Citrus Sinensis ID: 029230

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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-------
Protein Sequence
MASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKSQISEKPTPVQIAAES
Secondary Structure (PSIPRED)
cccccccccccccccccEEEEcEEEEEcccccccccccccccccccccccccccccEEEEccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccccEEEcccccccccccccccccccccccccccccccccHHHHHHHHccccccccccccccccccccccccccccccc
Secondary Structure Prediction (SSPRO)
cccccccccccccccccEEEEEEEEEEcccccccccEEEHcccccccccccccccccEEccccHHHHccccccccccccccccccccccccccccccccHHccccccccccccccEEEEcEEEEEcccccccccEEEHcccccccccccccccccEcccHHHHHHcccccccccccccccccccccccccccccccc
Coil and Loop (DISEMBL)
maspfggtqqkcmacdktvYLVDKLtadnrvyhkacfrchhckgtlklsnfnsfegvlycrphfdqLFKRTgsleksfegtpkivkpeklvenenaqkvsnkfvgtrdkcvgcdrtvyptekvsvngaayhrscfkcshggctispsnyiahegklYCKHHHIQlfrekgnysqLESDLeksqisekptpVQIAAES
Flexible Loop (DISEMBL)
maspfggtqqkcmacDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGsleksfegtpkivkpeklvenenaqkvsnkfvgtrdkcvgCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDleksqisekptpvqiaaes
Low Complexity Region (SEG)
MASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKSQISEKPTPVQIAAES
Disordered region (IsUnstruct)
**********KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTG***************************SNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFRE*****************************
Disordered Region (DISOPRED)
********QQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREK****************************
Disordered Region (DISEMBL)
*********QKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGN**************************
Disordered Region (DISPRO)
*********QKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKS******************************DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESD*******************
Transmembrane Helix (TMHMM)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (HMMTOP)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Transmembrane Helix (MEMSAT)
oooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooohhhhhhhhhhhhhhhhhhhhiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiiii
TM Helix, Signal Peptide (MEMSAT_SVM)
iiiiiiiiiiiiiiiiihhhhhhhhhhhhhhhhoooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
TM Helix, Signal Peptide (Phobius)
ooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooooo
Signal Peptide (SignalP HMM Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Signal Peptide (SignalP NN Mode)
xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx
Coiled Coils (COILS)
MASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKSQISEKPTPVQIAAES
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	197	2.2.26 [Sep-21-2011]
P29675	219	Pollen-specific protein S	N/A	no	0.934	0.840	0.700	6e-74
P50462	194	Cysteine and glycine-rich	yes	no	0.893	0.907	0.294	2e-18
P50461	194	Cysteine and glycine-rich	yes	no	0.893	0.907	0.294	2e-18
P50463	194	Cysteine and glycine-rich	yes	no	0.893	0.907	0.299	3e-18
Q16527	193	Cysteine and glycine-rich	no	no	0.908	0.927	0.284	9e-18
Q32LE9	193	Cysteine and glycine-rich	yes	no	0.908	0.927	0.284	9e-18
Q62908	193	Cysteine and glycine-rich	no	no	0.908	0.927	0.279	2e-17
P97314	193	Cysteine and glycine-rich	no	no	0.908	0.927	0.279	3e-17
Q05158	194	Cysteine and glycine-rich	N/A	no	0.908	0.922	0.288	6e-17
P50460	194	Cysteine and glycine-rich	yes	no	0.908	0.922	0.288	6e-17

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

 Score =  276 bits (706), Expect = 6e-74,   Method: Compositional matrix adjust.
 Identities = 131/187 (70%), Positives = 152/187 (81%), Gaps = 3/187 (1%)

Query: 5   FGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
           F GT QKC  C+KTVYLVDKL A+ RVYHKACFRCHHC  TLKLSNFNSF+GV+YCR HF
Sbjct: 4   FTGTTQKCTVCEKTVYLVDKLVANQRVYHKACFRCHHCNSTLKLSNFNSFDGVVYCRHHF 63

Query: 65  DQLFKRTGSLEKSFEGTPKIVKPEKLV--ENENAQKVSNKFVGTRDKCVGCDRTVYPTEK 122
           DQLFKRTGSLEKSF+GTPK  KPE+    E ++A ++S+ F GTRDKC  C + VYP E+
Sbjct: 64  DQLFKRTGSLEKSFDGTPKF-KPERTFSQETQSANRLSSFFEGTRDKCNACAKIVYPIER 122

Query: 123 VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKS 182
           V V+G AYHR+CFKC HGGCTISPSNYIAHEG+LYCKHHHIQLF++KGNYSQLE +   +
Sbjct: 123 VKVDGTAYHRACFKCCHGGCTISPSNYIAHEGRLYCKHHHIQLFKKKGNYSQLEVEETVA 182

Query: 183 QISEKPT 189
             +E  T
Sbjct: 183 APAESET 189

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 = 92.0 bits (227), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 58/197 (29%), Positives = 93/197 (47%), Gaps = 21/197 (10%)

Query: 4   PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
           P  G   KC AC+KTVY  +++  + R +HK CF C  C+  L  +   + E  +YC+  
Sbjct: 2   PNWGGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVC 61

Query: 64  FDQLFKRTG----------------SLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTR 107
           + + +   G                 L   F+ +PK   P +     N  K S KF G  
Sbjct: 62  YGRRYGPKGIGFGQGAGCLSTDTGEHLGLQFQQSPK---PARAATTSNPSKFSAKF-GES 117

Query: 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR 167
           +KC  C ++VY  EKV   G  +H++CF+C+  G ++  +N    +G+LYCK  + + F 
Sbjct: 118 EKCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFG 177

Query: 168 EKG-NYSQLESDLEKSQ 183
             G  +  L   +EK +
Sbjct: 178 PTGIGFGGLTQQVEKKE 194

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 = 92.0 bits (227), Expect = 2e-18,   Method: Compositional matrix adjust.
 Identities = 58/197 (29%), Positives = 94/197 (47%), Gaps = 21/197 (10%)

Query: 4   PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
           P  G   KC AC+KTVY  +++  + R +HK CF C  C+  L  +   + E  +YC+  
Sbjct: 2   PNWGGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVC 61

Query: 64  FDQLFKRTG----------------SLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTR 107
           + + +   G                 L   F+ +PK   P + V   N  K + KF G  
Sbjct: 62  YGRRYGPKGIGYGQGAGCLSTDTGEHLGLQFQQSPK---PARSVTTSNPSKFTAKF-GES 117

Query: 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR 167
           +KC  C ++VY  EKV   G  +H++CF+C+  G ++  +N    +G+LYCK  + + F 
Sbjct: 118 EKCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFG 177

Query: 168 EKG-NYSQLESDLEKSQ 183
             G  +  L   +EK +
Sbjct: 178 PTGIGFGGLTQQVEKKE 194

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 = 91.7 bits (226), Expect = 3e-18,   Method: Compositional matrix adjust.
 Identities = 59/197 (29%), Positives = 92/197 (46%), Gaps = 21/197 (10%)

Query: 4   PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
           P  G   KC ACDKTVY  +++  + R +HK CF C  C+  L  +   + E  +YC+  
Sbjct: 2   PNWGGGAKCGACDKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVC 61

Query: 64  FDQLFKRTG----------------SLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTR 107
           + + +   G                 L   F+ +P   KP +     N  K S KF G  
Sbjct: 62  YGRKYGPKGIGFGQGAGCLSTDTGEHLGLQFQQSP---KPARAATTSNPSKFSAKF-GES 117

Query: 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR 167
           +KC  C ++VY  EKV   G  +H++CF C+  G ++  +N    +G+LYCK  + + F 
Sbjct: 118 EKCPRCGKSVYAAEKVMGGGKPWHKTCFPCAICGKSLESTNVTDKDGELYCKVCYAKNFG 177

Query: 168 EKG-NYSQLESDLEKSQ 183
             G  +  L   +EK +
Sbjct: 178 PTGIGFGGLTHQVEKKE 194

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

 Score = 90.1 bits (222), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 55/193 (28%), Positives = 90/193 (46%), Gaps = 14/193 (7%)

Query: 4   PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
           P  G   KC AC +TVY  +++  D R +H+ CF C  C+  L  +     +  +YC+  
Sbjct: 2   PVWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDEEIYCKSC 61

Query: 64  FDQLFKRTGSLEKSFEGT------------PKIVKPEKLVENENAQKVSNKFVGTRDKCV 111
           + + +   G       GT            P+ V+P +   N N  K + K+ G  +KC 
Sbjct: 62  YGKKYGPKGYGYGQGAGTLNMDRGERLGIKPESVQPHRPTTNPNTSKFAQKYGGA-EKCS 120

Query: 112 GCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKG- 170
            C  +VY  EK+   G  +H++CF+C+  G ++  +     EG++YCK  + + F  KG 
Sbjct: 121 RCGDSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKGF 180

Query: 171 NYSQLESDLEKSQ 183
            Y Q    L  +Q
Sbjct: 181 GYGQGAGALVHAQ 193

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 = 90.1 bits (222), Expect = 9e-18,   Method: Compositional matrix adjust.
 Identities = 55/193 (28%), Positives = 90/193 (46%), Gaps = 14/193 (7%)

Query: 4   PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
           P  G   KC AC +TVY  +++  D R +H+ CF C  C+  L  +     +  +YC+  
Sbjct: 2   PVWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDEEIYCKSC 61

Query: 64  FDQLFKRTGSLEKSFEGT------------PKIVKPEKLVENENAQKVSNKFVGTRDKCV 111
           + + +   G       GT            P+ V+P +   N N  K + K+ G  +KC 
Sbjct: 62  YGKKYGPKGYGYGQGAGTLNMDRGERLGIKPESVQPHRPTTNPNTSKFAQKYGGA-EKCS 120

Query: 112 GCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKG- 170
            C  +VY  EK+   G  +H++CF+C+  G ++  +     EG++YCK  + + F  KG 
Sbjct: 121 RCGDSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKGF 180

Query: 171 NYSQLESDLEKSQ 183
            Y Q    L  +Q
Sbjct: 181 GYGQGAGALVHAQ 193

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 = 89.0 bits (219), Expect = 2e-17,   Method: Compositional matrix adjust.
 Identities = 54/193 (27%), Positives = 89/193 (46%), Gaps = 14/193 (7%)

Query: 4   PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
           P  G   KC AC +TVY  +++  D R +H+ CF C  C+  L  +     +  +YC+  
Sbjct: 2   PVWGGGNKCGACGRTVYHAEEVQCDGRTFHRCCFLCMVCRKNLDSTTVAIHDEEIYCKSC 61

Query: 64  FDQLFKRTGSLEKSFEGT------------PKIVKPEKLVENENAQKVSNKFVGTRDKCV 111
           + + +   G       GT            P+  +P +   N N  K + K+ G  +KC 
Sbjct: 62  YGKKYGPKGYGYGQGAGTLNMDRGERLGIKPESAQPHRPTTNPNTSKFAQKYGGA-EKCS 120

Query: 112 GCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKG- 170
            C  +VY  EK+   G  +H++CF+C+  G ++  +     EG++YCK  + + F  KG 
Sbjct: 121 RCGDSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKGF 180

Query: 171 NYSQLESDLEKSQ 183
            Y Q    L  +Q
Sbjct: 181 GYGQGAGALVHAQ 193

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

 Score = 88.6 bits (218), Expect = 3e-17,   Method: Compositional matrix adjust.
 Identities = 54/193 (27%), Positives = 89/193 (46%), Gaps = 14/193 (7%)

Query: 4   PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
           P  G   KC AC +TVY  +++  D R +H+ CF C  C+  L  +     +  +YC+  
Sbjct: 2   PVWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDEEIYCKSC 61

Query: 64  FDQLFKRTGSLEKSFEGT------------PKIVKPEKLVENENAQKVSNKFVGTRDKCV 111
           + + +   G       GT            P+  +P +   N N  K + K+ G  +KC 
Sbjct: 62  YGKKYGPKGYGYGQGAGTLNMDRGERLGIKPESAQPHRPTTNPNTSKFAQKYGGA-EKCS 120

Query: 112 GCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKG- 170
            C  +VY  EK+   G  +H++CF+C+  G ++  +     EG++YCK  + + F  KG 
Sbjct: 121 RCGDSVYAAEKIIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKGF 180

Query: 171 NYSQLESDLEKSQ 183
            Y Q    L  +Q
Sbjct: 181 GYGQGAGALVHAQ 193

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|Q05158|CSRP2_COTJA Cysteine and glycine-rich protein 2 OS=Coturnix coturnix japonica GN=CSRP2 PE=1 SV=2

 Score = 87.4 bits (215), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 56/194 (28%), Positives = 89/194 (45%), Gaps = 15/194 (7%)

Query: 4   PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
           P  G   KC AC +TVY  +++  D R +H+ CF C  C+  L  +     +  +YC+  
Sbjct: 2   PNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSC 61

Query: 64  FDQLFKRTGSLEKSFEGTPKIVKPEKL-------------VENENAQKVSNKFVGTRDKC 110
           + + +   G       GT  + + E+L               N N  K + KF G  +KC
Sbjct: 62  YGKKYGPKGYGYGQGAGTLNMDRGERLGIKPESSPSPHRPTTNPNTSKFAQKFGGA-EKC 120

Query: 111 VGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKG 170
             C  +VY  EKV   G  +H++CF+C+  G ++  +     EG++YCK  + + F  KG
Sbjct: 121 SRCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKG 180

Query: 171 -NYSQLESDLEKSQ 183
             Y Q    L  +Q
Sbjct: 181 FGYGQGAGALVHAQ 194

Interacts with zyxin. May be a component of a signal transduction pathway that mediates adhesion-stimulated changes in gene expression. Totally down-regulated in transformed cells.

Coturnix coturnix japonica (taxid: 93934)

>sp|P50460|CSRP2_CHICK Cysteine and glycine-rich protein 2 OS=Gallus gallus GN=CSRP2 PE=2 SV=3

 Score = 87.4 bits (215), Expect = 6e-17,   Method: Compositional matrix adjust.
 Identities = 56/194 (28%), Positives = 89/194 (45%), Gaps = 15/194 (7%)

Query: 4   PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
           P  G   KC AC +TVY  +++  D R +H+ CF C  C+  L  +     +  +YC+  
Sbjct: 2   PNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSC 61

Query: 64  FDQLFKRTGSLEKSFEGTPKIVKPEKL-------------VENENAQKVSNKFVGTRDKC 110
           + + +   G       GT  + + E+L               N N  K + KF G  +KC
Sbjct: 62  YGKKYGPKGYGYGQGAGTLNMDRGERLGIKPESTPSPHRPTTNPNTSKFAQKFGGA-EKC 120

Query: 111 VGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKG 170
             C  +VY  EKV   G  +H++CF+C+  G ++  +     EG++YCK  + + F  KG
Sbjct: 121 SRCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLESTTLTEKEGEIYCKGCYAKNFGPKG 180

Query: 171 -NYSQLESDLEKSQ 183
             Y Q    L  +Q
Sbjct: 181 FGYGQGAGALVHAQ 194

Totally down-regulated in transformed cells. May therefore take part in the control of cell growth and differentiation.

Gallus gallus (taxid: 9031)

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	197
224056260	196	predicted protein [Populus trichocarpa]	0.989	0.994	0.820	3e-93
118485459	196	unknown [Populus trichocarpa]	0.989	0.994	0.815	1e-92
117950163	196	LIM domain protein GLIM1b [Populus tremu	0.989	0.994	0.805	5e-92
118483314	195	unknown [Populus trichocarpa]	0.984	0.994	0.825	3e-91
117950161	195	LIM domain protein GLIM1a [Populus tremu	0.984	0.994	0.825	3e-91
224103769	195	predicted protein [Populus trichocarpa]	0.984	0.994	0.820	1e-90
255583325	196	Cysteine and glycine-rich protein, putat	0.994	1.0	0.802	1e-90
77556244	195	Pollen-specific protein SF3, putative, e	0.939	0.948	0.821	6e-88
225458850	197	PREDICTED: pollen-specific protein SF3 [	0.979	0.979	0.8	1e-87
225429013	194	PREDICTED: pollen-specific protein SF3 [	0.959	0.974	0.785	3e-87

>gi|224056260|ref|XP_002298780.1| predicted protein [Populus trichocarpa] gi|222846038|gb|EEE83585.1| predicted protein [Populus trichocarpa]

 Score =  346 bits (888), Expect = 3e-93,   Method: Compositional matrix adjust.
 Identities = 160/195 (82%), Positives = 180/195 (92%)

Query: 3   SPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRP 62
           + F GTQQKCMACDKTVYLVDKLTADNR+YHKACFRCHHC+GTLKLSN++SFEGVLYCRP
Sbjct: 2   AAFAGTQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCRGTLKLSNYSSFEGVLYCRP 61

Query: 63  HFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEK 122
           H+DQLFKRTGSL+KSFEGTPKIVKPEK V+NENA KVSN F GTR+KCVGC++TVYP EK
Sbjct: 62  HYDQLFKRTGSLDKSFEGTPKIVKPEKPVDNENASKVSNLFAGTREKCVGCNKTVYPIEK 121

Query: 123 VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKS 182
           V+VNG  YHRSCFKC+HGGCTISPSNYIAHEGKLYCKHHHIQLF+EKGNYSQLE++ EK+
Sbjct: 122 VTVNGTPYHRSCFKCTHGGCTISPSNYIAHEGKLYCKHHHIQLFKEKGNYSQLENEREKN 181

Query: 183 QISEKPTPVQIAAES 197
            ++   T V+IAAES
Sbjct: 182 PVTVSITAVEIAAES 196

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118485459|gb|ABK94586.1| unknown [Populus trichocarpa]

 Score =  344 bits (882), Expect = 1e-92,   Method: Compositional matrix adjust.
 Identities = 159/195 (81%), Positives = 179/195 (91%)

Query: 3   SPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRP 62
           + F GTQQKCMACDKTVYLVDKLTADNR+YHKACFRCHHC+GTLKLSN++SFEGVLYCRP
Sbjct: 2   AAFAGTQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCRGTLKLSNYSSFEGVLYCRP 61

Query: 63  HFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEK 122
           H+DQLFKRTGSL+KSFEGTPKIVKPEK V+NENA KVSN F GTR+KCVGC++TVYP EK
Sbjct: 62  HYDQLFKRTGSLDKSFEGTPKIVKPEKPVDNENASKVSNLFAGTREKCVGCNKTVYPIEK 121

Query: 123 VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKS 182
           V+VNG  YHRSCFKC+HGGCTISPSNYIAHEGKLYCKHHHIQLF+EKGNYSQLE++ EK+
Sbjct: 122 VTVNGTQYHRSCFKCTHGGCTISPSNYIAHEGKLYCKHHHIQLFKEKGNYSQLENEREKN 181

Query: 183 QISEKPTPVQIAAES 197
            ++   T V+IAA S
Sbjct: 182 PVTVNITAVEIAAGS 196

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|117950163|gb|ABK58465.1| LIM domain protein GLIM1b [Populus tremula x Populus alba]

 Score =  342 bits (877), Expect = 5e-92,   Method: Compositional matrix adjust.
 Identities = 157/195 (80%), Positives = 178/195 (91%)

Query: 3   SPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRP 62
           + F GTQQKCMACDKTVYLVDKLTADNR+YHKACFRCHHC+GTLKLSN++SFEGVLYCRP
Sbjct: 2   AAFAGTQQKCMACDKTVYLVDKLTADNRIYHKACFRCHHCRGTLKLSNYSSFEGVLYCRP 61

Query: 63  HFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEK 122
           H+DQLFKRTGSL+KSFEGTPKI KPEK V+NENA KVSN F GTR+KCVGC++TVYP EK
Sbjct: 62  HYDQLFKRTGSLDKSFEGTPKIAKPEKPVDNENASKVSNLFAGTREKCVGCNKTVYPIEK 121

Query: 123 VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKS 182
           V+VNG  YHR CFKC+HGGCT+SPSNYIAHEGKLYCKHHHIQLF+EKGNYSQLE++ EK+
Sbjct: 122 VTVNGTPYHRRCFKCTHGGCTVSPSNYIAHEGKLYCKHHHIQLFKEKGNYSQLENEREKN 181

Query: 183 QISEKPTPVQIAAES 197
            ++   T V+IAAES
Sbjct: 182 PVTVNITAVEIAAES 196

Source: Populus tremula x Populus alba

Species: Populus tremula x Populus alba

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|118483314|gb|ABK93559.1| unknown [Populus trichocarpa]

 Score =  340 bits (871), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 161/195 (82%), Positives = 178/195 (91%), Gaps = 1/195 (0%)

Query: 3   SPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRP 62
           + F GTQQKCMACDKTVYLVDKLTADNRV+HKACFRCHHC+GTLKLSN+ SFEGVLYCRP
Sbjct: 2   AAFAGTQQKCMACDKTVYLVDKLTADNRVFHKACFRCHHCRGTLKLSNYCSFEGVLYCRP 61

Query: 63  HFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEK 122
           H+DQLFKRTGSL+KSFEGTPKIVKPEK V+NENA KVSN F GTR+KCVGCD+TVYP EK
Sbjct: 62  HYDQLFKRTGSLDKSFEGTPKIVKPEKPVDNENASKVSNLFAGTREKCVGCDKTVYPIEK 121

Query: 123 VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKS 182
           V+VNG  YHRSCFKC+HGGCTISPSNYIAHEGKLYCKHHHIQLF+EKGNYSQLE++ EK+
Sbjct: 122 VTVNGTPYHRSCFKCTHGGCTISPSNYIAHEGKLYCKHHHIQLFKEKGNYSQLENEREKN 181

Query: 183 QISEKPTPVQIAAES 197
            +    T V+IAAES
Sbjct: 182 PVVS-ITAVEIAAES 195

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|117950161|gb|ABK58464.1| LIM domain protein GLIM1a [Populus tremula x Populus alba]

 Score =  339 bits (870), Expect = 3e-91,   Method: Compositional matrix adjust.
 Identities = 161/195 (82%), Positives = 178/195 (91%), Gaps = 1/195 (0%)

Query: 3   SPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRP 62
           + F GTQQKCMACDKTVYLVDKLTADNRV+HKACFRCHHC+GTLKLSN+ SFEGVLYCRP
Sbjct: 2   AAFSGTQQKCMACDKTVYLVDKLTADNRVFHKACFRCHHCRGTLKLSNYCSFEGVLYCRP 61

Query: 63  HFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEK 122
           H+DQLFKRTGSL+KSFEGTPKIVKPEK V+NENA KVSN F GTR+KCVGCD+TVYP EK
Sbjct: 62  HYDQLFKRTGSLDKSFEGTPKIVKPEKPVDNENASKVSNLFAGTREKCVGCDKTVYPIEK 121

Query: 123 VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKS 182
           V+VNG  YHRSCFKC+HGGCTISPSNYIAHEGKLYCKHHHIQLF+EKGNYSQLE++ EK+
Sbjct: 122 VTVNGTPYHRSCFKCTHGGCTISPSNYIAHEGKLYCKHHHIQLFKEKGNYSQLENEREKN 181

Query: 183 QISEKPTPVQIAAES 197
            +    T V+IAAES
Sbjct: 182 PVVS-ITAVEIAAES 195

Source: Populus tremula x Populus alba

Species: Populus tremula x Populus alba

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|224103769|ref|XP_002313186.1| predicted protein [Populus trichocarpa] gi|118487010|gb|ABK95336.1| unknown [Populus trichocarpa] gi|222849594|gb|EEE87141.1| predicted protein [Populus trichocarpa]

 Score =  338 bits (866), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 160/195 (82%), Positives = 178/195 (91%), Gaps = 1/195 (0%)

Query: 3   SPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRP 62
           + F GTQQKCMACDKTVYLVDKLTADNRV+HKACFRCHHC+GTLKLSN+ SFEGVLYCRP
Sbjct: 2   AAFAGTQQKCMACDKTVYLVDKLTADNRVFHKACFRCHHCRGTLKLSNYCSFEGVLYCRP 61

Query: 63  HFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEK 122
           H+DQLFKRTGSL+KSFEGTPKIVKPEK V+NENA KVSN F GTR+KCVGCD+TVYP EK
Sbjct: 62  HYDQLFKRTGSLDKSFEGTPKIVKPEKPVDNENASKVSNLFAGTREKCVGCDKTVYPIEK 121

Query: 123 VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKS 182
           V+VNG  YHRSCFKC+HGGCTISPSNYIAHEGKL+CKHHHIQLF+EKGNYSQLE++ EK+
Sbjct: 122 VTVNGTPYHRSCFKCTHGGCTISPSNYIAHEGKLHCKHHHIQLFKEKGNYSQLENEREKN 181

Query: 183 QISEKPTPVQIAAES 197
            +    T V+IAAES
Sbjct: 182 PVVS-ITAVEIAAES 195

Source: Populus trichocarpa

Species: Populus trichocarpa

Genus: Populus

Family: Salicaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|255583325|ref|XP_002532425.1| Cysteine and glycine-rich protein, putative [Ricinus communis] gi|223527874|gb|EEF29966.1| Cysteine and glycine-rich protein, putative [Ricinus communis]

 Score =  337 bits (865), Expect = 1e-90,   Method: Compositional matrix adjust.
 Identities = 158/197 (80%), Positives = 180/197 (91%), Gaps = 1/197 (0%)

Query: 1   MASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYC 60
           MA+ FGGTQQKCMACDKTVYLVDKLTADNRV+HKACFRCHHCKGTLKLSN+ SFEGVLYC
Sbjct: 1   MATTFGGTQQKCMACDKTVYLVDKLTADNRVFHKACFRCHHCKGTLKLSNYCSFEGVLYC 60

Query: 61  RPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPT 120
           RPH+DQLFK TGSL+KSFEGTPK+ KPEK +++ENA KVSNKF GTR+KCVGC +TVYP 
Sbjct: 61  RPHYDQLFKLTGSLDKSFEGTPKVAKPEKPIDSENASKVSNKFAGTREKCVGCSKTVYPI 120

Query: 121 EKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLE 180
           E+V+VNG  YHRSCFKC++GGCTISPSNYIAHEGKLYCKHHHIQLF+EKGNYSQLE++ +
Sbjct: 121 ERVTVNGTPYHRSCFKCTYGGCTISPSNYIAHEGKLYCKHHHIQLFKEKGNYSQLENERQ 180

Query: 181 KSQISEKPTPVQIAAES 197
            +  +EK T V+IAAES
Sbjct: 181 PA-TTEKITAVEIAAES 196

Source: Ricinus communis

Species: Ricinus communis

Genus: Ricinus

Family: Euphorbiaceae

Order: Malpighiales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|77556244|gb|ABA99040.1| Pollen-specific protein SF3, putative, expressed [Oryza sativa Japonica Group] gi|125579493|gb|EAZ20639.1| hypothetical protein OsJ_36255 [Oryza sativa Japonica Group]

 Score =  328 bits (841), Expect = 6e-88,   Method: Compositional matrix adjust.
 Identities = 152/185 (82%), Positives = 168/185 (90%)

Query: 1   MASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYC 60
           MA+ F GT  KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKL+N+NSFEGVLYC
Sbjct: 1   MATSFQGTTTKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLANYNSFEGVLYC 60

Query: 61  RPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPT 120
           RPHFDQLFKRTGSL+KSFEGTPK+VKPEK VENENA KVS+ F GTR+KCVGC++TVYP 
Sbjct: 61  RPHFDQLFKRTGSLDKSFEGTPKVVKPEKTVENENAIKVSSAFAGTREKCVGCNKTVYPI 120

Query: 121 EKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLE 180
           E+V+VN   YH+SCFKC HGGCTISPSNYIAHEGKLYCKHHHIQL +EKGN+SQLE+D E
Sbjct: 121 ERVTVNNTMYHKSCFKCCHGGCTISPSNYIAHEGKLYCKHHHIQLIKEKGNFSQLENDHE 180

Query: 181 KSQIS 185
           K+  S
Sbjct: 181 KASQS 185

Source: Oryza sativa Japonica Group

Species: Oryza sativa

Genus: Oryza

Family: Poaceae

Order: Poales

Class: Liliopsida

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225458850|ref|XP_002285355.1| PREDICTED: pollen-specific protein SF3 [Vitis vinifera] gi|147785329|emb|CAN72849.1| hypothetical protein VITISV_013939 [Vitis vinifera] gi|302142193|emb|CBI19396.3| unnamed protein product [Vitis vinifera]

 Score =  328 bits (840), Expect = 1e-87,   Method: Compositional matrix adjust.
 Identities = 156/195 (80%), Positives = 170/195 (87%), Gaps = 2/195 (1%)

Query: 5   FGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
           F GT QKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKL N+NSFEGVLYCRPHF
Sbjct: 3   FAGTTQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLGNYNSFEGVLYCRPHF 62

Query: 65  DQLFKRTGSLEKSFEGTPKIVKPEKLVENEN--AQKVSNKFVGTRDKCVGCDRTVYPTEK 122
           DQLFKRTGSL+KSFEGTPKIVKPEK +++E   A KVS+ F GTRDKCVGC  TVYPTEK
Sbjct: 63  DQLFKRTGSLDKSFEGTPKIVKPEKPIDSEKPIANKVSSMFAGTRDKCVGCKNTVYPTEK 122

Query: 123 VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKS 182
           V+VNG AYH+SCFKC+HGGCTISPSNYIAHEG+LYCKHHH QL +EKGN SQLE D EK 
Sbjct: 123 VTVNGTAYHKSCFKCTHGGCTISPSNYIAHEGRLYCKHHHTQLIKEKGNLSQLEGDHEKD 182

Query: 183 QISEKPTPVQIAAES 197
             +EK    ++AAES
Sbjct: 183 TANEKVNGREVAAES 197

Source: Vitis vinifera

Species: Vitis vinifera

Genus: Vitis

Family: Vitaceae

Order: Vitales

Phylum: Streptophyta

Superkingdom: Eukaryota

>gi|225429013|ref|XP_002266499.1| PREDICTED: pollen-specific protein SF3 [Vitis vinifera] gi|296083036|emb|CBI22440.3| unnamed protein product [Vitis vinifera]

 Score =  326 bits (835), Expect = 3e-87,   Method: Compositional matrix adjust.
 Identities = 154/196 (78%), Positives = 171/196 (87%), Gaps = 7/196 (3%)

Query: 5   FGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
           F GT QKCMAC+KTVYLVD+LTADNR+YHKACFRCHHC+GTLKL N+NSFEGVLYCRPHF
Sbjct: 3   FAGTTQKCMACEKTVYLVDRLTADNRIYHKACFRCHHCRGTLKLGNYNSFEGVLYCRPHF 62

Query: 65  DQLFKRTGSLEKSFEGTPKIVKPEKLV---ENENAQKVSNKFVGTRDKCVGCDRTVYPTE 121
           DQLFKRTGSL+KSFEGTPKIVKPEK     EN    KVSN FVGT+DKCVGC++T YP E
Sbjct: 63  DQLFKRTGSLDKSFEGTPKIVKPEKTTDHSENAATNKVSNMFVGTKDKCVGCNKTAYPLE 122

Query: 122 KVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEK 181
           KV+VNG  YH+SCFKC++GGCTISPSNYIAHEGKLYCKHHHIQLF+EKGNYSQLESD EK
Sbjct: 123 KVTVNGTPYHKSCFKCTYGGCTISPSNYIAHEGKLYCKHHHIQLFKEKGNYSQLESDNEK 182

Query: 182 SQISEKPTPVQIAAES 197
             +S     +Q+AAES
Sbjct: 183 DSVS----GIQVAAES 194

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	197
TAIR|locus:2012798	190	WLIM1 "AT1G10200" [Arabidopsis	0.903	0.936	0.822	5.8e-82
TAIR|locus:2061171	200	WLIM2a "WLIM2a" [Arabidopsis t	0.969	0.955	0.536	3.3e-56
TAIR|locus:2198210	205	PLIM2b "PLIM2b" [Arabidopsis t	0.847	0.814	0.514	1.1e-50
TAIR|locus:2050735	226	PLIM2a "PLIM2a" [Arabidopsis t	0.857	0.747	0.520	2e-49
TAIR|locus:2098871	213	PLIM2c "PLIM2c" [Arabidopsis t	0.873	0.807	0.497	1.8e-48
DICTYBASE|DDB_G0290575	472	DDB_G0290575 "LIM-type zinc fi	0.370	0.154	0.506	4.5e-32
RGD|71092	194	Csrp3 "cysteine and glycine-ri	0.893	0.907	0.324	3.9e-21
UNIPROTKB|P50463	194	Csrp3 "Cysteine and glycine-ri	0.893	0.907	0.324	3.9e-21
MGI|MGI:1330824	194	Csrp3 "cysteine and glycine-ri	0.893	0.907	0.319	3.9e-21
ZFIN|ZDB-GENE-030909-4	192	csrp1a "cysteine and glycine-r	0.903	0.927	0.305	4.9e-21

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

 Score = 822 (294.4 bits), Expect = 5.8e-82, P = 5.8e-82
 Identities = 148/180 (82%), Positives = 158/180 (87%)

Query:     5 FGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
             F GT QKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSN+NSFEGVLYCRPHF
Sbjct:     3 FAGTTQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNYNSFEGVLYCRPHF 62

Query:    65 DQLFKRTGSLEKSFEGTPKIVKPEKLVENEN--AQKVSNKFVGTRDKCVGCDRTVYPTEK 122
             DQ FKRTGSLEKSFEGTPKI KP++ +E E     KVSN F GTR+KCVGCD+TVYP EK
Sbjct:    63 DQNFKRTGSLEKSFEGTPKIGKPDRPLEGERPAGTKVSNMFGGTREKCVGCDKTVYPIEK 122

Query:   123 VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKS 182
             VSVNG  YH+SCFKC+HGGCTISPSNYIAHEGKLYCKHHHIQL +EKGN SQLE   E +
Sbjct:   123 VSVNGTLYHKSCFKCTHGGCTISPSNYIAHEGKLYCKHHHIQLIKEKGNLSQLEGGGENA 182

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

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

 Score = 579 (208.9 bits), Expect = 3.3e-56, P = 3.3e-56
 Identities = 104/194 (53%), Positives = 135/194 (69%)

Query:     5 FGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
             F GTQQKC AC+KTVY V+ L+AD   YHKACF+C HCK  L+LSN++S EGV+YCRPHF
Sbjct:     3 FTGTQQKCRACEKTVYPVELLSADGISYHKACFKCSHCKSRLQLSNYSSMEGVVYCRPHF 62

Query:    65 DQLFKRTGSLEKSFEGTPKIVKPEKLVE-NENAQKVSNKFVGTRDKCVGCDRTVYPTEKV 123
             +QLFK +GS  K+F+   K +  +   E N    +++  F GT+DKC  C +TVYP EKV
Sbjct:    63 EQLFKESGSFSKNFQSPAKPLTDKPTPELNRTPSRLAGMFSGTQDKCATCTKTVYPIEKV 122

Query:   124 SVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQL--ESDLEK 181
             +V    YH+SCFKCSHGGC ISPSNY A EG LYCKHH  QLF+EKG+Y+ L   + +++
Sbjct:   123 TVESQCYHKSCFKCSHGGCPISPSNYAALEGILYCKHHFAQLFKEKGSYNHLIKSASIKR 182

Query:   182 SQISEKPTPVQIAA 195
             +  +       +AA
Sbjct:   183 ATAAATAAAAAVAA 196

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

 Score = 527 (190.6 bits), Expect = 1.1e-50, P = 1.1e-50
 Identities = 88/171 (51%), Positives = 123/171 (71%)

Query:     5 FGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
             F GT  KC  CDKTVY+VD L+ +   YHK+CFRC HCKGTL++SN++S +GVLYC+ HF
Sbjct:     3 FTGTLDKCNVCDKTVYVVDMLSIEGMPYHKSCFRCTHCKGTLQMSNYSSMDGVLYCKTHF 62

