum_probs=60.4

Q ss_pred             CCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCC
Q 040947          102 TQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN  167 (210)
Q Consensus       102 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~  167 (210)
                      ..++|..|+++|. ++.|.++++.||++||+|..|+++|....|+..++++||+.||.++|++|+.
T Consensus        24 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~~   88 (89)
T 1x64_A           24 RMPLCDKCGSGIV-GAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSS   88 (89)
T ss_dssp             SCCBCTTTCCBCC-SCCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCCC
T ss_pred             cCCCcccCCCEec-ccEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            3479999999999 5779999999999999999999999988899999999999999999999974

>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=99.67  E-value=4.2e-17  Score=111.97  Aligned_cols=64  Identities=17%  Similarity=0.387  Sum_probs=59.9

Q ss_pred             CCccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCC
Q 040947          103 QDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN  167 (210)
Q Consensus       103 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~  167 (210)
                      .++|..|+++|. ++.|.++++.||++||+|..|+++|....|+..++++||+.||.++|++|+.
T Consensus        15 ~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g~   78 (79)
T 1x62_A           15 LPMCDKCGTGIV-GVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSS   78 (79)
T ss_dssp             CCCCSSSCCCCC-SSCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCCC
T ss_pred             CCccccCCCCcc-CcEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            379999999998 5789999999999999999999999877899999999999999999999974

>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=99.67  E-value=5.5e-17  Score=109.28  Aligned_cols=63  Identities=16%  Similarity=0.393  Sum_probs=58.6

Q ss_pred             Cccccccceeec---CceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCC
Q 040947          104 DKCAACEKTVYP---LEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKG  166 (210)
Q Consensus       104 ~~C~~C~~~I~~---~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~  166 (210)
                      ++|.+|+++|.+   .+.|.++++.||++||+|..|+++|.+..|+..+|++||+.||.++|++++
T Consensus         6 ~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p~~   71 (72)
T 1x4l_A            6 SGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPSS   71 (72)
T ss_dssp             CSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCSSC
T ss_pred             CCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCCCC
Confidence            799999999985   366899999999999999999999998889999999999999999999875

>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=99.66  E-value=3.7e-17  Score=108.32  Aligned_cols=62  Identities=24%  Similarity=0.621  Sum_probs=58.4

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE   68 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   68 (210)
                      ..++|.+|+++|. +++|.++|+.||++||+|..|+++|.+..|++++|++||+.||.++|++
T Consensus         4 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~   65 (66)
T 1nyp_A            4 GVPICGACRRPIE-GRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLFGD   65 (66)
T ss_dssp             CCCEETTTTEECC-SCEECCTTSBEETTTCBCTTTCCBCSSSCCEEETTEEECHHHHHHHCSC
T ss_pred             CCCCCcccCCEec-ceEEEECccccccCcCEECCCCCCCCCCceEeECCcEECHHHHHHHhCC
Confidence            3589999999999 8889999999999999999999999998999999999999999999974

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

Probab=99.66  E-value=6.8e-17  Score=110.12  Aligned_cols=64  Identities=30%  Similarity=0.633  Sum_probs=58.2

Q ss_pred             CccccccceeecCce-eEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCC
Q 040947          104 DKCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN  167 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~  167 (210)
                      ++|++|+++|.+.+. |.++|+.||++||+|..|+++|..+.|+..||++||+.||.++|++++.
T Consensus        12 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C~   76 (77)
T 1g47_A           12 ATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCWI   76 (77)
T ss_dssp             CBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC--
T ss_pred             CCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcccC
Confidence            799999999986555 6899999999999999999999988899999999999999999999974

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

Probab=99.66  E-value=4.5e-17  Score=111.03  Aligned_cols=68  Identities=25%  Similarity=0.597  Sum_probs=61.6

Q ss_pred             CCCCCCCCCcccCCcceecce-eEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947            1 MAFTGTLDKCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE   68 (210)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~-~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   68 (210)
                      |+.....++|.+|+++|+..+ ++.++|+.||++||+|..|+++|....|+.++|++||+.||.++|++
T Consensus         5 ~~~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~   73 (77)
T 1g47_A            5 MANALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAP   73 (77)
T ss_dssp             CCSCCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCC
T ss_pred             hccCCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhc
Confidence            456677899999999998644 57899999999999999999999988899999999999999999983

>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=99.66  E-value=8.4e-17  Score=118.07  Aligned_cols=68  Identities=18%  Similarity=0.390  Sum_probs=61.5

Q ss_pred             CCCccccccceeecCceeEecCccccccccccCCCCCcCCC--CCeeecCCeeecHhHHHhhhcCCCCcc
Q 040947          102 TQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTH--SSYAALDGVLYCKHHFAQLFMEKGNYS  169 (210)
Q Consensus       102 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~--~~f~~~dg~~yC~~c~~~~f~~k~~~~  169 (210)
                      +.++|++|+++|...+.|.++++.||++||+|+.|+++|..  ..|+.+||+|||+.||.++|++++...
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c   71 (114)
T 1j2o_A            2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMG   71 (114)
T ss_dssp             CCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSC
T ss_pred             cCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcC
Confidence            34899999999996668999999999999999999999974  579999999999999999999998643

>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=99.66  E-value=7e-17  Score=113.55  Aligned_cols=64  Identities=27%  Similarity=0.657  Sum_probs=59.5

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhcc
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKES   69 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~   69 (210)
                      ...++|..|+++|. +++|.++++.||++||+|..|+++|.+..|+++++++||+.||.++|+++
T Consensus        23 ~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~   86 (90)
T 2dar_A           23 KRTPMCAHCNQVIR-GPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASG   86 (90)
T ss_dssp             TCCCBBSSSCCBCC-SCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCC
T ss_pred             CCCCCCccCCCEec-ceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCC
Confidence            45789999999996 88899999999999999999999999989999999999999999999843

>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=99.66  E-value=3.4e-17  Score=111.54  Aligned_cols=62  Identities=19%  Similarity=0.535  Sum_probs=57.8

Q ss_pred             CCCCcccCCcceec---ceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947            6 TLDKCKACDKTVYV---VDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus         6 ~~~~C~~C~~~I~~---~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      .+++|..|+++|.+   .++|.++++.||++||+|..|+++|.+..|+++++++||+.||.++|+
T Consensus         4 ~~~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~   68 (76)
T 1x68_A            4 GSSGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDT   68 (76)
T ss_dssp             CCCCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCC
T ss_pred             cCCCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhC
Confidence            35899999999983   378999999999999999999999998899999999999999999998

>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=99.66  E-value=8.1e-17  Score=108.35  Aligned_cols=63  Identities=32%  Similarity=0.674  Sum_probs=58.7

Q ss_pred             CCCCcccCCcceecc-eeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947            6 TLDKCKACDKTVYVV-DMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE   68 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~-~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   68 (210)
                      .+++|..|+++|.++ ++|.++++.||++||+|..|+++|....|+++++++||+.||.++|++
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~   67 (72)
T 1wyh_A            4 GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFAS   67 (72)
T ss_dssp             CCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSC
T ss_pred             cCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccC
Confidence            458999999999975 679999999999999999999999998999999999999999999984

>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=99.66  E-value=9.4e-17  Score=107.55  Aligned_cols=63  Identities=17%  Similarity=0.486  Sum_probs=59.3

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE   68 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   68 (210)
                      ++.++|..|+++|. +++|.++++.||++||+|..|+++|....|+.+++++||+.||.++|++
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~   65 (70)
T 2d8x_A            3 SGSSGCHQCGEFII-GRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKAS   65 (70)
T ss_dssp             CCSSBCSSSCCBCC-SCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCC
T ss_pred             CCCCcCccCCCEec-ceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCC
Confidence            56789999999998 6789999999999999999999999998999999999999999999984

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

Probab=99.65  E-value=1.1e-16  Score=107.65  Aligned_cols=63  Identities=22%  Similarity=0.626  Sum_probs=58.5

Q ss_pred             CCCCcccCCcceecc-eeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947            6 TLDKCKACDKTVYVV-DMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE   68 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~-~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   68 (210)
                      .+++|..|+++|.+. .+|.++|+.||++||+|..|+++|.+..|+++++++||+.||.++|++
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~   67 (72)
T 1x4k_A            4 GSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHAS   67 (72)
T ss_dssp             CCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSS
T ss_pred             cCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCC
Confidence            358999999999976 479999999999999999999999998999999999999999999983

>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=99.64  E-value=1e-16  Score=108.01  Aligned_cols=64  Identities=19%  Similarity=0.463  Sum_probs=58.7

Q ss_pred             CCCCCcccCCcceec---ceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947            5 GTLDKCKACDKTVYV---VDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE   68 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~---~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   68 (210)
                      ..+++|..|+++|..   .++|.++++.||++||+|..|+++|.+..|+.+++++||..||.++|+|
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p   69 (72)
T 1x4l_A            3 SGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGP   69 (72)
T ss_dssp             SCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCS
T ss_pred             CCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCC
Confidence            457899999999984   3679999999999999999999999998999999999999999999884

>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=99.64  E-value=5e-17  Score=111.58  Aligned_cols=65  Identities=18%  Similarity=0.460  Sum_probs=59.6

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccC
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESG   70 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~   70 (210)
                      ...++|..|+++|+ +++|.++++.||++||+|..|+++|....|+++++++||+.||.++|++++
T Consensus        13 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g   77 (79)
T 1x62_A           13 QKLPMCDKCGTGIV-GVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPS   77 (79)
T ss_dssp             CCCCCCSSSCCCCC-SSCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCC
T ss_pred             CCCCccccCCCCcc-CcEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCC
Confidence            34689999999998 578999999999999999999999998889999999999999999998643

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

Probab=99.64  E-value=2e-16  Score=106.49  Aligned_cols=63  Identities=19%  Similarity=0.464  Sum_probs=58.2

Q ss_pred             CCCCCcccCCcceecc-eeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947            5 GTLDKCKACDKTVYVV-DMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~-~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      ...++|.+|+++|+.. .+|.++++.||+.||+|..|+++|.+..|+.+++++||+.||.++|+
T Consensus         3 ~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~~   66 (72)
T 1x61_A            3 SGSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLE   66 (72)
T ss_dssp             SCCCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHHH
T ss_pred             CCCCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHHc
Confidence            3568999999999965 47999999999999999999999998889999999999999999986

>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=99.64  E-value=1.6e-16  Score=111.47  Aligned_cols=65  Identities=22%  Similarity=0.498  Sum_probs=59.4

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccC
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESG   70 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~   70 (210)
                      ...++|..|+++|+ +++|.++++.||++||+|..|++.|....|+++++++||+.||.++|++++
T Consensus        23 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~   87 (89)
T 1x64_A           23 QRMPLCDKCGSGIV-GAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPS   87 (89)
T ss_dssp             CSCCBCTTTCCBCC-SCCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCC
T ss_pred             CcCCCcccCCCEec-ccEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCC
Confidence            34578999999999 578999999999999999999999998899999999999999999998543

>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=99.63  E-value=4.5e-16  Score=106.89  Aligned_cols=62  Identities=24%  Similarity=0.466  Sum_probs=57.3

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCC
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN  167 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~  167 (210)
                      ++|+.|+++|. ++.|.++++.||++||+|..|+++|....| .++|++||+.||.++|+++..
T Consensus        16 ~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f-~~~g~~yC~~cy~~~f~p~~s   77 (79)
T 2cor_A           16 YICQKCHAIID-EQPLIFKNDPYHPDHFNCANCGKELTADAR-ELKGELYCLPCHDKMGVSGPS   77 (79)
T ss_dssp             CBCTTTCCBCC-SCCCCCSSSCCCTTTSBCSSSCCBCCTTCE-EETTEEECHHHHHTTSCCSSC
T ss_pred             CCCccCCCEec-ceEEEECcceeCCCCCEeCCCCCccCCCCE-eECCEEeCHHHHHHhCCCCCC
Confidence            79999999999 788999999999999999999999997754 889999999999999998764

>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=99.62  E-value=2e-16  Score=109.43  Aligned_cols=65  Identities=35%  Similarity=0.756  Sum_probs=58.4

Q ss_pred             CCCCCccccccceeecCceeEecCccccccccccCCCCCcCCCCCee--ecCCeeecHhHHHhhhcC
Q 040947          100 SGTQDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYA--ALDGVLYCKHHFAQLFME  164 (210)
Q Consensus       100 ~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~--~~dg~~yC~~c~~~~f~~  164 (210)
                      .++.++|.+|+++|++.+.|.++++.||++||+|..|+++|....|.  ..||++||+.||.++|+.
T Consensus        12 ~~~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~   78 (82)
T 2co8_A           12 AGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSG   78 (82)
T ss_dssp             CCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCC
T ss_pred             CCCCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcC
Confidence            34458999999999988899999999999999999999999988887  479999999999988765

>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=99.62  E-value=1.2e-16  Score=110.49  Aligned_cols=64  Identities=36%  Similarity=0.801  Sum_probs=58.8

Q ss_pred             CCCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCee--ccCCeeeccchHHHhhh
Q 040947            4 TGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYS--SMDGVLYCKPHFEQLFK   67 (210)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~--~~~g~~yC~~cy~~~~~   67 (210)
                      .++.++|.+|+++|+..+.|.++++.||++||+|..|++.|....|+  +++|++||+.||.++|+
T Consensus        12 ~~~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~   77 (82)
T 2co8_A           12 AGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDS   77 (82)
T ss_dssp             CCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCC
T ss_pred             CCCCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhc
Confidence            45678999999999988889999999999999999999999998888  57999999999998876

>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=99.62  E-value=4.7e-16  Score=107.22  Aligned_cols=65  Identities=29%  Similarity=0.613  Sum_probs=59.7

Q ss_pred             CCCCcccCCcceecce-eEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccC
Q 040947            6 TLDKCKACDKTVYVVD-MLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESG   70 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~-~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~   70 (210)
                      .+++|.+|+++|..++ +|.++++.||++||+|..|+++|....|+++++++||+.||.++|++++
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~   79 (82)
T 1x63_A           14 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGP   79 (82)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCC
T ss_pred             cCCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCC
Confidence            3589999999998765 5899999999999999999999999899999999999999999999654

>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=99.62  E-value=4.2e-16  Score=106.95  Aligned_cols=61  Identities=25%  Similarity=0.617  Sum_probs=57.7

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      .+++|.+|+++|. ++.|.++++.||+.||+|..|+++|.+..|+.+++++||+.||.++|+
T Consensus        14 ~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~   74 (80)
T 1x3h_A           14 FSPKCGGCNRPVL-ENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRG   74 (80)
T ss_dssp             CSCBCTTTCCBCC-SSCEEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHHHS
T ss_pred             cCCccccCCCeec-ceeEEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHHcC
Confidence            3689999999998 578999999999999999999999998899999999999999999998

>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=99.62  E-value=5.3e-16  Score=111.02  Aligned_cols=70  Identities=24%  Similarity=0.449  Sum_probs=63.5

Q ss_pred             Cccccccceeec-CceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCcccccc
Q 040947          104 DKCAACEKTVYP-LEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLK  173 (210)
Q Consensus       104 ~~C~~C~~~I~~-~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~~~~~~  173 (210)
                      ++|++|+++|.+ ++.|.++++.||++||+|..|+++|.+..|+..+|++||+.||.++|++++......+
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I   76 (101)
T 2cup_A            6 SGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAI   76 (101)
T ss_dssp             CBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCSSSCCBC
T ss_pred             CcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccccCCCcc
Confidence            799999999985 6778999999999999999999999988899999999999999999999997554433

>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=99.61  E-value=4.6e-16  Score=107.13  Aligned_cols=62  Identities=27%  Similarity=0.630  Sum_probs=57.4

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeecc-CCeeeccchHHHhhh
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSM-DGVLYCKPHFEQLFK   67 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~-~g~~yC~~cy~~~~~   67 (210)
                      ...++|..|+++|. +++|.++++.||++||+|..|+++|.+..|+.. +|++||+.||.++|+
T Consensus        13 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~   75 (81)
T 2dlo_A           13 ATLEKCATCSQPIL-DRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFA   75 (81)
T ss_dssp             SSCCBCTTTCCBCC-SCCEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTT
T ss_pred             cCCCccccCCCeec-ceeEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhc
Confidence            46789999999998 678999999999999999999999998888876 799999999999998