Query:    65 DQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVS 124
             +QLFK +G+  K+F+   K  KPE         K+S+ F GT+DKC  C++TVYP EK+ 
Sbjct:    63 EQLFKESGNFSKNFQ-PGKTEKPEL---TRTPSKISSIFCGTQDKCAACEKTVYPLEKIQ 118

Query:   125 VNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQL 175
             + G  +H++CF+C+HGGCT++ S+Y + +  LYC+HH  QLF EKGNY+ +
Sbjct:   119 MEGECFHKTCFRCAHGGCTLTHSSYASLDSVLYCRHHFNQLFMEKGNYAHV 169

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 = 515 (186.3 bits), Expect = 2.0e-49, P = 2.0e-49
 Identities = 89/171 (52%), Positives = 122/171 (71%)

Query:     5 FGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
             F GT  KC ACDKTVY++D LT +   YHK+CFRC HCKGTL +SN++S +GVLYC+PHF
Sbjct:     3 FTGTLDKCKACDKTVYVMDLLTLEGNTYHKSCFRCTHCKGTLVISNYSSMDGVLYCKPHF 62

Query:    65 DQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVS 124
             +QLFK +G+  K+F+   K  KP   +      K+S+ F GT+DKC  C +TVYP EKV+
Sbjct:    63 EQLFKESGNYSKNFQAG-KTEKPNDHL-TRTPSKLSSFFSGTQDKCATCKKTVYPLEKVT 120

Query:   125 VNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQL 175
             + G +YH++CF+C+H GC ++ S+Y +  G LYCK H  QLF EKG+Y+ +
Sbjct:   121 MEGESYHKTCFRCTHSGCPLTHSSYASLNGVLYCKVHFNQLFLEKGSYNHV 171

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 = 506 (183.2 bits), Expect = 1.8e-48, P = 1.8e-48
 Identities = 87/175 (49%), Positives = 123/175 (70%)

Query:     1 MASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYC 60
             MA+ F GT  KC ACDKTVY++D +T +   YHK+CFRC HC GTL + N++S +GVLYC
Sbjct:     1 MAA-FTGTTDKCKACDKTVYVMDLMTLEGMPYHKSCFRCSHCNGTLVICNYSSMDGVLYC 59

Query:    61 RPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPT 120
             + HF+QLFK +G+  K+F+   K  K     +  N  ++S+ F GT+DKC  C +TVYP 
Sbjct:    60 KTHFEQLFKESGNFSKNFQTAGKTEKSNDATKAPN--RLSSFFSGTQDKCAACKKTVYPL 117

Query:   121 EKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQL 175
             EK+++ G +YH++CF+C+H GC ++ S+Y A +G LYCK H  QLF EKGNY+ +
Sbjct:   118 EKMTMEGESYHKTCFRCAHSGCPLTHSSYAALDGVLYCKVHFSQLFLEKGNYNHV 172

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

DICTYBASE|DDB_G0290575 DDB_G0290575 "LIM-type zinc finger-containing protein" [Dictyostelium discoideum (taxid:44689)]

 Score = 225 (84.3 bits), Expect = 4.5e-32, Sum P(2) = 4.5e-32
 Identities = 39/77 (50%), Positives = 50/77 (64%)

Query:     6 GGTQQKCMACDKTVYLVDKLTA----DNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR 61
             GGTQ+KC AC KTVYL +K+      D + +HK C +C HCK TL L N+ S  GV YC+
Sbjct:     5 GGTQEKCTACAKTVYLTEKIVVEDKEDKKTFHKLCLKCTHCKLTLSLGNYASLNGVFYCK 64

Query:    62 PHFDQLFKRTGSLEKSF 78
             PHF QLF   G+ ++ F
Sbjct:    65 PHFKQLFATKGNYDEGF 81

GO:0008270 "zinc ion binding" evidence=IEA

GO:0005575 "cellular_component" evidence=ND

GO:0046872 "metal ion binding" evidence=IEA

GO:0044351 "macropinocytosis" evidence=RCA

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

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 64/197 (32%), Positives = 94/197 (47%)

Query:     4 PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR-- 61
             P  G   KC ACDKTVY  +++  + R +HK CF C  C+  L  +   + E  +YC+  
Sbjct:     2 PNWGGGAKCGACDKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVC 61

Query:    62 ------PH---FDQ----LFKRTGS-LEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTR 107
                   P    F Q    L   TG  L   F+ +PK   P +     N  K S KF G  
Sbjct:    62 YGRKYGPKGIGFGQGAGCLSTDTGEHLGLQFQQSPK---PARAATTSNPSKFSAKF-GES 117

Query:   108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR 167
             +KC  C ++VY  EKV   G  +H++CF C+  G ++  +N    +G+LYCK  + + F 
Sbjct:   118 EKCPRCGKSVYAAEKVMGGGKPWHKTCFPCAICGKSLESTNVTDKDGELYCKVCYAKNFG 177

Query:   168 EKG-NYSQLESDLEKSQ 183
               G  +  L   +EK +
Sbjct:   178 PTGIGFGGLTHQVEKKE 194

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 = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 64/197 (32%), Positives = 94/197 (47%)

Query:     4 PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR-- 61
             P  G   KC ACDKTVY  +++  + R +HK CF C  C+  L  +   + E  +YC+  
Sbjct:     2 PNWGGGAKCGACDKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVC 61

Query:    62 ------PH---FDQ----LFKRTGS-LEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTR 107
                   P    F Q    L   TG  L   F+ +PK   P +     N  K S KF G  
Sbjct:    62 YGRKYGPKGIGFGQGAGCLSTDTGEHLGLQFQQSPK---PARAATTSNPSKFSAKF-GES 117

Query:   108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR 167
             +KC  C ++VY  EKV   G  +H++CF C+  G ++  +N    +G+LYCK  + + F 
Sbjct:   118 EKCPRCGKSVYAAEKVMGGGKPWHKTCFPCAICGKSLESTNVTDKDGELYCKVCYAKNFG 177

Query:   168 EKG-NYSQLESDLEKSQ 183
               G  +  L   +EK +
Sbjct:   178 PTGIGFGGLTHQVEKKE 194

GO:0008270 "zinc ion binding" evidence=IEA

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

 Score = 248 (92.4 bits), Expect = 3.9e-21, P = 3.9e-21
 Identities = 63/197 (31%), Positives = 95/197 (48%)

Query:     4 PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR-- 61
             P  G   KC AC+KTVY  +++  + R +HK CF C  C+  L  +   + E  +YC+  
Sbjct:     2 PNWGGGAKCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCKVC 61

Query:    62 ------PH---FDQ----LFKRTGS-LEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTR 107
                   P    F Q    L   TG  L   F+ +PK   P +     N  K S KF G  
Sbjct:    62 YGRRYGPKGIGFGQGAGCLSTDTGEHLGLQFQQSPK---PARAATTSNPSKFSAKF-GES 117

Query:   108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR 167
             +KC  C ++VY  EKV   G  +H++CF+C+  G ++  +N    +G+LYCK  + + F 
Sbjct:   118 EKCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNFG 177

Query:   168 EKG-NYSQLESDLEKSQ 183
               G  +  L   +EK +
Sbjct:   178 PTGIGFGGLTQQVEKKE 194

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

ZFIN|ZDB-GENE-030909-4 csrp1a "cysteine and glycine-rich protein 1a" [Danio rerio (taxid:7955)]

 Score = 247 (92.0 bits), Expect = 4.9e-21, P = 4.9e-21
 Identities = 59/193 (30%), Positives = 93/193 (48%)

Query:     4 PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
             P GG   KC  C KTVY  +++  + R +H++CF C  C+  L  +     E  +YC+  
Sbjct:     2 PLGGGN-KCGCCQKTVYFAEEVQCEGRSFHRSCFLCMVCRKNLDSTTVAVHENEIYCKAC 60

Query:    64 FDQLFKRTG----------SLEKSFEGTPKIVKPE--KLVENENAQKVSNKFVGTRDKCV 111
             + + +   G          S++K      K+V+P+  +   N N  K + KF G+ D C 
Sbjct:    61 YGKKYGPKGYGYGAGAGTLSMDKGESLGIKVVEPQNHQPTNNPNTSKFAQKFGGS-DVCP 119

Query:   112 GCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKG- 170
              C + VY  EKV   G A+HR CF+C+  G  +  +     +G++YCK  + + F  KG 
Sbjct:   120 RCSKAVYAAEKVIGAGNAWHRGCFRCAMCGKGLESTTLADKDGEIYCKGCYAKNFGPKGF 179

Query:   171 NYSQLESDLEKSQ 183
              Y Q    L  +Q
Sbjct:   180 GYGQGAGALSHTQ 192

GO:0008270 "zinc ion binding" evidence=IEA

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

GO:0007254 "JNK cascade" evidence=IMP

GO:0042074 "cell migration involved in gastrulation" evidence=IMP

GO:0016055 "Wnt receptor signaling pathway" evidence=IMP

GO:0003007 "heart morphogenesis" evidence=IMP

GO:0005622 "intracellular" evidence=IMP

GO:0046872 "metal 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

ID	Name	Annotated EC number	Identity	Query coverage	Hit coverage	RBH(Q2H)	RBH(H2Q)
P29675	SF3_HELAN	No assigned EC number	0.7005	0.9340	0.8401	N/A	no

EC Number Prediction by Ezypred Server

Original result from Ezypred Server

Fail to connect to Ezypred Server

EC Number Prediction by EFICAz Software

No EC number assignment, probably not an enzyme!

---

Prediction of Functionally Associated Proteins

Functionally Associated Proteins Detected by STRING

Original result from the STRING server

Fail to connect to STRING server

---

Conserved Domains and Related Protein Families

Conserved Domains Detected by RPS-BLAST

Original result of RPS-BLAST against CDD database part I

ID	Length	Definition	E-value
Query	197
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	2e-38
cd09441	61	cd09441, LIM2_SF3, The second Lim domain of pollen	2e-35
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	4e-23
cd09358	53	cd09358, LIM_Mical_like, The LIM domain of Mical (	6e-21
cd09440	63	cd09440, LIM1_SF3, The first Lim domain of pollen	1e-20
cd09441	61	cd09441, LIM2_SF3, The second Lim domain of pollen	3e-17
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	5e-16
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	4e-15
pfam00412	58	pfam00412, LIM, LIM domain	5e-15
cd09439	55	cd09439, LIM_Mical, The LIM domain of Mical (molec	6e-14
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	9e-13
cd09445	53	cd09445, LIM_Mical_like_2, This domain belongs to	2e-12
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	4e-12
pfam00412	58	pfam00412, LIM, LIM domain	7e-12
cd09439	55	cd09439, LIM_Mical, The LIM domain of Mical (molec	3e-11
cd09485	53	cd09485, LIM_Eplin_alpha_beta, The Lim domain of E	1e-10
cd09443	55	cd09443, LIM_Ltd-1, The LIM domain of LIM and tran	2e-10
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	5e-10
cd09442	53	cd09442, LIM_Eplin_like, The Lim domain of Epithel	7e-10
cd09443	55	cd09443, LIM_Ltd-1, The LIM domain of LIM and tran	1e-09
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	1e-09
smart00132	54	smart00132, LIM, Zinc-binding domain present in Li	5e-09
cd09445	53	cd09445, LIM_Mical_like_2, This domain belongs to	2e-08
cd09447	53	cd09447, LIM_LASP, The LIM domain of LIM and SH3 P	2e-08
cd08368	53	cd08368, LIM, LIM is a small protein-protein inter	2e-08
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	2e-08
cd09486	53	cd09486, LIM_Eplin_like_1, a LIM domain subfamily	6e-08
cd09401	53	cd09401, LIM_TLP_like, The LIM domains of thymus L	8e-08
cd09326	53	cd09326, LIM_CRP_like, The LIM domains of Cysteine	1e-07
cd09478	54	cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich	1e-07
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	2e-07
cd09326	53	cd09326, LIM_CRP_like, The LIM domains of Cysteine	5e-07
cd09359	53	cd09359, LIM_LASP_like, The LIM domain of LIM and	5e-07
cd09404	54	cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84	5e-07
cd09444	55	cd09444, LIM_Mical_like_1, This domain belongs to	7e-07
cd09476	54	cd09476, LIM1_TLP, The first LIM domain of thymus	1e-06
cd09446	53	cd09446, LIM_N_RAP, The LIM domain of N-RAP	1e-06
cd09482	54	cd09482, LIM2_CRP3, The second LIM domain of Cyste	2e-06
cd09404	54	cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84	3e-06
cd09403	54	cd09403, LIM2_CRP, The second LIM domain of Cystei	3e-06
cd09482	54	cd09482, LIM2_CRP3, The second LIM domain of Cyste	4e-06
cd09400	61	cd09400, LIM_like_1, LIM domain in proteins of unk	4e-06
cd09481	54	cd09481, LIM1_CRP3, The first LIM domain of Cystei	5e-06
cd09446	53	cd09446, LIM_N_RAP, The LIM domain of N-RAP	9e-06
cd09481	54	cd09481, LIM1_CRP3, The first LIM domain of Cystei	1e-05
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	1e-05
cd09444	55	cd09444, LIM_Mical_like_1, This domain belongs to	2e-05
cd09403	54	cd09403, LIM2_CRP, The second LIM domain of Cystei	2e-05
cd09402	53	cd09402, LIM1_CRP, The first LIM domain of Cystein	2e-05
cd09840	54	cd09840, LIM2_CRP2, The second LIM domain of Cyste	2e-05
cd09477	54	cd09477, LIM2_TLP, The second LIM domain of thymus	3e-05
cd09477	54	cd09477, LIM2_TLP, The second LIM domain of thymus	3e-05
cd09400	61	cd09400, LIM_like_1, LIM domain in proteins of unk	5e-05
cd09840	54	cd09840, LIM2_CRP2, The second LIM domain of Cyste	6e-05
cd09480	55	cd09480, LIM1_CRP2, The first LIM domain of Cystei	7e-05
cd09402	53	cd09402, LIM1_CRP, The first LIM domain of Cystein	8e-05
cd09480	55	cd09480, LIM1_CRP2, The first LIM domain of Cystei	1e-04
cd09479	56	cd09479, LIM1_CRP1, The first LIM domain of Cystei	1e-04
cd09479	56	cd09479, LIM1_CRP1, The first LIM domain of Cystei	2e-04
cd09463	53	cd09463, LIM1_LIMK2, The first LIM domain of LIMK2	2e-04
cd09367	52	cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of L	2e-04
cd09427	58	cd09427, LIM2_FHL3, The second LIM domain of Four	5e-04
cd09371	53	cd09371, LIM1_Lmx1b, The first LIM domain of Lmx1b	5e-04
cd09364	53	cd09364, LIM1_LIMK, The first LIM domain of LIMK (	7e-04
cd09379	55	cd09379, LIM2_AWH, The second LIM domain of Arrowh	7e-04
cd09478	54	cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich	0.001
cd09351	54	cd09351, LIM1_LPP, The first LIM domain of lipoma	0.001
cd09476	54	cd09476, LIM1_TLP, The first LIM domain of thymus	0.002
cd09462	74	cd09462, LIM1_LIMK1, The first LIM domain of LIMK1	0.002
cd09361	52	cd09361, LIM1_Enigma_like, The first LIM domain of	0.003

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

 Score =  126 bits (317), Expect = 2e-38
 Identities = 49/63 (77%), Positives = 56/63 (88%)

Query: 8  TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQL 67
          T QKC ACDKTVYLVD+L+AD  VYHK+CFRC HCKGTLKLSN++S EGVLYC+PHF+QL
Sbjct: 1  TTQKCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 60

Query: 68 FKR 70
          FK 
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 =  118 bits (298), Expect = 2e-35
 Identities = 48/61 (78%), Positives = 54/61 (88%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREK 169
           CV C +TVYP EKV+V G +YH+SCFKCSHGGCTISPSNY AHEG+LYCKHHH QLF+EK
Sbjct: 1   CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60

Query: 170 G 170
           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 = 86.9 bits (216), Expect = 4e-23
 Identities = 30/53 (56%), Positives = 40/53 (75%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
          C  C KTVY +++L AD +++HK+CFRC HC  TL+L N+ S EG LYC+PHF
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|188744 cd09358, LIM_Mical_like, The LIM domain of Mical (molecule interacting with CasL) like family

 Score = 81.2 bits (201), Expect = 6e-21
 Identities = 26/53 (49%), Positives = 35/53 (66%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH 162
           C  C +TVYP E++  +G  +H+SCF+CSH   T+   NY + EGKLYCK H 
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|188824 cd09440, LIM1_SF3, The first Lim domain of pollen specific protein SF3

 Score = 81.0 bits (200), Expect = 1e-20
 Identities = 33/63 (52%), Positives = 43/63 (68%)

Query: 106 TRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQL 165
           T  KC  CD+TVY  +++S +G  YH+SCF+CSH   T+  SNY + EG LYCK H  QL
Sbjct: 1   TTQKCKACDKTVYLVDQLSADGVVYHKSCFRCSHCKGTLKLSNYSSMEGVLYCKPHFEQL 60

Query: 166 FRE 168
           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|188825 cd09441, LIM2_SF3, The second Lim domain of pollen specific protein SF3

 Score = 71.7 bits (176), Expect = 3e-17
 Identities = 30/61 (49%), Positives = 41/61 (67%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRT 71
          C+AC KTVY ++K+T +   YHK+CF+C H   T+  SN+ + EG LYC+ H  QLFK  
Sbjct: 1  CVACGKTVYPIEKVTVEGTSYHKSCFKCSHGGCTISPSNYAAHEGRLYCKHHHSQLFKEK 60

Query: 72 G 72
          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|188826 cd09442, LIM_Eplin_like, The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins

 Score = 68.7 bits (168), Expect = 5e-16
 Identities = 26/53 (49%), Positives = 35/53 (66%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
          C  C K VY +++L AD + +HK+CFRC HC   L L N+ S  G +YC+PHF
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|188869 cd09485, LIM_Eplin_alpha_beta, The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin)

 Score = 66.1 bits (161), Expect = 4e-15
 Identities = 24/53 (45%), Positives = 37/53 (69%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
          C++C KTVY +++L A+ ++YH +CFRC +C   L L  + S  G +YC+PHF
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|215907 pfam00412, LIM, LIM domain

 Score = 65.8 bits (161), Expect = 5e-15
 Identities = 22/58 (37%), Positives = 33/58 (56%), Gaps = 1/58 (1%)

Query: 110 CVGCDRTVYPTEKVS-VNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF 166
           C GC + +Y  E V    G  +H  CF+C+  G  + P ++   +GKLYCKH + +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 = 63.1 bits (154), Expect = 6e-14
 Identities = 22/55 (40%), Positives = 37/55 (67%), Gaps = 2/55 (3%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSN--FNSFEGVLYCRPHF 64
          C  C K VY++++L+A+   +H++CF+C +C  TL+L    F+  +G  YC+PHF
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|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of proteins with unknown function

 Score = 60.0 bits (145), Expect = 9e-13
 Identities = 24/53 (45%), Positives = 34/53 (64%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
          C +C KTVY +++L AD  V+H +CF C HC   L L ++ +  G  YC+PHF
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|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 = 59.0 bits (143), Expect = 2e-12
 Identities = 25/53 (47%), Positives = 35/53 (66%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
          C +C K VY ++++ A+  +YHK CFRC  C   LK+ N+ S EG LYC+ 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|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 58.5 bits (142), Expect = 4e-12
 Identities = 22/54 (40%), Positives = 30/54 (55%), Gaps = 1/54 (1%)

Query: 109 KCVGCDRTVYPTEKV-SVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHH 161
           KC GC + +Y TE+V    G  +H  CFKC+  G  +S   +   +GKLYCK  
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 = 57.7 bits (140), Expect = 7e-12
 Identities = 20/58 (34%), Positives = 30/58 (51%), Gaps = 1/58 (1%)

Query: 12 CMACDKTVYLVDKLT-ADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
          C  C K +Y  + +  A  +V+H  CFRC  C   L   +F   +G LYC+  + +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 = 56.2 bits (136), Expect = 3e-11
 Identities = 24/54 (44%), Positives = 31/54 (57%), Gaps = 2/54 (3%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAH--EGKLYCKHH 161
           C  C + VY  E++S  G  +HRSCFKCS+ G T+    Y     +GK YCK H
Sbjct: 1   CYFCKKRVYVMERLSAEGLFFHRSCFKCSYCGTTLRLGAYAFDRDDGKFYCKPH 54

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

 Score = 54.5 bits (131), Expect = 1e-10
 Identities = 23/52 (44%), Positives = 31/52 (59%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHH 161
           CV C +TVYP E++  N   YH SCF+CS+    +S   Y +  G +YCK H
Sbjct: 1   CVSCQKTVYPLERLVANQQIYHNSCFRCSYCNTKLSLGTYASLHGNIYCKPH 52

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|188827 cd09443, LIM_Ltd-1, The LIM domain of LIM and transglutaminase domains protein (Ltd-1)

 Score = 54.0 bits (130), Expect = 2e-10
 Identities = 20/54 (37%), Positives = 29/54 (53%), Gaps = 2/54 (3%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNY--IAHEGKLYCKHH 161
           C  C +T YP E V  +G  YH+ CFKC   G  +S   +  +  +G++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 = 52.8 bits (127), Expect = 5e-10
 Identities = 20/53 (37%), Positives = 30/53 (56%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
          C  C KTVY  +KL   ++++HK CF+C  C  TL + N+  +    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|188826 cd09442, LIM_Eplin_like, The Lim domain of Epithelial Protein Lost in Neoplasm (Eplin) like proteins

 Score = 52.5 bits (126), Expect = 7e-10
 Identities = 20/52 (38%), Positives = 31/52 (59%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHH 161
           C  C + VYP E++  +   +H+SCF+C H    +S  NY +  G++YCK H
Sbjct: 1   CTVCQKRVYPMERLIADKQNFHKSCFRCEHCNSKLSLGNYASLHGRIYCKPH 52

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|188827 cd09443, LIM_Ltd-1, The LIM domain of LIM and transglutaminase domains protein (Ltd-1)

 Score = 52.0 bits (125), Expect = 1e-09
 Identities = 20/54 (37%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLS--NFNSFEGVLYCRPH 63
          C  C KT Y  + +  D   YHK CF+C  C   L L    F   +G +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 = 51.9 bits (125), Expect = 1e-09
 Identities = 16/53 (30%), Positives = 26/53 (49%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH 162
           C GC + +   E +   G  +H  CFKCS  G  +   ++   +GK 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|214528 smart00132, LIM, Zinc-binding domain present in Lin-11, Isl-1, Mec-3

 Score = 50.1 bits (120), Expect = 5e-09
 Identities = 19/54 (35%), Positives = 27/54 (50%), Gaps = 1/54 (1%)

Query: 11 KCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
          KC  C K +Y  ++ L A  +V+H  CF+C  C   L    F   +G LYC+  
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|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 = 48.6 bits (116), Expect = 2e-08
 Identities = 20/52 (38%), Positives = 28/52 (53%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHH 161
           C  C + VY  E++      YH++CF+C      +   NY +HEG LYCK H
Sbjct: 1   CRSCGKPVYKMEEIIAEKHIYHKNCFRCKDCNKQLKVDNYQSHEGNLYCKVH 52

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

 Score = 48.1 bits (115), Expect = 2e-08
 Identities = 22/53 (41%), Positives = 31/53 (58%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH 162
           C  C +TVYPTEK++     +H+ CFKC   G T++  NY  +  K 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 = 48.8 bits (117), Expect = 2e-08
 Identities = 15/53 (28%), Positives = 23/53 (43%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
          C  C K +   + L A  + +H  CF+C  C   L   +F   +G  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|188785 cd09401, LIM_TLP_like, The LIM domains of thymus LIM protein (TLP)

 Score = 48.1 bits (115), Expect = 2e-08
 Identities = 18/51 (35%), Positives = 26/51 (50%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKH 160
           C  C + VY  EK +  G  +H+ C +C     T++P  +  HEGK 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|188870 cd09486, LIM_Eplin_like_1, a LIM domain subfamily on a group of proteins with unknown function

 Score = 47.3 bits (112), Expect = 6e-08
 Identities = 21/52 (40%), Positives = 29/52 (55%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHH 161
           C  C +TVYP E++  +   +H SCF C H    +S  +Y A  G+ YCK H
Sbjct: 1   CSSCQKTVYPMERLVADKLVFHNSCFCCKHCNAKLSLGSYAALHGEFYCKPH 52

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

 Score = 47.0 bits (112), Expect = 8e-08
 Identities = 21/51 (41%), Positives = 25/51 (49%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRP 62
          C  C K VY  +K T+  R +HK C RC  CK TL     +  EG  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|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein (CRP) family

 Score = 46.0 bits (110), Expect = 1e-07
 Identities = 17/50 (34%), Positives = 29/50 (58%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCK 159
           C  C ++VY  E+V   G ++H+SCF C+     +  +    H+G++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|188862 cd09478, LIM_CRIP, The LIM domain of Cysteine-Rich Intestinal Protein (CRIP)

 Score = 46.0 bits (109), Expect = 1e-07
 Identities = 22/51 (43%), Positives = 31/51 (60%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKH 160
           C  CD+ VY  E+V+  G  +HR C KC   G T++P ++  H+GK 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|188745 cd09359, LIM_LASP_like, The LIM domain of LIM and SH3 Protein (LASP)-like proteins

 Score = 45.7 bits (108), Expect = 2e-07
 Identities = 20/53 (37%), Positives = 31/53 (58%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
          C  C K VY  +K+   ++ +HKACF C  CK TL ++N+  ++   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|188712 cd09326, LIM_CRP_like, The LIM domains of Cysteine Rich Protein (CRP) family

 Score = 44.5 bits (106), Expect = 5e-07
 Identities = 16/50 (32%), Positives = 27/50 (54%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR 61
          C  C K+VY  +++ A  + +HK+CF C  C   L  +     +G +YC+
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|188745 cd09359, LIM_LASP_like, The LIM domain of LIM and SH3 Protein (LASP)-like proteins

 Score = 44.6 bits (105), Expect = 5e-07
 Identities = 20/53 (37%), Positives = 31/53 (58%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH 162
           C  C + VYPTEKV+     +H++CF C     T++ +NY  ++ K 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|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A

 Score = 44.8 bits (106), Expect = 5e-07
 Identities = 21/54 (38%), Positives = 29/54 (53%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH 162
           KC  C ++VY  E+    G  +H+ CFKC      +  +N   HEG+LYCK  H
Sbjct: 1   KCPKCGKSVYAAEERLAGGYKWHKMCFKCGMCNKLLDSTNCAEHEGELYCKQCH 54

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|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 = 44.3 bits (105), Expect = 7e-07
 Identities = 19/55 (34%), Positives = 28/55 (50%), Gaps = 2/55 (3%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFE--GVLYCRPHF 64
          C AC + V+LV +   D ++YH+ CFRC  C  TL   ++ +    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|188860 cd09476, LIM1_TLP, The first LIM domain of thymus LIM protein (TLP)

 Score = 43.8 bits (103), Expect = 1e-06
 Identities = 23/49 (46%), Positives = 28/49 (57%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYC 158
           C  CD+TVY  EKVS  G  +HR C KC      +SP  +  H+GK 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|188830 cd09446, LIM_N_RAP, The LIM domain of N-RAP

 Score = 43.4 bits (102), Expect = 1e-06
 Identities = 17/53 (32%), Positives = 31/53 (58%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH 162
           C  C   VYP EK++     +H++CF C      ++ +N+++H+ K YC+ H+
Sbjct: 1   CARCGYGVYPAEKINCIDQTWHKACFHCEVCKMMLTVNNFVSHQKKPYCQAHN 53

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

 Score = 43.5 bits (102), Expect = 2e-06
 Identities = 18/50 (36%), Positives = 30/50 (60%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCK 159
           C  C ++VY  EKV   G  +H++CF+C+  G ++  +     +G+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|188788 cd09404, LIM1_MLP84B_like, The LIM domain of Mlp84B and Mlp60A

 Score = 42.5 bits (100), Expect = 3e-06
 Identities = 20/52 (38%), Positives = 27/52 (51%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRP 62
          KC  C K+VY  ++  A    +HK CF+C  C   L  +N    EG LYC+ 
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|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein (CRP)

 Score = 42.6 bits (100), Expect = 3e-06
 Identities = 16/50 (32%), Positives = 30/50 (60%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCK 159
           C  C ++VY  EK+   G  +H++CF+C+  G ++  +     +G++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|188866 cd09482, LIM2_CRP3, The second LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 42.3 bits (99), Expect = 4e-06
 Identities = 18/50 (36%), Positives = 28/50 (56%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR 61
          C  C K+VY  +K+    + +HK CFRC  C  +L+ +     +G LYC+
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|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function

 Score = 42.4 bits (100), Expect = 4e-06
 Identities = 18/52 (34%), Positives = 29/52 (55%)

Query: 107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYC 158
           R+ C  C   V+  E++ + G  YHR+CFKC+  G  ++P ++   E   YC
Sbjct: 2   REPCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 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|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 42.0 bits (98), Expect = 5e-06
 Identities = 19/51 (37%), Positives = 31/51 (60%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCK 159
           KC  C++TVY  E++  NG ++H++CF C      +  +   AHE ++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|188830 cd09446, LIM_N_RAP, The LIM domain of N-RAP

 Score = 41.4 bits (97), Expect = 9e-06
 Identities = 20/52 (38%), Positives = 29/52 (55%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
          C  C   VY  +K+   ++ +HKACF C  CK  L ++NF 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|188865 cd09481, LIM1_CRP3, The first LIM domain of Cysteine Rich Protein 3 (CRP3/MLP)

 Score = 41.3 bits (96), Expect = 1e-05
 Identities = 19/51 (37%), Positives = 30/51 (58%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR 61
          KC AC+KTVY  +++  + R +HK CF C  C+  L  +   + E  +YC+
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|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase )

 Score = 40.6 bits (95), Expect = 1e-05
 Identities = 19/54 (35%), Positives = 28/54 (51%), Gaps = 3/54 (5%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSN-YIAHEGKLYCKHHH 162
           C GC   +  ++ V      +H  CF+CS   C+ S SN Y   +GKLYC+  +
Sbjct: 1   CAGCRGKILDSQYVQALNQDWHCDCFRCSV--CSDSLSNWYFEKDGKLYCRKDY 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|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 = 40.1 bits (94), Expect = 2e-05
 Identities = 20/55 (36%), Positives = 29/55 (52%), Gaps = 2/55 (3%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIA--HEGKLYCKHHH 162
           C  C + V+  ++  V+G  YHR+CF+C     T+ P +Y A    G   C HHH
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|188787 cd09403, LIM2_CRP, The second LIM domain of Cysteine Rich Protein (CRP)

 Score = 40.6 bits (95), Expect = 2e-05
 Identities = 17/50 (34%), Positives = 28/50 (56%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR 61
          C  C K+VY  +K+    + +HK CFRC  C  +L+ +     +G +YC+
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|188786 cd09402, LIM1_CRP, The first LIM domain of Cysteine Rich Protein (CRP)

 Score = 40.3 bits (94), Expect = 2e-05
 Identities = 19/50 (38%), Positives = 29/50 (58%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCK 159
           C  C++TVY  E+V   G ++H+SCF C      +  +   AHE ++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|188871 cd09840, LIM2_CRP2, The second LIM domain of Cysteine Rich Protein 2 (CRP2)

 Score = 40.1 bits (93), Expect = 2e-05
 Identities = 17/50 (34%), Positives = 29/50 (58%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCK 159
           C  C  +VY  EK+   G  +H++CF+C+  G ++  +     EG++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|188861 cd09477, LIM2_TLP, The second LIM domain of thymus LIM protein (TLP)

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 18/49 (36%), Positives = 25/49 (51%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYC 158
           C GC + VY  EKV   G  +HR C +C     T++   +  H+G  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|188861 cd09477, LIM2_TLP, The second LIM domain of thymus LIM protein (TLP)

 Score = 40.0 bits (93), Expect = 3e-05
 Identities = 18/49 (36%), Positives = 24/49 (48%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYC 60
          C  C K VY  +K+ +  R +H+ C RC  CK TL        +G  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|188784 cd09400, LIM_like_1, LIM domain in proteins of unknown function

 Score = 39.3 bits (92), Expect = 5e-05
 Identities = 17/50 (34%), Positives = 26/50 (52%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYC 60
           C +C   V+L ++L  + +VYH+ CF+C  C   L   +F   E   YC
Sbjct: 4  PCASCGLPVFLAERLLIEGKVYHRTCFKCARCGVQLTPGSFYETEYGSYC 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|188871 cd09840, LIM2_CRP2, The second LIM domain of Cysteine Rich Protein 2 (CRP2)

 Score = 39.3 bits (91), Expect = 6e-05
 Identities = 17/50 (34%), Positives = 27/50 (54%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR 61
          C  C  +VY  +K+    + +HK CFRC  C  +L+ +     EG +YC+
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|188864 cd09480, LIM1_CRP2, The first LIM domain of Cysteine Rich Protein 2 (CRP2)

 Score = 38.8 bits (90), Expect = 7e-05
 Identities = 18/51 (35%), Positives = 28/51 (54%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR 61
          KC AC +TVY  +++  D R +HK CF C  C+  L  +     +  +YC+
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|188786 cd09402, LIM1_CRP, The first LIM domain of Cysteine Rich Protein (CRP)

 Score = 38.8 bits (90), Expect = 8e-05
 Identities = 18/50 (36%), Positives = 30/50 (60%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR 61
          C AC+KTVY  +++  + R +HK+CF C  C+  L  +   + E  +YC+
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|188864 cd09480, LIM1_CRP2, The first LIM domain of Cysteine Rich Protein 2 (CRP2)

 Score = 38.4 bits (89), Expect = 1e-04
 Identities = 18/51 (35%), Positives = 28/51 (54%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCK 159
           KC  C RTVY  E+V  +G ++H+ CF C      +  +    H+ ++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|188863 cd09479, LIM1_CRP1, The first LIM domain of Cysteine Rich Protein 1 (CRP1)

 Score = 38.1 bits (88), Expect = 1e-04
 Identities = 18/51 (35%), Positives = 27/51 (52%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCK 159
           KC  C +TVY  E+V   G ++H+SCF C      +  +    H  ++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|188863 cd09479, LIM1_CRP1, The first LIM domain of Cysteine Rich Protein 1 (CRP1)

 Score = 37.7 bits (87), Expect = 2e-04
 Identities = 18/52 (34%), Positives = 28/52 (53%)

Query: 10 QKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR 61
          +KC  C KTVY  +++  + R +HK+CF C  CK  L  +        +YC+
Sbjct: 1  KKCGVCQKTVYFAEEVQCEGRSFHKSCFLCMVCKKNLDSTTVAVHGEEIYCK 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|188847 cd09463, LIM1_LIMK2, The first LIM domain of LIMK2 (LIM domain Kinase 2)

 Score = 37.9 bits (88), Expect = 2e-04
 Identities = 20/54 (37%), Positives = 27/54 (50%), Gaps = 3/54 (5%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSN-YIAHEGKLYCKHHH 162
           C GC   +  +    V   A+H SCF+CS   C    +N Y   +GKLYC  H+
Sbjct: 1   CTGCGGRIQDSFHYRVVQEAWHNSCFQCSV--CQDLLTNWYYEKDGKLYCHKHY 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|188753 cd09367, LIM1_Lhx1_Lhx5, The first LIM domain of Lhx1 (also known as Lim1) and Lhx5

 Score = 37.4 bits (87), Expect = 2e-04
 Identities = 22/55 (40%), Positives = 28/55 (50%), Gaps = 5/55 (9%)

Query: 12 CMACDKTVYLVDK--LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
          C  CD+ +  +DK  L   +R +H  C +C  CK  L    F S EG LYCR  F
Sbjct: 1  CAGCDRPI--LDKFLLNVLDRAWHAKCVQCCDCKCPLTEKCF-SREGKLYCRNDF 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|188811 cd09427, LIM2_FHL3, The second LIM domain of Four and a half LIM domains protein 3 (FHL3)