>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=99.61  E-value=5.8e-16  Score=104.17  Aligned_cols=61  Identities=21%  Similarity=0.462  Sum_probs=56.6

Q ss_pred             CccccccceeecCc-eeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcC
Q 040947          104 DKCAACEKTVYPLE-KVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME  164 (210)
Q Consensus       104 ~~C~~C~~~I~~~e-~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~  164 (210)
                      ++|.+|+++|.+.+ .|.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+.
T Consensus         6 ~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~~~   67 (72)
T 1x61_A            6 SGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLES   67 (72)
T ss_dssp             CCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHHHT
T ss_pred             CCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHHcc
Confidence            79999999999654 68999999999999999999999888899999999999999999964

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

Probab=99.61  E-value=5.6e-16  Score=103.90  Aligned_cols=60  Identities=32%  Similarity=0.731  Sum_probs=56.1

Q ss_pred             CccccccceeecCce-eEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhc
Q 040947          104 DKCAACEKTVYPLEK-VTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~  163 (210)
                      ++|++|+++|.+.+. |.++++.||++||+|..|+++|..+.|+..+|++||+.||.++|+
T Consensus        12 ~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B           12 ATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             CBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHTC
T ss_pred             ccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhhC
Confidence            799999999997776 579999999999999999999998789999999999999999986

>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=99.61  E-value=3.9e-16  Score=105.58  Aligned_cols=62  Identities=15%  Similarity=0.259  Sum_probs=57.5

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCC-CCCeeecCCeeecHhHHHhhhcCCC
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLT-HSSYAALDGVLYCKHHFAQLFMEKG  166 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~-~~~f~~~dg~~yC~~c~~~~f~~k~  166 (210)
                      ++|++|+++|. ++.|.++++.||++||+|..|+++|. +..|++.++++||..||.++++++.
T Consensus         6 ~~C~~C~~~I~-~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~~~   68 (73)
T 1wig_A            6 SGCDSCEKYIT-GRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTEDS   68 (73)
T ss_dssp             CSCSSSCCCCS-SCCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSSSC
T ss_pred             CCcccCCCEec-CeeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhcccc
Confidence            79999999998 57899999999999999999999998 7789999999999999999988754

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

Probab=99.60  E-value=5.9e-16  Score=106.25  Aligned_cols=62  Identities=27%  Similarity=0.663  Sum_probs=58.0

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE   68 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   68 (210)
                      .+++|..|+++|. ++.|.++++.||++||+|..|+++|.+..|+++++++||+.||.++|++
T Consensus        14 ~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~   75 (80)
T 2cuq_A           14 FAPRCARCSKTLT-QGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFAS   75 (80)
T ss_dssp             SSCCCTTTCCCCC-SCCEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTC
T ss_pred             cCCcCCCCCCEec-CcEEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHcCC
Confidence            4689999999998 5689999999999999999999999988999999999999999999983

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

Probab=99.60  E-value=8e-16  Score=114.45  Aligned_cols=68  Identities=19%  Similarity=0.366  Sum_probs=63.3

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCcccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHV  171 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~~~~  171 (210)
                      ++|++|+++|..++.|.++|+.||++||+|..|+++|.+..|+..||++||+.||.++|++++.....
T Consensus         4 ~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~   71 (126)
T 2xqn_T            4 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHN   71 (126)
T ss_dssp             CBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCTTTCS
T ss_pred             CCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCcccCC
Confidence            79999999999778899999999999999999999999888999999999999999999999975443

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

Probab=99.60  E-value=6.2e-16  Score=104.60  Aligned_cols=61  Identities=16%  Similarity=0.315  Sum_probs=56.6

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCC-CCCeeccCCeeeccchHHHhhh
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLV-MSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~-~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      .+++|++|+++|. +++|.++++.||++||+|..|+++|. +..|+++++++||..||.++++
T Consensus         4 ~~~~C~~C~~~I~-~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~   65 (73)
T 1wig_A            4 GSSGCDSCEKYIT-GRVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAART   65 (73)
T ss_dssp             SCCSCSSSCCCCS-SCCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSS
T ss_pred             CcCCcccCCCEec-CeeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhc
Confidence            4689999999998 57899999999999999999999998 7789999999999999998876

>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=99.59  E-value=7.6e-16  Score=114.23  Aligned_cols=67  Identities=19%  Similarity=0.482  Sum_probs=60.8

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCC--CCCeeecCCeeecHhHHHhhhcC--CCCccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLT--HSSYAALDGVLYCKHHFAQLFME--KGNYSH  170 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~--~~~f~~~dg~~yC~~c~~~~f~~--k~~~~~  170 (210)
                      ++|++|+++|...+.|.++++.||++||+|..|+++|.  +..|+..+|++||+.||.++|++  +|..+.
T Consensus         6 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~   76 (122)
T 1m3v_A            6 KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGG   76 (122)
T ss_dssp             CCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSS
T ss_pred             CCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCC
Confidence            79999999999766799999999999999999999997  45799999999999999999999  886443

>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=99.59  E-value=5.1e-16  Score=107.08  Aligned_cols=63  Identities=22%  Similarity=0.583  Sum_probs=57.8

Q ss_pred             CCCCcccCCcceec-ceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947            6 TLDKCKACDKTVYV-VDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE   68 (210)
Q Consensus         6 ~~~~C~~C~~~I~~-~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   68 (210)
                      .+++|..|+++|.. +.+|.++++.||+.||+|..|+++|.+..|+.+++++||+.||.++|++
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~   77 (82)
T 2ehe_A           14 FANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSS   77 (82)
T ss_dssp             CSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGGG
T ss_pred             cCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCccEeeCCEEECHHHHhhhcCC
Confidence            46799999999984 4568899999999999999999999998999999999999999999983

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

Probab=99.59  E-value=6.9e-16  Score=122.98  Aligned_cols=62  Identities=32%  Similarity=0.770  Sum_probs=58.6

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      +.++|.+|+++|++++.|.++++.||++||+|..|+++|.+..|+.++|++||+.||.++|+
T Consensus       114 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~  175 (192)
T 1b8t_A          114 GSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFG  175 (192)
T ss_dssp             CCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHTC
T ss_pred             CCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccccCCEEeCHHHHHHhcC
Confidence            45679999999998888999999999999999999999998899999999999999999998

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

Probab=99.59  E-value=1.2e-15  Score=120.59  Aligned_cols=67  Identities=21%  Similarity=0.516  Sum_probs=60.6

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCcccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHV  171 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~~~~  171 (210)
                      ++|..|+++|...+.|.++++.||++||+|..|+++|....| .++|++||+.||.++|++++..+..
T Consensus        61 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~~kC~~C~~  127 (182)
T 2jtn_A           61 PMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTKCAACQL  127 (182)
T ss_dssp             CBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCE-EETTEEECHHHHHHTTSCCCTTTCC
T ss_pred             CcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCce-eECCEeeecCccccccccccccCCC
Confidence            799999999996667889999999999999999999998765 6899999999999999999975543

>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=99.59  E-value=8.6e-16  Score=105.46  Aligned_cols=62  Identities=24%  Similarity=0.542  Sum_probs=56.8

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE   68 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   68 (210)
                      ...++|..|+++|. ++.|.++|+.||++||+|..|+++|.... ++++|++||+.||.++|+|
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 LGKYICQKCHAIID-EQPLIFKNDPYHPDHFNCANCGKELTADA-RELKGELYCLPCHDKMGVS   74 (79)
T ss_dssp             CCCCBCTTTCCBCC-SCCCCCSSSCCCTTTSBCSSSCCBCCTTC-EEETTEEECHHHHHTTSCC
T ss_pred             cCCCCCccCCCEec-ceEEEECcceeCCCCCEeCCCCCccCCCC-EeECCEEeCHHHHHHhCCC
Confidence            45689999999999 78899999999999999999999999875 5899999999999999984

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

Probab=99.58  E-value=8.5e-16  Score=103.00  Aligned_cols=62  Identities=24%  Similarity=0.637  Sum_probs=57.1

Q ss_pred             CCCCcccCCcceeccee-EeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947            6 TLDKCKACDKTVYVVDM-LSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~-v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      ..++|.+|+++|...+. +.++|+.||++||+|..|+++|....|+.++|++||+.||.++|+
T Consensus        10 ~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B           10 ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             TTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHTC
T ss_pred             CCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhhC
Confidence            46899999999997775 689999999999999999999998889999999999999999874

>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=99.57  E-value=1e-15  Score=113.77  Aligned_cols=61  Identities=23%  Similarity=0.558  Sum_probs=56.1

Q ss_pred             CCCcccCCcceecceeEeeCCccccCCCcccccccCCCC--CCCeeccCCeeeccchHHHhhh
Q 040947            7 LDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLV--MSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus         7 ~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      .++|.+|+++|+...+|.++++.||+.||+|..|+++|.  +..|++++|++||+.||.++|+
T Consensus        61 ~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           61 WKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             CSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             CCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            579999999999666799999999999999999999997  4689999999999999999874

>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=99.57  E-value=1.5e-15  Score=112.91  Aligned_cols=61  Identities=20%  Similarity=0.490  Sum_probs=56.0

Q ss_pred             CCccccccceeecCceeEecCccccccccccCCCCCcCC--CCCeeecCCeeecHhHHHhhhc
Q 040947          103 QDKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLT--HSSYAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       103 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~--~~~f~~~dg~~yC~~c~~~~f~  163 (210)
                      .++|++|+++|...+.|.++++.||++||+|..|+++|.  +..|+.++|++||+.||.++||
T Consensus        61 ~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           61 WKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             CSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             CCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            379999999999666799999999999999999999997  4679999999999999999986

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

Probab=99.56  E-value=2.8e-15  Score=99.03  Aligned_cols=58  Identities=21%  Similarity=0.566  Sum_probs=54.1

Q ss_pred             CccccccceeecC-ceeEecCcccc--ccccccCCCCCcCCCCCeeecCCeeec-HhHHHhh
Q 040947          104 DKCAACEKTVYPL-EKVTMEGDCFH--KTCFRCAHGGCPLTHSSYAALDGVLYC-KHHFAQL  161 (210)
Q Consensus       104 ~~C~~C~~~I~~~-e~v~~~g~~~H--~~CF~C~~C~~~l~~~~f~~~dg~~yC-~~c~~~~  161 (210)
                      ++|++|+++|.++ +.|.++++.||  ++||+|..|+++|.+..|+.++|+||| ..||.++
T Consensus         3 ~~C~~C~~~I~~~~~~v~a~~~~wH~~~~CF~C~~C~~~L~~~~f~~~~g~~yC~~~C~~k~   64 (65)
T 2iyb_E            3 VVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM   64 (65)
T ss_dssp             EECTTTSSEECTTSCEEEETTEEEETTTTTSBCTTTCCBCTTSCCEEETTEEESSHHHHHTT
T ss_pred             CCCcCCCCeeccCceEEEECCCccCCCCCCEECCCCCCcCCCCceEEECCEEecCHHHhhhh
Confidence            6899999999974 67999999999  999999999999998899999999999 9999875

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

Probab=99.55  E-value=2.4e-15  Score=99.34  Aligned_cols=59  Identities=19%  Similarity=0.627  Sum_probs=54.4

Q ss_pred             CCCcccCCcceecc-eeEeeCCcccc--CCCcccccccCCCCCCCeeccCCeeec-cchHHHh
Q 040947            7 LDKCKACDKTVYVV-DMLSLEGMPYH--KSCFKCSHCKGTLVMSNYSSMDGVLYC-KPHFEQL   65 (210)
Q Consensus         7 ~~~C~~C~~~I~~~-~~v~~~g~~~H--~~CF~C~~C~~~L~~~~f~~~~g~~yC-~~cy~~~   65 (210)
                      +++|.+|+++|..+ +.|.++|+.||  ++||+|..|+++|.+..|++++|++|| .+||.++
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            47899999999974 78999999999  999999999999999999999999999 8898764

>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=99.54  E-value=4.2e-15  Score=101.17  Aligned_cols=60  Identities=23%  Similarity=0.618  Sum_probs=54.9

Q ss_pred             CCCCcccCCcceec----ceeEeeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHh
Q 040947            6 TLDKCKACDKTVYV----VDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQL   65 (210)
Q Consensus         6 ~~~~C~~C~~~I~~----~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~   65 (210)
                      .+++|++|+++|.+    .+.|.++++.||+.||+|..|+++|.+..|+++++++||+.||.++
T Consensus        14 ~~~~C~~C~~~I~~~g~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~l   77 (77)
T 2egq_A           14 VAKKCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKKL   77 (77)
T ss_dssp             CCCCCSSSCCCCCCCSSCCCEEEETTEEEETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHHC
T ss_pred             hCccCcccCCcccCCCCCceeEEECcceeCcccCEehhcCCCCCCCccEeECCEEEChHHhccC
Confidence            46899999999993    3789999999999999999999999998999999999999999753

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

Probab=99.53  E-value=9.1e-15  Score=109.35  Aligned_cols=67  Identities=18%  Similarity=0.393  Sum_probs=60.2

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCC--CCCeeecCCeeecHhHHHhhhcC--CCCccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLT--HSSYAALDGVLYCKHHFAQLFME--KGNYSH  170 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~--~~~f~~~dg~~yC~~c~~~~f~~--k~~~~~  170 (210)
                      ++|+.|+++|.+.+.|.++++.||++||+|..|+.+|.  +..|+..||+|||+.||.++|++  ++....
T Consensus         3 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~   73 (131)
T 2xjy_A            3 LTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCD   73 (131)
T ss_dssp             CBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTC
T ss_pred             ccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcC
Confidence            78999999999655789999999999999999999996  35799999999999999999999  776443

>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=99.50  E-value=1.6e-14  Score=99.29  Aligned_cols=61  Identities=21%  Similarity=0.515  Sum_probs=55.7

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCC-CCee-ccCCeeeccchHHHhhh
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVM-SNYS-SMDGVLYCKPHFEQLFK   67 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~-~~f~-~~~g~~yC~~cy~~~~~   67 (210)
                      .+++|..|+++|. ++.|.++++.||++||+|..|+++|.. ..|+ ++++++||+.||.++|+
T Consensus        14 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~   76 (81)
T 1x6a_A           14 FGEFCHGCSLLMT-GPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVS   76 (81)
T ss_dssp             SSCBCTTTCCBCC-SCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHC
T ss_pred             cCCcCccCCCCcC-ceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhc
Confidence            4579999999999 788999999999999999999999974 5677 58999999999999998

>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=99.50  E-value=2.3e-14  Score=111.92  Aligned_cols=67  Identities=21%  Similarity=0.516  Sum_probs=60.4

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCcccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHV  171 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~~~~  171 (210)
                      ++|.+|+++|...+.|.++|+.||++||+|..|+++|.+..| ..||++||+.||.++|+++|..+..
T Consensus         7 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~~~C~~C~~   73 (169)
T 2rgt_A            7 PMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTKCAACQL   73 (169)
T ss_dssp             CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCCE-ESSSCEECHHHHHHHHSCBCTTTCC
T ss_pred             CccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCCc-ccCCeeeeccccccccccccccccc
Confidence            799999999996667899999999999999999999998765 7899999999999999999975443

>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=99.44  E-value=5.7e-14  Score=111.51  Aligned_cols=67  Identities=18%  Similarity=0.448  Sum_probs=60.2

Q ss_pred             CccccccceeecCceeEecCccccccccccCCCCCcCCC--CCeeecCCeeecHhHHHhhhcC--CCCccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTH--SSYAALDGVLYCKHHFAQLFME--KGNYSH  170 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~--~~f~~~dg~~yC~~c~~~~f~~--k~~~~~  170 (210)
                      ++|+.|+++|...+.|.++++.||++||+|..|+++|..  ..|+..||++||+.||.++|++  +|..+.
T Consensus         6 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~   76 (188)
T 1rut_X            6 KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACG   76 (188)
T ss_dssp             CBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTC
T ss_pred             CcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCC
Confidence            799999999996556899999999999999999999985  6899999999999999999999  576433

>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=99.38  E-value=1.4e-13  Score=94.56  Aligned_cols=61  Identities=21%  Similarity=0.478  Sum_probs=53.2

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCcccccccCCCCCCCeeccCC-eeeccchHHHhhh
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCFKCSHCKGTLVMSNYSSMDG-VLYCKPHFEQLFK   67 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g-~~yC~~cy~~~~~   67 (210)
                      .+++|..|+++|. +++|.++++.||++||+|..|+++|....++..++ .+||..||.+++.
T Consensus        14 ~~~~C~~C~~~I~-~~~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~   75 (81)
T 1v6g_A           14 YGTRCFSCDQFIE-GEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSV   75 (81)
T ss_dssp             CCCBCTTTCCBCC-SCCEEETTEEECTTTSSCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSS
T ss_pred             hCCcCccccCEec-cceEEECCceeCccCCccccCCCCCCCCCEEEeCCCCEEChhhhcccCC
Confidence            3579999999998 78899999999999999999999999777776655 4799999987764

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

Probab=98.42  E-value=6.1e-08  Score=54.16  Aligned_cols=28  Identities=50%  Similarity=0.986  Sum_probs=27.0

Q ss_pred             CccccccceeecCceeEecCcccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      ++|++|++.|++.|.|.+.|+.||+.||
T Consensus         4 ~~C~~C~k~Vy~~Ek~~~~g~~~Hk~CF   31 (31)
T 1zfo_A            4 PNCARCGKIVYPTEKVNCLDKFWHKACF   31 (31)
T ss_dssp             CBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CcCCccCCEEecceeEEECCeEecccCC
Confidence            6999999999999999999999999998

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

Probab=98.36  E-value=8.5e-08  Score=53.56  Aligned_cols=29  Identities=31%  Similarity=0.675  Sum_probs=27.4

Q ss_pred             CCCcccCCcceecceeEeeCCccccCCCc
Q 040947            7 LDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         7 ~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      .++|.+|++.|+..|.+.++|+.||..||
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            46899999999999999999999999998

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=88.73  E-value=0.17  Score=36.16  Aligned_cols=92  Identities=13%  Similarity=0.296  Sum_probs=47.9

Q ss_pred             cccccccCCCCCC------CeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCCCCCCCCCCCcccccCCCCCcccc
Q 040947           35 FKCSHCKGTLVMS------NYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAA  108 (210)
Q Consensus        35 F~C~~C~~~L~~~------~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~C~~  108 (210)
                      +.|..|...+...      .....=|..||..|..+.+..+                                  ..|+.
T Consensus         8 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~----------------------------------~~CP~   53 (133)
T 4ap4_A            8 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNA----------------------------------NTCPT   53 (133)
T ss_dssp             CBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTTC----------------------------------SBCTT
T ss_pred             CCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHhC----------------------------------CCCCC
Confidence            5566665554321      1334457778888887765411                                  46777


Q ss_pred             ccceeecCceeEecCccccccccccCCCCCcCCCC----C--eeecCCeeecHhHHHhhhc
Q 040947          109 CEKTVYPLEKVTMEGDCFHKTCFRCAHGGCPLTHS----S--YAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       109 C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~----~--f~~~dg~~yC~~c~~~~f~  163 (210)
                      |++.+........   ..-.+=+.|..|...+...    .  ....=|..||..|..+.+.
T Consensus        54 Cr~~~~~~~l~~l---~i~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~  111 (133)
T 4ap4_A           54 CRKKINHKRYHPI---YIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLK  111 (133)
T ss_dssp             TCCBCTTTCEEEC---BCSSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHH
T ss_pred             CCCcCcccccccc---ccCCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHH
Confidence            7777653332211   1122334566666655321    1  1222377777777765543

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

Probab=85.45  E-value=0.27  Score=32.38  Aligned_cols=34  Identities=15%  Similarity=0.413  Sum_probs=25.0

Q ss_pred             CCCCCCCcccCCcceecceeEeeCCccccCCCcc
Q 040947            3 FTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCFK   36 (210)
Q Consensus         3 ~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF~   36 (210)
                      |......|+.|...|..+.....-+..||..|+.
T Consensus        11 y~~~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci~   44 (74)
T 2ct0_A           11 YPDAVKICNICHSLLIQGQSCETCGIRMHLPCVA   44 (74)
T ss_dssp             CSSSSCBCSSSCCBCSSSEECSSSCCEECHHHHH
T ss_pred             ccCCCCcCcchhhHcccCCccCCCCchhhHHHHH
Confidence            5667789999999998665444555667877763

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=84.98  E-value=1  Score=29.07  Aligned_cols=35  Identities=11%  Similarity=0.228  Sum_probs=27.3

Q ss_pred             CCCcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           32 KSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        32 ~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      +.-|.|..|...+.. .....-|..||..|..+.+.
T Consensus         6 ~~~~~C~IC~~~~~~-Pv~~~CgH~fc~~Ci~~~~~   40 (78)
T 1t1h_A            6 PEYFRCPISLELMKD-PVIVSTGQTYERSSIQKWLD   40 (78)
T ss_dssp             SSSSSCTTTSCCCSS-EEEETTTEEEEHHHHHHHHT
T ss_pred             cccCCCCCccccccC-CEEcCCCCeecHHHHHHHHH
Confidence            345888999888875 34457899999999998875

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

Probab=83.74  E-value=0.89  Score=29.83  Aligned_cols=33  Identities=15%  Similarity=0.371  Sum_probs=22.3

Q ss_pred             cCCCCCccccccceeecCceeEecCcccccccc
Q 040947           99 FSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus        99 ~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      +......|+.|...|.++..-..-+..||..|+
T Consensus        11 y~~~i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci   43 (74)
T 2ct0_A           11 YPDAVKICNICHSLLIQGQSCETCGIRMHLPCV   43 (74)
T ss_dssp             CSSSSCBCSSSCCBCSSSEECSSSCCEECHHHH
T ss_pred             ccCCCCcCcchhhHcccCCccCCCCchhhHHHH
Confidence            334457899999999865433344566777776

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=83.18  E-value=1  Score=28.65  Aligned_cols=34  Identities=26%  Similarity=0.417  Sum_probs=25.2

Q ss_pred             CcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           34 CFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        34 CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      -+.|..|...+........=|..||..|..+.+.
T Consensus        15 ~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~   48 (72)
T 2djb_A           15 YILCSICKGYLIDATTITECLHTFCKSCIVRHFY   48 (72)
T ss_dssp             GGSCTTTSSCCSSCEECSSSCCEECHHHHHHHHH
T ss_pred             CCCCCCCChHHHCcCEECCCCCHHHHHHHHHHHH
Confidence            4778888887776333336788999999988765

>2ysm_A Myeloid/lymphoid or mixed-lineage leukemia protein 3 homolog; PHD domain, histone-lysine N-methyltransferase, H3 lysine-4 specific MLL3; NMR {Homo sapiens}

Probab=82.65  E-value=2  Score=30.04  Aligned_cols=95  Identities=16%  Similarity=0.301  Sum_probs=54.2

Q ss_pred             CCCCcccCCcceecceeE--eeCCccccCCCcccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCC
Q 040947            6 TLDKCKACDKTVYVVDML--SLEGMPYHKSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPS   83 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v--~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~   83 (210)
                      ....|..|+..-...++|  ..=++.||..|+.=..     .    .+..+..+|..|.                     
T Consensus         6 ~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~~-----~----~~~~~~W~C~~C~---------------------   55 (111)
T 2ysm_A            6 SGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIAV-----T----PLKRAGWQCPECK---------------------   55 (111)
T ss_dssp             CCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCCC-----C----TTTSTTCCCTTTC---------------------
T ss_pred             CCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCcc-----c----cccccCccCCcCC---------------------
Confidence            456899998763212223  3345788988875321     1    1134566776552                     


Q ss_pred             CCCCCCCCCCCcccccCCCCCccccccceeecCceeE--ecCccccccccccCCCCCcCCCCCeeecCCeeecHhHHHh
Q 040947           84 SCSNQNRTPSKLSSLFSGTQDKCAACEKTVYPLEKVT--MEGDCFHKTCFRCAHGGCPLTHSSYAALDGVLYCKHHFAQ  160 (210)
Q Consensus        84 ~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~--~~g~~~H~~CF~C~~C~~~l~~~~f~~~dg~~yC~~c~~~  160 (210)
                                           .|..|++.-....+|.  .-++.||..|+.=     +|..    +..+.-||..|...
T Consensus        56 ---------------------~C~~C~~~~~~~~ll~Cd~C~~~yH~~Cl~p-----pl~~----~P~g~W~C~~C~~c  104 (111)
T 2ysm_A           56 ---------------------VCQNCKQSGEDSKMLVCDTCDKGYHTFCLQP-----VMKS----VPTNGWKCKNCRIC  104 (111)
T ss_dssp             ---------------------CCTTTCCCSCCTTEEECSSSCCEEEGGGSSS-----CCSS----CCSSCCCCHHHHCC
T ss_pred             ---------------------cccccCccCCCCCeeECCCCCcHHhHHhcCC-----cccc----CCCCCcCCcCCcCc
Confidence                                 5777777654333333  3367899987642     2321    22467789888654

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=82.46  E-value=1  Score=31.88  Aligned_cols=32  Identities=13%  Similarity=0.315  Sum_probs=20.5

Q ss_pred             CCCCCcccCCcceecc----e--eEeeCCccccCCCcc
Q 040947            5 GTLDKCKACDKTVYVV----D--MLSLEGMPYHKSCFK   36 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~----~--~v~~~g~~~H~~CF~   36 (210)
                      ...-.|..|...+...    +  ++..-|..||..|+.
T Consensus         5 ~~~~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~   42 (133)
T 4ap4_A            5 SGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLR   42 (133)
T ss_dssp             CCSCBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHH
T ss_pred             CCCCCCcccChhhhCccccccCeEecCCCChhhHHHHH
Confidence            4456899998887532    1  445567777766653

>1jjd_A Metallothionein, SMTA; zinc finger, zinc cluster, metal binding PR; NMR {Synechococcus elongatus} SCOP: g.46.1.1

Probab=81.71  E-value=1.2  Score=27.54  Aligned_cols=28  Identities=21%  Similarity=0.447  Sum_probs=22.8

Q ss_pred             cCCCCCcCCCCCeeecCCeeec-HhHHHh
Q 040947          133 CAHGGCPLTHSSYAALDGVLYC-KHHFAQ  160 (210)
Q Consensus       133 C~~C~~~l~~~~f~~~dg~~yC-~~c~~~  160 (210)
                      |..|+..++...-+..||+.|| +.|...
T Consensus        10 C~~C~c~Vs~~eai~~dGK~YCSe~Ca~g   38 (55)
T 1jjd_A           10 CEPCLCNVDPSKAIDRNGLYYCSEACADG   38 (55)
T ss_dssp             STTCCCCBCTTTSEESSSCEESSHHHHHT
T ss_pred             CCCCeeEechHHhhhcCCeEEehHHHHcc
Confidence            6778888887778888999998 777764

---

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	210
d2d8ya2	42	g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapie	8e-17
d2d8ya2	42	g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapie	9e-15
d1b8ta3	43	g.39.1.3 (A:101-143) Cysteine-rich (intestinal) pr	2e-11
d1b8ta3	43	g.39.1.3 (A:101-143) Cysteine-rich (intestinal) pr	2e-07
d2co8a2	36	g.39.1.3 (A:8-43) Nedd9 interacting protein with c	3e-11
d2co8a2	36	g.39.1.3 (A:8-43) Nedd9 interacting protein with c	3e-08
d2d8ya1	35	g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapien	2e-10
d2d8ya1	35	g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapien	4e-08
d1b8ta1	35	g.39.1.3 (A:1-35) Cysteine-rich (intestinal) prote	3e-05
d1b8ta1	35	g.39.1.3 (A:1-35) Cysteine-rich (intestinal) prote	0.001
d2cu8a1	30	g.39.1.3 (A:8-37) Cysteine-rich (intestinal) prote	2e-04
d1a7ia1	28	g.39.1.3 (A:8-35) Cysteine-rich (intestinal) prote	4e-04
d1zfoa_	30	g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 982	4e-04
d1ibia1	28	g.39.1.3 (A:117-144) Cysteine-rich (intestinal) pr	0.002
d1g47a2	35	g.39.1.3 (A:36-70) Pinch (particularly interesting	0.004

>d2d8ya2 g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 42

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]

 Score = 68.9 bits (169), Expect = 8e-17
 Identities = 20/41 (48%), Positives = 28/41 (68%)

Query: 36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNF 76
          +CS+C   L +  Y+S+ G +YCKPHF QLFK  GN+ + F
Sbjct: 1  RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGF 41

>d2d8ya2 g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]} Length = 42

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]

 Score = 63.5 bits (155), Expect = 9e-15
 Identities = 19/38 (50%), Positives = 25/38 (65%)

Query: 132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYS 169
           RC++    L+  +YA+L G +YCK HF QLF  KGNY 
Sbjct: 1   RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYD 38

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 43

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]

 Score = 54.9 bits (132), Expect = 2e-11
 Identities = 16/43 (37%), Positives = 23/43 (53%), Gaps = 1/43 (2%)

Query: 89  NRTPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCF 131
           N   S+++    G+ D C  C + VY  EKV   G  +HK+CF
Sbjct: 2   NPNASRMAQKVGGS-DGCPRCGQAVYAAEKVIGAGKSWHKSCF 43

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 43

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]

 Score = 44.1 bits (104), Expect = 2e-07
 Identities = 12/33 (36%), Positives = 16/33 (48%)

Query: 3  FTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCF 35
            G  D C  C + VY  + +   G  +HKSCF
Sbjct: 11 KVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF 43

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 54.0 bits (130), Expect = 3e-11
 Identities = 13/32 (40%), Positives = 21/32 (65%)

Query: 100 SGTQDKCAACEKTVYPLEKVTMEGDCFHKTCF 131
           +G  D CA C + +Y LE++ + G  FH++CF
Sbjct: 5   AGAGDLCALCGEHLYVLERLCVNGHFFHRSCF 36

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]} Length = 36

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.9 bits (109), Expect = 3e-08
 Identities = 12/31 (38%), Positives = 19/31 (61%)

Query: 5  GTLDKCKACDKTVYVVDMLSLEGMPYHKSCF 35
          G  D C  C + +YV++ L + G  +H+SCF
Sbjct: 6  GAGDLCALCGEHLYVLERLCVNGHFFHRSCF 36

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {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: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 52.1 bits (125), Expect = 2e-10
 Identities = 12/34 (35%), Positives = 20/34 (58%)

Query: 98  LFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCF 131
             +  ++ C  C+KTVYP+E++      FH +CF
Sbjct: 2   FQAPARETCVECQKTVYPMERLLANQQVFHISCF 35

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {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: Eplin, LIMA1
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 45.5 bits (108), Expect = 4e-08
 Identities = 11/31 (35%), Positives = 15/31 (48%)

Query: 5  GTLDKCKACDKTVYVVDMLSLEGMPYHKSCF 35
             + C  C KTVY ++ L      +H SCF
Sbjct: 5  PARETCVECQKTVYPMERLLANQQVFHISCF 35

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 35

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]

 Score = 37.6 bits (87), Expect = 3e-05
 Identities = 16/31 (51%), Positives = 19/31 (61%)

Query: 101 GTQDKCAACEKTVYPLEKVTMEGDCFHKTCF 131
           G   KC  C+K VY  E+V  EG  FHK+CF
Sbjct: 5   GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF 35

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]} Length = 35

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]

 Score = 33.0 bits (75), Expect = 0.001
 Identities = 15/35 (42%), Positives = 18/35 (51%)

Query: 1  MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCF 35
          M   G   KC  C K VY  + +  EG  +HKSCF
Sbjct: 1  MPNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF 35

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]} Length = 30

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]

 Score = 35.5 bits (82), Expect = 2e-04
 Identities = 14/26 (53%), Positives = 17/26 (65%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTC 130
           KC  C+KTVY  EKV+  G  +HK C
Sbjct: 4   KCPKCDKTVYFAEKVSSLGKDWHKFC 29

>d1a7ia1 g.39.1.3 (A:8-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]} Length = 28

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]

 Score = 34.6 bits (79), Expect = 4e-04
 Identities = 14/28 (50%), Positives = 19/28 (67%)

Query: 104 DKCAACEKTVYPLEKVTMEGDCFHKTCF 131
           +KC AC +TVY  E+V  +G  FH+ CF
Sbjct: 1   NKCGACGRTVYHAEEVQCDGRSFHRCCF 28

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]} Length = 30

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]