 Score = 36.8 bits (85), Expect = 5e-04
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 109 KCVGCDRTVYP-TEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYC 158
           KCV C +TV P + K+   G  +H  CF C      I   ++I  + + YC
Sbjct: 3   KCVACGKTVMPGSRKLEYEGQTWHEHCFICHGCEQPIGSRSFIPDKDEHYC 53

The second LIM domain of Four and a half LIM domains protein 3 (FHL3): FHL3 is highly expressed in the skeleton and cardiac muscles and possesses the transactivation and repression activities. FHL3 interacts with many transcription factors, such as CREB, BKLF/KLF3, CtBP2, MyoD, and MZF_1. Moreover, FHL3 interacts with alpha- and beta-subunits of the muscle alpha7beta1 integrin receptor. FHL3 was also proved to possess the auto-activation ability and was confirmed that the second zinc finger motif in fourth LIM domain was responsible for the auto-activation of FHL3. LIM domains are 50-60 amino acids in size and share two characteristic zinc finger motifs. The two zinc fingers contain eight conserved residues, mostly cysteines and histidines, which coordinately bond to two zinc atoms. LIM domains function as adaptors or scaffolds to support the assembly of multimeric protein complexes. Length = 58

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

 Score = 36.6 bits (85), Expect = 5e-04
 Identities = 17/51 (33%), Positives = 25/51 (49%), Gaps = 1/51 (1%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKH 160
           C GC R +     + VN  ++H  C +CS     ++ S Y   + KLYCK 
Sbjct: 1   CAGCQRPISDRYLLRVNERSWHEECLQCSVCQQPLTTSCY-FRDRKLYCKQ 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|188750 cd09364, LIM1_LIMK, The first LIM domain of LIMK (LIM domain Kinase )

 Score = 35.9 bits (83), Expect = 7e-04
 Identities = 17/53 (32%), Positives = 24/53 (45%), Gaps = 1/53 (1%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
          C  C   +     + A N+ +H  CFRC  C  +L    F   +G LYCR  +
Sbjct: 1  CAGCRGKILDSQYVQALNQDWHCDCFRCSVCSDSLSNWYFEK-DGKLYCRKDY 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|188765 cd09379, LIM2_AWH, The second LIM domain of Arrowhead (AWH)

 Score = 36.2 bits (84), Expect = 7e-04
 Identities = 18/55 (32%), Positives = 25/55 (45%), Gaps = 2/55 (3%)

Query: 12 CMACDKTVYLVDKL-TADNRVYHKACFRCHHCKGTLKL-SNFNSFEGVLYCRPHF 64
          C  C + +   D +  A + VYH ACF C  CK  L     F   E  + C+ H+
Sbjct: 1  CAKCSRNISASDWVRRARDHVYHLACFACDACKRQLSTGEEFALIEDRVLCKAHY 55

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

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

 Score = 35.6 bits (82), Expect = 0.001
 Identities = 16/49 (32%), Positives = 26/49 (53%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYC 60
          C  CDK VY  +++T+  + +H+ C +C  C  TL   +    +G  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|188737 cd09351, LIM1_LPP, The first LIM domain of lipoma preferred partner (LPP)

 Score = 35.5 bits (82), Expect = 0.001
 Identities = 15/35 (42%), Positives = 22/35 (62%)

Query: 26 TADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYC 60
          TA ++VYH +CF CH C+  L+   F + +G  YC
Sbjct: 16 TAMDQVYHISCFTCHQCQINLQGKPFYALDGKPYC 50

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

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

 Score = 34.9 bits (80), Expect = 0.002
 Identities = 16/49 (32%), Positives = 25/49 (51%)

Query: 12 CMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYC 60
          C  CDKTVY  +K+++  + +H+ C +C  C   L        +G  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|188846 cd09462, LIM1_LIMK1, The first LIM domain of LIMK1 (LIM domain Kinase 1)

 Score = 35.6 bits (82), Expect = 0.002
 Identities = 14/53 (26%), Positives = 28/53 (52%), Gaps = 1/53 (1%)

Query: 110 CVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH 162
           C  C +++Y  + +    + +H  CF+C   G ++S   Y   +G+L+CK  +
Sbjct: 22  CASCGQSIYDGQYLQALNSDWHADCFRCCECGASLS-HWYYEKDGRLFCKKDY 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|188747 cd09361, LIM1_Enigma_like, The first LIM domain of Enigma-like family

 Score = 34.3 bits (79), Expect = 0.003
 Identities = 14/40 (35%), Positives = 18/40 (45%)

Query: 25 LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
          L A  R +H   F C HC  +L    F   +G LYC   +
Sbjct: 13 LVALGRSWHPEEFTCSHCHCSLAEIGFVEEKGSLYCELCY 52

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

Conserved Domains Detected by HHsearch

Original result of HHsearch against CDD database

ID	Length	Definition	Probability
Query	197
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.95
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.92
KOG1701	468	consensus Focal adhesion adaptor protein Paxillin	99.91
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.88
KOG2272	332	consensus Focal adhesion protein PINCH-1, contains	99.87
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.86
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	99.84
KOG1700	200	consensus Regulatory protein MLP and related LIM p	99.82
KOG1703	479	consensus Adaptor protein Enigma and related PDZ-L	99.79
KOG1044	670	consensus Actin-binding LIM Zn-finger protein Lima	99.75
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.66
PF00412	58	LIM: LIM domain; InterPro: IPR001781 Zinc finger (	99.59
KOG4577	383	consensus Transcription factor LIM3, contains LIM	99.17
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.9
smart00132	39	LIM Zinc-binding domain present in Lin-11, Isl-1,	98.78
KOG1700	200	consensus Regulatory protein MLP and related LIM p	98.68
KOG1702	264	consensus Nebulin repeat protein [Cytoskeleton]	98.23
KOG0490	235	consensus Transcription factor, contains HOX domai	97.97
KOG1702	264	consensus Nebulin repeat protein [Cytoskeleton]	97.91
KOG0490	235	consensus Transcription factor, contains HOX domai	93.43
PF14446	54	Prok-RING_1: Prokaryotic RING finger family 1	92.52
PF09943	101	DUF2175: Uncharacterized protein conserved in arch	89.98
PF14471	51	DUF4428: Domain of unknown function (DUF4428)	86.54
PF10367	109	Vps39_2: Vacuolar sorting protein 39 domain 2; Int	86.31
smart00504	63	Ubox Modified RING finger domain. Modified RING fi	84.36
COG2888	61	Predicted Zn-ribbon RNA-binding protein with a fun	82.94
PF14835	65	zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM	81.69
PF01258	36	zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc f	81.61
PF08394	37	Arc_trans_TRASH: Archaeal TRASH domain; InterPro:	80.66

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

Probab=99.95  E-value=1.2e-29  Score=209.90  Aligned_cols=132  Identities=22%  Similarity=0.495  Sum_probs=120.6

Q ss_pred             Cccccccccceeccee-EEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCC
Q 029230            9 QQKCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKP   87 (197)
Q Consensus         9 ~~~C~~C~~~I~~~~~-~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~   87 (197)
                      ..+|.+|+|.|....- +.|+++.||..||+|..|++.|.++.||.+|+++||+.||++..                   
T Consensus       274 ~~iC~~C~K~V~g~~~ac~Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tl-------------------  334 (468)
T KOG1701|consen  274 FGICAFCHKTVSGQGLAVEAMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTL-------------------  334 (468)
T ss_pred             hhhhhhcCCcccCcchHHHHhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHH-------------------
Confidence            3589999999985433 79999999999999999999999999999999999999998876                   


Q ss_pred             CCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeee-CCeeecHHHHHhHh
Q 029230           88 EKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAH-EGKLYCKHHHIQLF  166 (197)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~-dg~~yC~~cy~~~~  166 (197)
                                          .+|..|+++|.+. .|.|+|+.||+.||+|..|++.|++..|.+. ++++||..||.++|
T Consensus       335 --------------------ekC~~Cg~~I~d~-iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kf  393 (468)
T KOG1701|consen  335 --------------------EKCNKCGEPIMDR-ILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKF  393 (468)
T ss_pred             --------------------HHHhhhhhHHHHH-HHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhc
Confidence                                7899999999642 3679999999999999999999999889764 79999999999999


Q ss_pred             cCCCCCCCCCCchh
Q 029230          167 REKGNYSQLESDLE  180 (197)
Q Consensus       167 ~~k~~~~~~~~~~~  180 (197)
                      ++||+.|.+.+.++
T Consensus       394 APrCs~C~~PI~P~  407 (468)
T KOG1701|consen  394 APRCSVCGNPILPR  407 (468)
T ss_pred             CcchhhccCCccCC
Confidence            99999999998876

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

Probab=99.92  E-value=4.4e-27  Score=182.86  Aligned_cols=175  Identities=19%  Similarity=0.283  Sum_probs=145.7

Q ss_pred             CCccccccccceeccee-EEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccC
Q 029230            8 TQQKCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVK   86 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~-~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~   86 (197)
                      ....|.+|.....+.+. +...|..||..||.|++|-.+|.++.|++.+|+.||+.+|+.+|+|-+..+..|+....+.+
T Consensus        11 ~~~~C~RC~~gF~~~e~~vns~ge~wH~~CFvCAQCf~pf~~g~~~efEgRkYCEhDF~~LfaPcC~kC~EFiiGrVika   90 (332)
T KOG2272|consen   11 ANMVCERCRDGFEPAEKIVNSNGELWHEQCFVCAQCFRPFPDGIFYEFEGRKYCEHDFHVLFAPCCGKCGEFIIGRVIKA   90 (332)
T ss_pred             HHHHHHHHhccCCchhhhhccCchhhHHHHHHHHHhcCcCCCceeEEecCcccccccchhhhchhhcccccchhhHHHHh
Confidence            34679999998877665 68889999999999999999999999999999999999999999999988888888888877


Q ss_pred             CCCcccccCc-------------------------------------------------------------c--------
Q 029230           87 PEKLVENENA-------------------------------------------------------------Q--------   97 (197)
Q Consensus        87 ~~~~~~~~~~-------------------------------------------------------------~--------   97 (197)
                      .+.+||+.+-                                                             .        
T Consensus        91 mnnSwHp~CF~Cd~Cn~~Lad~gf~rnqgr~LC~~Cn~k~Ka~~~g~YvC~KCh~~iD~~~l~fr~d~yH~yHFkCt~C~  170 (332)
T KOG2272|consen   91 MNNSWHPACFRCDLCNKHLADQGFYRNQGRALCRECNQKEKAKGRGRYVCQKCHAHIDEQPLTFRGDPYHPYHFKCTTCG  170 (332)
T ss_pred             hccccCcccchhHHHHHHHhhhhhHhhcchHHhhhhhhhhcccccceeehhhhhhhcccccccccCCCCCccceeccccc
Confidence            7777764310                                                             0        


Q ss_pred             ---------------ccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHH
Q 029230           98 ---------------KVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH  162 (197)
Q Consensus        98 ---------------~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy  162 (197)
                                     +....-..+.|+|..|.+||. ...|.++|+.||.++|+|+.|.+|+-+...+++.|.+||+.+|
T Consensus       171 keL~sdaRevk~eLyClrChD~mgipiCgaC~rpIe-ervi~amgKhWHveHFvCa~CekPFlGHrHYEkkGlaYCe~h~  249 (332)
T KOG2272|consen  171 KELTSDAREVKGELYCLRCHDKMGIPICGACRRPIE-ERVIFAMGKHWHVEHFVCAKCEKPFLGHRHYEKKGLAYCETHY  249 (332)
T ss_pred             ccccchhhhhccceeccccccccCCcccccccCchH-HHHHHHhccccchhheeehhcCCcccchhhhhhcCchhHHHHH
Confidence                           000000134589999999996 3446799999999999999999999999999999999999999


Q ss_pred             HhHhcCCCCCCCCCCchhhhc
Q 029230          163 IQLFREKGNYSQLESDLEKSQ  183 (197)
Q Consensus       163 ~~~~~~k~~~~~~~~~~~~~~  183 (197)
                      .++||.-|..|...+.-.+-.
T Consensus       250 ~qLfG~~CF~C~~~i~G~vv~  270 (332)
T KOG2272|consen  250 HQLFGNLCFICNRVIGGDVVS  270 (332)
T ss_pred             HHHhhhhheecCCccCccHHH
Confidence            999999999888776655443

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

Probab=99.91  E-value=1.4e-25  Score=185.74  Aligned_cols=124  Identities=27%  Similarity=0.647  Sum_probs=111.6

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccCCCeee-cCCeeeccccHHHHhhccCCcccccCCCCcccC
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNS-FEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVK   86 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~-~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~   86 (197)
                      ...+|..|++.|+ +..|.|+|+.||+.||+|..|++.|++..|.. .++++||..||++.|+                 
T Consensus       333 tlekC~~Cg~~I~-d~iLrA~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfA-----------------  394 (468)
T KOG1701|consen  333 TLEKCNKCGEPIM-DRILRALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFA-----------------  394 (468)
T ss_pred             HHHHHhhhhhHHH-HHHHHhcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcC-----------------
Confidence            3468999999998 78899999999999999999999999999965 4789999999999998                 


Q ss_pred             CCCcccccCccccccccCCCCCCCCCCCceeecCc------eeeecCccccccccccCcCCCCCC----CCCeeeeCCee
Q 029230           87 PEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTE------KVSVNGAAYHRSCFKCSHGGCTIS----PSNYIAHEGKL  156 (197)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e------~v~~~g~~~H~~CF~C~~C~~~l~----~~~~~~~dg~~  156 (197)
                                           ++|+.|+++|.+.+      +|++|++.||.+|++|..|+..|+    +...|..||.+
T Consensus       395 ---------------------PrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS~e~e~qgCyPld~Hl  453 (468)
T KOG1701|consen  395 ---------------------PRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLSSEEEGQGCYPLDGHL  453 (468)
T ss_pred             ---------------------cchhhccCCccCCCCCcceEEEEEccccccccceehhhcCccccccCCCCcceeccCce
Confidence                                 99999999998764      478999999999999999999998    34689999999


Q ss_pred             ecHHHHHhHhcCCC
Q 029230          157 YCKHHHIQLFREKG  170 (197)
Q Consensus       157 yC~~cy~~~~~~k~  170 (197)
                      +|+.|..++....+
T Consensus       454 lCk~Ch~~Rl~~~~  467 (468)
T KOG1701|consen  454 LCKTCHLKRLQAGS  467 (468)
T ss_pred             eechhhhhhhcccC
Confidence            99999998876543

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

Probab=99.88  E-value=1.1e-24  Score=172.26  Aligned_cols=125  Identities=26%  Similarity=0.567  Sum_probs=112.6

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCC
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKP   87 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~   87 (197)
                      ..++|++|++.|.+..++.++++.||..|++|+.|...|.+..|. ++|.+||+.+|.++|+                  
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~drCFs-R~~s~yCkedFfKrfG------------------   92 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLADRCFS-REGSVYCKEDFFKRFG------------------   92 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHHHHhh-cCCceeehHHHHHHhC------------------
Confidence            679999999999977778999999999999999999999976655 8999999999999998                  


Q ss_pred             CCcccccCccccccccCCCCCCCCCCCceeecCceee-ecCccccccccccCcCCCCCCC-CCee-eeCCeeecHHHHHh
Q 029230           88 EKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVS-VNGAAYHRSCFKCSHGGCTISP-SNYI-AHEGKLYCKHHHIQ  164 (197)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~-~~g~~~H~~CF~C~~C~~~l~~-~~~~-~~dg~~yC~~cy~~  164 (197)
                                          .+|..|...|.+.+.|. |.+.+||..||.|..|+++|.. +.|+ +.|+++.|+.+|++
T Consensus        93 --------------------TKCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~iC~R~L~TGdEFYLmeD~rLvCK~DYE~  152 (383)
T KOG4577|consen   93 --------------------TKCSACQEGIPPTQVVRKAQDFVYHLHCFACFICKRQLATGDEFYLMEDARLVCKDDYET  152 (383)
T ss_pred             --------------------CcchhhcCCCChHHHHHHhhcceeehhhhhhHhhhcccccCCeeEEeccceeehhhhHHH
Confidence                                89999999999998774 9999999999999999999985 4555 57899999999999


Q ss_pred             HhcCCCC
Q 029230          165 LFREKGN  171 (197)
Q Consensus       165 ~~~~k~~  171 (197)
                      .-...|.
T Consensus       153 Ak~k~~~  159 (383)
T KOG4577|consen  153 AKQKHCN  159 (383)
T ss_pred             HHhcccc
Confidence            8776664

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

Probab=99.87  E-value=8.5e-24  Score=164.58  Aligned_cols=117  Identities=24%  Similarity=0.490  Sum_probs=109.9

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCC
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKP   87 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~   87 (197)
                      +.++|..|.++|. +.++.++|+.||.+.|+|+.|.+|+-+...|++.|.+||+.+|.++|+                  
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            4689999999997 788999999999999999999999998899999999999999999998                  


Q ss_pred             CCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCC-CCeeeeCCeeecHHHHHh
Q 029230           88 EKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP-SNYIAHEGKLYCKHHHIQ  164 (197)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~-~~~~~~dg~~yC~~cy~~  164 (197)
                                          ..|..|+++|. ++.|.++++.|.++||.|+.|++.|.. .+|++.|-+|.|+.||.+
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                                89999999996 677899999999999999999999986 689999999999999974

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

Probab=99.86  E-value=8.9e-23  Score=174.43  Aligned_cols=161  Identities=21%  Similarity=0.367  Sum_probs=122.8

Q ss_pred             ccccccccceecceeEEeCCccccccccccccccccccCCCeeecCC-eeeccccHHHHhhccCCcccccCCCCcccCCC
Q 029230           10 QKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEG-VLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPE   88 (197)
Q Consensus        10 ~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g-~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~   88 (197)
                      ..|.+|.+.-. ++++.+.++.||..||+|..|+..|..+.|+.+++ ++|+.....           .++....+.++.
T Consensus        17 i~c~~c~~kc~-gevlrv~d~~fhi~cf~c~~cg~~la~~gff~k~~~~~ygt~~c~-----------~~~~gevvsa~g   84 (670)
T KOG1044|consen   17 IKCDKCRKKCS-GEVLRVNDNHFHINCFQCKKCGRNLAEGGFFTKPENRLYGTDDCR-----------AFVEGEVVSTLG   84 (670)
T ss_pred             eehhhhCCccc-cceeEeeccccceeeeeccccCCCcccccceecccceeecccchh-----------hhccceeEeccc
Confidence            46999999987 99999999999999999999999999999888765 567663322           122222222222


Q ss_pred             CcccccC------------------------------ccccccccCCCCCCCCCCCceeecCceeeecCccccccccccC
Q 029230           89 KLVENEN------------------------------AQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCS  138 (197)
Q Consensus        89 ~~~~~~~------------------------------~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~  138 (197)
                      +..|..+                              +.........+...|++|++.|..++.+.|+++.||+.||+|.
T Consensus        85 ktyh~~cf~cs~ck~pf~~g~~vt~~gk~~~c~~c~~~~~~~p~~~~~ps~cagc~~~lk~gq~llald~qwhv~cfkc~  164 (670)
T KOG1044|consen   85 KTYHPKCFSCSTCKSPFKSGDKVTFSGKECLCQTCSQPMPVSPAESYGPSTCAGCGEELKNGQALLALDKQWHVSCFKCK  164 (670)
T ss_pred             ceeccccceecccCCCCCCCCeeeecchhhhhhhhcCcccCCcccccCCccccchhhhhhccceeeeeccceeeeeeehh
Confidence            2222110                              0111111112457899999999999989999999999999999


Q ss_pred             cCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCCCCchhhhc
Q 029230          139 HGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLEKSQ  183 (197)
Q Consensus       139 ~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~~~~~~~~~  183 (197)
                      .|...|.+ .|+.+||.|||+.+|.+.||.||.+|..++..-|-+
T Consensus       165 ~c~~vL~g-ey~skdg~pyce~dy~~~fgvkc~~c~~fisgkvLq  208 (670)
T KOG1044|consen  165 SCSAVLNG-EYMSKDGVPYCEKDYQAKFGVKCEECEKFISGKVLQ  208 (670)
T ss_pred             hhcccccc-eeeccCCCcchhhhhhhhcCeehHHhhhhhhhhhhh
Confidence            99999887 899999999999999999999999999887655443

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

Probab=99.84  E-value=9.5e-22  Score=171.72  Aligned_cols=132  Identities=24%  Similarity=0.585  Sum_probs=121.9

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCC
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKP   87 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~   87 (197)
                      ..+.|..|+..|.....+.++++.||+.+|.|..|...|....|...+|.+||..||.+.++                  
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            45899999999984489999999999999999999999999999999999999999999987                  


Q ss_pred             CCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230           88 EKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                                          +.|.+|+++|. ++.|.+.++.||++||.|..|+++|....|+..||.|||+.||.++++
T Consensus       364 --------------------p~C~~C~~~i~-~~~v~a~~~~wH~~cf~C~~C~~~~~~~~~~~~~~~pyce~~~~~~~~  422 (479)
T KOG1703|consen  364 --------------------PNCKRCLLPIL-EEGVCALGRLWHPECFVCADCGKPLKNSSFFESDGEPYCEDHYKKLFT  422 (479)
T ss_pred             --------------------ccccccCCchH-HhHhhhccCeechhceeeecccCCCCCCcccccCCccchhhhHhhhcc
Confidence                                99999999998 556888899999999999999999999999999999999999999999


Q ss_pred             CCCCCCCCCCc
Q 029230          168 EKGNYSQLESD  178 (197)
Q Consensus       168 ~k~~~~~~~~~  178 (197)
                      ++|.+|.....
T Consensus       423 ~~~~~~~~p~~  433 (479)
T KOG1703|consen  423 TKCDYCKKPVE  433 (479)
T ss_pred             ccchhccchhH
Confidence            99988866543

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

Probab=99.82  E-value=3e-21  Score=150.20  Aligned_cols=179  Identities=44%  Similarity=0.840  Sum_probs=143.1

Q ss_pred             CCCCCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCC-cccccCCCC
Q 029230            4 PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGS-LEKSFEGTP   82 (197)
Q Consensus         4 ~~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~-~~~~~~~~~   82 (197)
                      ++......|..|++.|+..+.+...|..||..||+|..|.+.|....+..+++.+||+.+|...+++.+. ..+.++...
T Consensus         2 ~~~~~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~   81 (200)
T KOG1700|consen    2 SFTGTTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAG   81 (200)
T ss_pred             CcccccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCcccccccccccccC
Confidence            4556678999999999998999999999999999999999999999999999999999988888887653 233333222


Q ss_pred             cccCCCCcccccCc--cccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHH
Q 029230           83 KIVKPEKLVENENA--QKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKH  160 (197)
Q Consensus        83 ~~~~~~~~~~~~~~--~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~  160 (197)
                      .+.....+....+.  ......+.++...|.+|.+.+++.|.+...+..||..||+|+.|+..|+.+.+....|.+||..
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~c~~c~k~vy~~Ek~~~~~~~~hk~cfrc~~~~~~ls~~~~~~~~g~l~~~~  161 (200)
T KOG1700|consen   82 GLGKDGKSLNESKPNQSAKFQVFAGEKEKCARCQKTVYPLEKVTGNGLEFHKSCFRCTHCGKKLSPKNYAALEGVLYCKH  161 (200)
T ss_pred             CCCcccccccccccccchhHHhhhccccccccccceeeehHHHhhhhhhhhhhheeecccccccCCcchhhcCCccccch
Confidence            22122222222222  2344556777899999999999999999999999999999999999999999999999999999


Q ss_pred             HHHhHhcCCCCCCCCCCchhhh
Q 029230          161 HHIQLFREKGNYSQLESDLEKS  182 (197)
Q Consensus       161 cy~~~~~~k~~~~~~~~~~~~~  182 (197)
                      ++.+++..+..+-.+.......
T Consensus       162 ~~~~~~~~~~~~~~~~~~~~~~  183 (200)
T KOG1700|consen  162 HFAQLFKGKGNYNEGFGARENK  183 (200)
T ss_pred             hhheeecCCCcccccchhhhhh
Confidence            9999888888877776655533

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

Probab=99.79  E-value=1e-20  Score=165.28  Aligned_cols=117  Identities=26%  Similarity=0.645  Sum_probs=108.8

Q ss_pred             CCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccC
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVK   86 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~   86 (197)
                      ...++|.+|.++|. ++.|.+.++.||++||.|..|+++|....|+..++.+||+.||.++++                 
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            35689999999998 888999999999999999999999999999999999999999999986                 


Q ss_pred             CCCcccccCccccccccCCCCCCCCCCCceeecCce-eeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHH
Q 029230           87 PEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH  162 (197)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy  162 (197)
                                           ++|..|.++|..+.. |.+++..||..||+|..|.+.|.++.|+...++|+|..|+
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                                 789999999876654 7899999999999999999999999999999999999875

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

Probab=99.75  E-value=3.8e-19  Score=152.39  Aligned_cols=115  Identities=21%  Similarity=0.564  Sum_probs=105.3

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCC
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKP   87 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~   87 (197)
                      +...|++|++.|..++.+.|+++.||..||+|..|...|. +.|..++|.+||+.||++.|+                  
T Consensus       132 ~ps~cagc~~~lk~gq~llald~qwhv~cfkc~~c~~vL~-gey~skdg~pyce~dy~~~fg------------------  192 (670)
T KOG1044|consen  132 GPSTCAGCGEELKNGQALLALDKQWHVSCFKCKSCSAVLN-GEYMSKDGVPYCEKDYQAKFG------------------  192 (670)
T ss_pred             CCccccchhhhhhccceeeeeccceeeeeeehhhhccccc-ceeeccCCCcchhhhhhhhcC------------------
Confidence            5578999999999999999999999999999999999997 578899999999999999998                  


Q ss_pred             CCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCC-CCeeeeCCeeecHHHH
Q 029230           88 EKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP-SNYIAHEGKLYCKHHH  162 (197)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~-~~~~~~dg~~yC~~cy  162 (197)
                                          .+|..|.+-|. +..|.|.|++||+.|-+|..|+..++. ++.++.+..+|-..|-
T Consensus       193 --------------------vkc~~c~~fis-gkvLqag~kh~HPtCARCsRCgqmF~eGEEMYlQGs~iWHP~C~  247 (670)
T KOG1044|consen  193 --------------------VKCEECEKFIS-GKVLQAGDKHFHPTCARCSRCGQMFGEGEEMYLQGSEIWHPDCK  247 (670)
T ss_pred             --------------------eehHHhhhhhh-hhhhhccCcccCcchhhhhhhccccccchheeeccccccCCccc
Confidence                                89999999997 556789999999999999999999984 6788888888888885

>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=99.66  E-value=1.8e-16  Score=99.63  Aligned_cols=57  Identities=35%  Similarity=0.792  Sum_probs=53.4

Q ss_pred             CCCCCceeecCcee-eecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHh
Q 029230          110 CVGCDRTVYPTEKV-SVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF  166 (197)
Q Consensus       110 C~~C~~~I~~~e~v-~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~  166 (197)
                      |++|+++|.+.+.+ .++|+.||++||+|..|+++|.++.|+..+|++||+.||.++|
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            78999999988875 5999999999999999999999988999999999999999986

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=99.59  E-value=1.4e-15  Score=95.54  Aligned_cols=57  Identities=28%  Similarity=0.773  Sum_probs=53.0

Q ss_pred             ccccccceecceeE-EeCCccccccccccccccccccCCCeeecCCeeeccccHHHHh
Q 029230           12 CMACDKTVYLVDKL-TADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF   68 (197)
Q Consensus        12 C~~C~~~I~~~~~~-~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~   68 (197)
                      |.+|+++|..++.+ .++|+.||++||+|..|+++|.++.|+..+|++||+.||.++|
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            78999999977765 7999999999999999999999988999999999999998875

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=99.17  E-value=1.6e-12  Score=103.57  Aligned_cols=74  Identities=26%  Similarity=0.475  Sum_probs=65.3

Q ss_pred             CCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCCCCchh
Q 029230          106 TRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLE  180 (197)
Q Consensus       106 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~~~~~~  180 (197)
                      ..++|++|++.|.+.-.+.++++.||..|++|+.|+.+|.. ..+.++|.+||+++|-++||.||+.|+.-+++-
T Consensus        32 eip~CagC~q~IlDrFilKvl~R~wHs~CLkCs~C~~qL~d-rCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPt  105 (383)
T KOG4577|consen   32 EIPICAGCDQHILDRFILKVLDRHWHSSCLKCSDCHDQLAD-RCFSREGSVYCKEDFFKRFGTKCSACQEGIPPT  105 (383)
T ss_pred             ccccccchHHHHHHHHHHHHHhhhhhhhhcchhhhhhHHHH-HHhhcCCceeehHHHHHHhCCcchhhcCCCChH
Confidence            34899999999986544579999999999999999999987 789999999999999999999999888766543

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

Probab=98.90  E-value=1.1e-09  Score=62.65  Aligned_cols=37  Identities=32%  Similarity=0.769  Sum_probs=33.2

Q ss_pred             CCCCCCceeecC-ceeeecCccccccccccCcCCCCCC
Q 029230          109 KCVGCDRTVYPT-EKVSVNGAAYHRSCFKCSHGGCTIS  145 (197)
Q Consensus       109 ~C~~C~~~I~~~-e~v~~~g~~~H~~CF~C~~C~~~l~  145 (197)
                      +|.+|+++|.+. ..+.+.++.||++||+|..|+++|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            589999999987 5577999999999999999999985

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=98.78  E-value=4.1e-09  Score=60.19  Aligned_cols=37  Identities=35%  Similarity=0.729  Sum_probs=33.6

Q ss_pred             cccccccceecc-eeEEeCCcccccccccccccccccc
Q 029230           11 KCMACDKTVYLV-DKLTADNRVYHKACFRCHHCKGTLK   47 (197)
Q Consensus        11 ~C~~C~~~I~~~-~~~~~~g~~~H~~CF~C~~C~~~L~   47 (197)
                      +|.+|+++|.+. ..+.+.++.||+.||+|..|+.+|.
T Consensus         1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~   38 (39)
T smart00132        1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG   38 (39)
T ss_pred             CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence            589999999976 6788999999999999999999985

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=98.68  E-value=9e-09  Score=80.33  Aligned_cols=70  Identities=43%  Similarity=0.842  Sum_probs=63.1

Q ss_pred             CCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCC-CCCC
Q 029230          106 TRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGN-YSQL  175 (197)
Q Consensus       106 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~-~~~~  175 (197)
                      ...+|.+|++.|+..+.+...|..||+.||+|..|.+.|..+.+...++.+||+.||...++++.. +..+
T Consensus         6 ~~~kc~~c~k~vy~~e~~~~~g~~~hk~c~~c~~~~k~l~~~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~   76 (200)
T KOG1700|consen    6 TTDKCNACGKTVYFVEKVQKDGVDFHKECFKCEKCKKTLTLSGYSEHEGVPYCKNCHVAQFGPKGGGFGKG   76 (200)
T ss_pred             ccchhhhccCcchHHHHHhccCcchhhhHHhccccccccccccccccccccccccchHhhhCccccccccc
Confidence            346999999999999988899999999999999999999999999999999999999999998885 4444

>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]

Probab=98.23  E-value=6e-08  Score=74.32  Aligned_cols=59  Identities=34%  Similarity=0.660  Sum_probs=54.9

Q ss_pred             CCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHh
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF  166 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~  166 (197)
                      ..|..|++.+++.|.|.-+++.||..||+|..|+.+|.-..+...|.+|||..+|.+..
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            56889999999999999999999999999999999999888888999999999998765

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

Probab=97.97  E-value=9.7e-07  Score=70.17  Aligned_cols=111  Identities=18%  Similarity=0.478  Sum_probs=88.5

Q ss_pred             cccceecceeEEeCCcccccccccccccccccc--CCCeeecCCeeeccccHHH--HhhccCCcccccCCCCcccCCCCc
Q 029230           15 CDKTVYLVDKLTADNRVYHKACFRCHHCKGTLK--LSNFNSFEGVLYCRPHFDQ--LFKRTGSLEKSFEGTPKIVKPEKL   90 (197)
Q Consensus        15 C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~c~~~--~~~~~~~~~~~~~~~~~~~~~~~~   90 (197)
                      |+..|.+...+.+.+..||..|..|..|...|.  ...|.. +|..||..+|.+  .+.                     
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~---------------------   59 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFS---------------------   59 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhcc---------------------
Confidence            667777656677779999999999999999998  555666 999999999987  333                     


Q ss_pred             ccccCccccccccCCCCCCCCCCCceeecCceee-ecCccccccccccCcCCCCCC-CCCeeeeCC-eeecHHHHHhH
Q 029230           91 VENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVS-VNGAAYHRSCFKCSHGGCTIS-PSNYIAHEG-KLYCKHHHIQL  165 (197)
Q Consensus        91 ~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~-~~g~~~H~~CF~C~~C~~~l~-~~~~~~~dg-~~yC~~cy~~~  165 (197)
                                       .+|.+|...+...+.|. +..+. |..||.|..|...+. +..+.+.+. +.+|..++.+.
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                             78999999997666664 66666 999999999988665 456666554 99999888654

>KOG1702 consensus Nebulin repeat protein [Cytoskeleton]

Probab=97.91  E-value=9.3e-07  Score=67.86  Aligned_cols=61  Identities=33%  Similarity=0.802  Sum_probs=55.1

Q ss_pred             CccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230            9 QQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus         9 ~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      ...|..|++.+++.+.+..+++.||..||.|..|+.+|.-..|--.+.++||..+|....+
T Consensus         4 k~n~~~cgk~vYPvE~v~cldk~whk~cfkce~c~mtlnmKnyKgy~kkpycn~hYpkq~a   64 (264)
T KOG1702|consen    4 KCNREDCGKTVYPVEEVKCLDKVWHKQCFKCEVCGMTLNMKNYKGYDKKPYCNPHYPKQVA   64 (264)
T ss_pred             cchhhhhccccccHHHHhhHHHHHHHHhheeeeccCChhhhhccccccCCCcCccccccee
Confidence            4678899999999999999999999999999999999998888888999999999965443

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

Probab=93.43  E-value=0.025  Score=44.71  Aligned_cols=63  Identities=21%  Similarity=0.514  Sum_probs=49.6

Q ss_pred             CCceeecCceeeecCccccccccccCcCCCCCC--CCCeeeeCCeeecHHHHHh--HhcCCCCCCCCC
Q 029230          113 CDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTIS--PSNYIAHEGKLYCKHHHIQ--LFREKGNYSQLE  176 (197)
Q Consensus       113 C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~--~~~~~~~dg~~yC~~cy~~--~~~~k~~~~~~~  176 (197)
                      |+..|.+...+.+.+..||..|..|..|...|.  ...|.. +|..||...|..  .+..+|.-+...
T Consensus         2 ~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~g~~~~~~d~~~~~~~~~rr~rt~~~   68 (235)
T KOG0490|consen    2 CGRQILDRYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSK-DGSIYCKRDYQREFKFSKRCARCKFT   68 (235)
T ss_pred             CCccccchHHhhcccHHHHHHHHhhhhhcchhccCCCcccC-CCcccccccchhhhhccccccCCCCC
Confidence            666776555566779999999999999999997  445556 999999999998  777777644443

>PF14446 Prok-RING_1: Prokaryotic RING finger family 1

Probab=92.52  E-value=0.088  Score=32.08  Aligned_cols=36  Identities=33%  Similarity=0.696  Sum_probs=26.2

Q ss_pred             CCCCCCCceeecCce-ee--ecCcccccccc----ccCc--CCCC
Q 029230          108 DKCVGCDRTVYPTEK-VS--VNGAAYHRSCF----KCSH--GGCT  143 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~-v~--~~g~~~H~~CF----~C~~--C~~~  143 (197)
                      .+|..|+++|.+++- |.  .-+..||++|.    .|..  |+.+
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            789999999985543 43  56788999988    4655  5544

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

Probab=89.98  E-value=0.11  Score=35.86  Aligned_cols=31  Identities=23%  Similarity=0.548  Sum_probs=21.9

Q ss_pred             CCCCCCCceeecCceee-ecCccccccccccC
Q 029230          108 DKCVGCDRTVYPTEKVS-VNGAAYHRSCFKCS  138 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~-~~g~~~H~~CF~C~  138 (197)
                      -+|..|+++|+.++..+ ..+..-|.+||+=.
T Consensus         3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~   34 (101)
T PF09943_consen    3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREK   34 (101)
T ss_pred             eEEEecCCeeeecceEEEecCCcEeHHHHHHH
Confidence            35888888888887755 44467788888644

>PF14471 DUF4428: Domain of unknown function (DUF4428)

Probab=86.54  E-value=0.61  Score=28.10  Aligned_cols=29  Identities=28%  Similarity=0.515  Sum_probs=23.6

Q ss_pred             ccCcCCCCCCC-CCeeeeCCeeecHHHHHhH
Q 029230          136 KCSHGGCTISP-SNYIAHEGKLYCKHHHIQL  165 (197)
Q Consensus       136 ~C~~C~~~l~~-~~~~~~dg~~yC~~cy~~~  165 (197)
                      .|..|+..+.. ..+...|| ..|..|+.++
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            48889998875 34777888 6999999997

>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=86.31  E-value=0.57  Score=32.23  Aligned_cols=29  Identities=31%  Similarity=0.482  Sum_probs=21.7

Q ss_pred             CCCCCCCceeecCcee-eecCccccccccc
Q 029230          108 DKCVGCDRTVYPTEKV-SVNGAAYHRSCFK  136 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v-~~~g~~~H~~CF~  136 (197)
                      ..|+.|+++|.....+ ...|..+|..|++
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            6799999999765443 3667778888863

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 [].

>smart00504 Ubox Modified RING finger domain

Probab=84.36  E-value=1.4  Score=27.07  Aligned_cols=32  Identities=19%  Similarity=0.199  Sum_probs=25.8

Q ss_pred             cccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           37 FRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      |.|..|+..+.+ ......|..||+.|..+.+.
T Consensus         2 ~~Cpi~~~~~~~-Pv~~~~G~v~~~~~i~~~~~   33 (63)
T smart00504        2 FLCPISLEVMKD-PVILPSGQTYERRAIEKWLL   33 (63)
T ss_pred             cCCcCCCCcCCC-CEECCCCCEEeHHHHHHHHH
Confidence            578899988876 45567799999999988775

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

>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]

Probab=82.94  E-value=0.89  Score=28.17  Aligned_cols=34  Identities=15%  Similarity=0.337  Sum_probs=22.9

Q ss_pred             CCCCCCccccccccceecceeEEeCCccccccccccccccccc
Q 029230            4 PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTL   46 (197)
Q Consensus         4 ~~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L   46 (197)
                      ++....+.|..|+..|..++....         |.|-.|+..+
T Consensus         4 ~~~~~~~~CtSCg~~i~p~e~~v~---------F~CPnCGe~~   37 (61)
T COG2888           4 MEMKDPPVCTSCGREIAPGETAVK---------FPCPNCGEVE   37 (61)
T ss_pred             ccccCCceeccCCCEeccCCceeE---------eeCCCCCcee
Confidence            344457899999999966655433         7777777443

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

Probab=81.69  E-value=1.3  Score=28.08  Aligned_cols=33  Identities=18%  Similarity=0.304  Sum_probs=15.2

Q ss_pred             cccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           37 FRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      ++|+.|...|...--...=.+.+|..|-.+.++
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            578888887764322334457889888866665

>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule

Probab=81.61  E-value=0.29  Score=27.10  Aligned_cols=28  Identities=21%  Similarity=0.418  Sum_probs=13.0

Q ss_pred             cCcCCCCCCCCCeeeeCCeeecHHHHHh
Q 029230          137 CSHGGCTISPSNYIAHEGKLYCKHHHIQ  164 (197)
Q Consensus       137 C~~C~~~l~~~~~~~~dg~~yC~~cy~~  164 (197)
                      |..|+.+|.........+..+|..|+.+
T Consensus         6 C~~CGe~I~~~Rl~~~p~~~~C~~C~~~   33 (36)
T PF01258_consen    6 CEDCGEPIPEERLVAVPGATLCVECQER   33 (36)
T ss_dssp             -TTTSSBEEHHHHHHCTTECS-HHHHHH
T ss_pred             ccccCChHHHHHHHhCCCcEECHHHhCc
Confidence            4444544444444444555556555543

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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.

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

Probab=80.66  E-value=1.2  Score=24.90  Aligned_cols=28  Identities=21%  Similarity=0.488  Sum_probs=17.3

Q ss_pred             CCCCCceeecCce-eeecCcccccccccc
Q 029230          110 CVGCDRTVYPTEK-VSVNGAAYHRSCFKC  137 (197)
Q Consensus       110 C~~C~~~I~~~e~-v~~~g~~~H~~CF~C  137 (197)
                      |.-|+++|.+... +...++.||.-|-.|
T Consensus         1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC   29 (37)
T PF08394_consen    1 CDYCGGEITGEPIVVKIGNKVYYFCCPTC   29 (37)
T ss_pred             CCccCCcccCCEEEEEECCeEEEEECHHH
Confidence            5677888874433 347777777544444

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

---

Homologous Structure Templates

Structure Templates Detected by BLAST

Original result of BLAST against Protein Data Bank

ID	Length	Definition	E-value
Query	197
2d8y_A	91	Solution Structure Of The Lim Domain Of Epithelial		3e-15
2d8y_A	91	Solution Structure Of The Lim Domain Of Epithelial		3e-12
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		3e-09
1qli_A	113	Quail Cysteine And Glycine-Rich Protein, Nmr, 15 Mi		6e-09
1iml_A	76	Cysteine Rich Intestinal Protein, Nmr, 48 Structure		1e-06
1ctl_A	85	Structure Of The Carboxy-Terminal Lim Domain From T		3e-06
2cu8_A	76	Solution Structure Of The Lim Domain Of Human Cyste		6e-06
2o13_A	58	Solution Structure Of The C-Terminal Lim Domain Of		8e-06
2o13_A	58	Solution Structure Of The C-Terminal Lim Domain Of		2e-05
2co8_A	82	Solution Structures Of The Lim Domain Of Human Nedd		2e-05
2co8_A	82	Solution Structures Of The Lim Domain Of Human Nedd		2e-05
2o10_A	60	Solution Structure Of The N-Terminal Lim Domain Of		3e-05
1a7i_A	81	Amino-Terminal Lim Domain From Quail Cysteine And G		9e-05
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 = 78.2 bits (191), Expect = 3e-15,   Method: Compositional matrix adjust.
 Identities = 31/75 (41%), Positives = 49/75 (65%)
Query: 8  TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQL 67
           ++ C+ C KTVY +++L A+ +V+H +CFRC +C   L L  + S  G +YC+PHF+QL
Sbjct: 14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQL 73
Query: 68 FKRTGSLEKSFEGTP 82
          FK  G+ ++ F   P
Sbjct: 74 FKSKGNYDEGFGSGP 88

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

Iteration: 1
 Score = 68.2 bits (165), Expect = 3e-12,   Method: Compositional matrix adjust.
 Identities = 30/69 (43%), Positives = 43/69 (62%)
Query: 106 TRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQL 165
            R+ CV C +TVYP E++  N   +H SCF+CS+    +S   Y +  G++YCK H  QL
Sbjct: 14  ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQL 73
Query: 166 FREKGNYSQ 174
           F+ KGNY +
Sbjct: 74  FKSKGNYDE 82

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

Iteration: 1
 Score = 75.5 bits (184), Expect = 2e-14,   Method: Compositional matrix adjust.
 Identities = 51/177 (28%), Positives = 82/177 (46%), Gaps = 12/177 (6%)
Query: 4   PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
           P  G  +KC  C K VY  +++  +   +HK+CF C  CK  L  +        +YC+  
Sbjct: 2   PNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSC 61
Query: 64  FDQLFKRTGSLEKSFEGTPKIVKPEKL-----------VENENAQKVSNKFVGTRDKCVG 112
           + + +   G  +    GT    K E L             N NA +++ K VG  D C  
Sbjct: 62  YGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQK-VGGSDGCPR 120
Query: 113 CDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREK 169
           C + VY  EKV   G ++H+SCF+C+  G ++  +     +G++YCK  + + F  K
Sbjct: 121 CGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPK 177

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

Iteration: 1
 Score = 58.2 bits (139), Expect = 3e-09,   Method: Compositional matrix adjust.
 Identities = 33/98 (33%), Positives = 50/98 (51%), Gaps = 2/98 (2%)
Query: 87  PEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP 146
           P +   N N  K + KF G  +KC  C  +VY  EKV   G  +H++CF+C+  G ++  
Sbjct: 17  PHRPTTNPNTSKFAQKFGGA-EKCSACGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLES 75
Query: 147 SNYIAHEGKLYCKHHHIQLFREKG-NYSQLESDLEKSQ 183
           +     EG++YCK  + + F  KG  Y Q    L  +Q
Sbjct: 76  TTLTEKEGEIYCKGCYAKNFGPKGFGYGQGAGALVHAQ 113

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

Iteration: 1
 Score = 57.0 bits (136), Expect = 6e-09,   Method: Compositional matrix adjust.
 Identities = 33/98 (33%), Positives = 50/98 (51%), Gaps = 2/98 (2%)
Query: 87  PEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP 146
           P +   N N  K + KF G  +KC  C  +VY  EKV   G  +H++CF+C+  G ++  
Sbjct: 17  PHRPTTNPNTSKFAQKFGGA-EKCSRCGDSVYAAEKVIGAGKPWHKNCFRCAKCGKSLES 75
Query: 147 SNYIAHEGKLYCKHHHIQLFREKG-NYSQLESDLEKSQ 183
           +     EG++YCK  + + F  KG  Y Q    L  +Q
Sbjct: 76  TTLTEKEGEIYCKGCYAKNFGPKGFGYGQGAGALVHAQ 113

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

Iteration: 1
 Score = 49.3 bits (116), Expect = 1e-06,   Method: Compositional matrix adjust.
 Identities = 26/63 (41%), Positives = 35/63 (55%), Gaps = 1/63 (1%)
Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHH-HIQLFR 167
           KC  CD+ VY  E+V+  G  +HR C KC   G T++   +  HEGK YC H  +  +F 
Sbjct: 2   KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61
Query: 168 EKG 170
            KG
Sbjct: 62  PKG 64

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

Iteration: 1
 Score = 48.1 bits (113), Expect = 3e-06,   Method: Compositional matrix adjust.
 Identities = 23/66 (34%), Positives = 37/66 (56%)
Query: 104 VGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHI 163
           VG  D C  C + VY  EKV   G ++H+SCF+C+  G ++  +     +G++YCK  + 
Sbjct: 5   VGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYA 64
Query: 164 QLFREK 169
           + F  K
Sbjct: 65  KNFGPK 70

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 6e-06,   Method: Compositional matrix adjust.
 Identities = 22/50 (44%), Positives = 30/50 (60%)
Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYC 158
           KC  CD+TVY  EKVS  G  +H+ C KC     T++P  +  H+GK +C
Sbjct: 11  KCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFC 60

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

Iteration: 1
 Score = 47.0 bits (110), Expect = 8e-06,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 33/58 (56%)
Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
          KC  C K+VY  +K+    + +HK CFRC  C  +L+ +N    +G LYC+  + + 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 = 45.8 bits (107), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 21/58 (36%), Positives = 35/58 (60%)
Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF 166
           KC  C ++VY  EKV   G  +H++CF+C+  G ++  +N    +G+LYCK  + + F
Sbjct: 1   KCPRCGKSVYAAEKVMGGGKPWHKTCFRCAICGKSLESTNVTDKDGELYCKVCYAKNF 58

>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 = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 19/62 (30%), Positives = 32/62 (51%), Gaps = 2/62 (3%)
Query: 7  GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSF--EGVLYCRPHF 64
          G    C  C + +Y++++L  +   +H++CFRCH C+ TL    +     +G  YC  H 
Sbjct: 13 GAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHL 72
Query: 65 DQ 66
           Q
Sbjct: 73 PQ 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 = 45.4 bits (106), Expect = 2e-05,   Method: Compositional matrix adjust.
 Identities = 23/60 (38%), Positives = 30/60 (50%), Gaps = 2/60 (3%)
Query: 104 VGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAH--EGKLYCKHH 161
            G  D C  C   +Y  E++ VNG  +HRSCF+C     T+ P  Y  H  +G  YC  H
Sbjct: 12  AGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQH 71

>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 = 19/51 (37%), Positives = 31/51 (60%)
Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCK 159
           KC  C++TVY  E++  NG ++H++CF C      +  +   AHE ++YCK
Sbjct: 3   KCGACEKTVYHAEEIQCNGRSFHKTCFHCMACRKALDSTTVAAHESEIYCK 53

>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 = 9e-05,   Method: Compositional matrix adjust.
 Identities = 22/78 (28%), Positives = 36/78 (46%)
Query: 4  PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
          P  G   KC AC +TVY  +++  D R +H+ CF C  C+  L  +     +  +YC+  
Sbjct: 2  PNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSC 61
Query: 64 FDQLFKRTGSLEKSFEGT 81
          + + +   G       GT
Sbjct: 62 YGKKYGPKGYGYGQGAGT 79

>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 = 25/77 (32%), Positives = 38/77 (49%), Gaps = 1/77 (1%)
Query: 105 GTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQ 164
           G  +KC  C RTVY  E+V  +G ++HR CF C      +  +    H+ ++YCK  + +
Sbjct: 5   GGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGK 64
Query: 165 LFREKG-NYSQLESDLE 180
            +  KG  Y Q    L 
Sbjct: 65  KYGPKGYGYGQGAGTLN 81

Structure Templates Detected by RPS-BLAST

Original result of RPS-BLAST against PDB70 database

ID	Length	Definition	E-value
Query	197
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	1e-47
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	2e-25
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	1e-24
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	5e-24
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	1e-23
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	2e-22
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	5e-22
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	2e-19
2co8_A	82	NEDD9 interacting protein with calponin homology a	8e-22
2co8_A	82	NEDD9 interacting protein with calponin homology a	3e-19
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	1e-17
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	3e-14
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	5e-17
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	7e-08
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-15
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	1e-09
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	2e-15
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	1e-13
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	2e-14
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	2e-07
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	4e-13
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	4e-05
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	8e-13
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	3e-06
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	5e-06
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	4e-12
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	1e-10
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	6e-12
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	6e-11
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	7e-12
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	1e-09
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	9e-04
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	2e-11
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	1e-09
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	4e-11
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	6e-09
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	3e-10
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	7e-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	1e-09
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	1e-09
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	7e-09
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	2e-09
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	1e-08
2cuq_A	80	Four and A half LIM domains 3; structural genomics	3e-09
2cuq_A	80	Four and A half LIM domains 3; structural genomics	1e-07
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	3e-09
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	4e-08
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	3e-09
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	5e-09
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	3e-09
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	2e-08
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	7e-09
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	1e-08
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	9e-09
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	3e-07
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	2e-08
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	2e-06
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	2e-08
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	9e-07
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	2e-08
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	2e-07
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	5e-08
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	2e-06
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	6e-08
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	6e-07
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	9e-08
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	1e-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	9e-07
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	6e-07
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	1e-04
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	1e-06
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	2e-05
2cor_A	79	Pinch protein; LIM domain, particularly interestin	3e-05
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	7e-05
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	8e-05
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	6e-04
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	9e-04
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	8e-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 =  153 bits (388), Expect = 1e-47
 Identities = 48/178 (26%), Positives = 77/178 (43%), Gaps = 10/178 (5%)

Query: 4   PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
           P  G  +KC  C K VY  +++  +   +HK+CF C  CK  L  +        +YC+  
Sbjct: 2   PNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSC 61

Query: 64  FDQLFKRTGSLEKSFEGTPKIVKPEKL----------VENENAQKVSNKFVGTRDKCVGC 113
           + + +   G  +    GT    K E L                     + VG  D C  C
Sbjct: 62  YGKKYGPKGKGKGMGAGTLSTDKGESLGIKYEEGQSHRPTNPNASRMAQKVGGSDGCPRC 121

Query: 114 DRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGN 171
            + VY  EKV   G ++H+SCF+C+  G ++  +     +G++YCK  + + F  KG 
Sbjct: 122 GQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGF 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 = 71.6 bits (175), Expect = 6e-16
 Identities = 20/72 (27%), Positives = 33/72 (45%)

Query: 103 FVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH 162
             G   KC  C + VY  E+V   G+++H+SCF C      +  +    H  ++YCK  +
Sbjct: 3   NWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCY 62

Query: 163 IQLFREKGNYSQ 174
            + +  KG    
Sbjct: 63  GKKYGPKGKGKG 74

>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 = 98.4 bits (245), Expect = 2e-27
 Identities = 31/82 (37%), Positives = 49/82 (59%)

Query: 2  ASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR 61
                 ++ C+ C KTVY +++L A+ +V+H +CFRC +C   L L  + S  G +YC+
Sbjct: 8  MKFQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCK 67

Query: 62 PHFDQLFKRTGSLEKSFEGTPK 83
          PHF+QLFK  G+ ++ F   P 
Sbjct: 68 PHFNQLFKSKGNYDEGFGSGPS 89

>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 = 93.8 bits (233), Expect = 2e-25
 Identities = 30/77 (38%), Positives = 43/77 (55%)

Query: 98  KVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLY 157
                    R+ CV C +TVYP E++  N   +H SCF+CS+    +S   Y +  G++Y
Sbjct: 6   SGMKFQAPARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIY 65

Query: 158 CKHHHIQLFREKGNYSQ 174
           CK H  QLF+ KGNY +
Sbjct: 66  CKPHFNQLFKSKGNYDE 82

>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 = 90.9 bits (226), Expect = 1e-24
 Identities = 27/73 (36%), Positives = 38/73 (52%), Gaps = 1/73 (1%)

Query: 100 SNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYC- 158
           S+   G   KC  CD+TVY  EKVS  G  +H+ C KC     T++P  +  H+GK +C 
Sbjct: 2   SSGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCH 61

Query: 159 KHHHIQLFREKGN 171
           K  +  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 = 89.4 bits (222), Expect = 5e-24
 Identities = 24/73 (32%), Positives = 36/73 (49%), Gaps = 1/73 (1%)

Query: 2  ASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYC- 60
          +S   G   KC  CDKTVY  +K+++  + +HK C +C  C  TL        +G  +C 
Sbjct: 2  SSGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCH 61

Query: 61 RPHFDQLFKRTGS 73
          +P +  LF    S
Sbjct: 62 KPCYATLFGSGPS 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 = 88.6 bits (220), Expect = 1e-23
 Identities = 24/73 (32%), Positives = 37/73 (50%), Gaps = 1/73 (1%)

Query: 103 FVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH 162
             G  +KC  C RTVY  E+V  +G ++HR CF C      +  +    H+ ++YCK  +
Sbjct: 3   NWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCY 62

Query: 163 IQLFREKG-NYSQ 174
            + +  KG  Y Q
Sbjct: 63  GKKYGPKGYGYGQ 75

>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 = 85.2 bits (211), Expect = 2e-22
 Identities = 20/70 (28%), Positives = 34/70 (48%)

Query: 4  PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
          P  G   KC AC +TVY  +++  D R +H+ CF C  C+  L  +     +  +YC+  
Sbjct: 2  PNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSC 61

Query: 64 FDQLFKRTGS 73
          + + +   G 
Sbjct: 62 YGKKYGPKGY 71

>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 = 83.9 bits (208), Expect = 5e-22
 Identities = 26/65 (40%), Positives = 35/65 (53%), Gaps = 1/65 (1%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKH-HHIQLFR 167
           KC  CD+ VY  E+V+  G  +HR C KC   G T++   +  HEGK YC H  +  +F 
Sbjct: 2   KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61

Query: 168 EKGNY 172
            KG  
Sbjct: 62  PKGFG 66

>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 = 77.4 bits (191), Expect = 2e-19
 Identities = 21/63 (33%), Positives = 31/63 (49%), Gaps = 1/63 (1%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYC-RPHFDQLFK 69
          KC  CDK VY  +++T+  + +H+ C +C  C  TL        EG  YC  P +  +F 
Sbjct: 2  KCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFG 61

Query: 70 RTG 72
            G
Sbjct: 62 PKG 64

>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 = 83.8 bits (207), Expect = 8e-22
 Identities = 20/75 (26%), Positives = 33/75 (44%), Gaps = 2/75 (2%)

Query: 1  MASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSF--EGVL 58
                G    C  C + +Y++++L  +   +H++CFRCH C+ TL    +     +G  
Sbjct: 7  GQHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHF 66

Query: 59 YCRPHFDQLFKRTGS 73
          YC  H  Q      S
Sbjct: 67 YCLQHLPQTDSGPSS 81

>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 = 77.3 bits (190), Expect = 3e-19
 Identities = 24/79 (30%), Positives = 35/79 (44%), Gaps = 2/79 (2%)

Query: 95  NAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAH-- 152
           +     ++  G  D C  C   +Y  E++ VNG  +HRSCF+C     T+ P  Y  H  
Sbjct: 3   SGSSGQHQEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPG 62

Query: 153 EGKLYCKHHHIQLFREKGN 171
           +G  YC  H  Q      +
Sbjct: 63  DGHFYCLQHLPQTDSGPSS 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 = 72.8 bits (179), Expect = 1e-17
 Identities = 19/64 (29%), Positives = 25/64 (39%), Gaps = 1/64 (1%)

Query: 6  GGTQQKCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHF 64
          G     C  C       +K + ++  +YH+ CF C  C        F  FEG  YC   F
Sbjct: 8  GSASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDF 67

Query: 65 DQLF 68
            LF
Sbjct: 68 QMLF 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 = 64.0 bits (156), Expect = 3e-14
 Identities = 20/61 (32%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 107 RDKCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQL 165
              C  C     P EK V+ NG  YH  CF C+          +   EG+ YC+H    L
Sbjct: 11  SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQML 70

Query: 166 F 166
           F
Sbjct: 71  F 71

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

 Score = 72.9 bits (179), Expect = 5e-17
 Identities = 29/164 (17%), Positives = 46/164 (28%), Gaps = 40/164 (24%)

Query: 11  KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFE--GVLYCRPHFDQLF 68
            C  C + +     L A ++ +H+ C  C  C   L       +   G   CR  + +LF
Sbjct: 4   TCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLF 63

Query: 69  KRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKV-SVNG 127
                                               G    C  CD+ +   E    V  
Sbjct: 64  ------------------------------------GQDGLCASCDKRIRAYEMTMRVKD 87

Query: 128 AAYHRSCFKCSHGGCTISP-SNYIAHEGKLYCKHHHIQLFREKG 170
             YH  CFKC+           Y+     + C+    +  +  G
Sbjct: 88  KVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDIYEWTKING 131

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

 Score = 48.6 bits (116), Expect = 7e-08
 Identities = 15/68 (22%), Positives = 27/68 (39%), Gaps = 2/68 (2%)

Query: 7   GTQQKCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKL-SNFNSFEGVLYCRPHF 64
           G    C +CDK +   +  +   ++VYH  CF+C  C+    +   +      + C    
Sbjct: 64  GQDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDI 123

Query: 65  DQLFKRTG 72
            +  K  G
Sbjct: 124 YEWTKING 131

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

 Score = 69.4 bits (170), Expect = 1e-15
 Identities = 26/159 (16%), Positives = 49/159 (30%), Gaps = 41/159 (25%)

Query: 11  KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKR 70
           +C  CD+ ++  +   A+N+ +H   F C  C   L    +        C+P + +    
Sbjct: 5   RCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHA- 63

Query: 71  TGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEK-VSVNGAA 129
                                                  C GC   + P  + V+ N  +
Sbjct: 64  -------------------------------------VVCQGCHNAIDPEVQRVTYNNFS 86

Query: 130 YH--RSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF 166
           +H    CF CS     +    ++  EG ++C     +  
Sbjct: 87  WHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKKRM 125

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

 Score = 53.2 bits (128), Expect = 1e-09
 Identities = 12/61 (19%), Positives = 22/61 (36%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFRE 168
           +C GCD  ++  E        +H   F C      ++   Y+    K  CK  +++    
Sbjct: 5   RCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAV 64

Query: 169 K 169
            
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 = 67.0 bits (164), Expect = 2e-15
 Identities = 18/62 (29%), Positives = 24/62 (38%), Gaps = 1/62 (1%)

Query: 8  TQQKCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQ 66
              C  C       +K + ++  +YH+ CF C  C        F  FEG  YC   F  
Sbjct: 10 ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQM 69

Query: 67 LF 68
          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 = 1e-13
 Identities = 20/62 (32%), Positives = 25/62 (40%), Gaps = 1/62 (1%)

Query: 106 TRDKCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQ 164
               C  C     P EK V+ NG  YH  CF C+          +   EG+ YC+H    
Sbjct: 10  ASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQM 69

Query: 165 LF 166
           LF
Sbjct: 70  LF 71

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

 Score = 67.2 bits (164), Expect = 2e-14
 Identities = 32/162 (19%), Positives = 49/162 (30%), Gaps = 42/162 (25%)

Query: 11  KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKR 70
            C  CD+ +     L A +R +H  C +C  C   L    F S    +YC+  F + F  
Sbjct: 8   MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRF-- 64

Query: 71  TGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKV-SVNGAA 129
                                                 KC  C   + PT+ V       
Sbjct: 65  ------------------------------------GTKCAACQLGIPPTQVVRRAQDFV 88

Query: 130 YHRSCFKCSHGGCTISP--SNYIAHEGKLYCKHHHIQLFREK 169
           YH  CF C      ++     Y+  + +L CK  +    +  
Sbjct: 89  YHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETAKQGG 130

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

 Score = 47.9 bits (114), Expect = 2e-07
 Identities = 18/131 (13%), Positives = 30/131 (22%), Gaps = 42/131 (32%)

Query: 11  KCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKL--SNFNSFEGVLYCRPHFDQL 67
           KC AC   +        A + VYH  CF C  CK  L      +   +  L C+  ++  
Sbjct: 67  KCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYETA 126

Query: 68  FKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNG 127
                                                  +    G   +      +    
Sbjct: 127 K--------------------------------------QGGSGGSGGSG-GGTPMVAAS 147

Query: 128 AAYHRSCFKCS 138
              H    + +
Sbjct: 148 PERHDGGLQAN 158

>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 = 63.9 bits (155), Expect = 4e-13
 Identities = 32/164 (19%), Positives = 53/164 (32%), Gaps = 40/164 (24%)

Query: 10  QKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFE--GVLYCRPHFDQL 67
           ++C  C   +     L A +  +H  C +C  C+  L     +S+   G++ CR  + +L
Sbjct: 6   KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRL 65

Query: 68  FKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKV-SVN 126
           F                                    G    C  C +++  +E V    
Sbjct: 66  F------------------------------------GNSGACSACGQSIPASELVMRAQ 89

Query: 127 GAAYHRSCFKCSHGGCTISP-SNYIAHEGKLYCKHHHIQLFREK 169
           G  YH  CF CS     + P   +    G L+C+H         
Sbjct: 90  GNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEHDRPTALING 133

>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 = 41.9 bits (98), Expect = 4e-05
 Identities = 14/64 (21%), Positives = 27/64 (42%), Gaps = 2/64 (3%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP--SNYIAHEGKLYCKHHHIQLF 166
           +C GC   +     +    + +H  C KCS     +    ++     G + C++ +I+LF
Sbjct: 7   RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 66

Query: 167 REKG 170
              G
Sbjct: 67  GNSG 70

>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 = 63.0 bits (153), Expect = 8e-13
 Identities = 32/155 (20%), Positives = 48/155 (30%), Gaps = 42/155 (27%)

Query: 11  KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKR 70
            C  CD+ +     L A +R +H  C +C  C   L    F S    +YC+  F + F  
Sbjct: 62  MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRF-- 118

Query: 71  TGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKV-SVNGAA 129
                                                 KC  C   + PT+ V       
Sbjct: 119 ------------------------------------GTKCAACQLGIPPTQVVRRAQDFV 142

Query: 130 YHRSCFKCSHGGCTISP--SNYIAHEGKLYCKHHH 162
           YH  CF C      ++     Y+  + +L CK  +
Sbjct: 143 YHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADY 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 = 44.5 bits (105), Expect = 3e-06
 Identities = 14/61 (22%), Positives = 23/61 (37%), Gaps = 1/61 (1%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFRE 168
            C GCD+ +     +      +H  C KCS     ++     +    +YCK    + F  
Sbjct: 62  MCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLA-ERCFSRGESVYCKDDFFKRFGT 120

Query: 169 K 169
           K
Sbjct: 121 K 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 = 44.1 bits (104), Expect = 5e-06
 Identities = 16/59 (27%), Positives = 23/59 (38%), Gaps = 3/59 (5%)

Query: 11  KCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKL--SNFNSFEGVLYCRPHFDQ 66
           KC AC   +        A + VYH  CF C  CK  L      +   +  L C+  ++ 
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 = 58.2 bits (141), Expect = 4e-12
 Identities = 18/59 (30%), Positives = 28/59 (47%), Gaps = 1/59 (1%)

Query: 11 KCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
           C AC +TV    + L    + +H+ CF C  C+  L   +F   +G  YC P ++  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 = 53.9 bits (130), Expect = 1e-10
 Identities = 15/59 (25%), Positives = 24/59 (40%), Gaps = 1/59 (1%)

Query: 109 KCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF 166
            C  C  TV P  + +   G  +H  CF CS     +   +++  +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 = 58.1 bits (141), Expect = 6e-12
 Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 11 KCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
          KC  C K +   D+ +     V+HK CF C +CK  +   +F       YC    +  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 = 55.5 bits (134), Expect = 6e-11
 Identities = 16/59 (27%), Positives = 25/59 (42%), Gaps = 1/59 (1%)

Query: 109 KCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF 166
           KC GC + +   ++ V   G  +H+ CF CS+    I   ++       YC   H   F
Sbjct: 17  KCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKF 75

>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 = 58.2 bits (141), Expect = 7e-12
 Identities = 23/131 (17%), Positives = 37/131 (28%), Gaps = 40/131 (30%)

Query: 11  KCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK 69
            C+ C K +    K +   NR +H  CFRC  C   L    F + +  + C     +   
Sbjct: 7   GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS 66

Query: 70  RTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKV-SVNGA 128
                                                  KC GC + +   ++     G 
Sbjct: 67  --------------------------------------PKCKGCFKAIVAGDQNVEYKGT 88

Query: 129 AYHRSCFKCSH 139
            +H+ CF    
Sbjct: 89  VWHKDCFSGPS 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 = 52.4 bits (126), Expect = 1e-09
 Identities = 13/62 (20%), Positives = 26/62 (41%), Gaps = 1/62 (1%)

Query: 109 KCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR 167
            CV C + +    K V      +H +CF+C+     ++   ++A + K+ C     +   
Sbjct: 7   GCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS 66

Query: 168 EK 169
            K
Sbjct: 67  PK 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 = 36.2 bits (84), Expect = 9e-04
 Identities = 10/33 (30%), Positives = 14/33 (42%), Gaps = 1/33 (3%)

Query: 11  KCMACDKTVYLVDK-LTADNRVYHKACFRCHHC 42
           KC  C K +   D+ +     V+HK CF     
Sbjct: 68  KCKGCFKAIVAGDQNVEYKGTVWHKDCFSGPSS 100

>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 = 56.6 bits (137), Expect = 2e-11
 Identities = 13/59 (22%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 11 KCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
           C  C KT+    + +      +H+ CF CH C+  +   +F   +   +C P +++  
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 = 51.6 bits (124), Expect = 1e-09
 Identities = 12/59 (20%), Positives = 27/59 (45%), Gaps = 1/59 (1%)

Query: 109 KCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF 166
            C  C +T+ P  + +   G+++H +CF C      I   ++I  + + +C   + +  
Sbjct: 7   GCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQH 65

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

 Score = 53.6 bits (129), Expect = 3e-10
 Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF 166
            C GC   +   + +      +H SCFKC      ++   YI+ +G  YC+  +   F
Sbjct: 17  HCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILT-GEYISKDGVPYCESDYHAQF 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 = 49.7 bits (119), Expect = 7e-09
 Identities = 16/58 (27%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
           C  C + +     L A ++ +H +CF+C  C   L    + S +GV YC   +   F
Sbjct: 17 HCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILT-GEYISKDGVPYCESDYHAQF 73

>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 = 17/67 (25%), Positives = 26/67 (38%), Gaps = 4/67 (5%)

Query: 2  ASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR 61
           S        C+ C K +     +T   + +HK CF C  C+  L    F + +   YC 
Sbjct: 1  GSSGSS---GCVQCKKPI-TTGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCL 56

Query: 62 PHFDQLF 68
            F  L+
Sbjct: 57 NCFCDLY 63

>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 = 1e-09
 Identities = 14/61 (22%), Positives = 25/61 (40%), Gaps = 1/61 (1%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFRE 168
            CV C + +  T  V+     +H+ CF C+     +S   + A +   YC +    L+  
Sbjct: 7   GCVQCKKPIT-TGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYAS 65

Query: 169 K 169
            
Sbjct: 66  G 66

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

 Score = 51.5 bits (124), Expect = 1e-09
 Identities = 15/58 (25%), Positives = 25/58 (43%), Gaps = 1/58 (1%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
           C AC + +     + A  + +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 = 49.6 bits (119), Expect = 7e-09
 Identities = 15/58 (25%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF 166
            C  C R +     V+  G  +H   F C+          +   +G  YC+ H+ QLF
Sbjct: 7   ICGACRRPIE-GRVVNAMGKQWHVEHFVCAKCEKPFLGHRHYERKGLAYCETHYNQLF 63

>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 = 50.9 bits (122), Expect = 2e-09
 Identities = 16/61 (26%), Positives = 26/61 (42%), Gaps = 1/61 (1%)

Query: 11 KCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK 69
           C  C + V      + A +RV+H  CF C  C+  L+  +F + E   YC   +    +
Sbjct: 7  GCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLE 66

Query: 70 R 70
           
Sbjct: 67 S 67

>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 = 49.4 bits (118), Expect = 1e-08
 Identities = 14/62 (22%), Positives = 22/62 (35%), Gaps = 1/62 (1%)

Query: 106 TRDKCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQ 164
               C GC   V      V      +H  CF CS     +   ++ A E + YC+  ++ 
Sbjct: 4   GSSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVA 63

Query: 165 LF 166
             
Sbjct: 64  TL 65

>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 = 3e-09
 Identities = 17/58 (29%), Positives = 27/58 (46%), Gaps = 1/58 (1%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
          +C  C KT+     +T  ++ +H+ C  C  C+  L    F S +   YC   F +LF
Sbjct: 17 RCARCSKTL-TQGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELF 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 = 46.6 bits (111), Expect = 1e-07
 Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFRE 168
           +C  C +T+     V+     +HR C  C+     ++   + + +   YC     +LF  
Sbjct: 17  RCARCSKTLTQ-GGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFAS 75

Query: 169 K 169
            
Sbjct: 76  G 76

>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 = 50.8 bits (122), Expect = 3e-09
 Identities = 17/58 (29%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
          KC  C++ V L + L+A + V+H  CF C  C  +    +F   +G  +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 = 4e-08
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 1/58 (1%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF 166
           KC GC+R V     +S     +H  CF C     + S  ++   +G+ +C+ H+    
Sbjct: 17  KCGGCNRPVL-ENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRR 73