 Score = 34.5 bits (79), Expect = 4e-04
 Identities = 14/27 (51%), Positives = 15/27 (55%)

Query: 105 KCAACEKTVYPLEKVTMEGDCFHKTCF 131
            CA C K VYP EKV      +HK CF
Sbjct: 4   NCARCGKIVYPTEKVNCLDKFWHKACF 30

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]} Length = 28

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]

 Score = 32.2 bits (73), Expect = 0.002
 Identities = 12/27 (44%), Positives = 16/27 (59%)

Query: 104 DKCAACEKTVYPLEKVTMEGDCFHKTC 130
           +KC+ C  +VY  EKV   G  +HK C
Sbjct: 2   EKCSRCGDSVYAAEKVIGAGKPWHKNC 28

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {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: Pinch (particularly interesting new Cys-His) protein
species: Human (Homo sapiens) [TaxId: 9606]

 Score = 31.6 bits (72), Expect = 0.004
 Identities = 10/32 (31%), Positives = 13/32 (40%)

Query: 131 FRCAHGGCPLTHSSYAALDGVLYCKHHFAQLF 162
           F CA          +   +G  YC+H F  LF
Sbjct: 1   FVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLF 32

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	210
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.05
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	99.01
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.93
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.92
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.9
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.89
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.78
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.71
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.71
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.68
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.66
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.63
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.62
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.62
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.6
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.56
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.56
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.54
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.54
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.54
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.52
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.52
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.51
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.49
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.47
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.47
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.43
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.42
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.39
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.39
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.36
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.35
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.34
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.34
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.32
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.28
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.28
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.25
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.24
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.24
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.23
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.21
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.21
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.2
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.18
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.18
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.17
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.14
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.13
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.11
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.09
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	98.08
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.07
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.04
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.03
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.01
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.97
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.94
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.94
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.92
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.92
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.89
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.87
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.86
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.85
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	97.83
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.83
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	97.83
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.82
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.75
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.74
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.73
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.71
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.71
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.69
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.68
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.62
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.62
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.62
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.61
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.58
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.58
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.57
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.54
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.5
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.49
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.47
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.45
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.39
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.28
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.25
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.22
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.21
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.15
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.14
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.12
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.09
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.03
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.03
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.95
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.84
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.77
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.62
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.54
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.47
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.21
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	96.11
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.1
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	95.8
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	95.78
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	95.77
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	95.75
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	95.65
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	95.54
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	95.43
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	95.09
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	94.87
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	94.72
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	94.7
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	94.6
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	94.42
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	93.3
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	93.02
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	92.85
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	92.75
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	91.08
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	90.48
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	90.39
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	89.52
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	88.91
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	88.22
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	87.63
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	87.56
d2co8a1	33	Nedd9 interacting protein with calponin homology,	86.65
d2co8a1	33	Nedd9 interacting protein with calponin homology,	84.56
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	84.03
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	83.39
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	81.17
d2gvia2	33	Uncharacterized protein Ta1109 {Thermoplasma acido	81.02

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

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

Probab=99.05  E-value=1.3e-11  Score=69.50  Aligned_cols=27  Identities=26%  Similarity=0.712  Sum_probs=26.0

Q ss_pred             CccccccceeecCceeEecCcccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      ++|..|+++|. ++.|+|+|+.||++||
T Consensus         9 pkC~~C~~~I~-g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           9 PKCGGCNRPVL-ENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CBCTTTCCBCC-SSCEEETTEEECTTTC
T ss_pred             hhhhhcCCccc-chheeecCCccCcccC
Confidence            89999999998 8899999999999998

>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=99.01  E-value=1.1e-10  Score=67.67  Aligned_cols=42  Identities=45%  Similarity=0.842  Sum_probs=39.4

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCCcccccc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGNYSHVLK  173 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~~~~~~~  173 (210)
                      ||+.|++.|..+.|...+|.+||+.||.++|++|++++++++
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~kGny~~gfg   42 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFG   42 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhhcCCCCCCC
Confidence            699999999999999999999999999999999999988763

>d1g47a2 g.39.1.3 (A:36-70) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.93  E-value=2.4e-10  Score=64.16  Aligned_cols=34  Identities=29%  Similarity=0.625  Sum_probs=32.8

Q ss_pred             cccCCCCCcCCCCCeeecCCeeecHhHHHhhhcC
Q 040947          131 FRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME  164 (210)
Q Consensus       131 F~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~  164 (210)
                      |+|+.|+++|....|++.||+|||+.||.++|+|
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            7899999999999999999999999999999997

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

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

Probab=98.92  E-value=7.6e-10  Score=66.18  Aligned_cols=45  Identities=36%  Similarity=0.558  Sum_probs=39.1

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCC-ccccccccc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN-YSHVLKAAN  176 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~-~~~~~~~~~  176 (210)
                      +|..|++.|++....+.||+|||+.||.++|+||+. +..+.+...
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~g~G~gaG~l~   46 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQGAGALI   46 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCCCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCccCcccCccccc
Confidence            689999999988999999999999999999999997 665555443

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

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

Probab=98.90  E-value=3.5e-10  Score=65.51  Aligned_cols=42  Identities=48%  Similarity=1.111  Sum_probs=39.5

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCcc
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQ   77 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~   77 (210)
                      +|..|++.|..++|..++|.+||+.||.++|.++|.|+..|+
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~kGny~~gfg   42 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFG   42 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhhcCCCCCCC
Confidence            699999999999999999999999999999999999987764

>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=98.89  E-value=2.1e-10  Score=64.41  Aligned_cols=34  Identities=26%  Similarity=0.683  Sum_probs=32.6

Q ss_pred             cccccccCCCCCCCeeccCCeeeccchHHHhhhc
Q 040947           35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKE   68 (210)
Q Consensus        35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~   68 (210)
                      |+|+.|+++|.+..|++++|++||+.||.++|+|
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            7999999999999999999999999999999984

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

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

Probab=98.78  E-value=1.2e-08  Score=64.30  Aligned_cols=44  Identities=18%  Similarity=0.272  Sum_probs=38.1

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhhhcCCCC-cccccccc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFMEKGN-YSHVLKAA  175 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~k~~-~~~~~~~~  175 (210)
                      .|..|++.|+...+...+++|||+.||.++|+||+. +..+....
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG~G~G~gag~l   45 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGTL   45 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCcccccccccee
Confidence            388999999999999999999999999999999997 65555443

>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=98.71  E-value=3e-09  Score=59.58  Aligned_cols=30  Identities=30%  Similarity=0.606  Sum_probs=27.7

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCc
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      -.+++|..|+++|. +++|.|+|+.||++||
T Consensus         6 ~fapkC~~C~~~I~-g~~v~Al~~~wHpeCF   35 (35)
T d1x3ha1           6 MFSPKCGGCNRPVL-ENYLSAMDTVWHPECF   35 (35)
T ss_dssp             CCSCBCTTTCCBCC-SSCEEETTEEECTTTC
T ss_pred             HhChhhhhcCCccc-chheeecCCccCcccC
Confidence            35799999999997 8899999999999998

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

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

Probab=98.71  E-value=4.7e-09  Score=61.42  Aligned_cols=40  Identities=38%  Similarity=0.825  Sum_probs=33.0

Q ss_pred             CCCCcccccCCCCCccccccceeecCceeEecCcccccccc
Q 040947           91 TPSKLSSLFSGTQDKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus        91 ~~~~~~~~~~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      .+.+..+.+.+ .++|.+|++.|++.|.+.+.|+.||+.||
T Consensus         4 ~~sk~~~~~g~-~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3           4 NASRMAQKVGG-SDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCCCCCCCCCC-CEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             CccccccccCC-CCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            34444544544 48999999999999999999999999998

>d1b8ta4 g.39.1.3 (A:144-192) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

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

Probab=98.68  E-value=4.3e-09  Score=62.83  Aligned_cols=36  Identities=28%  Similarity=0.685  Sum_probs=33.7

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHhhhccCC
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGN   71 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~   71 (210)
                      +|..|++.|++....++|+++||+.||.++|+|++.
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~   36 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGF   36 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCcc
Confidence            699999999999999999999999999999998764

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

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

Probab=98.66  E-value=8e-09  Score=60.93  Aligned_cols=37  Identities=30%  Similarity=0.536  Sum_probs=34.5

Q ss_pred             ccCCCCCcCCCCCeeecCCeeec-HhHHHhhhcCCCCc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYC-KHHFAQLFMEKGNY  168 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC-~~c~~~~f~~k~~~  168 (210)
                      +|..|++.|+.+...+.||+||| +.||.++|+||+.-
T Consensus         1 kC~~C~K~L~sg~~aeHdg~pYC~k~CY~~~FGPkG~g   38 (48)
T d1imla2           1 KCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFG   38 (48)
T ss_dssp             BCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSS
T ss_pred             CchhcCcCcCCCChhhcCCcccccccchhhccCCCccc
Confidence            68999999999999999999999 77999999999973

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

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

Probab=98.63  E-value=2.6e-09  Score=60.20  Aligned_cols=28  Identities=36%  Similarity=0.831  Sum_probs=26.2

Q ss_pred             CccccccceeecCce-eEecCcccccccc
Q 040947          104 DKCAACEKTVYPLEK-VTMEGDCFHKTCF  131 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~-v~~~g~~~H~~CF  131 (210)
                      ++|..|+++|.++.. |++.|+.||..||
T Consensus         9 ~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           9 PKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             cccccCCCccCCCCeEeEeCCccchhccC
Confidence            799999999998776 9999999999998

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

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

Probab=98.62  E-value=2.5e-09  Score=58.57  Aligned_cols=27  Identities=33%  Similarity=0.726  Sum_probs=25.1

Q ss_pred             CccccccceeecCceeEecCcccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      ++|..|+++|. ...|++.++.||++||
T Consensus         9 ~~C~~Ckk~It-~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           9 PRCARCSKTLT-QGGVTYRDQPWHRECL   35 (35)
T ss_dssp             CCCTTTCCCCC-SCCEESSSSEECTTTC
T ss_pred             HHHhhcCCccc-cCceeecCCcchhhhC
Confidence            79999999998 5679999999999998

>d2d8za2 g.39.1.3 (A:33-64) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.62  E-value=1.4e-08  Score=54.71  Aligned_cols=32  Identities=25%  Similarity=0.531  Sum_probs=30.0

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhhhc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~  163 (210)
                      +|..|.++|.+.+|+++|++|||..||..+|+
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            47889999999999999999999999999986

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.60  E-value=1e-08  Score=56.36  Aligned_cols=33  Identities=33%  Similarity=0.852  Sum_probs=30.3

Q ss_pred             CCCCCCCCcccCCcceecceeEeeCCccccCCCc
Q 040947            2 AFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         2 ~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      .|..++.+|.+|+++|. ..+|.|+|+.||+.||
T Consensus         3 Cy~~tlEkC~~C~~~I~-driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           3 CYVATLEKCATCSQPIL-DRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCCSSCCBCTTTCCBCC-SCCEEETTEEECTTTC
T ss_pred             hHHHHHHHHHHhchHHH-HHHHHHhCCCCCCCCC
Confidence            37788999999999997 7789999999999998

>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=98.56  E-value=1.4e-08  Score=59.06  Aligned_cols=31  Identities=19%  Similarity=0.398  Sum_probs=28.2

Q ss_pred             CCCCCCcccCCcceecceeEeeCCccccCCCc
Q 040947            4 TGTLDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      .+..++|+.|+++|. +.+|.|+|+.||++||
T Consensus        15 ~~r~P~C~~C~~pI~-g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          15 GKRTPMCAHCNQVIR-GPFLVALGKSWHPEEF   45 (45)
T ss_dssp             TTCCCBBSSSCCBCC-SCEEEETTEEECTTTC
T ss_pred             CCCCeeccccCCccc-CceeeecCCccCcCCC
Confidence            345799999999997 9999999999999998

>d1b8ta3 g.39.1.3 (A:101-143) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

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

Probab=98.56  E-value=1.1e-08  Score=59.81  Aligned_cols=33  Identities=36%  Similarity=0.763  Sum_probs=30.4

Q ss_pred             CCCCCCCcccCCcceecceeEeeCCccccCCCc
Q 040947            3 FTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         3 ~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      ..++.+.|.+|++.||..|.+.++|+.||+.||
T Consensus        11 ~~g~~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          11 KVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCCCCEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             ccCCCCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            346679999999999999999999999999998

>d2cuqa1 g.39.1.3 (A:43-74) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.54  E-value=3e-08  Score=52.65  Aligned_cols=32  Identities=28%  Similarity=0.570  Sum_probs=30.3

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhhhc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~  163 (210)
                      +|..|+++|.+.+|..+|..|||..||..+|+
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            58999999999999999999999999999986

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.54  E-value=1.3e-08  Score=56.82  Aligned_cols=33  Identities=36%  Similarity=0.839  Sum_probs=30.9

Q ss_pred             CCCCCCCcccCCcceecceeEeeCCccccCCCc
Q 040947            3 FTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         3 ~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      .+|+..+|..|++.|+..|.+.++|+.||+.||
T Consensus         4 ~~g~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           4 EAGAGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CCCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             cCCCCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            357889999999999999999999999999998

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

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

Probab=98.54  E-value=4.2e-08  Score=57.80  Aligned_cols=36  Identities=31%  Similarity=0.712  Sum_probs=33.7

Q ss_pred             ccccccCCCCCCCeeccCCeeec-cchHHHhhhccCC
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYC-KPHFEQLFKESGN   71 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC-~~cy~~~~~~~~~   71 (210)
                      +|..|++.|++....+++++||| +.||..+|+|++.
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 7799999999875

>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=98.52  E-value=2.4e-08  Score=58.07  Aligned_cols=28  Identities=21%  Similarity=0.434  Sum_probs=26.3

Q ss_pred             CCccccccceeecCceeEecCcccccccc
Q 040947          103 QDKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       103 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      .|+|..|+++|. +..|+++|+.||++||
T Consensus        18 ~P~C~~C~~pI~-g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          18 TPMCAHCNQVIR-GPFLVALGKSWHPEEF   45 (45)
T ss_dssp             CCBBSSSCCBCC-SCEEEETTEEECTTTC
T ss_pred             CeeccccCCccc-CceeeecCCccCcCCC
Confidence            389999999998 8899999999999998

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.52  E-value=2.1e-08  Score=53.15  Aligned_cols=28  Identities=50%  Similarity=0.912  Sum_probs=26.7

Q ss_pred             CccccccceeecCceeEecCcccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      ++|++|+++|+++|.+..+|+.||+.|+
T Consensus         3 ~~CprC~K~VYfaEk~~~lgk~WHk~Cl   30 (30)
T d2cu8a1           3 SKCPKCDKTVYFAEKVSSLGKDWHKFCL   30 (30)
T ss_dssp             CBCTTTCCBCCTTTEEEETTEEEETTTC
T ss_pred             CcCCCCCCceeeHHhhccCCcccccccC
Confidence            7999999999999999999999999885

>d2dloa1 g.39.1.3 (A:8-42) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.51  E-value=2.5e-08  Score=54.74  Aligned_cols=28  Identities=29%  Similarity=0.761  Sum_probs=25.7

Q ss_pred             CCccccccceeecCceeEecCcccccccc
Q 040947          103 QDKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       103 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      ..+|.+|+++|+ +.++.++|+.||+.||
T Consensus         8 lEkC~~C~~~I~-driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           8 LEKCATCSQPIL-DRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCBCTTTCCBCC-SCCEEETTEEECTTTC
T ss_pred             HHHHHHhchHHH-HHHHHHhCCCCCCCCC
Confidence            479999999997 7778999999999998

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LASP-1
domain: LASP-1
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=98.49  E-value=1.6e-08  Score=52.89  Aligned_cols=28  Identities=50%  Similarity=0.986  Sum_probs=27.0

Q ss_pred             CccccccceeecCceeEecCcccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      +.|++|++.++|.|.+..+++.||+.||
T Consensus         3 ~~CaRC~k~VYp~Ekl~ClDk~WHK~CF   30 (30)
T d1zfoa_           3 PNCARCGKIVYPTEKVNCLDKFWHKACF   30 (30)
T ss_dssp             CBCSSSCSBCCGGGCCCSSSSCCCGGGC
T ss_pred             CcccccCCccccHHHhhhhHHHHhhccC
Confidence            6899999999999999999999999998

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.47  E-value=3.9e-08  Score=54.64  Aligned_cols=32  Identities=34%  Similarity=0.704  Sum_probs=29.8

Q ss_pred             CCCCCCcccCCcceecceeEeeCCccccCCCc
Q 040947            4 TGTLDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         4 ~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      .+...+|..|++.|+..|.+.++|+.||..||
T Consensus         4 ~p~~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           4 APARETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SSSSCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CCCCcccccCCCEEeeeeeEecCCeehhhccC
Confidence            35678999999999999999999999999998

>d2co8a2 g.39.1.3 (A:8-43) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=98.47  E-value=2.7e-08  Score=55.52  Aligned_cols=32  Identities=41%  Similarity=1.020  Sum_probs=29.5

Q ss_pred             CCCCCccccccceeecCceeEecCcccccccc
Q 040947          100 SGTQDKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       100 ~g~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      .|+..+|..|++.|++.|.+.+.|+.||+.||
T Consensus         5 ~g~~~~C~~C~K~VY~~Erl~a~g~~yHk~CF   36 (36)
T d2co8a2           5 AGAGDLCALCGEHLYVLERLCVNGHFFHRSCF   36 (36)
T ss_dssp             CCSSCBCSSSCCBCCTTTBCCBTTBCCBTTTC
T ss_pred             CCCCCcccccCCEEeeeeEEEecCcEeccccC
Confidence            45568999999999999999999999999998

>d2d8ya1 g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.43  E-value=6e-08  Score=53.85  Aligned_cols=29  Identities=41%  Similarity=1.082  Sum_probs=27.8

Q ss_pred             CCccccccceeecCceeEecCcccccccc
Q 040947          103 QDKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       103 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      .++|..|++.|++.|.+.+.|+.||+.||
T Consensus         7 ~~kC~~C~K~VY~~E~~~a~g~~~Hk~CF   35 (35)
T d2d8ya1           7 RETCVECQKTVYPMERLLANQQVFHISCF   35 (35)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSSEEETTTC
T ss_pred             CcccccCCCEEeeeeeEecCCeehhhccC
Confidence            37999999999999999999999999998

>d2cu8a1 g.39.1.3 (A:8-37) Cysteine-rich (intestinal) protein, CRP, CRIP {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.42  E-value=4.7e-08  Score=51.73  Aligned_cols=29  Identities=45%  Similarity=0.864  Sum_probs=27.2

Q ss_pred             CCCcccCCcceecceeEeeCCccccCCCc
Q 040947            7 LDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         7 ~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      ++.|++|+++||..|.+..+|+.||+.|+
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            47899999999999999999999999996

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=98.39  E-value=8.5e-08  Score=49.84  Aligned_cols=30  Identities=37%  Similarity=0.806  Sum_probs=28.4

Q ss_pred             cccCCCCCcCCCCCeeecCCeeecHhHHHh
Q 040947          131 FRCAHGGCPLTHSSYAALDGVLYCKHHFAQ  160 (210)
Q Consensus       131 F~C~~C~~~l~~~~f~~~dg~~yC~~c~~~  160 (210)
                      |+|+.|++.|.+.....+||.+||+.||.+
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            899999999999999999999999999976

>d2dj7a1 g.39.1.3 (A:44-74) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.39  E-value=1e-07  Score=50.50  Aligned_cols=31  Identities=32%  Similarity=0.644  Sum_probs=28.2

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhhhc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~  163 (210)
                      +|..|++.|.++ |..+||.|||+.+|.++|+
T Consensus         1 kC~~C~~vL~gE-Ym~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVILTGE-YISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBCSSC-CEEETTEEECTTHHHHHTT
T ss_pred             CccccCccccce-eecCCCCcccHHHHHHhcC
Confidence            589999999874 9999999999999999986

>d1zfoa_ g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LASP-1
domain: LASP-1
species: Pig (Sus scrofa) [TaxId: 9823]

Probab=98.36  E-value=4e-08  Score=51.33  Aligned_cols=29  Identities=31%  Similarity=0.675  Sum_probs=27.4

Q ss_pred             CCCcccCCcceecceeEeeCCccccCCCc
Q 040947            7 LDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         7 ~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      .+.|++|++.|++.|.|.-+++.||..||
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

>d2d8za2 g.39.1.3 (A:33-64) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.35  E-value=1e-07  Score=51.23  Aligned_cols=32  Identities=25%  Similarity=0.645  Sum_probs=29.8

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      .|..|.++|.++.|..+|++|||-.||..+|+
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            48899999999999999999999999999874

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

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

Probab=98.34  E-value=2e-07  Score=50.07  Aligned_cols=34  Identities=32%  Similarity=0.641  Sum_probs=32.1

Q ss_pred             cccCCCCCcCCCCCeeecCCeeecHhHHHhhhcC
Q 040947          131 FRCAHGGCPLTHSSYAALDGVLYCKHHFAQLFME  164 (210)
Q Consensus       131 F~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~~  164 (210)
                      |+|+.|.+++-+...+++.|..||+.+|.++|+.
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            7899999999998999999999999999999974

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.34  E-value=2.1e-07  Score=50.21  Aligned_cols=32  Identities=22%  Similarity=0.430  Sum_probs=29.2

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhhhc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~  163 (210)
                      +|..|.+++.++.|++.||+|||+.||.++-|
T Consensus         1 VC~~C~~PF~~~~Fy~~~g~PyCe~HyH~~~G   32 (32)
T d1x3ha2           1 VCGDCFTSFSTGSFFELDGRPFCELHYHHRRG   32 (32)
T ss_dssp             BCSSSCCBSCSSCCEESSSCEECHHHHHHHHS
T ss_pred             CcCccCCcCCCCCeEeECCccchHHhhhhhcC
Confidence            58999999999999999999999999998643

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

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

Probab=98.32  E-value=1.2e-07  Score=59.65  Aligned_cols=36  Identities=22%  Similarity=0.528  Sum_probs=33.8

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHhhhccCC
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGN   71 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~   71 (210)
                      .|..|++.|++....++++++||+.||.++|+|+|.
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG~   36 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGK   36 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCcc
Confidence            388999999999999999999999999999999874

>d1ibia2 g.39.1.3 (A:145-175) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=98.28  E-value=1e-07  Score=49.50  Aligned_cols=30  Identities=27%  Similarity=0.812  Sum_probs=28.4

Q ss_pred             cccccccCCCCCCCeeccCCeeeccchHHH
Q 040947           35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFEQ   64 (210)
Q Consensus        35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~   64 (210)
                      |+|+.|++.|.+.....+||++||+.||.+
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            899999999999999999999999999975

>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=98.28  E-value=2e-07  Score=49.87  Aligned_cols=35  Identities=43%  Similarity=0.822  Sum_probs=33.4

Q ss_pred             CCCCCCCCCcccCCcceecceeEeeCCccccCCCc
Q 040947            1 MAFTGTLDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      |+-.|+..+|..|.+.|+..|-|.-.|+.||..||
T Consensus         1 mpn~ggg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           1 MPNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCCCCCCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CCccCCCceeccccceEeeeeeeeecCcccccccC
Confidence            78889999999999999999999999999999998

>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=98.25  E-value=2.9e-07  Score=49.14  Aligned_cols=32  Identities=34%  Similarity=0.776  Sum_probs=29.2

Q ss_pred             ccccccCCCCCCCeeccCCeeecc-chHHHhhh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCK-PHFEQLFK   67 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~-~cy~~~~~   67 (210)
                      +|..|++.|..+...+++|++||. +||..+|+
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            689999999999999999999995 69998874

>d2dj7a1 g.39.1.3 (A:44-74) Actin-binding LIM protein 3, abLIM-3 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.24  E-value=3.3e-07  Score=48.50  Aligned_cols=31  Identities=39%  Similarity=0.793  Sum_probs=28.2

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      +|..|++.|.+ .|..+||.|||+.||+..|+
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            68999999987 78899999999999999874

>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=98.24  E-value=1.6e-07  Score=49.91  Aligned_cols=26  Identities=23%  Similarity=0.429  Sum_probs=23.9

Q ss_pred             CccccccceeecCceeEecCccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTC  130 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~C  130 (210)
                      ++|+.|++||. ++.|+++|+.||+++
T Consensus         6 p~C~~C~~PI~-~~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           6 PICGACRRPIE-GRVVNAMGKQWHVEH   31 (31)
T ss_dssp             CEETTTTEECC-SCEECCTTSBEETTT
T ss_pred             cchhhcCCchh-hhHhhhhccccCCCC
Confidence            89999999998 788999999999874

>d2cuqa1 g.39.1.3 (A:43-74) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.23  E-value=2.9e-07  Score=48.76  Aligned_cols=32  Identities=31%  Similarity=0.670  Sum_probs=30.0

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      .|+.|+++|.++.|..+|..+||..||.++|+
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            48999999999999999999999999999874

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.21  E-value=2.2e-07  Score=52.90  Aligned_cols=26  Identities=27%  Similarity=0.698  Sum_probs=24.7

Q ss_pred             CccccccceeecCceeEecCccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTC  130 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~C  130 (210)
                      .+|..|++.|. ++.|.+.+++||+.|
T Consensus        16 ~~C~~C~~~It-G~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          16 TRCFSCDQFIE-GEVVSALGKTYHPDC   41 (41)
T ss_dssp             CBCTTTCCBCC-SCCEEETTEEECTTT
T ss_pred             cccccccCEee-eeeeEecCcccCCCC
Confidence            79999999997 999999999999987

>d1x3ha2 g.39.1.3 (A:43-74) Leupaxin {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=98.21  E-value=3.4e-07  Score=49.37  Aligned_cols=31  Identities=19%  Similarity=0.603  Sum_probs=28.7

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHhh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQLF   66 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~   66 (210)
                      .|..|.+++.+..|++++|+|||+.+|+++.
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            4899999999999999999999999999874

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

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

Probab=98.20  E-value=2.8e-07  Score=51.67  Aligned_cols=30  Identities=37%  Similarity=0.762  Sum_probs=27.3

Q ss_pred             CCCCcccCCcceeccee-EeeCCccccCCCc
Q 040947            6 TLDKCKACDKTVYVVDM-LSLEGMPYHKSCF   35 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~-v~~~g~~~H~~CF   35 (210)
                      .+++|..|+++|.++.. |++.|+.||..||
T Consensus         7 ~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           7 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             cCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            46899999999998764 9999999999998

>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=98.18  E-value=2.5e-07  Score=49.12  Aligned_cols=28  Identities=18%  Similarity=0.417  Sum_probs=25.4

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCC
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSC   34 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~C   34 (210)
                      +.++|+.|.+||. +..|.|+|+.||++.
T Consensus         4 g~p~C~~C~~PI~-~~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           4 GVPICGACRRPIE-GRVVNAMGKQWHVEH   31 (31)
T ss_dssp             CCCEETTTTEECC-SCEECCTTSBEETTT
T ss_pred             CCcchhhcCCchh-hhHhhhhccccCCCC
Confidence            5689999999998 789999999999974

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

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

Probab=98.17  E-value=4.7e-07  Score=49.23  Aligned_cols=31  Identities=23%  Similarity=0.454  Sum_probs=28.6

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCc
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      .+...|+.|++.|..+..+.|+++.||.+||
T Consensus         6 ~g~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           6 RGPSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             cCCccccccchhhhCCceeeeeecceeeeeC
Confidence            4567899999999988999999999999998

>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=98.14  E-value=7.3e-07  Score=47.53  Aligned_cols=32  Identities=31%  Similarity=0.561  Sum_probs=29.1

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHh-HHHhhhc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKH-HFAQLFM  163 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~-c~~~~f~  163 (210)
                      +|..|++.|..+...+.||+|||.. ||..+|+
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            6899999999989999999999954 9999986

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

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

Probab=98.13  E-value=7.6e-07  Score=48.37  Aligned_cols=28  Identities=21%  Similarity=0.592  Sum_probs=26.7

Q ss_pred             CccccccceeecCceeEecCcccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      ..|+.|++.|..++.+.++++.||.+||
T Consensus         9 ~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           9 SHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             SCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             ccccccchhhhCCceeeeeecceeeeeC
Confidence            6899999999989899999999999998

>d1j2oa1 g.39.1.3 (A:1-30) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=98.09  E-value=1.1e-06  Score=46.46  Aligned_cols=30  Identities=23%  Similarity=0.512  Sum_probs=26.4

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCC
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSC   34 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~C   34 (210)
                      |....|+.|+++|.+..++.++++.||..|
T Consensus         1 G~~~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           1 GSLLTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             CCCBCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             CCCcccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            456789999999986677999999999987

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

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

Probab=98.08  E-value=1.7e-06  Score=46.01  Aligned_cols=32  Identities=16%  Similarity=0.362  Sum_probs=29.7

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhhhc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~  163 (210)
                      .|..|+.+|....|..+++..||..||+++|+
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            37889999999999999999999999999986

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

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

Probab=98.07  E-value=1.6e-06  Score=46.00  Aligned_cols=32  Identities=25%  Similarity=0.636  Sum_probs=29.3

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhhhc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~  163 (210)
                      .|+.|+++|....|++..|++||+.||++.|+
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            38899999998899999999999999999875

>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=98.04  E-value=2.1e-06  Score=45.57  Aligned_cols=31  Identities=26%  Similarity=0.542  Sum_probs=29.3

Q ss_pred             cCCCCCcCCCCCeeecCCeeecHhHHHhhhc
Q 040947          133 CAHGGCPLTHSSYAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       133 C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~  163 (210)
                      |..|..+|....|..+++..||..||+++|+
T Consensus         2 C~~C~qPIGtkSFip~~~~~yCvpCYE~kfA   32 (32)
T d1wyha1           2 CSGCEQPLGSRSFVPDKGAHYCVPCYENKFA   32 (32)
T ss_dssp             CTTTCCBTTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             cccccCcccccccccCCCcEEEEeccccccC
Confidence            7889999999999999999999999999986

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

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

Probab=98.03  E-value=1.2e-06  Score=46.92  Aligned_cols=33  Identities=30%  Similarity=0.787  Sum_probs=31.5

Q ss_pred             cccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      |.|+.|.+++-+...+++.|..||+.+|.++|+
T Consensus         1 FvCA~CekPF~G~rhyE~~g~ayCe~Hy~qLfg   33 (35)
T d1u5sb2           1 FVCAKCEKPFLGHRHYERKGLAYCETHYNQLFG   33 (35)
T ss_dssp             CBCTTTCCBCSSSCCEEETTEEECHHHHHHHCS
T ss_pred             CcccccCCccCCchhhhhcCchHHHHHHHHHhc
Confidence            789999999999999999999999999999986

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

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

Probab=98.01  E-value=1.5e-06  Score=46.18  Aligned_cols=32  Identities=34%  Similarity=0.911  Sum_probs=29.4

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      .|+.|+.+|....|.+..|.+||+.||++.|+
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            38899999999999999999999999998763

>d1x4ka2 g.39.1.3 (A:8-34) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.97  E-value=1.4e-06  Score=44.11  Aligned_cols=26  Identities=38%  Similarity=1.023  Sum_probs=23.7

Q ss_pred             cccccceeecCce-eEecCcccccccc
Q 040947          106 CAACEKTVYPLEK-VTMEGDCFHKTCF  131 (210)
Q Consensus       106 C~~C~~~I~~~e~-v~~~g~~~H~~CF  131 (210)
                      |..|.+.|.|+.+ +++.|..||..||
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            7789999999765 8999999999998

>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=97.94  E-value=2.2e-06  Score=45.39  Aligned_cols=29  Identities=17%  Similarity=0.426  Sum_probs=25.6

Q ss_pred             CCCcccCCcceecceeEeeCCccccCCCc
Q 040947            7 LDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         7 ~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      ...|++|+++|.+.-++.++++.||..|+
T Consensus         2 ~~~CaGC~~~I~DRflL~v~dr~WH~~CL   30 (30)
T d1rutx1           2 WKRCAGCGGKIADRFLLYAMDSYWHSRCL   30 (30)
T ss_dssp             CCBBTTTCCBCCCSEEEEETTEEECGGGC
T ss_pred             ccccCCCCCccchhhhhccchhhhhhhhC
Confidence            35799999999966779999999999985

>d1a7ia2 g.39.1.3 (A:36-67) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.92  E-value=1.8e-06  Score=45.34  Aligned_cols=31  Identities=23%  Similarity=0.589  Sum_probs=28.6