>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 = 50.5 bits (121), Expect = 3e-09
 Identities = 14/58 (24%), Positives = 23/58 (39%), Gaps = 1/58 (1%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
           C+ C+K +     +T  ++ +H  CF C  C   L    F + E   YC   +    
Sbjct: 7  GCVKCNKAI-TSGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFV 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 = 49.7 bits (119), Expect = 5e-09
 Identities = 11/62 (17%), Positives = 23/62 (37%), Gaps = 1/62 (1%)

Query: 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR 167
             CV C++ +  +  ++     +H  CF C      ++   + A E + YC   +     
Sbjct: 6   SGCVKCNKAIT-SGGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVS 64

Query: 168 EK 169
             
Sbjct: 65  GP 66

>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 = 50.6 bits (121), Expect = 3e-09
 Identities = 15/59 (25%), Positives = 26/59 (44%), Gaps = 1/59 (1%)

Query: 11 KCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
           C  C + +    + L  ++R +H+ CFRC  C+ +L    F   +  L C   +   F
Sbjct: 17 TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAF 75

>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 = 48.6 bits (116), Expect = 2e-08
 Identities = 9/62 (14%), Positives = 22/62 (35%), Gaps = 1/62 (1%)

Query: 109 KCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR 167
            C  C + +    + +      +H  CF+C     +++   +   + +L C   +   F 
Sbjct: 17  TCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFS 76

Query: 168 EK 169
             
Sbjct: 77  SG 78

>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 = 50.9 bits (121), Expect = 7e-09
 Identities = 13/60 (21%), Positives = 26/60 (43%), Gaps = 2/60 (3%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTIS--PSNYIAHEGKLYCKHHHIQLF 166
           +C GC   +     +    + +H  C KCS     +    ++     G + C++ +I+LF
Sbjct: 63  RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 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 = 50.5 bits (120), Expect = 1e-08
 Identities = 16/68 (23%), Positives = 30/68 (44%), Gaps = 2/68 (2%)

Query: 3   SPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFE--GVLYC 60
              G + ++C  C   +     L A +  +H  C +C  C+  L     +S+   G++ C
Sbjct: 55  GSGGLSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILC 114

Query: 61  RPHFDQLF 68
           R  + +LF
Sbjct: 115 RNDYIRLF 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 = 49.8 bits (119), Expect = 9e-09
 Identities = 16/67 (23%), Positives = 22/67 (32%), Gaps = 1/67 (1%)

Query: 2  ASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR 61
           +        C  C   +     + A ++  H  CF C  C   LK   +   EG LYC 
Sbjct: 18 GAGSAQRMPLCDKCGSGIVGAV-VKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCE 76

Query: 62 PHFDQLF 68
           H     
Sbjct: 77 THARART 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 = 45.9 bits (109), Expect = 3e-07
 Identities = 14/61 (22%), Positives = 19/61 (31%), Gaps = 1/61 (1%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFRE 168
            C  C   +     V       H  CF C+     +    Y   EG+LYC+ H       
Sbjct: 27  LCDKCGSGIV-GAVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSG 85

Query: 169 K 169
            
Sbjct: 86  P 86

>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 = 48.7 bits (116), Expect = 2e-08
 Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 3/61 (4%)

Query: 11 KCMACDKTVYLVDK---LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQL 67
           C  C   +  +     ++ + R +H  CF C  C  +L    F +    + C      +
Sbjct: 7  GCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDI 66

Query: 68 F 68
           
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 = 42.9 bits (101), Expect = 2e-06
 Identities = 10/61 (16%), Positives = 20/61 (32%), Gaps = 3/61 (4%)

Query: 109 KCVGCDRTV---YPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQL 165
            C GC   +     T+ +S     +H  CF C     ++    ++     + C      +
Sbjct: 7   GCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDI 66

Query: 166 F 166
            
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 = 49.0 bits (117), Expect = 2e-08
 Identities = 17/59 (28%), Positives = 27/59 (45%), Gaps = 3/59 (5%)

Query: 11 KCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
           C  C++ +      L A  + +H   F C HCK T+    F   +G LYC   +++ F
Sbjct: 27 MCAHCNQVI--RGPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFF 83

>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 = 44.4 bits (105), Expect = 9e-07
 Identities = 13/58 (22%), Positives = 28/58 (48%), Gaps = 1/58 (1%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLF 166
            C  C++ +     +   G ++H   F C+H   T++   ++  +G LYC+  + + F
Sbjct: 27  MCAHCNQVIRG-PFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFF 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 = 48.6 bits (116), Expect = 2e-08
 Identities = 16/58 (27%), Positives = 24/58 (41%), Gaps = 1/58 (1%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF 68
           C  C + + +   + A N  +H  CFRC  C+  L    F    G   CRP  ++  
Sbjct: 7  GCHQCGEFI-IGRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREK 63

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

 Score = 45.5 bits (108), Expect = 2e-07
 Identities = 9/61 (14%), Positives = 22/61 (36%), Gaps = 1/61 (1%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFRE 168
            C  C   +     +     ++H  CF+C      ++   ++ + G+  C+  H +    
Sbjct: 7   GCHQCGEFII-GRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKAS 65

Query: 169 K 169
            
Sbjct: 66  G 66

>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 = 47.7 bits (114), Expect = 5e-08
 Identities = 18/65 (27%), Positives = 26/65 (40%), Gaps = 2/65 (3%)

Query: 5  FGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFN-SFEGVLYCRPH 63
          +  T +KC  C + + L   L A  + YH  CF C  C   L    F       ++C   
Sbjct: 11 YVATLEKCATCSQPI-LDRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIED 69

Query: 64 FDQLF 68
          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 = 43.5 bits (103), Expect = 2e-06
 Identities = 14/65 (21%), Positives = 25/65 (38%), Gaps = 2/65 (3%)

Query: 103 FVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSN-YIAHEGKLYCKHH 161
           +V T +KC  C + +     +   G AYH  CF C      +      +    +++C   
Sbjct: 11  YVATLEKCATCSQPILD-RILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIED 69

Query: 162 HIQLF 166
             + F
Sbjct: 70  FHRKF 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 = 48.4 bits (115), Expect = 6e-08
 Identities = 14/64 (21%), Positives = 25/64 (39%), Gaps = 2/64 (3%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSN--YIAHEGKLYCKHHHIQLF 166
           +C GC   +     +    + +H  C KCS     +           G + C++ +I+LF
Sbjct: 7   RCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLF 66

Query: 167 REKG 170
              G
Sbjct: 67  GNSG 70

>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 = 6e-07
 Identities = 16/68 (23%), Positives = 32/68 (47%), Gaps = 2/68 (2%)

Query: 8  TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFE--GVLYCRPHFD 65
          + ++C  C   +     L A +  +H  C +C  C+  L     +S+   G++ CR  + 
Sbjct: 4  SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYI 63

Query: 66 QLFKRTGS 73
          +LF  +G+
Sbjct: 64 RLFGNSGA 71

>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 = 9e-08
 Identities = 14/69 (20%), Positives = 21/69 (30%), Gaps = 3/69 (4%)

Query: 2  ASPFGGTQQKCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYC 60
          +         C  C   +  V   +   +R  H  C+ C  C   LK       E  +YC
Sbjct: 8  SIGNAQKLPMCDKCGTGI--VGVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYC 65

Query: 61 RPHFDQLFK 69
            H  +   
Sbjct: 66 EKHARERVS 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 = 46.7 bits (111), Expect = 1e-07
 Identities = 11/61 (18%), Positives = 21/61 (34%), Gaps = 1/61 (1%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFRE 168
            C  C   +     V +     H  C+ C+  G  +    +   E ++YC+ H  +    
Sbjct: 17  MCDKCGTGIVG-VFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSG 75

Query: 169 K 169
            
Sbjct: 76  P 76

>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 = 22/61 (36%), Gaps = 4/61 (6%)

Query: 11 KCMACDKTVYLVDK----LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQ 66
          KC  C   +    K    +  + + +H  CF C  C   L    F   +  +YC     +
Sbjct: 17 KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

Query: 67 L 67
          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 = 44.0 bits (104), Expect = 9e-07
 Identities = 14/61 (22%), Positives = 27/61 (44%), Gaps = 4/61 (6%)

Query: 109 KCVGCDRTVYP----TEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQ 164
           KC GC   +      +  V+  G ++H  CF C      ++   ++ H+ ++YC     +
Sbjct: 17  KCAGCKNPITGFGKGSSVVAYEGQSWHDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKK 76

Query: 165 L 165
           L
Sbjct: 77  L 77

>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 = 45.4 bits (107), Expect = 6e-07
 Identities = 13/72 (18%), Positives = 25/72 (34%), Gaps = 2/72 (2%)

Query: 105 GTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTIS--PSNYIAHEGKLYCKHHH 162
           G+   C GC + +     +      +H  C  C   GC +           G+  C+  +
Sbjct: 1   GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 60

Query: 163 IQLFREKGNYSQ 174
           ++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 = 39.3 bits (91), Expect = 1e-04
 Identities = 15/68 (22%), Positives = 25/68 (36%), Gaps = 2/68 (2%)

Query: 7  GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFE--GVLYCRPHF 64
          G+   C  C + +     L A ++ +H+ C  C  C   L       +   G   CR  +
Sbjct: 1  GSLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDY 60

Query: 65 DQLFKRTG 72
           +L    G
Sbjct: 61 LRLGGSGG 68

>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 = 43.7 bits (103), Expect = 1e-06
 Identities = 12/61 (19%), Positives = 24/61 (39%), Gaps = 3/61 (4%)

Query: 11 KCMACDKTVYLVDK---LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQL 67
           C+AC K +  +     +   +  +H  CF C  C  +L    F +    ++C+     +
Sbjct: 7  GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGM 66

Query: 68 F 68
           
Sbjct: 67 D 67

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

 Score = 40.6 bits (95), Expect = 2e-05
 Identities = 9/68 (13%), Positives = 25/68 (36%), Gaps = 3/68 (4%)

Query: 109 KCVGCDRTVYP---TEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQL 165
            CV C + +      + +    + +H  CF C     ++    ++    +++C+     +
Sbjct: 7   GCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGM 66

Query: 166 FREKGNYS 173
             +    S
Sbjct: 67  DTDISGPS 74

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

 Score = 39.8 bits (93), Expect = 3e-05
 Identities = 17/65 (26%), Positives = 25/65 (38%), Gaps = 2/65 (3%)

Query: 4  PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPH 63
            G  +  C  C   +     L   N  YH   F C +C   L  ++    +G LYC P 
Sbjct: 10 ARGLGKYICQKC-HAIIDEQPLIFKNDPYHPDHFNCANCGKELT-ADARELKGELYCLPC 67

Query: 64 FDQLF 68
           D++ 
Sbjct: 68 HDKMG 72

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

 Score = 39.0 bits (91), Expect = 7e-05
 Identities = 13/61 (21%), Positives = 21/61 (34%), Gaps = 5/61 (8%)

Query: 11 KCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKL--SNFNSFEGVLYCRPHFDQL 67
           C  C     +    + A    YH  CF C  CK  ++   +        LYC    +++
Sbjct: 17 FCHGCSL--LMTGPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEV 74

Query: 68 F 68
           
Sbjct: 75 V 75

>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 = 38.6 bits (90), Expect = 8e-05
 Identities = 13/60 (21%), Positives = 19/60 (31%), Gaps = 3/60 (5%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP--SNYIAHEGKLYCKHHHIQLF 166
            C GC   +     +      YH  CF C      I    +  +     LYC   H ++ 
Sbjct: 17  FCHGCSLLMTGPF-MVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVV 75

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

 Score = 36.3 bits (84), Expect = 6e-04
 Identities = 14/55 (25%), Positives = 22/55 (40%), Gaps = 2/55 (3%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSN-YIAHEGKLYCKHHH 162
           +C  CD+ +   E VS  G  YH  CF C+       P +    +  +  C+   
Sbjct: 17  RCFSCDQFI-EGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKCS 70

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

 Score = 35.9 bits (83), Expect = 9e-04
 Identities = 13/54 (24%), Positives = 25/54 (46%), Gaps = 2/54 (3%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEG-VLYCRPH 63
          +C +CD+ +   + ++A  + YH  CF C  C+      +  +F G    C+  
Sbjct: 17 RCFSCDQFI-EGEVVSALGKTYHPDCFVCAVCRLPFPPGDRVTFNGKECMCQKC 69

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

 Score = 35.0 bits (80), Expect = 8e-04
 Identities = 11/28 (39%), Positives = 16/28 (57%)

Query: 10 QKCMACDKTVYLVDKLTADNRVYHKACF 37
            C  C K VY  +K+   ++ +HKACF
Sbjct: 4  PNCARCGKIVYPTEKVNCLDKFWHKACF 31

Structure Templates Detected by HHsearch

Original result of HHsearch against PDB70 database

ID	Length	Definition	Probability
Query	197
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	100.0
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	100.0
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.98
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	99.97
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.97
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.94
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.91
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.86
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.86
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.86
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.86
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.86
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.84
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.82
2egq_A	77	FHL1 protein; LIM domain, four and A half LIM doma	99.82
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.8
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.8
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.78
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.77
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.77
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.77
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.76
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.76
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.76
1a7i_A	81	QCRP2 (LIM1); LIM domain containing proteins, meta	99.76
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.75
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.75
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.75
1iml_A	76	CRIP, cysteine rich intestinal protein; metal-bind	99.75
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.75
2cu8_A	76	Cysteine-rich protein 2; CRP2, CRIP2, ESP1 protein	99.74
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.74
2cup_A	101	Skeletal muscle LIM-protein 1; four and half LIM d	99.74
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.73
1j2o_A	114	FLIN2, fusion of rhombotin-2 and LIM domain-bindin	99.73
2xqn_T	126	Testin, TESS; metal-binding protein, cytoskeleton,	99.73
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.73
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.73
1m3v_A	122	FLIN4, fusion of the LIM interacting domain of LDB	99.72
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.72
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.69
2cur_A	69	Skeletal muscle LIM-protein 1; four and A half LIM	99.69
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.69
2jtn_A	182	LIM domain-binding protein 1, LIM/homeobox protein	99.69
2dj7_A	80	Actin-binding LIM protein 3; LIM domain, Zn bindin	99.69
2d8y_A	91	Eplin protein; LIM domain, epithelial protein LOST	99.69
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.69
2d8z_A	70	Four and A half LIM domains 2; skeletal muscle LIM	99.68
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.67
1x62_A	79	C-terminal LIM domain protein 1; PDZ and LIM domai	99.67
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.67
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.67
1x68_A	76	FHL5 protein; four-and-A-half LIM protein 5, zinc	99.67
1nyp_A	66	Pinch protein; LIM domain, protein recognition, ce	99.67
2d8x_A	70	Protein pinch; LIM domain, pinch protein, structur	99.67
2dar_A	90	PDZ and LIM domain protein 5; enigma homolog prote	99.66
1wyh_A	72	SLIM 2, skeletal muscle LIM-protein 2; structural	99.66
1x4k_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.66
2xjy_A	131	Rhombotin-2; oncoprotein, T-cell leukemia, proto-o	99.66
1x4l_A	72	Skeletal muscle LIM-protein 3; LIM domain, structu	99.66
1g47_A	77	Pinch protein; LIM domain, Zn finger, cell adhesio	99.65
1x64_A	89	Alpha-actinin-2 associated LIM protein; LIM domain	99.65
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.64
2rgt_A	169	Fusion of LIM/homeobox protein LHX3, linker, INSU	99.64
2iyb_E	65	Testin, TESS, TES; LIM domain, SH3-binding, tumour	99.63
1x61_A	72	Thyroid receptor interacting protein 6; LIM domain	99.63
1x3h_A	80	Leupaxin; paxillin family, protein-protein interac	99.63
1b8t_A	192	Protein (CRP1); LIM domain, muscle differentiation	99.62
1x63_A	82	Skeletal muscle LIM-protein 1; LIM domain, four an	99.62
2dlo_A	81	Thyroid receptor-interacting protein 6; LIM domain	99.61
2cor_A	79	Pinch protein; LIM domain, particularly interestin	99.61
2co8_A	82	NEDD9 interacting protein with calponin homology a	99.61
2cuq_A	80	Four and A half LIM domains 3; structural genomics	99.61
2ehe_A	82	Four and A half LIM domains 3; FHL-3, skeletal mus	99.6
1wig_A	73	KIAA1808 protein; LIM domain, zinc finger, metal-b	99.59
3f6q_B	72	LIM and senescent cell antigen-like-containing dom	99.59
1rut_X	188	Flinc4, fusion protein of LMO4 protein and LIM dom	99.59
2l4z_A	123	DNA endonuclease RBBP8, LIM domain transcription L	99.59
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	99.55
1x6a_A	81	LIMK-2, LIM domain kinase 2; LIM-kinase 2, zinc fi	99.53
2l3k_A	123	Rhombotin-2, linker, LIM domain-binding protein 1;	99.51
1v6g_A	81	Actin binding LIM protein 2; LIM domain, zinc bind	99.4
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.68
1zfo_A	31	LAsp-1; LIM domain, zinc-finger, metal-binding pro	98.33
1jjd_A	55	Metallothionein, SMTA; zinc finger, zinc cluster,	87.84
2ysm_A	111	Myeloid/lymphoid or mixed-lineage leukemia protein	87.63
1t1h_A	78	Gspef-atpub14, armadillo repeat containing protein	86.08
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	85.6
2ct0_A	74	Non-SMC element 1 homolog; ring domain, structural	84.77
4ap4_A	133	E3 ubiquitin ligase RNF4; ligase-signalling protei	84.41
2ecy_A	66	TNF receptor-associated factor 3; metal binding pr	82.6
2ysl_A	73	Tripartite motif-containing protein 31; ring-type	81.1
1g25_A	65	CDK-activating kinase assembly factor MAT1; ring f	80.6
3vk6_A	101	E3 ubiquitin-protein ligase hakai; HYB, phosphotyr	80.6
2djb_A	72	Polycomb group ring finger protein 6; PCGF6, ring	80.42

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

Probab=100.00  E-value=6.2e-35  Score=225.81  Aligned_cols=169  Identities=27%  Similarity=0.573  Sum_probs=137.9

Q ss_pred             CCCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCccc
Q 029230            6 GGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIV   85 (197)
Q Consensus         6 ~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~   85 (197)
                      .++.++|.+|+++|..++.+.++|+.||++||+|..|+++|.+..|+.++|++||+.||.++|++++..+...   ..+.
T Consensus         4 ~~~~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~c~~c~~~---~g~~   80 (192)
T 1b8t_A            4 WGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMG---AGTL   80 (192)
T ss_dssp             CCCCEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCC---CCCC
T ss_pred             CCCCCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCccccccccc---cccE
Confidence            4457899999999988888999999999999999999999999999999999999999999999987543221   1222


Q ss_pred             CCCCccccc--------------CccccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeee
Q 029230           86 KPEKLVENE--------------NAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIA  151 (197)
Q Consensus        86 ~~~~~~~~~--------------~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~  151 (197)
                      ..+++|+..              ....+...+ ++.++|++|+++|.+++.|.++++.||++||+|..|+++|.++.|+.
T Consensus        81 ~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~-~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~  159 (192)
T 1b8t_A           81 STDKGESLGIKYEEGQSHRPTNPNASRMAQKV-GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCFRCAKCGKSLESTTLAD  159 (192)
T ss_dssp             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCEECTTTSCEECSSSCEEETTEEECTTTCBCTTTCCBCCSSSEEE
T ss_pred             ecCCCcccccccccccccCCCCcCcccccccc-CCCCcCCCCCCEecCcEEEecCCCccchhcCCccccCCCCCCCcccc
Confidence            233333311              111111111 23468999999999888899999999999999999999999889999


Q ss_pred             eCCeeecHHHHHhHhcCCCCCCCCCCc
Q 029230          152 HEGKLYCKHHHIQLFREKGNYSQLESD  178 (197)
Q Consensus       152 ~dg~~yC~~cy~~~~~~k~~~~~~~~~  178 (197)
                      .||++||+.||.++|+++|..|...+.
T Consensus       160 ~~g~~yC~~cy~~~f~~kc~~C~~~~g  186 (192)
T 1b8t_A          160 KDGEIYCKGCYAKNFGPKGFGFGQGAG  186 (192)
T ss_dssp             ETTEEEEHHHHHHHTCCCCCCCCCCCC
T ss_pred             cCCEEeCHHHHHHhcCCcCCCCCCccc
Confidence            999999999999999999998886644

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

Probab=100.00  E-value=1e-33  Score=206.21  Aligned_cols=124  Identities=23%  Similarity=0.492  Sum_probs=113.9

Q ss_pred             CccccccccceecceeEEeCCccccccccccccccccccC--CCeeecCCeeeccccHHHHhhccCCcccccCCCCcccC
Q 029230            9 QQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKL--SNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVK   86 (197)
Q Consensus         9 ~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~--~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~   86 (197)
                      .++|.+|+++|.+.+.+.++|+.||++||+|..|+.+|..  ..|+.++|++||+.||.++++                 
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            5789999999997667999999999999999999999974  579999999999999999997                 


Q ss_pred             CCCcccccCccccccccCCCCC--CCCCCCceeecCce-eeecCccccccccccCcCCCCCC-CCCeeeeCCeeecHHHH
Q 029230           87 PEKLVENENAQKVSNKFVGTRD--KCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTIS-PSNYIAHEGKLYCKHHH  162 (197)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~--~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~l~-~~~~~~~dg~~yC~~cy  162 (197)
                                           +  +|.+|+++|.+.+. |.++++.||++||+|..|+++|. +..|+..+|++||..||
T Consensus        65 ---------------------~~~~C~~C~~~I~~~e~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~C~~c~  123 (131)
T 2xjy_A           65 ---------------------QDGLCASCDKRIRAYEMTMRVKDKVYHLECFKCAACQKHFCVGDRYLLINSDIVCEQDI  123 (131)
T ss_dssp             ---------------------CCEECTTTCCEECTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEEETTEEEEGGGH
T ss_pred             ---------------------CccChhhcCCccCccceeEeeCCceECccCcccCCCCCCCCCCCEEEEECCEEEcHHHH
Confidence                                 6  89999999997664 67999999999999999999995 66799999999999999


Q ss_pred             HhHhcCCC
Q 029230          163 IQLFREKG  170 (197)
Q Consensus       163 ~~~~~~k~  170 (197)
                      .++|+++|
T Consensus       124 ~~~~~~~~  131 (131)
T 2xjy_A          124 YEWTKING  131 (131)
T ss_dssp             HHHHHHHC
T ss_pred             HHHhhccC
Confidence            99998765

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

Probab=99.98  E-value=1.1e-32  Score=199.61  Aligned_cols=121  Identities=21%  Similarity=0.540  Sum_probs=113.1

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCC
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKP   87 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~   87 (197)
                      ..++|.+|+++|..++.+.++|+.||++||+|..|+++|.+..|+.++|++||+.||.++++                  
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            35899999999998889999999999999999999999998899999999999999999997                  


Q ss_pred             CCcccccCccccccccCCCCCCCCCCCceeecCc-eeeecCcccc--ccccccCcCCCCCCCCCeeeeCCeeecHHHHHh
Q 029230           88 EKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTE-KVSVNGAAYH--RSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQ  164 (197)
Q Consensus        88 ~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e-~v~~~g~~~H--~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~  164 (197)
                                          ++|++|+++|.+++ .|.++++.||  ++||+|..|+++|.+..|+..||++||..+|.+
T Consensus        64 --------------------~~C~~C~~~I~~~~~~~~a~~~~~H~~~~CF~C~~C~~~l~~~~f~~~~~~~yC~~~~~~  123 (126)
T 2xqn_T           64 --------------------VVCQGCHNAIDPEVQRVTYNNFSWHASTECFLCSCCSKCLIGQKFMPVEGMVFCSVECKK  123 (126)
T ss_dssp             --------------------CBCTTTCSBCCTTSCEEEETTEEEESSTTTSBCTTTCCBCTTSEEEEETTEEESSHHHHH
T ss_pred             --------------------ccCcccCCcCCcCceEEECCCCEeeCCCCCcCcCCCCCccCCCeeEeECCEEcchHHhhh
Confidence                                99999999999754 4789999999  999999999999998889999999999988887


Q ss_pred             Hh
Q 029230          165 LF  166 (197)
Q Consensus       165 ~~  166 (197)
                      +|
T Consensus       124 ~f  125 (126)
T 2xqn_T          124 RM  125 (126)
T ss_dssp             SC
T ss_pred             hc
Confidence            65

>1rut_X Flinc4, fusion protein of LMO4 protein and LIM domain- binding protein 1; B-tandem zipper, protein binding; 1.30A {Mus musculus} SCOP: g.39.1.3 g.39.1.3 g.39.1.3 g.39.1.3 PDB: 2dfy_X 2xjz_I 2xjy_B

Probab=99.97  E-value=4.5e-32  Score=209.11  Aligned_cols=129  Identities=22%  Similarity=0.524  Sum_probs=112.8

Q ss_pred             CCCccccccccceecceeEEeCCccccccccccccccccccC--CCeeecCCeeeccccHHHHhhccCCcccccCCCCcc
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKL--SNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKI   84 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~--~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~   84 (197)
                      ...++|.+|+++|...+++.++++.||++||+|..|+++|..  ..|+.++|++||+.||.++|+               
T Consensus         3 l~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~---------------   67 (188)
T 1rut_X            3 LSWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG---------------   67 (188)
T ss_dssp             -CCCBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHS---------------
T ss_pred             CCCCcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccc---------------
Confidence            346899999999997667999999999999999999999986  689999999999999999997               


Q ss_pred             cCCCCcccccCccccccccCCCCC--CCCCCCceeecCce-eeecCccccccccccCcCCCCCC-CCCeeeeCCeeecHH
Q 029230           85 VKPEKLVENENAQKVSNKFVGTRD--KCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTIS-PSNYIAHEGKLYCKH  160 (197)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~--~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~l~-~~~~~~~dg~~yC~~  160 (197)
                                             +  +|.+|+++|.+.+. |.++++.||++||+|..|+++|. +..|+..++++||..
T Consensus        68 -----------------------~~~~C~~C~~~I~~~e~~i~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~g~~yC~~  124 (188)
T 1rut_X           68 -----------------------NSGACSACGQSIPASELVMRAQGNVYHLKCFTCSTCRNRLVPGDRFHYINGSLFCEH  124 (188)
T ss_dssp             -----------------------CCEECTTTCCEECTTSEEEEETTEEECGGGCBCTTTCCBCCTTCEEEEETTEEEEGG
T ss_pred             -----------------------cCCccccCCCccccCcEEEEcCCCEEeCCCCeECCCCCCCCCCCeEEEECCeEECHH
Confidence                                   5  79999999998775 57999999999999999999996 567999999999999


Q ss_pred             HHHhHhcCCCCCC
Q 029230          161 HHIQLFREKGNYS  173 (197)
Q Consensus       161 cy~~~~~~k~~~~  173 (197)
                      ||.++|++++...
T Consensus       125 c~~~~~~~~~~~~  137 (188)
T 1rut_X          125 DRPTALINGHLNS  137 (188)
T ss_dssp             GCCTTTC------
T ss_pred             HHHHHhccccccc
Confidence            9999999999643

>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=99.97  E-value=7.9e-31  Score=198.90  Aligned_cols=124  Identities=25%  Similarity=0.515  Sum_probs=109.8

Q ss_pred             CCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccC
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVK   86 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~   86 (197)
                      .+.++|.+|+++|...+++.++|+.||+.||+|..|+++|.+..| .++|++||+.||.++|+                 
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            356899999999997677899999999999999999999998775 79999999999999998                 


Q ss_pred             CCCcccccCccccccccCCCCCCCCCCCceeecCcee-eecCccccccccccCcCCCCCC-CCCee-eeCCeeecHHHHH
Q 029230           87 PEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKV-SVNGAAYHRSCFKCSHGGCTIS-PSNYI-AHEGKLYCKHHHI  163 (197)
Q Consensus        87 ~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v-~~~g~~~H~~CF~C~~C~~~l~-~~~~~-~~dg~~yC~~cy~  163 (197)
                                           ++|.+|+++|.+.+.+ .++++.||++||+|..|+++|. +..|+ ..||++||+.||.
T Consensus        66 ---------------------~~C~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~~C~~c~~  124 (169)
T 2rgt_A           66 ---------------------TKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVCKADYE  124 (169)
T ss_dssp             ---------------------CBCTTTCCBCCTTSEEEEETTEEEEGGGCBCTTTCCBCCTTCEEEECTTSCEEEHHHHH
T ss_pred             ---------------------ccccccccccCCCcEEEEcCCceEeeCCCcCCCCCCCCCCCCceEEccCCeEECHHHHH
Confidence                                 9999999999987764 6999999999999999999998 44565 4689999999999


Q ss_pred             hHhcCC
Q 029230          164 QLFREK  169 (197)
Q Consensus       164 ~~~~~k  169 (197)
                      ++++..
T Consensus       125 ~~~~~~  130 (169)
T 2rgt_A          125 TAKQGG  130 (169)
T ss_dssp             HHHHCC
T ss_pred             HHhhcc
Confidence            998764

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

Probab=99.97  E-value=1e-30  Score=200.57  Aligned_cols=126  Identities=25%  Similarity=0.485  Sum_probs=111.1

Q ss_pred             CCCCCCCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCC
Q 029230            2 ASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGT   81 (197)
Q Consensus         2 ~~~~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~   81 (197)
                      ++......++|.+|+++|...+++.++|+.||+.||+|..|+++|.+..| .++|++||+.||.++|+            
T Consensus        53 ~~~~~~~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~------------  119 (182)
T 2jtn_A           53 GSGGTPEIPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFG------------  119 (182)
T ss_dssp             CCCCCCSCCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCE-EETTEEECHHHHHHTTS------------
T ss_pred             ccCCCCCCCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCce-eECCEeeecCccccccc------------
Confidence            34445667999999999997777899999999999999999999998776 68999999999999997            


Q ss_pred             CcccCCCCcccccCccccccccCCCCCCCCCCCceeecCce-eeecCccccccccccCcCCCCCCC-CCee-eeCCeeec
Q 029230           82 PKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISP-SNYI-AHEGKLYC  158 (197)
Q Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~l~~-~~~~-~~dg~~yC  158 (197)
                                                ++|.+|+++|.+.+. +.++++.||++||+|..|+++|.. ..|+ ..||++||
T Consensus       120 --------------------------~kC~~C~~~I~~~~~v~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~g~~yC  173 (182)
T 2jtn_A          120 --------------------------TKCAACQLGIPPTQVVRRAQDFVYHLHCFACVVCKRQLATGDEFYLMEDSRLVC  173 (182)
T ss_dssp             --------------------------CCCTTTCCCCCSSCCCCEETTEECCTTTCCCTTTCCCCCTTCEEEECTTSCEEC
T ss_pred             --------------------------cccccCCCccCCCceEEecCCCCEEeCCCcCCCCCCCCCCCCceEEccCCEEEC
Confidence                                      999999999998775 469999999999999999999984 4565 46899999


Q ss_pred             HHHHHhHh
Q 029230          159 KHHHIQLF  166 (197)
Q Consensus       159 ~~cy~~~~  166 (197)
                      ..||.++.
T Consensus       174 ~~cy~~~~  181 (182)
T 2jtn_A          174 KADYETAK  181 (182)
T ss_dssp             HHHHHHHT
T ss_pred             HHHHHHhh
Confidence            99998763

>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=99.94  E-value=1.5e-27  Score=165.98  Aligned_cols=98  Identities=24%  Similarity=0.610  Sum_probs=90.2

Q ss_pred             CCCCccccccccceec-ceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcc
Q 029230            6 GGTQQKCMACDKTVYL-VDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKI   84 (197)
Q Consensus         6 ~~~~~~C~~C~~~I~~-~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~   84 (197)
                      +...++|.+|+++|.. ++.+.++|+.||++||+|..|+++|.+..|+.++|++||+.||.++|+               
T Consensus         2 s~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~---------------   66 (101)
T 2cup_A            2 SSGSSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDS---------------   66 (101)
T ss_dssp             CSCCCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCC---------------
T ss_pred             CCCCCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcC---------------
Confidence            3456899999999975 788999999999999999999999998889999999999999999887               


Q ss_pred             cCCCCcccccCccccccccCCCCCCCCCCCceeecCc-eeeecCccccccccccCcCC
Q 029230           85 VKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTE-KVSVNGAAYHRSCFKCSHGG  141 (197)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e-~v~~~g~~~H~~CF~C~~C~  141 (197)
                                             ++|.+|+++|.+++ .|.++|+.||++||+|..|+
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                                   99999999999765 47899999999999999986

>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=99.91  E-value=1.1e-25  Score=161.76  Aligned_cols=113  Identities=19%  Similarity=0.327  Sum_probs=100.1

Q ss_pred             CCCccccccccceecceeEEeCCcccccccccccccccccc--CCCeeecCCeeeccccHHHHhhccCCcccccCCCCcc
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLK--LSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKI   84 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~   84 (197)
                      ...++|.+|+++|...+++.++++.||++||+|..|+.+|.  +..|+.++|++||+.||.++|+               
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            45689999999999777799999999999999999999997  3579999999999999999997               


Q ss_pred             cCCCCcccccCccccccccCCCCC--CCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHH
Q 029230           85 VKPEKLVENENAQKVSNKFVGTRD--KCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHH  162 (197)
Q Consensus        85 ~~~~~~~~~~~~~~~~~~~~~~~~--~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy  162 (197)
                                             +  +|++|+++|.+.+ |++.|+             ..|.++.|+.++++|||..||
T Consensus        68 -----------------------~~~~C~~C~~~I~~~~-~~~~g~-------------~~l~g~~f~~~~~~~yC~~~~  110 (122)
T 1m3v_A           68 -----------------------NSGAGGSGGHMGSGGD-VMVVGE-------------PTLMGGEFGDEDERLITRLEN  110 (122)
T ss_dssp             -----------------------CCCSSSCSSCCSCCEE-SSSSSS-------------SSCCSCTTCCTTCCCCEECTT
T ss_pred             -----------------------CCCccccCCCCcCchh-eEEcCC-------------cCCCCCccEecCCEeEccCcc
Confidence                                   6  9999999998654 566663             367888999999999999999


Q ss_pred             HhHhcCCCC
Q 029230          163 IQLFREKGN  171 (197)
Q Consensus       163 ~~~~~~k~~  171 (197)
                      .+++..+++
T Consensus       111 ~~~~~~~g~  119 (122)
T 1m3v_A          111 TQFDAANGI  119 (122)
T ss_dssp             TTTTCCSCC
T ss_pred             hhchhhcCC
Confidence            999988875

>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=99.86  E-value=1.2e-22  Score=135.23  Aligned_cols=79  Identities=18%  Similarity=0.451  Sum_probs=73.7

Q ss_pred             CCeeeccccHHHHhhccCCcccccCCCCcccCCCCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccc
Q 029230           55 EGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSC  134 (197)
Q Consensus        55 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~C  134 (197)
                      +|++||+.||.++++                                      ++|++|+++|.+ +.|.++++.||++|
T Consensus         1 gg~~yC~~cy~~~~~--------------------------------------~~C~~C~~~I~~-~~v~a~~~~~H~~C   41 (80)
T 2cuq_A            1 GSSGSSGPCYENKFA--------------------------------------PRCARCSKTLTQ-GGVTYRDQPWHREC   41 (80)
T ss_dssp             CCCCSCCCCCCCCSS--------------------------------------CCCTTTCCCCCS-CCEESSSSEECTTT
T ss_pred             CCcEEcHHHHccccC--------------------------------------CcCCCCCCEecC-cEEEECCchhhhhh
Confidence            588999999998886                                      899999999985 57899999999999