Q ss_pred             cccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           37 CSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        37 C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      |-.|++.|++....++++++||+.||.+.|+
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            7889999999999999999999999998763

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.92  E-value=1.7e-06  Score=44.19  Aligned_cols=27  Identities=44%  Similarity=0.935  Sum_probs=25.3

Q ss_pred             CccccccceeecCceeEecCccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTC  130 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~C  130 (210)
                      .+|++|++.++.+|.|.-.|+.||+.|
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            589999999999999999999999987

>d1a7ia2 g.39.1.3 (A:36-67) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.89  E-value=3.1e-06  Score=44.46  Aligned_cols=31  Identities=23%  Similarity=0.433  Sum_probs=28.7

Q ss_pred             cCCCCCcCCCCCeeecCCeeecHhHHHhhhc
Q 040947          133 CAHGGCPLTHSSYAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       133 C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~  163 (210)
                      |-.|++.|++......++.+||+.||.++|+
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            6789999999999999999999999999885

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

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

Probab=97.86  E-value=1.9e-06  Score=43.45  Aligned_cols=26  Identities=38%  Similarity=0.966  Sum_probs=23.6

Q ss_pred             cccccceeecCce-eEecCcccccccc
Q 040947          106 CAACEKTVYPLEK-VTMEGDCFHKTCF  131 (210)
Q Consensus       106 C~~C~~~I~~~e~-v~~~g~~~H~~CF  131 (210)
                      |..|.+.|.|+.+ +++.|..||..||
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            7789999999765 8999999999998

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.85  E-value=2.7e-06  Score=43.47  Aligned_cols=27  Identities=37%  Similarity=0.954  Sum_probs=25.3

Q ss_pred             CCcccCCcceecceeEeeCCccccCCC
Q 040947            8 DKCKACDKTVYVVDMLSLEGMPYHKSC   34 (210)
Q Consensus         8 ~~C~~C~~~I~~~~~v~~~g~~~H~~C   34 (210)
                      .+|.+|++.|+..|.|.-.|+.||+.|
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            579999999999999999999999987

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

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

Probab=97.83  E-value=4.8e-06  Score=44.22  Aligned_cols=32  Identities=19%  Similarity=0.563  Sum_probs=29.5

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      .|..|.++|+..+|..+++..||..||++.|+
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            37899999999999999999999999999874

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

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

Probab=97.83  E-value=3.1e-06  Score=42.66  Aligned_cols=26  Identities=38%  Similarity=0.836  Sum_probs=23.8

Q ss_pred             cccCCcceecce-eEeeCCccccCCCc
Q 040947           10 CKACDKTVYVVD-MLSLEGMPYHKSCF   35 (210)
Q Consensus        10 C~~C~~~I~~~~-~v~~~g~~~H~~CF   35 (210)
                      |..|.+.|+++. .++..|..||..||
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            788999999986 49999999999998

>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=97.83  E-value=4.4e-06  Score=44.05  Aligned_cols=28  Identities=14%  Similarity=0.402  Sum_probs=24.0

Q ss_pred             CCccccccceeecCceeEecCccccccc
Q 040947          103 QDKCAACEKTVYPLEKVTMEGDCFHKTC  130 (210)
Q Consensus       103 ~~~C~~C~~~I~~~e~v~~~g~~~H~~C  130 (210)
                      ...|+.|+++|...-.+.++++.||..|
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            3689999999985555899999999987

>d1x4ka2 g.39.1.3 (A:8-34) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.82  E-value=3.4e-06  Score=42.63  Aligned_cols=26  Identities=31%  Similarity=0.874  Sum_probs=23.9

Q ss_pred             cccCCcceecce-eEeeCCccccCCCc
Q 040947           10 CKACDKTVYVVD-MLSLEGMPYHKSCF   35 (210)
Q Consensus        10 C~~C~~~I~~~~-~v~~~g~~~H~~CF   35 (210)
                      |..|.+.|+++. .++..|..||..||
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            788999999986 49999999999998

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=97.75  E-value=5.9e-06  Score=43.98  Aligned_cols=28  Identities=32%  Similarity=0.818  Sum_probs=25.6

Q ss_pred             CccccccceeecCcee-EecCcccccccc
Q 040947          104 DKCAACEKTVYPLEKV-TMEGDCFHKTCF  131 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v-~~~g~~~H~~CF  131 (210)
                      ..|++|++.|.+.|.| .+.+..||..||
T Consensus         3 g~Ca~C~~~I~~~e~VmRA~~~VyHl~CF   31 (31)
T d1rutx3           3 GACSACGQSIPASELVMRAQGNVYHLKCF   31 (31)
T ss_dssp             EECTTTCCEECTTSEEEEETTEEECGGGC
T ss_pred             cccccccCcCChhHhheecccceeeeccC
Confidence            4799999999998984 899999999998

>d1wyha1 g.39.1.3 (A:35-66) Four and a half LIM domains 3, FHL3 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.74  E-value=7.7e-06  Score=43.34  Aligned_cols=32  Identities=31%  Similarity=0.694  Sum_probs=29.4

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      .|..|.++|+..+|..+++..||..||+..|+
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            37889999999999999999999999999874

>d2dloa2 g.39.1.3 (A:43-75) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.73  E-value=1.3e-05  Score=43.03  Aligned_cols=32  Identities=16%  Similarity=0.281  Sum_probs=28.7

Q ss_pred             ccCCCCCcCCCCCeeec-CCeeecHhHHHhhhc
Q 040947          132 RCAHGGCPLTHSSYAAL-DGVLYCKHHFAQLFM  163 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~-dg~~yC~~c~~~~f~  163 (210)
                      .|..|++.|++..|.+. ++++||..+|.++|+
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            48889999999999876 699999999999986

>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=97.71  E-value=7.7e-06  Score=44.42  Aligned_cols=29  Identities=24%  Similarity=0.675  Sum_probs=25.4

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCc
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      .+++|..|+++|. ..-|...++.||++||
T Consensus         7 fa~~C~~Ckk~It-~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           7 FAPRCARCSKTLT-QGGVTYRDQPWHRECL   35 (35)
T ss_dssp             SSCCCTTTCCCCC-SCCEESSSSEECTTTC
T ss_pred             HHHHHhhcCCccc-cCceeecCCcchhhhC
Confidence            4689999999998 4458899999999998

>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=97.71  E-value=8.9e-06  Score=42.98  Aligned_cols=28  Identities=18%  Similarity=0.472  Sum_probs=24.3

Q ss_pred             CccccccceeecCceeEecCcccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      ..|++|+++|.+.-.+.++++.||..|+
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            5899999999855558999999999985

>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=97.69  E-value=7.1e-06  Score=42.37  Aligned_cols=26  Identities=27%  Similarity=0.760  Sum_probs=22.4

Q ss_pred             cccccceeec---CceeEecCcccccccc
Q 040947          106 CAACEKTVYP---LEKVTMEGDCFHKTCF  131 (210)
Q Consensus       106 C~~C~~~I~~---~e~v~~~g~~~H~~CF  131 (210)
                      |+.|.+||+.   +..|.+.++.||.+||
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            7899999985   2358999999999998

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=97.62  E-value=9.4e-06  Score=43.17  Aligned_cols=29  Identities=28%  Similarity=0.768  Sum_probs=26.0

Q ss_pred             CCCcccCCcceeccee-EeeCCccccCCCc
Q 040947            7 LDKCKACDKTVYVVDM-LSLEGMPYHKSCF   35 (210)
Q Consensus         7 ~~~C~~C~~~I~~~~~-v~~~g~~~H~~CF   35 (210)
                      +..|++|++.|...|. +.|.+..||..||
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            4579999999998886 6999999999998

>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=97.62  E-value=1.1e-05  Score=41.61  Aligned_cols=26  Identities=27%  Similarity=0.769  Sum_probs=22.8

Q ss_pred             cccCCcceec---ceeEeeCCccccCCCc
Q 040947           10 CKACDKTVYV---VDMLSLEGMPYHKSCF   35 (210)
Q Consensus        10 C~~C~~~I~~---~~~v~~~g~~~H~~CF   35 (210)
                      |+.|.+||..   ..+|...++.||..||
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            8899999974   2479999999999998

>d1x61a2 g.39.1.3 (A:35-66) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.62  E-value=1.6e-05  Score=41.52  Aligned_cols=30  Identities=20%  Similarity=0.556  Sum_probs=27.4

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQL   65 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~   65 (210)
                      .|..|+..|.++.|+..+++.||++||...
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi~t   30 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYVAT   30 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceeeee
Confidence            378999999999999999999999999754

>d1a7ia1 g.39.1.3 (A:8-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.61  E-value=1.2e-05  Score=40.60  Aligned_cols=28  Identities=39%  Similarity=1.022  Sum_probs=26.3

Q ss_pred             CCcccCCcceecceeEeeCCccccCCCc
Q 040947            8 DKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         8 ~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      .+|+.|.+.|+..+-|.-+|+.||+.||
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

>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=97.58  E-value=2.5e-05  Score=41.84  Aligned_cols=30  Identities=20%  Similarity=0.496  Sum_probs=27.5

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCc
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      ...|.|.+|+..|. +.+|.+.++.+|++||
T Consensus         6 qklp~CdkCg~GIV-G~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           6 QKLPMCDKCGTGIV-GVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCCCSSSCCCCC-SSCEECSSCEECTTTT
T ss_pred             ccCccccccCCCcE-eEEEEeccccCCCCCC
Confidence            35799999999998 8899999999999998

>d1b8ta1 g.39.1.3 (A:1-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Chicken (Gallus gallus) [TaxId: 9031]}

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

Probab=97.58  E-value=1.6e-05  Score=42.27  Aligned_cols=30  Identities=50%  Similarity=1.012  Sum_probs=27.6

Q ss_pred             CCCccccccceeecCceeEecCcccccccc
Q 040947          102 TQDKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       102 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      +..+|..|.+.++.+|-|...|+.||+.||
T Consensus         6 gg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           6 GGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CCceeccccceEeeeeeeeecCcccccccC
Confidence            346999999999999999999999999998

>d2cura1 g.39.1.3 (A:33-63) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.57  E-value=1.8e-05  Score=41.25  Aligned_cols=29  Identities=17%  Similarity=0.614  Sum_probs=27.1

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHH
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQ   64 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~   64 (210)
                      .|..|.+.|.+..|..+++++||-+||..
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            48899999999999999999999999975

>d2cura1 g.39.1.3 (A:33-63) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.54  E-value=3.7e-05  Score=40.03  Aligned_cols=29  Identities=17%  Similarity=0.470  Sum_probs=27.0

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHh
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQ  160 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~  160 (210)
                      +|..|.++|.+.+|...+++.||-.||..
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            48899999999999999999999999975

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

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

Probab=97.50  E-value=1.9e-05  Score=40.61  Aligned_cols=26  Identities=27%  Similarity=0.737  Sum_probs=22.1

Q ss_pred             cccccceeec---CceeEecCcccccccc
Q 040947          106 CAACEKTVYP---LEKVTMEGDCFHKTCF  131 (210)
Q Consensus       106 C~~C~~~I~~---~e~v~~~g~~~H~~CF  131 (210)
                      |..|.+||..   ...|.+.++.||.+||
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            7889999985   2358999999999998

>d2dloa2 g.39.1.3 (A:43-75) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.47  E-value=3.2e-05  Score=41.50  Aligned_cols=32  Identities=19%  Similarity=0.424  Sum_probs=28.5

Q ss_pred             ccccccCCCCCCCeec-cCCeeeccchHHHhhh
Q 040947           36 KCSHCKGTLVMSNYSS-MDGVLYCKPHFEQLFK   67 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~-~~g~~yC~~cy~~~~~   67 (210)
                      +|..|++.|++..|.+ .++++||-.+|+++|+
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 4889999999999874

>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=97.45  E-value=4.2e-05  Score=43.61  Aligned_cols=29  Identities=17%  Similarity=0.472  Sum_probs=27.1

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCCc
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      ..+.|.+|+-.|. +.+|.+.++.+|++||
T Consensus        17 kLP~CdkCg~GIV-G~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          17 RMPLCDKCGSGIV-GAVVKARDKYRHPECF   45 (45)
T ss_dssp             SCCBCTTTCCBCC-SCCEESSSCEECTTTC
T ss_pred             cCccccccCCCcE-EEEEEeccccCCCCCC
Confidence            4689999999998 8899999999999998

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

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

Probab=97.39  E-value=2.7e-05  Score=40.04  Aligned_cols=26  Identities=27%  Similarity=0.790  Sum_probs=22.7

Q ss_pred             cccCCcceec---ceeEeeCCccccCCCc
Q 040947           10 CKACDKTVYV---VDMLSLEGMPYHKSCF   35 (210)
Q Consensus        10 C~~C~~~I~~---~~~v~~~g~~~H~~CF   35 (210)
                      |..|.+||..   ..+|...++.||.+||
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            7899999974   2479999999999998

>d1a7ia1 g.39.1.3 (A:8-35) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=97.28  E-value=6e-05  Score=37.98  Aligned_cols=27  Identities=52%  Similarity=1.141  Sum_probs=25.6

Q ss_pred             ccccccceeecCceeEecCcccccccc
Q 040947          105 KCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       105 ~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      +|..|.+.++-+|-|...|+.||+.||
T Consensus         2 kcg~c~ktvy~aeevqc~grsfhk~cf   28 (28)
T d1a7ia1           2 KCGACGRTVYHAEEVQCDGRSFHRCCF   28 (28)
T ss_dssp             BCSSSCCBCSSTTEEEETTEEEESSSE
T ss_pred             ccccccceEeeeeeeeecCceeccccC
Confidence            699999999999999999999999998

>d1v6ga1 g.39.1.3 (A:1-41) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.25  E-value=5.5e-05  Score=42.73  Aligned_cols=27  Identities=30%  Similarity=0.679  Sum_probs=25.1

Q ss_pred             CCCcccCCcceecceeEeeCCccccCCC
Q 040947            7 LDKCKACDKTVYVVDMLSLEGMPYHKSC   34 (210)
Q Consensus         7 ~~~C~~C~~~I~~~~~v~~~g~~~H~~C   34 (210)
                      ..+|..|++-|. +++|.|.++.||+.|
T Consensus        15 G~~C~~C~~~It-G~V~~Ag~~~yHP~C   41 (41)
T d1v6ga1          15 GTRCFSCDQFIE-GEVVSALGKTYHPDC   41 (41)
T ss_dssp             CCBCTTTCCBCC-SCCEEETTEEECTTT
T ss_pred             CcccccccCEee-eeeeEecCcccCCCC
Confidence            468999999996 999999999999998

>d2cupa3 g.39.1.3 (A:8-34) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.22  E-value=6.9e-05  Score=37.52  Aligned_cols=26  Identities=35%  Similarity=0.770  Sum_probs=21.5

Q ss_pred             cccccceeecCce-eEecCcccccccc
Q 040947          106 CAACEKTVYPLEK-VTMEGDCFHKTCF  131 (210)
Q Consensus       106 C~~C~~~I~~~e~-v~~~g~~~H~~CF  131 (210)
                      |.-|.+||-.+.. +...++.||..||
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            6789999974333 7899999999998

>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=97.21  E-value=6.9e-05  Score=40.06  Aligned_cols=27  Identities=19%  Similarity=0.429  Sum_probs=25.3

Q ss_pred             CccccccceeecCceeEecCcccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      |.|.+|+..|. +-.|.+.++.+|++||
T Consensus         9 p~CdkCg~GIV-G~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           9 PMCDKCGTGIV-GVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCSSSCCCCC-SSCEECSSCEECTTTT
T ss_pred             ccccccCCCcE-eEEEEeccccCCCCCC
Confidence            89999999998 7789999999999998

>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=97.15  E-value=0.00014  Score=37.51  Aligned_cols=32  Identities=25%  Similarity=0.553  Sum_probs=29.4

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      +|+.|.+.++.+.|+.+...+||-.|++..|+
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtche~kfa   32 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA   32 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcchhhhhcccccccCCCCcEEEEEeeccccC
Confidence            58999999999999999999999999998773

>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=97.14  E-value=0.00025  Score=40.31  Aligned_cols=28  Identities=21%  Similarity=0.436  Sum_probs=25.8

Q ss_pred             CCccccccceeecCceeEecCcccccccc
Q 040947          103 QDKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       103 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      .+.|.+|+..|. +-.|.+.++.+|++||
T Consensus        18 LP~CdkCg~GIV-G~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          18 MPLCDKCGSGIV-GAVVKARDKYRHPECF   45 (45)
T ss_dssp             CCBCTTTCCBCC-SCCEESSSCEECTTTC
T ss_pred             CccccccCCCcE-EEEEEeccccCCCCCC
Confidence            389999999998 7789999999999998

>d1x61a2 g.39.1.3 (A:35-66) Thyroid receptor interacting protein 6, TRIP6 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.12  E-value=0.00026  Score=36.87  Aligned_cols=30  Identities=17%  Similarity=0.413  Sum_probs=27.2

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhh
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQL  161 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~  161 (210)
                      .|..|+..|.+..|+..+.+.||+.||...
T Consensus         1 vC~tC~~kLRGqpFYAvekkayCE~CYi~t   30 (32)
T d1x61a2           1 VCSTCRAQLRGQHFYAVERRAYCEGCYVAT   30 (32)
T ss_dssp             BCSSSCCBCTTSCEEESSSCEEEHHHHHHH
T ss_pred             CeeEeCceecCCcceEeeccccccceeeee
Confidence            488999999999999999999999999753

>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=97.09  E-value=0.00031  Score=36.12  Aligned_cols=32  Identities=16%  Similarity=0.312  Sum_probs=29.3

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhhhc
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~f~  163 (210)
                      .|+.|+..|..+.|+.+....||..|.+.+|+
T Consensus         1 tcs~ckq~igsgsffpkg~d~ycvtche~kfa   32 (32)
T d1x63a2           1 TCSNCKQVIGTGSFFPKGEDFYCVTCHETKFA   32 (32)
T ss_dssp             CCSSSCCCCTTSCEEEETTEEEEHHHHHHHTS
T ss_pred             CcchhhhhcccccccCCCCcEEEEEeeccccC
Confidence            48899999999999999999999999999885

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

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

Probab=97.03  E-value=0.00014  Score=37.84  Aligned_cols=29  Identities=28%  Similarity=0.578  Sum_probs=26.1

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCC
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSC   34 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~C   34 (210)
                      +++.-|..|.+-|. +.++++.++.||+.|
T Consensus         3 sgssgC~~C~~~It-GkVLEAG~khYHP~C   31 (32)
T d1wiga1           3 SGSSGCDSCEKYIT-GRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCCSCSSSCCCCS-SCCBCCSSCCBCTTT
T ss_pred             Cccchhhhhhhhhh-hhhhhccccccCCCC
Confidence            45677999999997 899999999999988

>d2cupa3 g.39.1.3 (A:8-34) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=97.03  E-value=0.00013  Score=36.47  Aligned_cols=26  Identities=23%  Similarity=0.608  Sum_probs=22.0

Q ss_pred             cccCCcceecce-eEeeCCccccCCCc
Q 040947           10 CKACDKTVYVVD-MLSLEGMPYHKSCF   35 (210)
Q Consensus        10 C~~C~~~I~~~~-~v~~~g~~~H~~CF   35 (210)
                      |..|.+||..+. -|...++.||..||
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            788999997443 48999999999998

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.95  E-value=7.2e-05  Score=39.96  Aligned_cols=26  Identities=15%  Similarity=0.313  Sum_probs=23.3

Q ss_pred             CccccccceeecCceeEecCccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTC  130 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~C  130 (210)
                      ..|..|.+.|+ +-.|.+.+.+||++|
T Consensus         9 e~C~~C~~~it-GpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           9 EFCHGCSLLMT-GPFMVAGEFKYHPEC   34 (34)
T ss_dssp             CBCTTTCCBCC-SCCBCCTTCCBCTTS
T ss_pred             HHhhhhHhhcc-cceeeecccccCCCC
Confidence            78999999887 777889999999998

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.84  E-value=0.00061  Score=35.29  Aligned_cols=29  Identities=31%  Similarity=0.616  Sum_probs=26.0

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHh
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQ  160 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~  160 (210)
                      .|+.|+..|....+++.++++||+.|...
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            48999999998889999999999998764

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

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

Probab=96.77  E-value=0.0003  Score=36.51  Aligned_cols=26  Identities=23%  Similarity=0.586  Sum_probs=23.9

Q ss_pred             CccccccceeecCceeEecCccccccc
Q 040947          104 DKCAACEKTVYPLEKVTMEGDCFHKTC  130 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~v~~~g~~~H~~C  130 (210)
                      .-|..|.+.|. +..+++.+++||+.|
T Consensus         6 sgC~~C~~~It-GkVLEAG~khYHP~C   31 (32)
T d1wiga1           6 SGCDSCEKYIT-GRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CSCSSSCCCCS-SCCBCCSSCCBCTTT
T ss_pred             chhhhhhhhhh-hhhhhccccccCCCC
Confidence            57999999998 888999999999987

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=96.62  E-value=0.00068  Score=35.12  Aligned_cols=30  Identities=30%  Similarity=0.656  Sum_probs=26.3

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQL   65 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~   65 (210)
                      .|+.|+..|....++..++++||+.+...+
T Consensus         1 vC~dCg~NLKqrG~Ffv~~~lyCE~HAr~R   30 (31)
T d1x64a2           1 VCADCNLNLKQKGYFFVEGELYCETHARAR   30 (31)
T ss_dssp             CCSSSCCCTTTSCCEEETTEEECHHHHHHH
T ss_pred             CccccccChhhcceEEeccEEeehhhhhcc
Confidence            489999999999999999999999887643

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

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

Probab=96.54  E-value=0.00058  Score=33.54  Aligned_cols=26  Identities=23%  Similarity=0.489  Sum_probs=21.9

Q ss_pred             cccCCcceecce-eEeeCCccccCCCc
Q 040947           10 CKACDKTVYVVD-MLSLEGMPYHKSCF   35 (210)
Q Consensus        10 C~~C~~~I~~~~-~v~~~g~~~H~~CF   35 (210)
                      |..|++.+.... -+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            788999987443 48999999999998

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=96.47  E-value=0.00046  Score=36.69  Aligned_cols=32  Identities=28%  Similarity=0.678  Sum_probs=28.1

Q ss_pred             ccccccCCCC--CCCeeccCCeeeccchHHHhhh
Q 040947           36 KCSHCKGTLV--MSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        36 ~C~~C~~~L~--~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      +|.-|+..|.  +.+.|.+.|.++|+.+|.++|+
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            5888999997  5688899999999999999984

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

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

Probab=96.21  E-value=0.0007  Score=35.13  Aligned_cols=30  Identities=20%  Similarity=0.471  Sum_probs=26.0

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhh
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQL  161 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~  161 (210)
                      .|+.|+..|....++..++++||+.|...+
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr~r   30 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHARER   30 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhhhc
Confidence            489999999887888899999999987654

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.11  E-value=0.0018  Score=34.54  Aligned_cols=34  Identities=24%  Similarity=0.472  Sum_probs=28.7

Q ss_pred             CCCCCCCCCcccCCcceeccee-EeeCCccccCCC
Q 040947            1 MAFTGTLDKCKACDKTVYVVDM-LSLEGMPYHKSC   34 (210)
Q Consensus         1 ~~~~~~~~~C~~C~~~I~~~~~-v~~~g~~~H~~C   34 (210)
                      |+-+-....|.+|+....+.|. |...|..||..|
T Consensus         1 m~~sL~~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           1 MANALASATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCSCCCCCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             CchHHHHHHHHHHccCCCchHHhhcCCCccccccC
Confidence            5556677889999999988774 899999999987

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=96.10  E-value=0.0017  Score=34.36  Aligned_cols=32  Identities=22%  Similarity=0.549  Sum_probs=27.8

Q ss_pred             ccCCCCCcCC--CCCeeecCCeeecHhHHHhhhc
Q 040947          132 RCAHGGCPLT--HSSYAALDGVLYCKHHFAQLFM  163 (210)
Q Consensus       132 ~C~~C~~~l~--~~~f~~~dg~~yC~~c~~~~f~  163 (210)
                      +|+-|+..|.  +...+.+.|.++|+.+|.++|+
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            5788899986  6678889999999999999986

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

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

Probab=95.80  E-value=0.00077  Score=34.98  Aligned_cols=30  Identities=20%  Similarity=0.497  Sum_probs=25.9

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQL   65 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~   65 (210)
                      .|+.|+..|....++..++++||+.+...+
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr~r   30 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHARER   30 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhhhc
Confidence            489999999988888899999999887653

>d2cupa2 g.39.1.3 (A:35-65) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.78  E-value=0.0024  Score=32.84  Aligned_cols=28  Identities=18%  Similarity=0.533  Sum_probs=25.4

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHH
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFE   63 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~   63 (210)
                      +|..|-.+|....|..+|++++|..|..
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHHT
T ss_pred             CchhhccccccCcccccCCeEeeccccc
Confidence            5889999999999999999999998864

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

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

Probab=95.77  E-value=0.0022  Score=31.41  Aligned_cols=26  Identities=31%  Similarity=0.621  Sum_probs=20.7

Q ss_pred             cccccceeecC-ceeEecCcccccccc
Q 040947          106 CAACEKTVYPL-EKVTMEGDCFHKTCF  131 (210)
Q Consensus       106 C~~C~~~I~~~-e~v~~~g~~~H~~CF  131 (210)
                      |..|++.+... ..|.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            66788877643 348999999999998

>d2cupa2 g.39.1.3 (A:35-65) Four and a half LIM domains protein 1, FHL-1 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.75  E-value=0.0044  Score=31.83  Aligned_cols=28  Identities=29%  Similarity=0.576  Sum_probs=25.3

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHH
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFA  159 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~  159 (210)
                      +|+.|-.+|..+.|..+|++++|..|-.
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~s   28 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCTT   28 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHHT
T ss_pred             CchhhccccccCcccccCCeEeeccccc
Confidence            5888999999999999999999998864

>d1g47a1 g.39.1.3 (A:1-35) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.65  E-value=0.0024  Score=34.00  Aligned_cols=27  Identities=33%  Similarity=0.831  Sum_probs=24.1

Q ss_pred             CccccccceeecCce-eEecCccccccc
Q 040947          104 DKCAACEKTVYPLEK-VTMEGDCFHKTC  130 (210)
Q Consensus       104 ~~C~~C~~~I~~~e~-v~~~g~~~H~~C  130 (210)
                      ..|.+|+....|.|. |...|..||..|
T Consensus         8 ~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           8 ATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHccCCCchHHhhcCCCccccccC
Confidence            589999999998876 689999999987

>d2cora1 g.39.1.3 (A:43-73) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.54  E-value=0.0059  Score=31.32  Aligned_cols=29  Identities=34%  Similarity=0.598  Sum_probs=23.9

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhh
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQL  161 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~  161 (210)
                      .|+.|++.|... -.+..|.+||..|..++
T Consensus         1 nC~~Cgkeltad-ArEl~geLyCLpChdKm   29 (31)
T d2cora1           1 NCANCGKELTAD-ARELKGELYCLPCHDKM   29 (31)
T ss_dssp             BCSSSCCBCCTT-CEEETTEEECHHHHHTT
T ss_pred             Cccccccccchh-HHHhcCCEEEEeccccc
Confidence            388999999875 56778999999998864

>d2cora1 g.39.1.3 (A:43-73) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.43  E-value=0.0038  Score=32.06  Aligned_cols=29  Identities=28%  Similarity=0.799  Sum_probs=23.9

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQL   65 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~   65 (210)
                      .|+.|++.|.. .-.+..|.+||.+|+.+.
T Consensus         1 nC~~Cgkelta-dArEl~geLyCLpChdKm   29 (31)
T d2cora1           1 NCANCGKELTA-DARELKGELYCLPCHDKM   29 (31)
T ss_dssp             BCSSSCCBCCT-TCEEETTEEECHHHHHTT
T ss_pred             Cccccccccch-hHHHhcCCEEEEeccccc
Confidence            38899999987 456789999999998753

>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=95.09  E-value=0.013  Score=30.90  Aligned_cols=31  Identities=23%  Similarity=0.549  Sum_probs=25.5

Q ss_pred             cccCCCCCcCC-CCCeeecC-CeeecHhHHHhh
Q 040947          131 FRCAHGGCPLT-HSSYAALD-GVLYCKHHFAQL  161 (210)
Q Consensus       131 F~C~~C~~~l~-~~~f~~~d-g~~yC~~c~~~~  161 (210)
                      |.|..|+.-|. ++.|.+.+ .++||-.||.+.
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy~~~   33 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCHNEV   33 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecchhcc
Confidence            77999999886 66787765 899999999874

>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=94.87  E-value=0.0081  Score=31.15  Aligned_cols=27  Identities=30%  Similarity=0.800  Sum_probs=22.0

Q ss_pred             ccccccCCCCCC-CeeccCCeeeccchH
Q 040947           36 KCSHCKGTLVMS-NYSSMDGVLYCKPHF   62 (210)
Q Consensus        36 ~C~~C~~~L~~~-~f~~~~g~~yC~~cy   62 (210)
                      +|+.|...|.++ .|...+|.+||+.+.
T Consensus         1 tC~tC~n~LVPGDRFHyvNG~lfCE~D~   28 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYINGSLFCEHDR   28 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEETTEEEEGGGC
T ss_pred             CcccccccccCCceeEEecCEEEEecCC
Confidence            488898888754 788899999999764

>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=94.72  E-value=0.0088  Score=31.62  Aligned_cols=28  Identities=18%  Similarity=0.432  Sum_probs=24.3

Q ss_pred             CCCCcccCCcceecceeEeeCCccccCCC
Q 040947            6 TLDKCKACDKTVYVVDMLSLEGMPYHKSC   34 (210)
Q Consensus         6 ~~~~C~~C~~~I~~~~~v~~~g~~~H~~C   34 (210)
                      ....|..|...|. +-++.|.+..||++|
T Consensus         7 fge~C~~C~~~it-GpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           7 FGEFCHGCSLLMT-GPFMVAGEFKYHPEC   34 (34)
T ss_dssp             SSCBCTTTCCBCC-SCCBCCTTCCBCTTS
T ss_pred             HHHHhhhhHhhcc-cceeeecccccCCCC
Confidence            3578999999776 888899999999998

>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=94.70  E-value=0.011  Score=30.68  Aligned_cols=27  Identities=22%  Similarity=0.581  Sum_probs=22.2

Q ss_pred             ccCCCCCcCC-CCCeeecCCeeecHhHH
Q 040947          132 RCAHGGCPLT-HSSYAALDGVLYCKHHF  158 (210)
Q Consensus       132 ~C~~C~~~l~-~~~f~~~dg~~yC~~c~  158 (210)
                      .|+.|..+|- +.+|...+|.+||+.+-
T Consensus         1 tC~tC~n~LVPGDRFHyvNG~lfCE~D~   28 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYINGSLFCEHDR   28 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEETTEEEEGGGC
T ss_pred             CcccccccccCCceeEEecCEEEEecCC
Confidence            4888888885 77899999999998753

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.60  E-value=0.0057  Score=33.72  Aligned_cols=28  Identities=18%  Similarity=0.422  Sum_probs=19.7

Q ss_pred             ccccccceeecCceeE-ecCccccccccc
Q 040947          105 KCAACEKTVYPLEKVT-MEGDCFHKTCFR  132 (210)
Q Consensus       105 ~C~~C~~~I~~~e~v~-~~g~~~H~~CF~  132 (210)
                      .|++|++....+|-|. -.+..||+.|-.
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            4888888887666554 455689988743

>d2d8xa1 g.39.1.3 (A:33-64) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.42  E-value=0.014  Score=30.20  Aligned_cols=30  Identities=20%  Similarity=0.546  Sum_probs=27.2

Q ss_pred             ccccccCCCCCCCeeccCCeeeccchHHHh
Q 040947           36 KCSHCKGTLVMSNYSSMDGVLYCKPHFEQL   65 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~   65 (210)
                      +|..|...|.+..|....|+.+|.+|..+.
T Consensus         1 rC~~C~~~LAD~GFvKnagR~LCrpch~re   30 (32)
T d2d8xa1           1 RCDLCQEVLADIGFVKNAGRHLCRPCHNRE   30 (32)
T ss_dssp             BCSSSCCBCSSSCCEEETTEEECHHHHHHH
T ss_pred             CchHHHhHHHHhhhhhcccccccchhhhhc
Confidence            589999999999999999999999998753