Q ss_pred             cccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCC
Q 029230          135 FKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNY  172 (197)
Q Consensus       135 F~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~  172 (197)
                      |+|..|+++|.++.|+..|++|||+.||.++|+++|+.
T Consensus        42 F~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~s   79 (80)
T 2cuq_A           42 LVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGPSS   79 (80)
T ss_dssp             CBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCSTTC
T ss_pred             CCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCCCCC
Confidence            99999999999889999999999999999999999964

>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=99.86  E-value=1.2e-22  Score=135.34  Aligned_cols=79  Identities=22%  Similarity=0.439  Sum_probs=73.6

Q ss_pred             CCeeeccccHHHHhhccCCcccccCCCCcccCCCCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccc
Q 029230           55 EGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSC  134 (197)
Q Consensus        55 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~C  134 (197)
                      +|++||+.||.++++                                      ++|++|+++|.+ +.|.++++.||++|
T Consensus         1 gg~~yC~~~y~~~~~--------------------------------------~~C~~C~~~I~~-~~v~a~~~~~H~~C   41 (80)
T 1x3h_A            1 GSSGSSGKDFLAMFS--------------------------------------PKCGGCNRPVLE-NYLSAMDTVWHPEC   41 (80)
T ss_dssp             CCCCCCCCCCCCCCS--------------------------------------CBCTTTCCBCCS-SCEEETTEEECTTT
T ss_pred             CCCccchhHHhhhcC--------------------------------------CccccCCCeecc-eeEEECCCeEecCc
Confidence            478999999988886                                      899999999995 66899999999999


Q ss_pred             cccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCC
Q 029230          135 FKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNY  172 (197)
Q Consensus       135 F~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~  172 (197)
                      |+|..|+++|.++.|+..+++|||+.||.++|+++|..
T Consensus        42 F~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~~C~~   79 (80)
T 1x3h_A           42 FVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGSGPSS   79 (80)
T ss_dssp             CBCSSSCCBSCSSCCEESSSCEECHHHHHHHHSSSCCC
T ss_pred             CChhhCCCCCCCCcEEeECCEEECHHHHHHHcCCCCCC
Confidence            99999999999888999999999999999999999963

>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=99.86  E-value=1.6e-22  Score=135.31  Aligned_cols=80  Identities=20%  Similarity=0.426  Sum_probs=74.1

Q ss_pred             CCeeeccccHHHHhhccCCcccccCCCCcccCCCCcccccCccccccccCCCCCCCCCCCceeecCce-eeecCcccccc
Q 029230           55 EGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEK-VSVNGAAYHRS  133 (197)
Q Consensus        55 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~-v~~~g~~~H~~  133 (197)
                      ++.+||+.||.++++                                      ++|++|+++|.+++. |.++++.||++
T Consensus         1 ~~~~yC~~cy~~~~~--------------------------------------~~C~~C~~~I~~~~~~~~a~~~~~H~~   42 (82)
T 1x63_A            1 GSSGSSGKCTTREDS--------------------------------------PKCKGCFKAIVAGDQNVEYKGTVWHKD   42 (82)
T ss_dssp             CCSCCCCCCCSCCCS--------------------------------------CBCSSSCCBCCSSSCEEECSSCEEETT
T ss_pred             CCCcCchhHHccccC--------------------------------------CcCccCCcccccCceEEEECccccccc
Confidence            467999999988876                                      899999999998765 78999999999


Q ss_pred             ccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCC
Q 029230          134 CFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNY  172 (197)
Q Consensus       134 CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~  172 (197)
                      ||+|..|+++|.++.|+..++++||+.||.++|++++++
T Consensus        43 CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~~   81 (82)
T 1x63_A           43 CFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPSS   81 (82)
T ss_dssp             TCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCSC
T ss_pred             cCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCCC
Confidence            999999999999989999999999999999999999975

>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=1.7e-22  Score=143.47  Aligned_cols=108  Identities=16%  Similarity=0.218  Sum_probs=90.6

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccC--CCeeecCCeeeccccHHHHhhccCCcccccCCCCccc
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKL--SNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIV   85 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~--~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~   85 (197)
                      +.++|.+|+++|...+.+.++++.||+.||+|..|+++|..  ..|+.++|++||+.||.++|+                
T Consensus         2 ~~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~----------------   65 (114)
T 1j2o_A            2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGG----------------   65 (114)
T ss_dssp             CCBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHT----------------
T ss_pred             cCCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhC----------------
Confidence            46899999999997778999999999999999999999985  589999999999999999998                


Q ss_pred             CCCCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCC-CCCCCeeeeCCeeecHHHHHh
Q 029230           86 KPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCT-ISPSNYIAHEGKLYCKHHHIQ  164 (197)
Q Consensus        86 ~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~-l~~~~~~~~dg~~yC~~cy~~  164 (197)
                                            ++|..|..    ++.+.               |+.+ |.++.|+..|++|||..||.+
T Consensus        66 ----------------------~~c~~c~~----~~~~~---------------~~~~~~~g~~f~~~~~~~~C~~~~~~  104 (114)
T 1j2o_A           66 ----------------------SGGHMGSG----GDVMV---------------VGEPTLMGGEFGDEDERLITRLENTQ  104 (114)
T ss_dssp             ----------------------SCCSSCBS----CSCCC---------------SSCSSTTSSBCCCSSSCCCEEEECTT
T ss_pred             ----------------------cccCcCCC----CceeE---------------cCCccCCCCeeEEcCCEeecchhhhc
Confidence                                  77777752    22111               2344 667799999999999999999


Q ss_pred             HhcCCCCC
Q 029230          165 LFREKGNY  172 (197)
Q Consensus       165 ~~~~k~~~  172 (197)
                      +.+.+++-
T Consensus       105 ~~~~~g~~  112 (114)
T 1j2o_A          105 FDAANGID  112 (114)
T ss_dssp             CCCTTSSC
T ss_pred             cccccCCC
Confidence            88877653

>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=99.86  E-value=6.8e-23  Score=137.14  Aligned_cols=80  Identities=15%  Similarity=0.440  Sum_probs=73.4

Q ss_pred             CCeeeccccHHHHhhccCCcccccCCCCcccCCCCcccccCccccccccCCCCCCCCCCCceeecC-ceeeecCcccccc
Q 029230           55 EGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPT-EKVSVNGAAYHRS  133 (197)
Q Consensus        55 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~-e~v~~~g~~~H~~  133 (197)
                      +|++||+.||.++|+                                      ++|++|+++|.+. ..|.++++.||++
T Consensus         1 ~g~~yC~~~y~~~~~--------------------------------------~~C~~C~~~I~~~~~~~~a~~~~~H~~   42 (82)
T 2ehe_A            1 GSSGSSGPCYDNTFA--------------------------------------NTCAECQQLIGHDSRELFYEDRHFHEG   42 (82)
T ss_dssp             CCCCCCCCCCCCCCS--------------------------------------CBCTTTCCBCCSSCCBCCCSSCCCBTT
T ss_pred             CCceechhHhCcccC--------------------------------------CcCccCCCccccCcEEEEeCCcccccc
Confidence            589999999998887                                      8999999999954 4467899999999


Q ss_pred             ccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCC
Q 029230          134 CFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNY  172 (197)
Q Consensus       134 CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~  172 (197)
                      ||+|..|+++|.++.|+..+++|||+.||.++|+++|..
T Consensus        43 CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C~~   81 (82)
T 2ehe_A           43 CFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGPSS   81 (82)
T ss_dssp             TSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGGGSSCC
T ss_pred             CCeecCCCCccCCCccEeeCCEEECHHHHhhhcCCCCCC
Confidence            999999999999989999999999999999999999963

>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=99.84  E-value=9.5e-22  Score=131.24  Aligned_cols=64  Identities=19%  Similarity=0.469  Sum_probs=58.8

Q ss_pred             CCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeee-CCeeecHHHHHhHhcCCCCC
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAH-EGKLYCKHHHIQLFREKGNY  172 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~-dg~~yC~~cy~~~~~~k~~~  172 (197)
                      ++|++|+++|. ++.|.++++.||++||+|..|+++|.+..|+.. ||+|||+.||.++|+++|..
T Consensus        16 ~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~~~C~~   80 (81)
T 2dlo_A           16 EKCATCSQPIL-DRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFASGPSS   80 (81)
T ss_dssp             CBCTTTCCBCC-SCCEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTTSSSCC
T ss_pred             CccccCCCeec-ceeEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhcCcCCC
Confidence            89999999998 456889999999999999999999998888876 79999999999999999963

>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=99.82  E-value=5.8e-21  Score=127.35  Aligned_cols=78  Identities=19%  Similarity=0.380  Sum_probs=70.0

Q ss_pred             CCeeeccccHHHHhhccCCcccccCCCCcccCCCCcccccCccccccccCCCCCCCCCCCceeecCceeeecCccccccc
Q 029230           55 EGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSC  134 (197)
Q Consensus        55 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~C  134 (197)
                      ++.+||+.||.++|+                                      ++|++|+++|. ++.|.++++.||++|
T Consensus         1 g~~~yC~~~y~~~~~--------------------------------------~~C~~C~~~I~-~~~~~a~~~~~H~~C   41 (81)
T 1x6a_A            1 GSSGSSGKDYWGKFG--------------------------------------EFCHGCSLLMT-GPFMVAGEFKYHPEC   41 (81)
T ss_dssp             CCCCCCCCCSSCCSS--------------------------------------CBCTTTCCBCC-SCCBCCTTCCBCTTS
T ss_pred             CCCccchhHHhhhcC--------------------------------------CcCccCCCCcC-ceEEEECCceecccc
Confidence            367999999999887                                      89999999999 666889999999999


Q ss_pred             cccCcCCCCCCC-CCee-eeCCeeecHHHHHhHhcCCCC
Q 029230          135 FKCSHGGCTISP-SNYI-AHEGKLYCKHHHIQLFREKGN  171 (197)
Q Consensus       135 F~C~~C~~~l~~-~~~~-~~dg~~yC~~cy~~~~~~k~~  171 (197)
                      |+|..|+++|.. ..|. ..+++|||+.||.++|+++++
T Consensus        42 F~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~~~s   80 (81)
T 1x6a_A           42 FACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSGPSS   80 (81)
T ss_dssp             CBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCTTSC
T ss_pred             CCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcCCCC
Confidence            999999999974 5677 489999999999999998874

>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=99.82  E-value=4.9e-21  Score=126.51  Aligned_cols=73  Identities=19%  Similarity=0.554  Sum_probs=66.8

Q ss_pred             CCeeeccccHHHHhhccCCcccccCCCCcccCCCCcccccCccccccccCCCCCCCCCCCceeec----CceeeecCccc
Q 029230           55 EGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYP----TEKVSVNGAAY  130 (197)
Q Consensus        55 ~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~----~e~v~~~g~~~  130 (197)
                      ++++||+.||.++++                                      ++|++|+++|.+    .+.|.++++.|
T Consensus         1 g~~~yC~~cy~~~~~--------------------------------------~~C~~C~~~I~~~g~~~~~~~a~~~~~   42 (77)
T 2egq_A            1 GSSGSSGDCYKNFVA--------------------------------------KKCAGCKNPITGFGKGSSVVAYEGQSW   42 (77)
T ss_dssp             CCSSCCTTCCCSCCC--------------------------------------CCCSSSCCCCCCCSSCCCEEEETTEEE
T ss_pred             CCCeEchhHhchhhC--------------------------------------ccCcccCCcccCCCCCceeEEECccee
Confidence            478999999998886                                      899999999994    36688999999


Q ss_pred             cccccccCcCCCCCCCCCeeeeCCeeecHHHHHhH
Q 029230          131 HRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQL  165 (197)
Q Consensus       131 H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~  165 (197)
                      |++||+|..|+++|.+..|+..+|+|||+.||.++
T Consensus        43 H~~CF~C~~C~~~L~~~~f~~~~~~~yC~~cy~~l   77 (77)
T 2egq_A           43 HDYCFHCKKCSVNLANKRFVFHQEQVYCPDCAKKL   77 (77)
T ss_dssp             ETTTCBCSSSCCBCTTSCCCEETTEECCHHHHHHC
T ss_pred             CcccCEehhcCCCCCCCccEeECCEEEChHHhccC
Confidence            99999999999999998899999999999999763

>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=99.80  E-value=6.3e-20  Score=125.04  Aligned_cols=74  Identities=41%  Similarity=0.816  Sum_probs=69.6

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCCCCchh
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLE  180 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~~~~~~  180 (197)
                      .++|++|+++|.+++.|.++++.||++||+|..|+++|..+.|+..|+++||+.||.++|+++|+++.++....
T Consensus        15 ~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~g~g~~~   88 (91)
T 2d8y_A           15 RETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFGSGP   88 (91)
T ss_dssp             SCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCCCCC
T ss_pred             CCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccCCcCCCC
Confidence            38999999999988889999999999999999999999988899999999999999999999999999988753

>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=99.80  E-value=8.7e-20  Score=120.19  Aligned_cols=69  Identities=36%  Similarity=0.680  Sum_probs=64.1

Q ss_pred             cCCCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecH-HHHHhHhcCCCC
Q 029230          103 FVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCK-HHHIQLFREKGN  171 (197)
Q Consensus       103 ~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~-~cy~~~~~~k~~  171 (197)
                      |.+..++|++|+++|.+++.|.++++.||++||+|..|+++|.+..|+..|++|||+ .||.++|+++|.
T Consensus         5 ~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~kc~   74 (76)
T 2cu8_A            5 SSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSGPS   74 (76)
T ss_dssp             CCCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSSCS
T ss_pred             cCCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccccC
Confidence            444568999999999988889999999999999999999999998899999999999 799999999996

>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=99.78  E-value=1.9e-19  Score=118.50  Aligned_cols=70  Identities=36%  Similarity=0.658  Sum_probs=65.5

Q ss_pred             CCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecH-HHHHhHhcCCCCCCCCCC
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCK-HHHIQLFREKGNYSQLES  177 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~-~cy~~~~~~k~~~~~~~~  177 (197)
                      |+|++|+++|.+++.|.++|+.||++||+|..|+++|.++.|+..||++||+ .||.++|+++|..|.+..
T Consensus         1 p~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~~C~~C~~~~   71 (76)
T 1iml_A            1 PKCPKCDKEVYFAERVTSLGKDWHRPCLKCEKCGKTLTSGGHAEHEGKPYCNHPCYSAMFGPKGFGRGGAE   71 (76)
T ss_dssp             CBCTTTSSBCCGGGEEEETTEEEETTTCBCTTTCCBCCTTTEEEETTEEEETTTHHHHHSSCCCSSCCCSS
T ss_pred             CcCCCCCCEEECceEEEECCccccCCCCCccccCccCCCCceECcCCeEeeCHHHHHHHhCccCCCcCCce
Confidence            5799999999988889999999999999999999999998999999999999 699999999999998654

>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=99.77  E-value=1.3e-19  Score=120.77  Aligned_cols=71  Identities=31%  Similarity=0.626  Sum_probs=58.2

Q ss_pred             CCCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCC
Q 029230          105 GTRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQL  175 (197)
Q Consensus       105 ~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~  175 (197)
                      +..++|.+|+++|.+++.|.++++.||++||+|..|+++|..+.|+..++++||+.||.++|+++|..|..
T Consensus         5 ~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~gcg~   75 (81)
T 1a7i_A            5 GGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYGPKGYGYGQ   75 (81)
T ss_dssp             ---CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC--------
T ss_pred             CCCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhCCcccccCC
Confidence            34589999999999888899999999999999999999999888999999999999999999999986653

>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=99.77  E-value=2.8e-19  Score=118.94  Aligned_cols=65  Identities=23%  Similarity=0.556  Sum_probs=61.1

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCC
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNY  172 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~  172 (197)
                      .++|++|+++|++++.|.++++.||++||+|..|+++|.+ .|+.+||+|||+.||.++|+++|..
T Consensus        15 ~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C~~   79 (80)
T 2dj7_A           15 PSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGPSS   79 (80)
T ss_dssp             CSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCSTT
T ss_pred             CCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCCCC
Confidence            4899999999998888999999999999999999999986 7999999999999999999999964

>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=99.77  E-value=9e-19  Score=119.04  Aligned_cols=65  Identities=20%  Similarity=0.478  Sum_probs=60.9

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCC
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNY  172 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~  172 (197)
                      .++|++|+++|. ++.|.++|+.||++||+|..|+++|.+..|+..++++||+.||.++|+++|+.
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            489999999996 67789999999999999999999999888999999999999999999999964

>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=99.76  E-value=1.2e-18  Score=112.52  Aligned_cols=64  Identities=17%  Similarity=0.494  Sum_probs=60.1

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCC
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGN  171 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~  171 (197)
                      .++|++|+++|.+ +.|.++++.||++||+|..|+++|.+..|+..|+++||+.||.++|+++|.
T Consensus         5 ~~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C~   68 (69)
T 2cur_A            5 SSGCVKCNKAITS-GGITYQDQPWHADCFVCVTCSKKLAGQRFTAVEDQYYCVDCYKNFVSGPSS   68 (69)
T ss_dssp             CCCCSSSCCCCCT-TCEEETTEEECTTTTBCTTTCCBCTTSCEEECSSCEEEHHHHHHHHTCSCC
T ss_pred             cCCCcccCCEeCc-ceEEECccccccCcCEECCCCCCCCCCccEeECCEEECHHHhHHHhcCCCC
Confidence            3899999999984 678999999999999999999999988999999999999999999999985

>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=99.76  E-value=4.7e-19  Score=116.69  Aligned_cols=68  Identities=13%  Similarity=0.473  Sum_probs=63.2

Q ss_pred             CCCCCCCceeec---CceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCC
Q 029230          108 DKCVGCDRTVYP---TEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQL  175 (197)
Q Consensus       108 ~~C~~C~~~I~~---~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~  175 (197)
                      ++|++|+++|.+   .+.|.++++.||++||+|..|+++|.+..|+..|++|||+.||.++|+++|..+++
T Consensus         6 ~~C~~C~~~I~~~g~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~C~~~sg   76 (76)
T 1x68_A            6 SGCVACSKPISGLTGAKFICFQDSQWHSECFNCGKCSVSLVGKGFLTQNKEIFCQKCGSGMDTDISGPSSG   76 (76)
T ss_dssp             CCCTTTCCCCCTTTTCCEEEETTEEEEGGGCBCTTTCCBCSSSCEEEETTEEEETTTTCCCCCCSSSSSCC
T ss_pred             CCCccCCCcccCCCCceeEEECCcccCcccCChhhCCCcCCCCceEeECCEEECHHHhhhhhCCcCCCCCC
Confidence            899999999995   36688999999999999999999999888999999999999999999999987754

>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=99.76  E-value=3.5e-19  Score=118.68  Aligned_cols=77  Identities=21%  Similarity=0.493  Sum_probs=66.8

Q ss_pred             CeeeccccHHHHhhccCCcccccCCCCcccCCCCcccccCccccccccCCCCCCCCCCCceeecCceeeecCcccccccc
Q 029230           56 GVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus        56 g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      ..+||+.||.++|+                                      ++|++|+++|. ++.|.++++.||++||
T Consensus         2 ~~~yC~~dy~~~~~--------------------------------------~~C~~C~~~I~-~~~v~a~~~~wH~~CF   42 (81)
T 1v6g_A            2 SSGSSGLDYQRLYG--------------------------------------TRCFSCDQFIE-GEVVSALGKTYHPDCF   42 (81)
T ss_dssp             CCCCCCSCGGGSCC--------------------------------------CBCTTTCCBCC-SCCEEETTEEECTTTS
T ss_pred             CCCcchHHHHhHhC--------------------------------------CcCccccCEec-cceEEECCceeCccCC
Confidence            46899999999997                                      89999999999 5678999999999999


Q ss_pred             ccCcCCCCCCCCCeeeeCC-eeecHHHHHhHhcCCCC
Q 029230          136 KCSHGGCTISPSNYIAHEG-KLYCKHHHIQLFREKGN  171 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg-~~yC~~cy~~~~~~k~~  171 (197)
                      +|..|+++|..+.++..++ .+||..||.++++..++
T Consensus        43 ~C~~C~~~L~~~~~~~~~~~~~~C~~C~~~~~~~~~s   79 (81)
T 1v6g_A           43 VCAVCRLPFPPGDRVTFNGKECMCQKCSLPVSVSGPS   79 (81)
T ss_dssp             SCSSSCCCCCSSSCEEEETTEEEEHHHHSCCSSCCCC
T ss_pred             ccccCCCCCCCCCEEEeCCCCEEChhhhcccCCCCCC
Confidence            9999999998766666555 57999999988876653

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

Probab=99.76  E-value=3e-19  Score=119.03  Aligned_cols=66  Identities=29%  Similarity=0.747  Sum_probs=58.1

Q ss_pred             CCCCCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230            4 PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus         4 ~~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      ++.+..++|.+|+++|..++.+.++++.||++||+|..|+++|....|+.+++++||+.||.++|+
T Consensus         2 ~~~~~~~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~   67 (81)
T 1a7i_A            2 PNWGGGNKCGACGRTVYHAEEVQCDGRSFHRCCFLCMVCRKNLDSTTVAIHDAEVYCKSCYGKKYG   67 (81)
T ss_dssp             ------CBCSSSCCBCSSTTEEEETTEEEESSSEECSSSCCEECSSCCEEETTEEECSHHHHHHCC
T ss_pred             CCCCCCCcCcCcCccccCceeEEeCCcccccccCccCCCCCCCCCCCeEeeCCEEECHHHHHHHhC
Confidence            356678999999999988889999999999999999999999998899999999999999999998

>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=99.75  E-value=1.3e-18  Score=113.31  Aligned_cols=65  Identities=25%  Similarity=0.569  Sum_probs=61.1

Q ss_pred             CCCCCCCceeecC-ceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCC
Q 029230          108 DKCVGCDRTVYPT-EKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNY  172 (197)
Q Consensus       108 ~~C~~C~~~I~~~-e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~  172 (197)
                      ++|++|+++|.++ +.|.++|+.||++||+|..|+++|.++.|+..+|++||+.||.++|+++|+.
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            8999999999985 5678999999999999999999999989999999999999999999999964

>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=99.75  E-value=8.4e-19  Score=112.31  Aligned_cols=61  Identities=25%  Similarity=0.452  Sum_probs=58.2

Q ss_pred             CCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCC
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREK  169 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k  169 (197)
                      ++|++|+++|. ++.|.++|+.||++||+|..|+++|.++.|+..||++||+.||.++|++|
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            89999999999 67789999999999999999999999989999999999999999999986

>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=99.75  E-value=1.8e-18  Score=111.99  Aligned_cols=64  Identities=20%  Similarity=0.514  Sum_probs=60.1

Q ss_pred             CCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCC
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNY  172 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~  172 (197)
                      ++|++|+++|.+ +.|.++++.||++||+|..|+++|.+..|+..|+++||+.||.++|+++|..
T Consensus         6 ~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c~~   69 (70)
T 2d8z_A            6 SGCVQCKKPITT-GGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGPSS   69 (70)
T ss_dssp             CBCSSSCCBCCS-SEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCCTT
T ss_pred             CCCcccCCeecc-ceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhccccCC
Confidence            899999999984 5689999999999999999999999889999999999999999999999963

>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=99.75  E-value=1.3e-18  Score=114.54  Aligned_cols=60  Identities=33%  Similarity=0.853  Sum_probs=57.2

Q ss_pred             ccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeecc-ccHHHHhh
Q 029230           10 QKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR-PHFDQLFK   69 (197)
Q Consensus        10 ~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~-~c~~~~~~   69 (197)
                      |+|.+|+++|..++.+.++|+.||++||+|..|+++|.++.|+.++|.+||+ .||.++|+
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            5899999999988899999999999999999999999988999999999999 69999998

>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=99.75  E-value=2.1e-18  Score=112.21  Aligned_cols=65  Identities=20%  Similarity=0.534  Sum_probs=61.1

Q ss_pred             CCCCCCCceeecCc-eeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCC
Q 029230          108 DKCVGCDRTVYPTE-KVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNY  172 (197)
Q Consensus       108 ~~C~~C~~~I~~~e-~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~  172 (197)
                      ++|++|+++|.+++ .|.++|+.||++||+|..|+++|.++.|+..||++||+.||.++|+++|..
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            89999999999875 578999999999999999999999989999999999999999999999964

>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=1.8e-18  Score=113.84  Aligned_cols=70  Identities=33%  Similarity=0.743  Sum_probs=65.0

Q ss_pred             CCCCCCCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeecc-ccHHHHhhcc
Q 029230            2 ASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCR-PHFDQLFKRT   71 (197)
Q Consensus         2 ~~~~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~-~c~~~~~~~~   71 (197)
                      |+.++...++|.+|+++|..++.|.++++.||++||+|..|+++|.+..|+.+++++||+ .||.++|+++
T Consensus         2 s~~~~~~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~cy~~~f~~k   72 (76)
T 2cu8_A            2 SSGSSGMASKCPKCDKTVYFAEKVSSLGKDWHKFCLKCERCSKTLTPGGHAEHDGKPFCHKPCYATLFGSG   72 (76)
T ss_dssp             CCSCCCCCCBCTTTCCBCCTTTEEEETTEEEETTTCBCSSSCCBCCTTSCEEETTEEECTTTHHHHHSCSS
T ss_pred             ccccCCCCCCCcCCCCEeECCeEEEECCeEeeCCCCCCCCCCCccCCCceEeECCEEecchHHHHHhcccc
Confidence            567788899999999999988899999999999999999999999988999999999999 7999999843

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

Probab=99.74  E-value=1.7e-18  Score=114.17  Aligned_cols=65  Identities=31%  Similarity=0.598  Sum_probs=59.0

Q ss_pred             CCCCCCCCceeecCce-eeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCC
Q 029230          107 RDKCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGN  171 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~  171 (197)
                      .++|++|+++|.+.+. +.++|+.||++||+|..|+++|.++.|+..||++||+.||.++|+++|.
T Consensus        11 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~C~   76 (77)
T 1g47_A           11 SATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPCWI   76 (77)
T ss_dssp             CCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC--
T ss_pred             CCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcccC
Confidence            4899999999997665 5799999999999999999999988899999999999999999999986

>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=99.74  E-value=2.7e-18  Score=118.91  Aligned_cols=73  Identities=16%  Similarity=0.388  Sum_probs=68.0

Q ss_pred             CCCCCCCCceeec-CceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCCCCch
Q 029230          107 RDKCVGCDRTVYP-TEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDL  179 (197)
Q Consensus       107 ~~~C~~C~~~I~~-~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~~~~~  179 (197)
                      .++|++|+++|++ ++.|.++|+.||++||+|..|+++|.+..|+..||++||+.||.++|+++|..|...+.+
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~   78 (101)
T 2cup_A            5 SSGCVECRKPIGADSKEVHYKNRFWHDTCFRCAKCLHPLANETFVAKDNKILCNKCTTREDSPKCKGCFKAIVA   78 (101)
T ss_dssp             CCBCSSSCCBCCSSSCEEEETTEEEETTTCCCSSSCCCTTSSCCEEETTEEECHHHHTTCCCCBCSSSCCBCCS
T ss_pred             CCcCcccCCcccCCceEEEECccChhhcCCcccccCCCCCcCeeECcCCEEEChhHhhhhcCCccccCCCcccc
Confidence            3899999999985 667889999999999999999999998889999999999999999999999999998874

>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=99.73  E-value=8.6e-18  Score=113.92  Aligned_cols=64  Identities=22%  Similarity=0.445  Sum_probs=59.9

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCC
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGN  171 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~  171 (197)
                      .++|.+|+++|++ +.|.++++.||++||+|..|+++|.++.|+..|+++||+.||.++|++||.
T Consensus        25 ~~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~p~~~   88 (89)
T 1x64_A           25 MPLCDKCGSGIVG-AVVKARDKYRHPECFVCADCNLNLKQKGYFFVEGELYCETHARARTSGPSS   88 (89)
T ss_dssp             CCBCTTTCCBCCS-CCEESSSCEECTTTCCCSSSCCCTTTSCCEEETTEEECHHHHHHHSSSCCC
T ss_pred             CCCcccCCCEecc-cEEEECCceECccCCEecCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            4899999999995 668899999999999999999999988899999999999999999999984

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

Probab=99.73  E-value=3.2e-18  Score=121.29  Aligned_cols=68  Identities=18%  Similarity=0.443  Sum_probs=62.6

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCCC--CCeeeeCCeeecHHHHHhHhcCCCCCCC
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP--SNYIAHEGKLYCKHHHIQLFREKGNYSQ  174 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~--~~~~~~dg~~yC~~cy~~~~~~k~~~~~  174 (197)
                      .++|++|+++|.+.+.|.++++.||++||+|..|+++|..  ..|+.+||+|||+.||.++|+++|..|.
T Consensus         3 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~~y~~~f~~~c~~c~   72 (114)
T 1j2o_A            3 LLTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLGGSGGHMGS   72 (114)
T ss_dssp             CBCBSSSCSCBCSSEEEECSSSEECTTTCCCSSSCSCCCCSSSCCCCBTTBCCCHHHHHHHHTSCCSSCB
T ss_pred             CCCCcCCCCeeCCcEEEEECchhHHHhcCcccccCCchhcCCCeeEEECCeeechHHHHHHhCcccCcCC
Confidence            4899999999997777899999999999999999999984  5899999999999999999999987664

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

Probab=99.73  E-value=4.2e-18  Score=122.64  Aligned_cols=73  Identities=19%  Similarity=0.358  Sum_probs=69.3

Q ss_pred             CCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCCCCchh
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDLE  180 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~~~~~~  180 (197)
                      ++|++|+++|.+++.|.++|+.||++||+|..|+++|.+..|+.+||+|||+.||.++|+++|..|...+.+.
T Consensus         4 ~~C~~C~~~I~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~~~~~C~~C~~~I~~~   76 (126)
T 2xqn_T            4 PRCAGCDELIFSNEYTQAENQNWHLKHFCCFDCDSILAGEIYVMVNDKPVCKPCYVKNHAVVCQGCHNAIDPE   76 (126)
T ss_dssp             CBBTTTSSBCCSSCEEEETTEEECGGGSBCTTTCCBCTTSEEEEETTEEEEHHHHHHHSCCBCTTTCSBCCTT
T ss_pred             CCCccCCCEeCCceEEeeCCCCccCCCCCcCCCCCCCCcCEEEeECCEEechHHhCcCcCccCcccCCcCCcC
Confidence            8999999999988888999999999999999999999988999999999999999999999999999988853

>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=99.73  E-value=3.1e-18  Score=111.48  Aligned_cols=64  Identities=16%  Similarity=0.498  Sum_probs=59.0

Q ss_pred             CCCCCCCCceeec---CceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCC
Q 029230          107 RDKCVGCDRTVYP---TEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKG  170 (197)
Q Consensus       107 ~~~C~~C~~~I~~---~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~  170 (197)
                      .++|++|+++|.+   .+.|.++++.||++||+|..|+++|.+..|+.+||+|||+.||.++|++++
T Consensus         5 ~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p~~   71 (72)
T 1x4l_A            5 SSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGPSS   71 (72)
T ss_dssp             SCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCSSC
T ss_pred             CCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCCCC
Confidence            3899999999995   356789999999999999999999999899999999999999999999876

>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=99.73  E-value=8.7e-18  Score=108.77  Aligned_cols=64  Identities=14%  Similarity=0.422  Sum_probs=59.5

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCC
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGN  171 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~  171 (197)
                      .++|++|+++|. ++.|.++++.||++||+|..|+++|....|+..||++||+.||.++|+++..
T Consensus         5 ~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~   68 (70)
T 2d8x_A            5 SSGCHQCGEFII-GRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASGPS   68 (70)
T ss_dssp             SSBCSSSCCBCC-SCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCCSC
T ss_pred             CCcCccCCCEec-ceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCCCC
Confidence            489999999998 4678999999999999999999999998899999999999999999998764

>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=99.72  E-value=5.3e-18  Score=121.57  Aligned_cols=74  Identities=19%  Similarity=0.431  Sum_probs=68.0

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCC--CCCeeeeCCeeecHHHHHhHhcC--CCCCCCCCCchh
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTIS--PSNYIAHEGKLYCKHHHIQLFRE--KGNYSQLESDLE  180 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~--~~~~~~~dg~~yC~~cy~~~~~~--k~~~~~~~~~~~  180 (197)
                      .++|++|+++|.+.+.|.++++.||++||+|..|+++|.  +..|+.+||+|||+.||.++|++  +|..|...+...
T Consensus         5 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~cy~~~f~~~~~C~~C~~~I~~~   82 (122)
T 1m3v_A            5 WKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGAGGSGGHMGSGG   82 (122)
T ss_dssp             CCCBSSSSSCCCSSCCEEETTEEECHHHHCCSSSCCCTTTSEECCEEETTEEECHHHHHHHHCCCCSSSCSSCCSCCE
T ss_pred             CCCCcccCCEeCCcEEEEECCceeHhhCCCcCCCCCcccccCCeEEEECCeeecHHHHHHHcCCCCccccCCCCcCch
Confidence            389999999999877789999999999999999999997  46799999999999999999999  999999888754

>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=99.72  E-value=3e-18  Score=113.61  Aligned_cols=64  Identities=17%  Similarity=0.409  Sum_probs=59.7

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCC
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGN  171 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~  171 (197)
                      .++|++|+++|++ +.|.++++.||++||+|..|+++|.+..|+.+|+++||+.||.++|++++.
T Consensus        15 ~~~C~~C~~~I~~-~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g~   78 (79)
T 1x62_A           15 LPMCDKCGTGIVG-VFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPSS   78 (79)
T ss_dssp             CCCCSSSCCCCCS-SCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCCC
T ss_pred             CCccccCCCCccC-cEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCCC
Confidence            4899999999995 578999999999999999999999887899999999999999999999974

>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=99.69  E-value=2.8e-17  Score=108.98  Aligned_cols=63  Identities=19%  Similarity=0.432  Sum_probs=57.7

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCC
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGN  171 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~  171 (197)
                      .++|++|+++|. ++.|.++|+.||++||+|..|+++|.+.. +.+||++||+.||.++|+++++
T Consensus        15 ~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~-f~~~g~~yC~~cy~~~f~p~~s   77 (79)
T 2cor_A           15 KYICQKCHAIID-EQPLIFKNDPYHPDHFNCANCGKELTADA-RELKGELYCLPCHDKMGVSGPS   77 (79)
T ss_dssp             CCBCTTTCCBCC-SCCCCCSSSCCCTTTSBCSSSCCBCCTTC-EEETTEEECHHHHHTTSCCSSC
T ss_pred             CCCCccCCCEec-ceEEEECcceeCCCCCEeCCCCCccCCCC-EeECCEEeCHHHHHHhCCCCCC
Confidence            389999999999 66789999999999999999999999865 5999999999999999999875

>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=1.8e-17  Score=106.97  Aligned_cols=62  Identities=23%  Similarity=0.613  Sum_probs=58.3

Q ss_pred             CCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      ...++|.+|+++|. ++.|.++++.||++||+|..|+++|.+..|+++++++||+.||.++|+
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            45689999999998 678999999999999999999999998899999999999999999998

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

Probab=99.69  E-value=1.7e-17  Score=126.74  Aligned_cols=72  Identities=22%  Similarity=0.465  Sum_probs=66.0

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCCCCch
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDL  179 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~~~~~  179 (197)
                      .++|.+|+++|...+.|.++|+.||++||+|..|+++|.+..| .+||+|||+.||.++|+++|..|...+.+
T Consensus        60 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f-~~~g~~yC~~~y~~~f~~kC~~C~~~I~~  131 (182)
T 2jtn_A           60 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERCF-SRGESVYCKDDFFKRFGTKCAACQLGIPP  131 (182)
T ss_dssp             CCBCBTSSSBCCCSEEEEETTEEECSSTTSCTTTCCCCSSCCE-EETTEEECHHHHHHTTSCCCTTTCCCCCS
T ss_pred             CCcCccCCCCccCceeEEecCCeEccccCccCCCCCccCCCce-eECCEeeecCccccccccccccCCCccCC
Confidence            3899999999997766789999999999999999999998665 79999999999999999999999988764

>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=109.48  Aligned_cols=65  Identities=25%  Similarity=0.587  Sum_probs=59.5

Q ss_pred             CCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccC
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTG   72 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   72 (197)
                      ...++|.+|+++|..++.|.++++.||++||+|..|+++|.+ .|+.+++++||+.||.++|++++
T Consensus        13 ~~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~-~~~~~~g~~yC~~~y~~~fg~~C   77 (80)
T 2dj7_A           13 RGPSHCAGCKEEIKHGQSLLALDKQWHVSCFKCQTCSVILTG-EYISKDGVPYCESDYHAQFGSGP   77 (80)
T ss_dssp             SSCSCCTTTCCCCSSSCCEEETTEEECTTTCBCSSSCCBCSS-CCEEETTEEECTTHHHHHTTCCS
T ss_pred             CCCCCCcCcCCeeCCCeEEEECCcccccccCCcCcCCCCcCC-CeEEECCEEECHHHHHHHcCCCC
Confidence            456899999999998899999999999999999999999985 69999999999999999998443

>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=99.69  E-value=2.3e-17  Score=112.20  Aligned_cols=72  Identities=42%  Similarity=1.038  Sum_probs=65.5

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccC
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFE   79 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~   79 (197)
                      ..++|.+|+++|...+.|.++++.||++||+|..|+++|....|+.+++++||+.||.++|+++++.+..|.
T Consensus        14 ~~~~C~~C~~~I~~~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~kc~~~~g~g   85 (91)
T 2d8y_A           14 ARETCVECQKTVYPMERLLANQQVFHISCFRCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGFG   85 (91)
T ss_dssp             SSCBCTTTCCBCCTTSEEECSSSEEETTTCBCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCCC
T ss_pred             CCCcCccCCCccCCceeEEECCCEECCCCCeeCCCCCCCCCCCcEeECCEEECHHHHHHHhCCCcCccCCcC
Confidence            468999999999987899999999999999999999999988899999999999999999998776655554

>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=99.69  E-value=3.6e-17  Score=106.36  Aligned_cols=61  Identities=23%  Similarity=0.504  Sum_probs=56.5

Q ss_pred             CCCCCCCCceeecCc-eeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230          107 RDKCVGCDRTVYPTE-KVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e-~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      .++|++|+++|.+.+ .|.++++.||++||+|..|+++|.+..|+..++++||+.||.++|+
T Consensus         5 ~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~~~   66 (72)
T 1x61_A            5 SSGCGGCGEDVVGDGAGVVALDRVFHVGCFVCSTCRAQLRGQHFYAVERRAYCEGCYVATLE   66 (72)
T ss_dssp             CCCCSSSCSCCCSSSCCEECSSSEECTTTCBCSSSCCBCTTSCEEESSSCEEEHHHHHHHHH
T ss_pred             CCCCccCCCccCCCceEEEECCCeEcccCCcccccCCcCCcCcCEeeCCeEECHHHHHHHHc
Confidence            389999999999754 5789999999999999999999988889999999999999999995

>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=99.68  E-value=3.7e-17  Score=105.71  Aligned_cols=65  Identities=25%  Similarity=0.592  Sum_probs=59.3

Q ss_pred             CCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccC
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTG   72 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   72 (197)
                      ...++|.+|+++|. ++.+.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|++++
T Consensus         3 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c   67 (70)
T 2d8z_A            3 SGSSGCVQCKKPIT-TGGVTYREQPWHKECFVCTACRKQLSGQRFTARDDFAYCLNCFCDLYASGP   67 (70)
T ss_dssp             CCCCBCSSSCCBCC-SSEEESSSSEEETTTSBCSSSCCBCTTSCCEESSSSEECHHHHHHHTCCCC
T ss_pred             CCCCCCcccCCeec-cceEEECccccCCCCCccCCCCCcCCcCceEeeCCeEECHHHHHHHhcccc
Confidence            45689999999998 677999999999999999999999998899999999999999999998433

>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=99.67  E-value=5e-17  Score=105.48  Aligned_cols=60  Identities=33%  Similarity=0.705  Sum_probs=56.4

Q ss_pred             CCCCCCCceeecCce-eeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230          108 DKCVGCDRTVYPTEK-VSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~-v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      ++|++|+++|.+.+. |.++|+.||++||+|..|+++|.++.|+..||++||+.||.++|+
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            899999999998886 469999999999999999999998889999999999999999986

>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=2.3e-17  Score=109.34  Aligned_cols=66  Identities=20%  Similarity=0.402  Sum_probs=60.2

Q ss_pred             CCCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccC
Q 029230            6 GGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTG   72 (197)
Q Consensus         6 ~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   72 (197)
                      ....++|.+|+++|. +++|.++++.||++||+|..|+++|....|+.+++++||+.||.++|++++
T Consensus        12 ~~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~~~p~g   77 (79)
T 1x62_A           12 AQKLPMCDKCGTGIV-GVFVKLRDRHRHPECYVCTDCGTNLKQKGHFFVEDQIYCEKHARERVSGPS   77 (79)
T ss_dssp             CCCCCCCSSSCCCCC-SSCEECSSCEECTTTTSCSSSCCCHHHHCCEESSSCEECHHHHHHHHSSCC
T ss_pred             CCCCCccccCCCCcc-CcEEEECcceeCcCcCeeCCCCCCCCCCCeEeECCEEECHHHHHHHhCCCC
Confidence            345689999999999 578999999999999999999999998889999999999999999998654

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

Probab=99.67  E-value=1.6e-17  Score=110.85  Aligned_cols=64  Identities=34%  Similarity=0.708  Sum_probs=58.2

Q ss_pred             CCCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCee--eeCCeeecHHHHHhHhcCC
Q 029230          106 TRDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYI--AHEGKLYCKHHHIQLFREK  169 (197)
Q Consensus       106 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~--~~dg~~yC~~cy~~~~~~k  169 (197)
                      +.++|.+|+++|++++.|.++++.||++||+|..|+++|....|+  ..||++||+.||.++|+.-
T Consensus        14 ~~~~C~~C~~~I~~~e~v~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~   79 (82)
T 2co8_A           14 AGDLCALCGEHLYVLERLCVNGHFFHRSCFRCHTCEATLWPGGYEQHPGDGHFYCLQHLPQTDSGP   79 (82)
T ss_dssp             SSCBCSSSCCBCCTTTBCCBTTBCCBTTTCBCSSSCCBCCTTSEECCTTTCCCEETTTCCCCCCCC
T ss_pred             CCCCCcccCCCcccceEEEECCCeeCCCcCEEcCCCCCcCCCceeEeCcCCEEEChHHHHhhhcCC
Confidence            358999999999988889999999999999999999999998887  4799999999999988653

>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=99.67  E-value=4.7e-17  Score=106.23  Aligned_cols=61  Identities=15%  Similarity=0.321  Sum_probs=56.2

Q ss_pred             CCCCCCCceeecCceeeecCccccccccccCcCCCCCC-CCCeeeeCCeeecHHHHHhHhcCC
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTIS-PSNYIAHEGKLYCKHHHIQLFREK  169 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~-~~~~~~~dg~~yC~~cy~~~~~~k  169 (197)
                      ++|++|+++|.+ +.|.++|+.||++||+|..|+++|. +..|+..++++||..||.++++.+
T Consensus         6 ~~C~~C~~~I~~-~~v~a~~~~wH~~CF~C~~C~~~L~~~~~f~~~~~~~yC~~C~~~~~~~~   67 (73)
T 1wig_A            6 SGCDSCEKYITG-RVLEAGEKHYHPSCALCVRCGQMFAEGEEMYLQGSSIWHPACRQAARTED   67 (73)
T ss_dssp             CSCSSSCCCCSS-CCBCCSSCCBCTTTSCCSSSCCCCCSSCCCEEETTEEECTTHHHHTSSSS
T ss_pred             CCcccCCCEecC-eeEEeCCCCCCCCcCEeCCCCCCCCCCCeeEeeCCEEEChHHChHhhccc
Confidence            899999999985 6688999999999999999999998 778999999999999999987654

>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=99.67  E-value=3.1e-17  Score=107.87  Aligned_cols=62  Identities=19%  Similarity=0.457  Sum_probs=57.8

Q ss_pred             CCccccccccceec---ceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230            8 TQQKCMACDKTVYL---VDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus         8 ~~~~C~~C~~~I~~---~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      ..++|.+|+++|.+   .+.+.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|+
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            46899999999993   488999999999999999999999998899999999999999999987

>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=99.67  E-value=3.1e-17  Score=104.89  Aligned_cols=62  Identities=24%  Similarity=0.527  Sum_probs=58.3

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhc
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKR   70 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~   70 (197)
                      ..++|.+|+++|. ++.+.++|+.||++||+|..|+++|.+..|+.++|.+||+.||.++|++
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            4689999999999 8889999999999999999999999988999999999999999999873

>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=99.67  E-value=5.6e-17  Score=104.89  Aligned_cols=65  Identities=25%  Similarity=0.503  Sum_probs=60.1

Q ss_pred             CCCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhcc
Q 029230            6 GGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRT   71 (197)
Q Consensus         6 ~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~   71 (197)
                      +++.++|..|+++|. ++.+.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|++.
T Consensus         2 s~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~   66 (70)
T 2d8x_A            2 SSGSSGCHQCGEFII-GRVIKAMNNSWHPECFRCDLCQEVLADIGFVKNAGRHLCRPCHNREKASG   66 (70)
T ss_dssp             CCCSSBCSSSCCBCC-SCCEEETTEEECTTTSBCSSSCCBCSSSCCEEETTEEECHHHHHHHHCCC
T ss_pred             CCCCCcCccCCCEec-ceEEEECcccccccCCEeCCCCCcCCCCccEeECCeEECHHHhhhhcCCC
Confidence            356789999999998 68899999999999999999999999989999999999999999999843

>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=7.8e-17  Score=109.38  Aligned_cols=65  Identities=26%  Similarity=0.585  Sum_probs=60.0

Q ss_pred             CCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccC
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTG   72 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   72 (197)
                      ...++|.+|+++|. ++.|.++|+.||++||+|..|+++|.+..|+.+++++||+.||.++|++++
T Consensus        23 ~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~cy~~~f~~~c   87 (90)
T 2dar_A           23 KRTPMCAHCNQVIR-GPFLVALGKSWHPEEFNCAHCKNTMAYIGFVEEKGALYCELCYEKFFASGP   87 (90)
T ss_dssp             TCCCBBSSSCCBCC-SCEEEETTEEECTTTCBCSSSCCBCSSSCBEESSSCEECHHHHHHHTSCCC
T ss_pred             CCCCCCccCCCEec-ceEEEECCccccccCCccCCCCCCCCCCEeEeECCEEECHHHHHHHcCCCC
Confidence            45689999999997 888999999999999999999999998899999999999999999998544

>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=7e-17  Score=104.94  Aligned_cols=65  Identities=29%  Similarity=0.619  Sum_probs=59.6

Q ss_pred             CCccccccccceecc-eeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccC
Q 029230            8 TQQKCMACDKTVYLV-DKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTG   72 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~-~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   72 (197)
                      ..++|.+|+++|... +++.++|+.||++||+|..|+++|....|+.+++++||+.||.++|++++
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C   69 (72)
T 1wyh_A            4 GSSGCSACGETVMPGSRKLEYGGQTWHEHCFLCSGCEQPLGSRSFVPDKGAHYCVPCYENKFASGP   69 (72)
T ss_dssp             CCCBCSSSCCBCCSSSCEECSTTCCEETTTCBCTTTCCBTTTSCEEEETTEEEEHHHHHHHTSCCC
T ss_pred             cCCCCccCCCccccCccEEEECccccCcccCeECCCCCcCCCCccCCcCCeEECHHHHHHHccCcC
Confidence            468999999999974 78999999999999999999999999899999999999999999998443

>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=99.66  E-value=9.3e-17  Score=104.35  Aligned_cols=65  Identities=22%  Similarity=0.572  Sum_probs=59.6

Q ss_pred             CCccccccccceecc-eeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccC
Q 029230            8 TQQKCMACDKTVYLV-DKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTG   72 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~-~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   72 (197)
                      ..++|.+|+++|... ..+.++|+.||++||+|..|+++|.++.|+.+++.+||+.||.++|++++
T Consensus         4 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~C   69 (72)
T 1x4k_A            4 GSSGCQECKKTIMPGTRKMEYKGSSWHETCFICHRCQQPIGTKSFIPKDNQNFCVPCYEKQHASGP   69 (72)
T ss_dssp             CCCCBSSSCCCCCSSSCEEEETTEEEETTTTCCSSSCCCCCSSSEEEETTEEEEHHHHHHHTSSCC
T ss_pred             cCCCCccCCCcccCCceEEEECcCeecccCCcccccCCccCCCccCccCCeEECHHHHhHHhCCCC
Confidence            458999999999975 57999999999999999999999999999999999999999999998443

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

Probab=99.66  E-value=1.2e-16  Score=115.60  Aligned_cols=72  Identities=17%  Similarity=0.406  Sum_probs=66.4

Q ss_pred             CCCCCCCceeecCceeeecCccccccccccCcCCCCCC--CCCeeeeCCeeecHHHHHhHhcC--CCCCCCCCCch
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTIS--PSNYIAHEGKLYCKHHHIQLFRE--KGNYSQLESDL  179 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~--~~~~~~~dg~~yC~~cy~~~~~~--k~~~~~~~~~~  179 (197)
                      ++|++|+++|.+.+.|.++|+.||++||+|..|+++|.  +..|+.+||+|||+.||.++|++  +|..|...+..
T Consensus         3 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~~~~~~~~g~~yC~~~y~~~~~~~~~C~~C~~~I~~   78 (131)
T 2xjy_A            3 LTCGGCQQNIGDRYFLKAIDQYWHEDCLSCDLCGCRLGEVGRRLYYKLGRKLCRRDYLRLFGQDGLCASCDKRIRA   78 (131)
T ss_dssp             CBBTTTCCBCCSSEEEEETTEEEETTTCBCTTTCCBCSSTTCCEEEETTEEECHHHHHHHHCCCEECTTTCCEECT
T ss_pred             ccCcCCCCEeCCcEEEEECCCcccHHHcccCcCCCccccCCCeEEEECCEEeecCchhhhCCCccChhhcCCccCc
Confidence            78999999999776688999999999999999999996  36899999999999999999999  99999988764

>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=99.66  E-value=5.3e-17  Score=105.62  Aligned_cols=65  Identities=17%  Similarity=0.413  Sum_probs=59.2

Q ss_pred             CCCCccccccccceec---ceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhc
Q 029230            6 GGTQQKCMACDKTVYL---VDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKR   70 (197)
Q Consensus         6 ~~~~~~C~~C~~~I~~---~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~   70 (197)
                      +...++|.+|+++|..   .+++.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|++
T Consensus         2 s~~~~~C~~C~~~I~~~~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~p   69 (72)
T 1x4l_A            2 SSGSSGCAGCTNPISGLGGTKYISFEERQWHNDCFNCKKCSLSLVGRGFLTERDDILCPDCGKDISGP   69 (72)
T ss_dssp             CSCSCSBTTTTBCCCCSSSCSCEECSSCEECTTTCBCSSSCCBCTTSCCEECSSSEECHHHHHTCCCS
T ss_pred             CCCCCCCcCCCccccCCCCcceEEECCcccCcccCEeccCCCcCCCCccEeECCEEEChhHcCcccCC
Confidence            3457899999999994   3779999999999999999999999988999999999999999999874

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

Probab=99.65  E-value=7.2e-17  Score=106.25  Aligned_cols=67  Identities=25%  Similarity=0.563  Sum_probs=60.0

Q ss_pred             CCCCCccccccccceec-ceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhcc
Q 029230            5 FGGTQQKCMACDKTVYL-VDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRT   71 (197)
Q Consensus         5 ~~~~~~~C~~C~~~I~~-~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~   71 (197)
                      .....++|.+|+++|.. +..+.++|+.||++||+|..|+++|.++.|+.++|++||+.||.++|+++
T Consensus         7 ~~~~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~~f~~~   74 (77)
T 1g47_A            7 NALASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFAPC   74 (77)
T ss_dssp             SCCCCCBCSSSCCBCCSTTTCEEETTEEECTTTCCCTTTCCCCGGGCSEEETTEEECHHHHHHHCCCC
T ss_pred             cCCCCCCchhcCCccCCCceEEEeCccEeccccCeECCCCCCCCCCCeEeECCeEeCHHHHHHHhhcc
Confidence            44567899999999985 45578999999999999999999999889999999999999999999843

>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=99.65  E-value=1.2e-16  Score=108.22  Aligned_cols=65  Identities=25%  Similarity=0.484  Sum_probs=59.5

Q ss_pred             CCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccC
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTG   72 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   72 (197)
                      ...++|.+|+++|. ++.+.++++.||++||+|..|+++|....|+.+++.+||+.||.++|++++
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            45578999999999 588999999999999999999999998899999999999999999998544

>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=99.64  E-value=1e-16  Score=114.93  Aligned_cols=61  Identities=21%  Similarity=0.539  Sum_probs=56.4

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCC--CCCeeeeCCeeecHHHHHhHhc
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTIS--PSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~--~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      .++|++|+++|+..+.|.++|+.||++||+|..|+++|.  +..|+.+||+|||+.||.++||
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            389999999999776789999999999999999999997  4689999999999999999986

>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=99.64  E-value=2.3e-16  Score=119.12  Aligned_cols=72  Identities=22%  Similarity=0.446  Sum_probs=65.5

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCCCCch
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLESDL  179 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~~~~~  179 (197)
                      .++|++|+++|.+.+.|.++|+.||++||+|..|+++|.+.. +.+||++||+.||.++|+++|..|...+..
T Consensus         6 ~~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~~-f~~~g~~yC~~~y~~~f~~~C~~C~~~I~~   77 (169)
T 2rgt_A            6 IPMCAGCDQHILDRFILKALDRHWHSKCLKCSDCHVPLAERC-FSRGESVYCKDDFFKRFGTKCAACQLGIPP   77 (169)
T ss_dssp             -CBBSSSSSBCCSSSCEECSSCEECTTTSBCTTTCCBCCSCC-EESSSCEECHHHHHHHHSCBCTTTCCBCCT
T ss_pred             CCccccCCCccCCcEEEEECCcEEccccCccCCCCCcCCCCC-cccCCeeeecccccccccccccccccccCC
Confidence            389999999999776688999999999999999999999866 478999999999999999999999987765

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

Probab=99.63  E-value=1.8e-16  Score=101.13  Aligned_cols=58  Identities=24%  Similarity=0.641  Sum_probs=54.1

Q ss_pred             CCCCCCCceeecC-ceeeecCcccc--ccccccCcCCCCCCCCCeeeeCCeeec-HHHHHhH
Q 029230          108 DKCVGCDRTVYPT-EKVSVNGAAYH--RSCFKCSHGGCTISPSNYIAHEGKLYC-KHHHIQL  165 (197)
Q Consensus       108 ~~C~~C~~~I~~~-e~v~~~g~~~H--~~CF~C~~C~~~l~~~~~~~~dg~~yC-~~cy~~~  165 (197)
                      ++|++|+++|.++ +.|.++|+.||  ++||+|..|+++|.+..|+.+||+||| ..||.++
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            7899999999975 66889999999  999999999999999899999999999 9999875

>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=99.63  E-value=2.2e-16  Score=102.58  Aligned_cols=63  Identities=25%  Similarity=0.565  Sum_probs=58.0

Q ss_pred             CCCccccccccceecc-eeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230            7 GTQQKCMACDKTVYLV-DKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~-~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      ...++|.+|+++|... ..+.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|+
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            4568999999999864 57999999999999999999999988889999999999999999986

>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=99.63  E-value=2.7e-16  Score=104.22  Aligned_cols=62  Identities=26%  Similarity=0.629  Sum_probs=58.0

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhc
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKR   70 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~   70 (197)
                      .+++|.+|+++|. ++.|.++++.||+.||+|..|+++|.++.|+.+++++||+.||.++|++
T Consensus        14 ~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~~y~~~f~~   75 (80)
T 1x3h_A           14 FSPKCGGCNRPVL-ENYLSAMDTVWHPECFVCGDCFTSFSTGSFFELDGRPFCELHYHHRRGS   75 (80)
T ss_dssp             CSCBCTTTCCBCC-SSCEEETTEEECTTTCBCSSSCCBSCSSCCEESSSCEECHHHHHHHHSS
T ss_pred             cCCccccCCCeec-ceeEEECCCeEecCcCChhhCCCCCCCCcEEeECCEEECHHHHHHHcCC
Confidence            4589999999999 5789999999999999999999999988999999999999999999983

>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=99.62  E-value=4.6e-16  Score=119.79  Aligned_cols=68  Identities=28%  Similarity=0.592  Sum_probs=63.8

Q ss_pred             CCCCCCCCceeecCceeeecCccccccccccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCC
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQ  174 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~  174 (197)
                      .++|.+|+++|+.++.|.++|+.||++||+|..|+++|.+..|+.+||++||+.||.++|+++|..|.
T Consensus         7 ~~~C~~C~~~I~~~~~v~a~g~~wH~~CF~C~~C~~~L~~~~~~~~~g~~yC~~cy~~~f~~~c~~c~   74 (192)
T 1b8t_A            7 GKKCGVCQKAVYFAEEVQCEGSSFHKSCFLCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKG   74 (192)
T ss_dssp             CEECTTTCCEECSSCCEEETTEEECTTTCBCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCC
T ss_pred             CCcCccCCCeecceeEEEeCCceecCCCCcCcccCCcCCCCeeEecCCEeeChhhhHhhcCccccccc
Confidence            47899999999988888999999999999999999999998899999999999999999999997554

>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=3.4e-16  Score=104.27  Aligned_cols=66  Identities=27%  Similarity=0.563  Sum_probs=60.1

Q ss_pred             CCccccccccceecce-eEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCC
Q 029230            8 TQQKCMACDKTVYLVD-KLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGS   73 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~-~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~   73 (197)
                      ..++|.+|+++|..++ .+.++++.||++||+|..|+++|..+.|+.+++++||+.||.++|+++++
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~~~   80 (82)
T 1x63_A           14 DSPKCKGCFKAIVAGDQNVEYKGTVWHKDCFTCSNCKQVIGTGSFFPKGEDFYCVTCHETKFASGPS   80 (82)
T ss_dssp             CSCBCSSSCCBCCSSSCEEECSSCEEETTTCCCSSSCCCCTTSCEEEETTEEEEHHHHHHHTSCCCS
T ss_pred             cCCcCccCCcccccCceEEEECccccccccCchhhCCCccCCCccEeeCCEEECHHHHHHHhCCCCC
Confidence            4589999999998755 58999999999999999999999998999999999999999999986653

>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=4.8e-16  Score=103.36  Aligned_cols=63  Identities=27%  Similarity=0.561  Sum_probs=57.5

Q ss_pred             CCCccccccccceecceeEEeCCccccccccccccccccccCCCeeec-CCeeeccccHHHHhhc
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSF-EGVLYCRPHFDQLFKR   70 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~-~g~~yC~~c~~~~~~~   70 (197)
                      ...++|.+|+++|. ++.|.++++.||+.||+|..|+++|.+..|+.. +|++||+.||.++|++
T Consensus        13 ~~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~g~~yC~~cy~~~f~~   76 (81)
T 2dlo_A           13 ATLEKCATCSQPIL-DRILRAMGKAYHPGCFTCVVCHRGLDGIPFTVDATSQIHCIEDFHRKFAS   76 (81)
T ss_dssp             SSCCBCTTTCCBCC-SCCEEETTEEECTTTCBCSSSCCBCTTSCEECCTTCCCEEHHHHHHHTTS
T ss_pred             cCCCccccCCCeec-ceeEEECCccccHHhcCcccCCCccCCCeeEECCCCEEECHHHHHHHhcC
Confidence            35789999999998 678999999999999999999999998888866 7899999999999983

>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=99.61  E-value=3.1e-16  Score=103.91  Aligned_cols=65  Identities=26%  Similarity=0.495  Sum_probs=58.0

Q ss_pred             CCCCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccC
Q 029230            6 GGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTG   72 (197)
Q Consensus         6 ~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   72 (197)
                      ....++|.+|+++|. ++.|.++|+.||++||+|..|+++|....| +++|.+||+.||.++|++..
T Consensus        12 ~~~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~f-~~~g~~yC~~cy~~~f~p~~   76 (79)
T 2cor_A           12 GLGKYICQKCHAIID-EQPLIFKNDPYHPDHFNCANCGKELTADAR-ELKGELYCLPCHDKMGVSGP   76 (79)
T ss_dssp             CCCCCBCTTTCCBCC-SCCCCCSSSCCCTTTSBCSSSCCBCCTTCE-EETTEEECHHHHHTTSCCSS
T ss_pred             ccCCCCCccCCCEec-ceEEEECcceeCCCCCEeCCCCCccCCCCE-eECCEEeCHHHHHHhCCCCC
Confidence            345689999999999 788999999999999999999999997754 89999999999999998543

>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=99.61  E-value=1.6e-16  Score=106.07  Aligned_cols=64  Identities=30%  Similarity=0.806  Sum_probs=58.2

Q ss_pred             CCCCccccccccceecceeEEeCCccccccccccccccccccCCCee--ecCCeeeccccHHHHhh
Q 029230            6 GGTQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFN--SFEGVLYCRPHFDQLFK   69 (197)
Q Consensus         6 ~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~--~~~g~~yC~~c~~~~~~   69 (197)
                      .+..++|.+|+++|+..+.+.++++.||++||+|..|+++|....|+  +++|++||+.||.++|+
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            34568999999999988899999999999999999999999998887  57999999999988876

>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=99.61  E-value=6.7e-16  Score=102.34  Aligned_cols=64  Identities=27%  Similarity=0.580  Sum_probs=58.8

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccC
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTG   72 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   72 (197)
                      ..++|.+|+++|. ++.|.++++.||++||+|..|+++|.+..|+.+++++||+.||.++|++++
T Consensus        14 ~~~~C~~C~~~I~-~~~v~a~~~~~H~~CF~C~~C~~~L~~~~~~~~~~~~yC~~cy~~~f~~~c   77 (80)
T 2cuq_A           14 FAPRCARCSKTLT-QGGVTYRDQPWHRECLVCTGCQTPLAGQQFTSRDEDPYCVACFGELFASGP   77 (80)
T ss_dssp             SSCCCTTTCCCCC-SCCEESSSSEECTTTCBCSSSCCBCTTCCEEECSSSEEEHHHHHHHTTCST
T ss_pred             cCCcCCCCCCEec-CcEEEECCchhhhhhCCcccCCCcCCCCeeEeECCEEECHHHHHHHcCCCC
Confidence            4589999999998 568999999999999999999999998899999999999999999998444

>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=99.60  E-value=3.1e-16  Score=104.46  Aligned_cols=65  Identities=23%  Similarity=0.567  Sum_probs=58.7

Q ss_pred             CCccccccccceec-ceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhhccC
Q 029230            8 TQQKCMACDKTVYL-VDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTG   72 (197)
Q Consensus         8 ~~~~C~~C~~~I~~-~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   72 (197)
                      ..++|.+|+++|.. +.++.++++.||+.||+|..|+++|.+..|+.+++++||+.||.++|++++
T Consensus        14 ~~~~C~~C~~~I~~~~~~~~a~~~~~H~~CF~C~~C~~~L~~~~f~~~~~~~~C~~c~~~~~~~~C   79 (82)
T 2ehe_A           14 FANTCAECQQLIGHDSRELFYEDRHFHEGCFRCCRCQRSLADEPFTCQDSELLCNDCYCSAFSSGP   79 (82)
T ss_dssp             CSCBCTTTCCBCCSSCCBCCCSSCCCBTTTSBCTTTCCBCSSCCEEEETTEEEETTTSSCCGGGSS
T ss_pred             cCCcCccCCCccccCcEEEEeCCccccccCCeecCCCCccCCCccEeeCCEEECHHHHhhhcCCCC
Confidence            45799999999984 567889999999999999999999998899999999999999999998433

>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=99.59  E-value=4.8e-16  Score=101.39  Aligned_cols=61  Identities=16%  Similarity=0.311  Sum_probs=56.4

Q ss_pred             CCccccccccceecceeEEeCCcccccccccccccccccc-CCCeeecCCeeeccccHHHHhh
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLK-LSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~-~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      ..++|.+|+++|. ++.|.++|+.||++||+|..|+++|. +..|+.+++++||..||.++++
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 58899999999999999999999998 6789999999999999998876

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

Probab=99.59  E-value=5.8e-16  Score=100.38  Aligned_cols=63  Identities=29%  Similarity=0.695  Sum_probs=57.4

Q ss_pred             CCCccccccccceeccee-EEeCCccccccccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230            7 GTQQKCMACDKTVYLVDK-LTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~-~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      ...++|.+|+++|...+. +.+.|+.||++||+|..|+++|..+.|+.++|++||+.||.++|+
T Consensus         9 ~~~~~C~~C~~~i~~~e~~~~~~~~~~H~~CF~C~~C~~~L~~~~~~~~~g~~yC~~~y~~lf~   72 (72)
T 3f6q_B            9 SASATCERCKGGFAPAEKIVNSNGELYHEQCFVCAQCFQQFPEGLFYEFEGRKYCEHDFQMLFA   72 (72)
T ss_dssp             CTTCBCTTTCCBCCTTCEEEEETTEEEETTTSSCTTTCCCCGGGCCEEETTEEECHHHHHHHTC
T ss_pred             cCCccchhcCccccCCceEEEeCcCeeCcCCCcccCCCCCCCCCCeEeECCeEeCHHHHHHhhC
Confidence            356899999999997665 689999999999999999999998899999999999999999874

>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=99.59  E-value=6.3e-16  Score=118.64  Aligned_cols=72  Identities=18%  Similarity=0.428  Sum_probs=66.4

Q ss_pred             CCCCCCCceeecCceeeecCccccccccccCcCCCCCCC--CCeeeeCCeeecHHHHHhHhcC--CCCCCCCCCch
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISP--SNYIAHEGKLYCKHHHIQLFRE--KGNYSQLESDL  179 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~--~~~~~~dg~~yC~~cy~~~~~~--k~~~~~~~~~~  179 (197)
                      ++|++|+++|.+.+.|.++|+.||++||+|..|+++|..  ..|+.+||++||+.||.++|++  +|..|...+..
T Consensus         6 ~~C~~C~~~I~~~~~~~a~~~~wH~~CF~C~~C~~~L~~~g~~~~~~~g~~yC~~cy~~~~~~~~~C~~C~~~I~~   81 (188)
T 1rut_X            6 KRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFGNSGACSACGQSIPA   81 (188)
T ss_dssp             CBBTTTCCBCCCSEEEEETTEEECGGGCBCTTTCCBHHHHCSEEEEETTEEECHHHHHHHHSCCEECTTTCCEECT
T ss_pred             CcCccCCCEeCCceeEEecCcEecccCcccCCCCcccccCCceEEEeCCccccccccccccccCCccccCCCcccc
Confidence            899999999997666889999999999999999999985  6899999999999999999999  79999987764

>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=99.59  E-value=8.6e-16  Score=110.12  Aligned_cols=62  Identities=23%  Similarity=0.541  Sum_probs=56.4

Q ss_pred             CCccccccccceecceeEEeCCcccccccccccccccccc--CCCeeecCCeeeccccHHHHhh
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLK--LSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~--~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      ..++|.+|+++|....++.++|+.||+.||+|..|+++|.  +..|+.++|++||+.||.++|+
T Consensus        60 ~~~~C~~C~~~I~~~~~v~a~~~~wH~~CF~C~~C~~~L~~~g~~f~~~dg~~yC~~cy~~~Fg  123 (123)
T 2l4z_A           60 SWKRCAGCGGKIADRFLLYAMDSYWHSRCLKCSSCQAQLGDIGTSSYTKSGMILCRNDYIRLFG  123 (123)
T ss_dssp             SCSBBSSSSSBCCSSSEEEETTEEEETTTSBCTTTCCBGGGTTCCCBCSSSCCBCHHHHHHHCC
T ss_pred             cCCcCcCCCCCcCCcEEEEeCCcEEcccccCcCcCCCcccccCCceEEECCEEeCHHHhhhhcC
Confidence            3579999999999766799999999999999999999997  3589999999999999999874

>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=1.7e-15  Score=96.56  Aligned_cols=59  Identities=25%  Similarity=0.611  Sum_probs=54.1

Q ss_pred             Cccccccccceec-ceeEEeCCcccc--ccccccccccccccCCCeeecCCeeec-cccHHHH
Q 029230            9 QQKCMACDKTVYL-VDKLTADNRVYH--KACFRCHHCKGTLKLSNFNSFEGVLYC-RPHFDQL   67 (197)
Q Consensus         9 ~~~C~~C~~~I~~-~~~~~~~g~~~H--~~CF~C~~C~~~L~~~~f~~~~g~~yC-~~c~~~~   67 (197)
                      +++|.+|+++|.. ++.|.++|+.||  ++||+|..|+++|.+..|+.++|++|| .+||.++
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            4789999999997 478999999999  999999999999998899999999999 8888654

>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=99.55  E-value=2.9e-15  Score=98.48  Aligned_cols=60  Identities=22%  Similarity=0.558  Sum_probs=54.8

Q ss_pred             CCccccccccceec----ceeEEeCCccccccccccccccccccCCCeeecCCeeeccccHHHH
Q 029230            8 TQQKCMACDKTVYL----VDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQL   67 (197)
Q Consensus         8 ~~~~C~~C~~~I~~----~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~   67 (197)
                      ..++|.+|+++|.+    .+.+.++++.||+.||+|..|+++|.+..|+.+++++||+.||.++
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            45899999999993    4789999999999999999999999988999999999999999753

>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=99.53  E-value=6.6e-15  Score=97.73  Aligned_cols=62  Identities=21%  Similarity=0.472  Sum_probs=56.1

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccC-CCee-ecCCeeeccccHHHHhhc
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKL-SNFN-SFEGVLYCRPHFDQLFKR   70 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~-~~f~-~~~g~~yC~~c~~~~~~~   70 (197)
                      ..++|.+|+++|. ++.+.++++.||++||+|..|+++|.. ..|. ++++++||+.||.++|++
T Consensus        14 ~~~~C~~C~~~I~-~~~~~a~~~~~H~~CF~C~~C~~~L~~g~~f~~~~~~~~~C~~c~~~~~~~   77 (81)
T 1x6a_A           14 FGEFCHGCSLLMT-GPFMVAGEFKYHPECFACMSCKVIIEDGDAYALVQHATLYCGKCHNEVVSG   77 (81)
T ss_dssp             SSCBCTTTCCBCC-SCCBCCTTCCBCTTSCBCTTTCCBCCTTSCEEECSSSCEEEHHHHHHHHCT
T ss_pred             cCCcCccCCCCcC-ceEEEECCceeccccCCccCCCCccCCCCcEEEeeCCEEECHHHHHHHhcC
Confidence            4579999999999 888999999999999999999999975 5676 589999999999999984

>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=99.40  E-value=6.2e-14  Score=93.02  Aligned_cols=61  Identities=21%  Similarity=0.495  Sum_probs=53.3

Q ss_pred             CCccccccccceecceeEEeCCccccccccccccccccccCCCeeecCC-eeeccccHHHHhh
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACFRCHHCKGTLKLSNFNSFEG-VLYCRPHFDQLFK   69 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF~C~~C~~~L~~~~f~~~~g-~~yC~~c~~~~~~   69 (197)
                      ..++|.+|+++|. ++.|.++++.||++||+|..|+++|..+.|+..++ .+||..||.+++.
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            4579999999999 78899999999999999999999998777666655 4799999987765