>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=93.30  E-value=0.061  Score=27.65  Aligned_cols=30  Identities=17%  Similarity=0.269  Sum_probs=26.4

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHHHhh
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHFAQL  161 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~~~~  161 (210)
                      +|..|...|....|...-|+.+|+.|..+.
T Consensus         1 rC~~C~~~LAD~GFvKnagR~LCrpch~re   30 (32)
T d2d8xa1           1 RCDLCQEVLADIGFVKNAGRHLCRPCHNRE   30 (32)
T ss_dssp             BCSSSCCBCSSSCCEEETTEEECHHHHHHH
T ss_pred             CchHHHhHHHHhhhhhcccccccchhhhhc
Confidence            589999999988899989999999998753

>d1wiga2 g.39.1.3 (A:33-73) Actin-binding LIM protein 2, abLIM2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=93.02  E-value=0.01  Score=32.64  Aligned_cols=28  Identities=14%  Similarity=0.336  Sum_probs=19.7

Q ss_pred             CcccCCcceecceeE-eeCCccccCCCcc
Q 040947            9 KCKACDKTVYVVDML-SLEGMPYHKSCFK   36 (210)
Q Consensus         9 ~C~~C~~~I~~~~~v-~~~g~~~H~~CF~   36 (210)
                      .|.+|++....+|-+ .-.+..||+.|-.
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            488898888777654 4445679988743

>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=92.85  E-value=0.039  Score=28.97  Aligned_cols=31  Identities=26%  Similarity=0.637  Sum_probs=25.0

Q ss_pred             cccccccCCCCCC-Ceecc-CCeeeccchHHHh
Q 040947           35 FKCSHCKGTLVMS-NYSSM-DGVLYCKPHFEQL   65 (210)
Q Consensus        35 F~C~~C~~~L~~~-~f~~~-~g~~yC~~cy~~~   65 (210)
                      |.|..|+.-+.++ +|..+ ..++||-.||.+.
T Consensus         1 F~C~~C~~fIgdgdsyaLVerskLYCG~Cy~~~   33 (34)
T d1x6aa2           1 FACMSCKVIIEDGDAYALVQHATLYCGKCHNEV   33 (34)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHH
T ss_pred             CcccccccEEecCceEEEEeeceeeeecchhcc
Confidence            7899999999865 66644 6689999999864

>d1j2oa2 g.39.1.3 (A:31-63) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=92.75  E-value=0.038  Score=28.51  Aligned_cols=31  Identities=19%  Similarity=0.367  Sum_probs=25.1

Q ss_pred             cccccccCCCCC--CCeeccCCeeeccchHHHh
Q 040947           35 FKCSHCKGTLVM--SNYSSMDGVLYCKPHFEQL   65 (210)
Q Consensus        35 F~C~~C~~~L~~--~~f~~~~g~~yC~~cy~~~   65 (210)
                      ++|.-|+..|+.  ...|.+.+.++|+.+|.++
T Consensus         1 LkC~cC~cRLGEVG~tlytk~nliLCkrDYlRl   33 (33)
T d1j2oa2           1 LSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL   33 (33)
T ss_dssp             CCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHH
T ss_pred             CccccccccccchhhHHHhhcceeeehhhhhcC
Confidence            468888888884  4677889999999999763

>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=91.08  E-value=0.067  Score=28.27  Aligned_cols=28  Identities=18%  Similarity=0.468  Sum_probs=23.5

Q ss_pred             CCccccccceeecCceeEecCcccccccc
Q 040947          103 QDKCAACEKTVYPLEKVTMEGDCFHKTCF  131 (210)
Q Consensus       103 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  131 (210)
                      .-.|..|...|. .+-+.+.+..||+..|
T Consensus         8 k~vC~KCh~iId-d~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           8 KYICQKCHAIID-EQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCBCTTTCCBCC-SCCCCCSSSCCCTTTS
T ss_pred             hHHHHHHHhhhh-cCcceecCCCCCCCCC
Confidence            368999998885 5668999999999876

>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=90.48  E-value=0.1  Score=34.33  Aligned_cols=33  Identities=15%  Similarity=0.343  Sum_probs=24.6

Q ss_pred             cccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      |+|..|...+........=|..||..|..+.+.
T Consensus        23 l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~   55 (97)
T d1jm7b_          23 LRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG   55 (97)
T ss_dssp             TSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT
T ss_pred             CCCccCCchhhcCceeCCCCCchhHHHHHHHHh
Confidence            688888888876433335689999999877664

>d2baya1 g.44.1.2 (A:1-56) Pre-mRNA splicing factor Prp19 {Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: Pre-mRNA splicing factor Prp19
species: Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]

Probab=90.39  E-value=0.11  Score=30.71  Aligned_cols=52  Identities=15%  Similarity=0.139  Sum_probs=37.8

Q ss_pred             cccccccCCCCCCCeeccCCeeeccchHHHhhhccCCCCCCccCCCCCCCCCCCCCCCCCcccccCCCCCccccccceee
Q 040947           35 FKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFKESGNFSKNFQTGKNPSSCSNQNRTPSKLSSLFSGTQDKCAACEKTVY  114 (210)
Q Consensus        35 F~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~C~~C~~~I~  114 (210)
                      +.|..|...+.+.......|..||..|..+-+..+                                  ..|..|++++.
T Consensus         1 l~C~Ic~~~~~~Pv~~~~cGh~fc~~cI~~~l~~~----------------------------------~~CP~c~~~l~   46 (56)
T d2baya1           1 MLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVKDT----------------------------------GNDPITNEPLS   46 (56)
T ss_dssp             CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHHHH----------------------------------SBCTTTCCBCC
T ss_pred             CCCccCCchHHhcCccCCCCCcccHHHHHHHHhhc----------------------------------cCCCccCCcCC
Confidence            35788888777633334689999999998877632                                  47999999987


Q ss_pred             cCceeE
Q 040947          115 PLEKVT  120 (210)
Q Consensus       115 ~~e~v~  120 (210)
                      ..+.+.
T Consensus        47 ~~dLip   52 (56)
T d2baya1          47 IEEIVE   52 (56)
T ss_dssp             GGGCEE
T ss_pred             HHhcee
Confidence            655554

>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=89.52  E-value=0.11  Score=27.44  Aligned_cols=30  Identities=23%  Similarity=0.420  Sum_probs=24.4

Q ss_pred             CCCCCcccCCcceecceeEeeCCccccCCCc
Q 040947            5 GTLDKCKACDKTVYVVDMLSLEGMPYHKSCF   35 (210)
Q Consensus         5 ~~~~~C~~C~~~I~~~~~v~~~g~~~H~~CF   35 (210)
                      .+--+|.+|...|. .+-+...+..||+..|
T Consensus         6 lGk~vC~KCh~iId-d~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           6 LGKYICQKCHAIID-EQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCBCTTTCCBCC-SCCCCCSSSCCCTTTS
T ss_pred             hhhHHHHHHHhhhh-cCcceecCCCCCCCCC
Confidence            34568999999985 5568899999999877

>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=88.91  E-value=0.19  Score=27.06  Aligned_cols=29  Identities=17%  Similarity=0.219  Sum_probs=18.2

Q ss_pred             cccCCCCCcCC-CCCeeecCCeeecHhHHH
Q 040947          131 FRCAHGGCPLT-HSSYAALDGVLYCKHHFA  159 (210)
Q Consensus       131 F~C~~C~~~l~-~~~f~~~dg~~yC~~c~~  159 (210)
                      |+|+.|.+++. +++.........|..|-.
T Consensus         1 FvC~vCr~pFP~GDRVTFnGKeC~CQ~Cs~   30 (40)
T d1v6ga2           1 FVCAVCRLPFPPGDRVTFNGKECMCQKCSL   30 (40)
T ss_dssp             SSCSSSCCCCCSSSCEEEETTEEEEHHHHS
T ss_pred             CcccccCCCCCCCCeEEEcCceeehhhcCC
Confidence            56777777776 444555555667777654

>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=88.22  E-value=0.15  Score=26.15  Aligned_cols=26  Identities=19%  Similarity=0.554  Sum_probs=23.0

Q ss_pred             cccccCCCCCCCeeccCCeeeccchH
Q 040947           37 CSHCKGTLVMSNYSSMDGVLYCKPHF   62 (210)
Q Consensus        37 C~~C~~~L~~~~f~~~~g~~yC~~cy   62 (210)
                      |..|+-.|.+..|......++|.+|-
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            67888899999999999999999874

>d2c2la2 g.44.1.2 (A:225-304) STIP1 homology and U box-containing protein 1, STUB1 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: STIP1 homology and U box-containing protein 1, STUB1
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.63  E-value=0.31  Score=30.57  Aligned_cols=35  Identities=9%  Similarity=0.089  Sum_probs=28.8

Q ss_pred             CCCcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           32 KSCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        32 ~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      ++-|.|..|...+... ....-|..||..|..+.+.
T Consensus         5 P~~l~CpIc~~l~~dP-v~~~cGhtfc~~ci~~~l~   39 (80)
T d2c2la2           5 PDYLCGKISFELMREP-CITPSGITYDRKDIEEHLQ   39 (80)
T ss_dssp             CSTTBCTTTCSBCSSE-EECSSCCEEETTHHHHHHH
T ss_pred             CccccCcCcCchhhhh-cccCCcCeecHHHHHHHHh
Confidence            5679999999988873 4567899999999988765

>d1j2oa2 g.39.1.3 (A:31-63) Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Rhombotin-2 (Lmo2)
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=87.56  E-value=0.31  Score=24.93  Aligned_cols=30  Identities=23%  Similarity=0.468  Sum_probs=23.9

Q ss_pred             ccCCCCCcCC--CCCeeecCCeeecHhHHHhh
Q 040947          132 RCAHGGCPLT--HSSYAALDGVLYCKHHFAQL  161 (210)
Q Consensus       132 ~C~~C~~~l~--~~~f~~~dg~~yC~~c~~~~  161 (210)
                      +|.-|++.|.  +...+.+.+.++|+.+|.++
T Consensus         2 kC~cC~cRLGEVG~tlytk~nliLCkrDYlRl   33 (33)
T d1j2oa2           2 SCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRL   33 (33)
T ss_dssp             CCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHH
T ss_pred             ccccccccccchhhHHHhhcceeeehhhhhcC
Confidence            5777888886  55677788999999999753

>d2co8a1 g.39.1.3 (A:44-76) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=86.65  E-value=0.12  Score=26.67  Aligned_cols=28  Identities=32%  Similarity=0.653  Sum_probs=20.9

Q ss_pred             ccCCCCCcCCCCCee--ecCCeeecHhHHH
Q 040947          132 RCAHGGCPLTHSSYA--ALDGVLYCKHHFA  159 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~--~~dg~~yC~~c~~  159 (210)
                      +|..|...|..+.|.  ..||..||..++.
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hlp   30 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHLP   30 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTCC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeeccC
Confidence            477788888766664  4589999987754

>d2co8a1 g.39.1.3 (A:44-76) Nedd9 interacting protein with calponin homology, NICAL (MICAL1) {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Nedd9 interacting protein with calponin homology, NICAL (MICAL1)
species: Human (Homo sapiens) [TaxId: 9606]

Probab=84.56  E-value=0.27  Score=25.28  Aligned_cols=27  Identities=37%  Similarity=0.893  Sum_probs=21.6

Q ss_pred             ccccccCCCCCCCeecc--CCeeeccchH
Q 040947           36 KCSHCKGTLVMSNYSSM--DGVLYCKPHF   62 (210)
Q Consensus        36 ~C~~C~~~L~~~~f~~~--~g~~yC~~cy   62 (210)
                      +|..|...|..+.|..+  ||.+||..+.
T Consensus         1 rC~~CeatL~pG~Y~qhp~dghfyc~~hl   29 (33)
T d2co8a1           1 RCHTCEATLWPGGYEQHPGDGHFYCLQHL   29 (33)
T ss_dssp             BCSSSCCBCCTTSEECCTTTCCCEETTTC
T ss_pred             CceeeeeEEccCcccCCCCCceEeeeecc
Confidence            57889999998877754  8899998654

>d1t1ha_ g.44.1.2 (A:) E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsis thaliana) [TaxId: 3702]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: U-box
domain: E3 ubiquitin ligase PUB14
species: Thale-cress (Arabidopsis thaliana) [TaxId: 3702]

Probab=84.03  E-value=0.67  Score=28.70  Aligned_cols=34  Identities=12%  Similarity=0.254  Sum_probs=27.7

Q ss_pred             CCcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           33 SCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        33 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      +=|.|..|...+... .....|..||..|..+.+.
T Consensus         7 ~~l~CpIc~~~m~dP-V~~~cgh~fc~~ci~~~~~   40 (78)
T d1t1ha_           7 EYFRCPISLELMKDP-VIVSTGQTYERSSIQKWLD   40 (78)
T ss_dssp             SSSSCTTTSCCCSSE-EEETTTEEEEHHHHHHHHT
T ss_pred             ccCCCcCcCchhhCc-eEccCCCcchHHHHHHHHH
Confidence            458999999988773 4557999999999988765

>d1rmda2 g.44.1.1 (A:1-86) V(D)J recombination activating protein 1 (RAG1), dimerization domain {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: V(D)J recombination activating protein 1 (RAG1), dimerization domain
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=83.39  E-value=0.45  Score=30.55  Aligned_cols=34  Identities=18%  Similarity=0.368  Sum_probs=26.9

Q ss_pred             CCcccccccCCCCCCCeeccCCeeeccchHHHhhh
Q 040947           33 SCFKCSHCKGTLVMSNYSSMDGVLYCKPHFEQLFK   67 (210)
Q Consensus        33 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~   67 (210)
                      .-|.|..|...+.. .....=|..||..|..+.+.
T Consensus        22 ~~l~C~IC~~~~~~-pv~~~CgH~FC~~Ci~~~~~   55 (86)
T d1rmda2          22 KSISCQICEHILAD-PVETSCKHLFCRICILRCLK   55 (86)
T ss_dssp             HHTBCTTTCSBCSS-EEECTTSCEEEHHHHHHHHH
T ss_pred             cCcCCccCCcchhc-ceecCCCChhhHHHHHHHHh
Confidence            44889999888765 45567899999999988764

>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=81.17  E-value=0.52  Score=24.08  Aligned_cols=25  Identities=12%  Similarity=0.492  Sum_probs=20.3

Q ss_pred             cCCCCCcCCCCCeeecCCeeecHhH
Q 040947          133 CAHGGCPLTHSSYAALDGVLYCKHH  157 (210)
Q Consensus       133 C~~C~~~l~~~~f~~~dg~~yC~~c  157 (210)
                      |..|...|-+..|.-....++|..|
T Consensus         2 cgkcsvslvg~gfltq~~~i~c~~c   26 (34)
T d1x68a2           2 CGKCSVSLVGKGFLTQNKEIFCQKC   26 (34)
T ss_dssp             CTTTCCBCSSSCEEEETTEEEETTT
T ss_pred             CccceEEEEeeeeeeccCcEEehhc
Confidence            6677778888888888888999877

>d2gvia2 g.39.1.18 (A:169-201) Uncharacterized protein Ta1109 {Thermoplasma acidophilum [TaxId: 2303]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: FwdE C-terminal domain-like
domain: Uncharacterized protein Ta1109
species: Thermoplasma acidophilum [TaxId: 2303]

Probab=81.02  E-value=0.37  Score=24.23  Aligned_cols=27  Identities=26%  Similarity=0.423  Sum_probs=15.8

Q ss_pred             ccCCCCCcCCCCCeeecCCeeecHhHH
Q 040947          132 RCAHGGCPLTHSSYAALDGVLYCKHHF  158 (210)
Q Consensus       132 ~C~~C~~~l~~~~f~~~dg~~yC~~c~  158 (210)
                      +|..|+.---...-.+.+|+|.|+.+|
T Consensus         5 rcdvcgeytyeadakllngkpvckpdy   31 (33)
T d2gvia2           5 RCDVCGEYTYEADAKLLNGKPVCKPDY   31 (33)
T ss_dssp             ECTTTCCEEEGGGCEEETTEEECHHHH
T ss_pred             EEeeccceeeccchhhhCCCcccCccc
Confidence            455555422222334568899998877