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

Probab=98.68  E-value=6.7e-09  Score=55.81  Aligned_cols=28  Identities=43%  Similarity=0.994  Sum_probs=27.1

Q ss_pred             CCCCCCCceeecCceeeecCcccccccc
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      ++|++|++.|+++|.+.+.|+.||..||
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            7899999999999999999999999998

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

Probab=98.33  E-value=1.3e-07  Score=50.70  Aligned_cols=29  Identities=38%  Similarity=0.902  Sum_probs=27.5

Q ss_pred             CccccccccceecceeEEeCCcccccccc
Q 029230            9 QQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         9 ~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      .++|..|++.|+..+.+.++|+.||..||
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            47999999999999999999999999998

>1jjd_A Metallothionein, SMTA; zinc finger, zinc cluster, metal binding PR; NMR {Synechococcus elongatus} SCOP: g.46.1.1

Probab=87.84  E-value=0.43  Score=28.37  Aligned_cols=30  Identities=27%  Similarity=0.539  Sum_probs=24.0

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeec-HHHHHhH
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYC-KHHHIQL  165 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC-~~cy~~~  165 (197)
                      .|..|+..++...-+..||+.|| +.|...-
T Consensus         9 aC~~C~c~Vs~~eai~~dGK~YCSe~Ca~gH   39 (55)
T 1jjd_A            9 ACEPCLCNVDPSKAIDRNGLYYCSEACADGH   39 (55)
T ss_dssp             SSTTCCCCBCTTTSEESSSCEESSHHHHHTS
T ss_pred             cCCCCeeEechHHhhhcCCeEEehHHHHccC
Confidence            37788888888788899999998 7887653

>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=87.63  E-value=1.1  Score=30.33  Aligned_cols=97  Identities=19%  Similarity=0.410  Sum_probs=55.9

Q ss_pred             CCCCccccccccceecceeEEeC--CccccccccccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCc
Q 029230            6 GGTQQKCMACDKTVYLVDKLTAD--NRVYHKACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPK   83 (197)
Q Consensus         6 ~~~~~~C~~C~~~I~~~~~~~~~--g~~~H~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~   83 (197)
                      ......|..|+..-...+.|.-.  ++.||..|+.=.     +..    ...+.-+|..|                    
T Consensus         4 ~~~~~~C~~C~~~g~~~~ll~C~~C~~~~H~~Cl~~~-----~~~----~~~~~W~C~~C--------------------   54 (111)
T 2ysm_A            4 GSSGANCAVCDSPGDLLDQFFCTTCGQHYHGMCLDIA-----VTP----LKRAGWQCPEC--------------------   54 (111)
T ss_dssp             CCCCSCBTTTCCCCCTTTSEECSSSCCEECTTTTTCC-----CCT----TTSTTCCCTTT--------------------
T ss_pred             CCCCCCCcCCCCCCCCcCCeECCCCCCCcChHHhCCc-----ccc----ccccCccCCcC--------------------
Confidence            34557899998764322234333  477888886532     110    13455667665                    


Q ss_pred             ccCCCCcccccCccccccccCCCCCCCCCCCceeecCceee--ecCccccccccccCcCCCCCCCCCeeeeCCeeecHHH
Q 029230           84 IVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTVYPTEKVS--VNGAAYHRSCFKCSHGGCTISPSNYIAHEGKLYCKHH  161 (197)
Q Consensus        84 ~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I~~~e~v~--~~g~~~H~~CF~C~~C~~~l~~~~~~~~dg~~yC~~c  161 (197)
                                              ..|..|++.-.....|.  .=++.||..|..=     +|..    .-.+.-||..|
T Consensus        55 ------------------------~~C~~C~~~~~~~~ll~Cd~C~~~yH~~Cl~p-----pl~~----~P~g~W~C~~C  101 (111)
T 2ysm_A           55 ------------------------KVCQNCKQSGEDSKMLVCDTCDKGYHTFCLQP-----VMKS----VPTNGWKCKNC  101 (111)
T ss_dssp             ------------------------CCCTTTCCCSCCTTEEECSSSCCEEEGGGSSS-----CCSS----CCSSCCCCHHH
T ss_pred             ------------------------CcccccCccCCCCCeeECCCCCcHHhHHhcCC-----cccc----CCCCCcCCcCC
Confidence                                    35788887654434443  4567899988742     2322    12367889888


Q ss_pred             HHh
Q 029230          162 HIQ  164 (197)
Q Consensus       162 y~~  164 (197)
                      ...
T Consensus       102 ~~c  104 (111)
T 2ysm_A          102 RIC  104 (111)
T ss_dssp             HCC
T ss_pred             cCc
Confidence            554

>1t1h_A Gspef-atpub14, armadillo repeat containing protein; ubiquitin ligase, E3 ligase, U-BOX,; NMR {Arabidopsis thaliana} SCOP: g.44.1.2

Probab=86.08  E-value=0.96  Score=28.16  Aligned_cols=34  Identities=21%  Similarity=0.281  Sum_probs=26.3

Q ss_pred             cccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           35 ACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        35 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      .-|.|..|...+.+ .....-|..||..|..+.+.
T Consensus         7 ~~~~C~IC~~~~~~-Pv~~~CgH~fc~~Ci~~~~~   40 (78)
T 1t1h_A            7 EYFRCPISLELMKD-PVIVSTGQTYERSSIQKWLD   40 (78)
T ss_dssp             SSSSCTTTSCCCSS-EEEETTTEEEEHHHHHHHHT
T ss_pred             ccCCCCCccccccC-CEEcCCCCeecHHHHHHHHH
Confidence            45788899887764 44456899999999988774

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=85.60  E-value=0.49  Score=32.54  Aligned_cols=104  Identities=11%  Similarity=0.219  Sum_probs=60.0

Q ss_pred             cccccccccccCC----C--eeecCCeeeccccHHHHhhccCCcccccCCCCcccCCCCcccccCccccccccCCCCCCC
Q 029230           37 FRCHHCKGTLKLS----N--FNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKC  110 (197)
Q Consensus        37 F~C~~C~~~L~~~----~--f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C  110 (197)
                      +.|..|...+...    .  ....=|..||..|..+.+..                                    ...|
T Consensus         8 ~~C~IC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~------------------------------------~~~C   51 (133)
T 4ap4_A            8 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKN------------------------------------ANTC   51 (133)
T ss_dssp             CBCTTTCCBHHHHHHTTCCEEEETTCCEEEHHHHHHHHTT------------------------------------CSBC
T ss_pred             CCCcccChhhhCccccccCeEecCCCChhhHHHHHHHHHh------------------------------------CCCC
Confidence            5677776665432    1  33445788888888776541                                    1468


Q ss_pred             CCCCceeecCceeeecCccccccccccCcCCCCCCCC----C--eeeeCCeeecHHHHHhHh--cCCCCCCCCCCch
Q 029230          111 VGCDRTVYPTEKVSVNGAAYHRSCFKCSHGGCTISPS----N--YIAHEGKLYCKHHHIQLF--REKGNYSQLESDL  179 (197)
Q Consensus       111 ~~C~~~I~~~e~v~~~g~~~H~~CF~C~~C~~~l~~~----~--~~~~dg~~yC~~cy~~~~--~~k~~~~~~~~~~  179 (197)
                      +.|.+.+...+....   ..-.+=+.|..|...+...    .  ....=|..||..|..+.+  ...|-.|......
T Consensus        52 P~Cr~~~~~~~l~~l---~i~~~~~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~  125 (133)
T 4ap4_A           52 PTCRKKINHKRYHPI---YIGSGTVSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINH  125 (133)
T ss_dssp             TTTCCBCTTTCEEEC---BCSSSSCBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCG
T ss_pred             CCCCCcCcccccccc---ccCCCCCCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCCh
Confidence            888888765443211   1122345677776665421    1  222348889998876654  3456666665544

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

Probab=84.77  E-value=0.71  Score=29.16  Aligned_cols=29  Identities=17%  Similarity=0.374  Sum_probs=19.0

Q ss_pred             CCCCCCCCceeecCceeeecCcccccccc
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      ...|+.|...|.+++.-..-+..||..|+
T Consensus        15 i~~C~IC~~~i~~g~~C~~C~h~fH~~Ci   43 (74)
T 2ct0_A           15 VKICNICHSLLIQGQSCETCGIRMHLPCV   43 (74)
T ss_dssp             SCBCSSSCCBCSSSEECSSSCCEECHHHH
T ss_pred             CCcCcchhhHcccCCccCCCCchhhHHHH
Confidence            47899999999765432334455666665

>4ap4_A E3 ubiquitin ligase RNF4; ligase-signalling protein complex, chimera; 2.21A {Rattus norvegicus}

Probab=84.41  E-value=1.5  Score=30.02  Aligned_cols=42  Identities=17%  Similarity=0.335  Sum_probs=29.2

Q ss_pred             CCCCCCCceeecC----c--eeeecCcccccccc--------ccCcCCCCCCCCCe
Q 029230          108 DKCVGCDRTVYPT----E--KVSVNGAAYHRSCF--------KCSHGGCTISPSNY  149 (197)
Q Consensus       108 ~~C~~C~~~I~~~----e--~v~~~g~~~H~~CF--------~C~~C~~~l~~~~~  149 (197)
                      ..|+.|...+...    .  .+..-|..||..|.        .|-.|...+.....
T Consensus        73 ~~C~iC~~~~~~~~~~~~~~~~~~CgH~fc~~Ci~~~~~~~~~CP~Cr~~~~~~~~  128 (133)
T 4ap4_A           73 VSCPICMDGYSEIVQNGRLIVSTECGHVFCSQCLRDSLKNANTCPTCRKKINHKRY  128 (133)
T ss_dssp             CBCTTTCCBHHHHHHTTCCEEEETTSBEEEHHHHHHHHHHCSBCTTTCCBCCGGGE
T ss_pred             CCCCCCCCccccccccCcceEeCCCCChhhHHHHHHHHHcCCCCCCCCCcCChhcc
Confidence            6799998877532    1  23456788888887        58888888766443

>2ecy_A TNF receptor-associated factor 3; metal binding protein, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=82.60  E-value=1.2  Score=26.79  Aligned_cols=33  Identities=18%  Similarity=0.429  Sum_probs=24.1

Q ss_pred             ccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           36 CFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        36 CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      =+.|..|...+... ....=|..||..|..+.+.
T Consensus        15 ~~~C~IC~~~~~~p-~~~~CgH~fC~~Ci~~~~~   47 (66)
T 2ecy_A           15 KYKCEKCHLVLCSP-KQTECGHRFCESCMAALLS   47 (66)
T ss_dssp             CEECTTTCCEESSC-CCCSSSCCCCHHHHHHHHT
T ss_pred             CCCCCCCChHhcCe-eECCCCCHHHHHHHHHHHH
Confidence            47788888777643 3346688999999988763

>2ysl_A Tripartite motif-containing protein 31; ring-type zinc finger domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=81.10  E-value=1.5  Score=26.81  Aligned_cols=33  Identities=18%  Similarity=0.226  Sum_probs=24.0

Q ss_pred             ccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           36 CFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        36 CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      =+.|..|...+.. .....=|+.||..|..+.+.
T Consensus        20 ~~~C~IC~~~~~~-~~~~~CgH~fC~~Ci~~~~~   52 (73)
T 2ysl_A           20 EVICPICLDILQK-PVTIDCGHNFCLKCITQIGE   52 (73)
T ss_dssp             CCBCTTTCSBCSS-EEECTTCCEEEHHHHHHHCS
T ss_pred             CCEeccCCcccCC-eEEcCCCChhhHHHHHHHHH
Confidence            3778888887764 33335688999999987763

>1g25_A CDK-activating kinase assembly factor MAT1; ring finger (C3HC4), metal binding protein; NMR {Homo sapiens} SCOP: g.44.1.1

Probab=80.60  E-value=1.9  Score=25.69  Aligned_cols=33  Identities=24%  Similarity=0.469  Sum_probs=22.4

Q ss_pred             cccccccc-cccCCC---eeecCCeeeccccHHHHhh
Q 029230           37 FRCHHCKG-TLKLSN---FNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        37 F~C~~C~~-~L~~~~---f~~~~g~~yC~~c~~~~~~   69 (197)
                      +.|..|.. .+.+..   ....=|..+|..|..+.+.
T Consensus         4 ~~C~IC~~~~~~~~~~~~~~~~CgH~fC~~Ci~~~~~   40 (65)
T 1g25_A            4 QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV   40 (65)
T ss_dssp             TCCSTTTTHHHHCSSCCEEECTTCCCEEHHHHHHHHH
T ss_pred             CcCCcCCCCccCCCccCeecCCCCCHhHHHHHHHHHH
Confidence            56778877 554432   2345688999999988764

>3vk6_A E3 ubiquitin-protein ligase hakai; HYB, phosphotyrosine binding domain; 1.90A {Mus musculus}

Probab=80.60  E-value=1.3  Score=29.70  Aligned_cols=67  Identities=22%  Similarity=0.309  Sum_probs=41.6

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHHhhccCCcccccCCCCcccCCCCcccccCccccccccCCCCCCCCCCCcee
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSFEGTPKIVKPEKLVENENAQKVSNKFVGTRDKCVGCDRTV  117 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~I  117 (197)
                      -|..|+.++..-.-...=+.++|-+|+.......                                   ...|+.|..+|
T Consensus         3 fC~~C~~Pi~iygRmIPCkHvFCydCa~~~~~~~-----------------------------------~k~Cp~C~~~V   47 (101)
T 3vk6_A            3 FCDKCGLPIKVYGRMIPCKHVFCYDCAILHEKKG-----------------------------------DKMCPGCSDPV   47 (101)
T ss_dssp             BCTTTCSBCSEEEEEETTCCEEEHHHHHHHHHTT-----------------------------------CCBCTTTCCBC
T ss_pred             ecCccCCCeEEEeeeccccccHHHHHHHHHHhcc-----------------------------------CCCCcCcCCee
Confidence            3677888875322233345788999987654311                                   16799999999


Q ss_pred             ecCceeeecCccccccccccC---cCCCCCC
Q 029230          118 YPTEKVSVNGAAYHRSCFKCS---HGGCTIS  145 (197)
Q Consensus       118 ~~~e~v~~~g~~~H~~CF~C~---~C~~~l~  145 (197)
                      ..-|.. .+|..     |.|.   .|.+..-
T Consensus        48 ~rVe~~-~~~~i-----f~C~~~~~CkrtyL   72 (101)
T 3vk6_A           48 QRIEQC-TRGSL-----FMCSIVQGCKRTYL   72 (101)
T ss_dssp             SEEEEE-EGGGC-----CCCCCCCCCCCCCS
T ss_pred             eeeEEe-ccCCE-----EECCCCCCHHHHhc
Confidence            765543 44555     4565   4666543

>2djb_A Polycomb group ring finger protein 6; PCGF6, ring domain, structural genomics, NPPSFA; NMR {Homo sapiens}

Probab=80.42  E-value=1.7  Score=26.63  Aligned_cols=35  Identities=20%  Similarity=0.282  Sum_probs=24.5

Q ss_pred             cccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           35 ACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        35 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      .-+.|..|...+.+......=|+.||..|..+.+.
T Consensus        14 ~~~~C~IC~~~~~~p~~~~~CgH~fC~~Ci~~~~~   48 (72)
T 2djb_A           14 PYILCSICKGYLIDATTITECLHTFCKSCIVRHFY   48 (72)
T ss_dssp             GGGSCTTTSSCCSSCEECSSSCCEECHHHHHHHHH
T ss_pred             CCCCCCCCChHHHCcCEECCCCCHHHHHHHHHHHH
Confidence            34778888877765322235688999999887764

---

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	197
d2d8ya2	42	g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapie	2e-15
d2d8ya2	42	g.39.1.3 (A:44-85) Eplin, LIMA1 {Human (Homo sapie	1e-14
d2co8a2	36	g.39.1.3 (A:8-43) Nedd9 interacting protein with c	2e-10
d2co8a2	36	g.39.1.3 (A:8-43) Nedd9 interacting protein with c	7e-09
d2d8ya1	35	g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapien	4e-10
d2d8ya1	35	g.39.1.3 (A:9-43) Eplin, LIMA1 {Human (Homo sapien	2e-08
d1b8ta3	43	g.39.1.3 (A:101-143) Cysteine-rich (intestinal) pr	5e-10
d1b8ta3	43	g.39.1.3 (A:101-143) Cysteine-rich (intestinal) pr	1e-09
d2cu8a1	30	g.39.1.3 (A:8-37) Cysteine-rich (intestinal) prote	2e-04
d2cu8a1	30	g.39.1.3 (A:8-37) Cysteine-rich (intestinal) prote	0.003
d1b8ta1	35	g.39.1.3 (A:1-35) Cysteine-rich (intestinal) prote	5e-04
d1b8ta1	35	g.39.1.3 (A:1-35) Cysteine-rich (intestinal) prote	6e-04
d1a7ia1	28	g.39.1.3 (A:8-35) Cysteine-rich (intestinal) prote	0.003
d1zfoa_	30	g.39.1.4 (A:) LASP-1 {Pig (Sus scrofa) [TaxId: 982	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 = 65.1 bits (159), Expect = 2e-15
 Identities = 16/39 (41%), Positives = 24/39 (61%)

Query: 136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQ 174
           +CS+    +S   Y +  G++YCK H  QLF+ KGNY +
Sbjct: 1   RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDE 39

>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 = 62.8 bits (153), Expect = 1e-14
 Identities = 18/41 (43%), Positives = 26/41 (63%)

Query: 38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSF 78
          RC +C   L L  + S  G +YC+PHF+QLFK  G+ ++ F
Sbjct: 1  RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGF 41

>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 = 51.7 bits (124), Expect = 2e-10
 Identities = 8/34 (23%), Positives = 18/34 (52%)

Query: 4  PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACF 37
             G    C  C + +Y++++L  +   +H++CF
Sbjct: 3  QEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCF 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 = 47.5 bits (113), Expect = 7e-09
 Identities = 14/34 (41%), Positives = 19/34 (55%)

Query: 102 KFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCF 135
           +  G  D C  C   +Y  E++ VNG  +HRSCF
Sbjct: 3   QEAGAGDLCALCGEHLYVLERLCVNGHFFHRSCF 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 = 50.5 bits (121), Expect = 4e-10
 Identities = 12/31 (38%), Positives = 22/31 (70%)

Query: 7  GTQQKCMACDKTVYLVDKLTADNRVYHKACF 37
            ++ C+ C KTVY +++L A+ +V+H +CF
Sbjct: 5  PARETCVECQKTVYPMERLLANQQVFHISCF 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 = 46.3 bits (110), Expect = 2e-08
 Identities = 14/32 (43%), Positives = 19/32 (59%)

Query: 104 VGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCF 135
              R+ CV C +TVYP E++  N   +H SCF
Sbjct: 4   APARETCVECQKTVYPMERLLANQQVFHISCF 35

>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 = 50.6 bits (121), Expect = 5e-10
 Identities = 18/43 (41%), Positives = 26/43 (60%), Gaps = 1/43 (2%)

Query: 93  NENAQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCF 135
           N NA +++ K  G+ D C  C + VY  EKV   G ++H+SCF
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 = 49.5 bits (118), Expect = 1e-09
 Identities = 10/36 (27%), Positives = 17/36 (47%)

Query: 2  ASPFGGTQQKCMACDKTVYLVDKLTADNRVYHKACF 37
           +   G    C  C + VY  +K+    + +HK+CF
Sbjct: 8  MAQKVGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF 43

>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 = 35.2 bits (81), Expect = 2e-04
 Identities = 14/26 (53%), Positives = 17/26 (65%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSC 134
           KC  CD+TVY  EKVS  G  +H+ C
Sbjct: 4   KCPKCDKTVYFAEKVSSLGKDWHKFC 29

>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 = 32.1 bits (73), Expect = 0.003
 Identities = 12/26 (46%), Positives = 18/26 (69%)

Query: 11 KCMACDKTVYLVDKLTADNRVYHKAC 36
          KC  CDKTVY  +K+++  + +HK C
Sbjct: 4  KCPKCDKTVYFAEKVSSLGKDWHKFC 29

>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 = 34.1 bits (78), Expect = 5e-04
 Identities = 12/34 (35%), Positives = 19/34 (55%)

Query: 4  PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACF 37
          P  G  +KC  C K VY  +++  +   +HK+CF
Sbjct: 2  PNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF 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 = 34.1 bits (78), Expect = 6e-04
 Identities = 13/31 (41%), Positives = 19/31 (61%)

Query: 105 GTRDKCVGCDRTVYPTEKVSVNGAAYHRSCF 135
           G   KC  C + VY  E+V   G+++H+SCF
Sbjct: 5   GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF 35

>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 = 31.9 bits (72), Expect = 0.003
 Identities = 14/28 (50%), Positives = 19/28 (67%)

Query: 108 DKCVGCDRTVYPTEKVSVNGAAYHRSCF 135
           +KC  C RTVY  E+V  +G ++HR 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 = 31.8 bits (72), Expect = 0.004
 Identities = 12/27 (44%), Positives = 17/27 (62%)

Query: 109 KCVGCDRTVYPTEKVSVNGAAYHRSCF 135
            C  C + VYPTEKV+     +H++CF
Sbjct: 4   NCARCGKIVYPTEKVNCLDKFWHKACF 30

Homologous Domains Detected by HHsearch

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

ID	Length	Definition	Probability
Query	197
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	99.21
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	99.14
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	99.08
d1g47a2	35	Pinch (particularly interesting new Cys-His) prote	98.99
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.97
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.88
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.82
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.81
d2d8ya2	42	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.77
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.77
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.76
d1x3ha1	35	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.75
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.72
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.71
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.71
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.7
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.7
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.69
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.67
d2dara2	45	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.66
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.62
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.59
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.58
d1b8ta4	49	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.57
d2d8za2	32	Four and a half LIM domains protein 2, FHL2 {Human	98.53
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.53
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.48
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.47
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.46
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	98.46
d2dloa1	35	Thyroid receptor interacting protein 6, TRIP6 {Hum	98.45
d1b8ta3	43	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.45
d1imla2	48	Cysteine-rich (intestinal) protein, CRP, CRIP {Rat	98.45
d1ibia2	31	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.44
d1zfoa_	30	LASP-1 {Pig (Sus scrofa) [TaxId: 9823]}	98.41
d1x3ha2	32	Leupaxin {Human (Homo sapiens) [TaxId: 9606]}	98.41
d2d8ya1	35	Eplin, LIMA1 {Human (Homo sapiens) [TaxId: 9606]}	98.41
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.41
d2co8a2	36	Nedd9 interacting protein with calponin homology,	98.4
d2cu8a1	30	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.39
d1b8ta2	65	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	98.39
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	98.39
d2cuqa1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.36
d2dj7a1	31	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.34
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	98.31
d2dj7a2	36	Actin-binding LIM protein 3, abLIM-3 {Human (Homo	98.31
d1u5sb1	31	Pinch (particularly interesting new Cys-His) prote	98.29
d1u5sb2	35	Pinch (particularly interesting new Cys-His) prote	98.28
d1x63a1	37	Four and a half LIM domains protein 1, FHL-1 {Huma	98.28
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.27
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	98.26
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.22
d2cu8a2	33	Cysteine-rich (intestinal) protein, CRP, CRIP {Hum	98.19
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.17
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.17
d1x4ka1	32	Four and a half LIM domains protein 2, FHL2 {Human	98.16
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.15
d1wyha1	32	Four and a half LIM domains 3, FHL3 {Human (Homo s	98.13
d2d8xa2	26	Pinch (particularly interesting new Cys-His) prote	98.13
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.13
d2dara1	32	PDZ and LIM domain protein 5, Enigma {Human (Homo	98.12
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	98.11
d1j2oa1	30	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	98.09
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.08
d1rutx1	30	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	98.0
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.97
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.95
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.94
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.93
d1b8ta1	35	Cysteine-rich (intestinal) protein, CRP, CRIP {Chi	97.93
d1x4ka2	27	Four and a half LIM domains protein 2, FHL2 {Human	97.93
d1wyha2	27	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.88
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.84
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.83
d1a7ia2	32	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.81
d1x4la1	29	Four and a half LIM domains protein 2, FHL2 {Human	97.77
d1ibia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.77
d2d8za1	26	Four and a half LIM domains protein 2, FHL2 {Human	97.74
d2cuqa2	35	Four and a half LIM domains 3, FHL3 {Human (Homo s	97.74
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.66
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.66
d2cura1	31	Four and a half LIM domains protein 1, FHL-1 {Huma	97.63
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.63
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.6
d2cura2	26	Four and a half LIM domains protein 1, FHL-1 {Huma	97.6
d2dloa2	33	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.59
d1a7ia1	28	Cysteine-rich (intestinal) protein, CRP, CRIP {Jap	97.59
d1x68a1	29	Four and a half LIM domains protein 5, FHL-5 {Huma	97.57
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.54
d1rutx3	31	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	97.46
d1x61a2	32	Thyroid receptor interacting protein 6, TRIP6 {Hum	97.45
d1x62a2	35	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	97.39
d1v6ga1	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.38
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.38
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.37
d1x63a2	32	Four and a half LIM domains protein 1, FHL-1 {Huma	97.37
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.35
d1x64a1	45	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	97.3
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	97.24
d2cupa3	27	Four and a half LIM domains protein 1, FHL-1 {Huma	97.2
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	97.14
d1x64a2	31	PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus m	96.95
d1wiga1	32	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	96.9
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.82
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	96.64
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.63
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.61
d2cupa2	31	Four and a half LIM domains protein 1, FHL-1 {Huma	96.45
d1x62a1	31	PDZ and LIM domain protein 1 Elfin {Human (Homo sa	96.43
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	96.29
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	96.25
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	96.23
d1x61a1	27	Thyroid receptor interacting protein 6, TRIP6 {Hum	96.21
d1g47a1	35	Pinch (particularly interesting new Cys-His) prote	96.07
d1rutx2	34	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	95.98
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	95.28
d2d8xa1	32	Pinch (particularly interesting new Cys-His) prote	95.22
d1x6aa1	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	95.15
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	95.08
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	94.98
d2cora1	31	Pinch (particularly interesting new Cys-His) prote	94.63
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	94.53
d1x6aa2	34	Lim domain kinase 2 {Human (Homo sapiens) [TaxId:	94.51
d1rutx4	33	LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10	93.77
d2cora2	35	Pinch (particularly interesting new Cys-His) prote	93.43
d1wiga2	41	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	93.01
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	91.92
d1jm7b_	97	bard1 RING domain {Human (Homo sapiens) [TaxId: 96	90.75
d1x68a2	34	Four and a half LIM domains protein 5, FHL-5 {Huma	90.03
d2co8a1	33	Nedd9 interacting protein with calponin homology,	89.89
d1j2oa2	33	Rhombotin-2 (Lmo2) {Mouse (Mus musculus) [TaxId: 1	89.18
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	88.57
d2c2la2	80	STIP1 homology and U box-containing protein 1, STU	88.29
d2baya1	56	Pre-mRNA splicing factor Prp19 {Baker's yeast (Sac	86.89
d2gvia2	33	Uncharacterized protein Ta1109 {Thermoplasma acido	86.09
d1rmda2	86	V(D)J recombination activating protein 1 (RAG1), d	85.85
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	85.64
d1t1ha_	78	E3 ubiquitin ligase PUB14 {Thale-cress (Arabidopsi	84.02
d1x4la2	30	Four and a half LIM domains protein 2, FHL2 {Human	83.06
d1jm7a_	103	brca1 RING domain {Human (Homo sapiens) [TaxId: 96	81.36
d1v6ga2	40	Actin-binding LIM protein 2, abLIM2 {Human (Homo s	80.47

>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=99.21  E-value=4.5e-12  Score=70.52  Aligned_cols=42  Identities=38%  Similarity=0.714  Sum_probs=39.9

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCCCCCCCC
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGNYSQLES  177 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~~~~~~~  177 (197)
                      +|..|+++|..+.|...+|.+||++||.++|++|++|++++.
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            699999999999999999999999999999999999999874

>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=99.14  E-value=2.6e-12  Score=69.46  Aligned_cols=27  Identities=37%  Similarity=0.845  Sum_probs=25.4

Q ss_pred             CCCCCCCceeecCceeeecCcccccccc
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      ++|++|+++|. ++.|+|+|+.||++||
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            99999999997 6679999999999998

>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=99.08  E-value=2.7e-11  Score=65.27  Aligned_cols=34  Identities=26%  Similarity=0.556  Sum_probs=32.9

Q ss_pred             cccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcC
Q 029230          135 FKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFRE  168 (197)
Q Consensus       135 F~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~  168 (197)
                      |+|+.|+++|.++.|+++||+|||+.||.++|+|
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            7899999999999999999999999999999987

>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=98.99  E-value=5.4e-11  Score=64.07  Aligned_cols=34  Identities=35%  Similarity=0.731  Sum_probs=32.4

Q ss_pred             cccccccccccCCCeeecCCeeeccccHHHHhhc
Q 029230           37 FRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKR   70 (197)
Q Consensus        37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~   70 (197)
                      |+|+.|+++|.+..|++++|++||+.||.++|+|
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            7899999999999999999999999999999973

>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=98.97  E-value=3.8e-10  Score=64.70  Aligned_cols=42  Identities=24%  Similarity=0.549  Sum_probs=37.0

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCC-CCCCCC
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGN-YSQLES  177 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~-~~~~~~  177 (197)
                      +|..|++.|++....++|++|||+.||.++|+||+. +..+..
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG~g~G~gaG   43 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKGFGFGQGAG   43 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCCCCCCCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCccCcccCcc
Confidence            689999999998999999999999999999999997 444433

>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=98.88  E-value=1.5e-10  Score=60.80  Aligned_cols=27  Identities=26%  Similarity=0.746  Sum_probs=25.2

Q ss_pred             CCCCCCCceeecCceeeecCcccccccc
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      ++|..|+++|+.+. |.+.++.||.+||
T Consensus         9 ~~C~~Ckk~It~GG-vtY~dqpWHkeCF   35 (35)
T d2cuqa2           9 PRCARCSKTLTQGG-VTYRDQPWHRECL   35 (35)
T ss_dssp             CCCTTTCCCCCSCC-EESSSSEECTTTC
T ss_pred             HHHhhcCCccccCc-eeecCCcchhhhC
Confidence            89999999999764 9999999999998

>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=98.82  E-value=8.6e-10  Score=62.01  Aligned_cols=39  Identities=41%  Similarity=0.863  Sum_probs=32.1

Q ss_pred             ccccccccCCCCCCCCCCCceeecCceeeecCcccccccc
Q 029230           96 AQKVSNKFVGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus        96 ~~~~~~~~~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      ++++...+ ++.++|..|++.|++.|++.+.|+.||+.||
T Consensus         5 ~sk~~~~~-g~~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3           5 ASRMAQKV-GGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCCCCCCC-CCCEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             cccccccc-CCCCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            34444444 3458999999999999999999999999998

>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=98.81  E-value=1.3e-09  Score=61.62  Aligned_cols=36  Identities=36%  Similarity=0.627  Sum_probs=34.1

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeec-HHHHHhHhcCCCC
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYC-KHHHIQLFREKGN  171 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC-~~cy~~~~~~k~~  171 (197)
                      +|..|++.|+.+...++|++||| +.||.++|+||+.
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 7899999999996

>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=98.77  E-value=1.4e-09  Score=60.32  Aligned_cols=41  Identities=44%  Similarity=1.078  Sum_probs=37.8

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHHhhccCCccccc
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGSLEKSF   78 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~~~~~~   78 (197)
                      +|..|+..|..++|...+|.+||++||.++|+++++.++.|
T Consensus         1 rC~~C~~~Ls~~~yas~~G~lYCkpHf~qLF~~kGny~~gf   41 (42)
T d2d8ya2           1 RCSYCNNKLSLGTYASLHGRIYCKPHFNQLFKSKGNYDEGF   41 (42)
T ss_dssp             BCTTTCCBCCTTTCCCSSSCCCCHHHHHHHSCCCSCCCSCC
T ss_pred             CcCcCCCCccCCcchhhCCEeccHHHHHHHHHhhcCCCCCC
Confidence            69999999999999999999999999999999998876654

>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=98.77  E-value=2.6e-09  Score=55.12  Aligned_cols=32  Identities=19%  Similarity=0.415  Sum_probs=30.0

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      .|..|.++|.+.+|+++|++|||..||..+|+
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            48889999999999999999999999999985

>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=98.76  E-value=6.4e-10  Score=60.10  Aligned_cols=28  Identities=32%  Similarity=0.916  Sum_probs=26.3

Q ss_pred             CCCCCCCceeecCce-eeecCcccccccc
Q 029230          108 DKCVGCDRTVYPTEK-VSVNGAAYHRSCF  135 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~-v~~~g~~~H~~CF  135 (197)
                      ++|.+|+++|.++.+ |.+.|+.||.+||
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            899999999998876 8899999999998

>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=98.75  E-value=1.3e-09  Score=58.58  Aligned_cols=30  Identities=33%  Similarity=0.693  Sum_probs=27.9

Q ss_pred             CCCccccccccceecceeEEeCCcccccccc
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      ..+++|.+|+++|. ++.|.|+|+.||++||
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            45799999999997 8999999999999998

>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=98.72  E-value=3e-09  Score=56.94  Aligned_cols=32  Identities=44%  Similarity=0.934  Sum_probs=29.6

Q ss_pred             CCCCCCCCCCCceeecCceeeecCcccccccc
Q 029230          104 VGTRDKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       104 ~~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      +|+..+|..|+|.|++.|++.+.|+.||+.||
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

>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=98.71  E-value=5.7e-09  Score=53.07  Aligned_cols=32  Identities=16%  Similarity=0.407  Sum_probs=30.3

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      .|..|+++|.+..|..+|..|||..||..+|+
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            48999999999999999999999999999985

>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=98.71  E-value=2.9e-09  Score=59.38  Aligned_cols=28  Identities=18%  Similarity=0.454  Sum_probs=25.6

Q ss_pred             CCCCCCCCceeecCceeeecCcccccccc
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      .++|+.|+++|. +..|+|+|+.||++||
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            489999999997 6679999999999998

>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=98.70  E-value=3.8e-09  Score=53.61  Aligned_cols=28  Identities=50%  Similarity=0.946  Sum_probs=26.7

Q ss_pred             CCCCCCCceeecCceeeecCcccccccc
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      ++|++|+++|+++|.+..+|+.||+.|+
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            7899999999999999999999999885

>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=98.70  E-value=2.2e-08  Score=60.50  Aligned_cols=47  Identities=17%  Similarity=0.284  Sum_probs=39.7

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcCCCC-CCCCCCchhhh
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFREKGN-YSQLESDLEKS  182 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~k~~-~~~~~~~~~~~  182 (197)
                      .|..|++.|+.....+++++|||+.||.++|+||+. +..+......+
T Consensus         1 ~C~~C~K~LdS~~~~eh~~e~YCk~CY~k~fGPkG~G~G~gag~l~~d   48 (65)
T d1b8ta2           1 LCMVCKKNLDSTTVAVHGDEIYCKSCYGKKYGPKGKGKGMGAGTLSTD   48 (65)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHHSCCCCCCCCCCCCCCCC
T ss_pred             CchhcCCccCCCccccCCCcccchhhhccccCCCccccccccceeeec
Confidence            388999999999999999999999999999999997 55555554433

>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=98.69  E-value=5.1e-09  Score=53.17  Aligned_cols=31  Identities=26%  Similarity=0.595  Sum_probs=28.7

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      +|..|++.|.+ .|+.+||.|||+.+|.++||
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            58999999988 89999999999999999986

>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=98.67  E-value=6e-09  Score=55.55  Aligned_cols=29  Identities=48%  Similarity=1.098  Sum_probs=27.9

Q ss_pred             CCCCCCCCceeecCceeeecCcccccccc
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      ..+|..|++.|++.|++.+.|+.||+.||
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            48999999999999999999999999998

>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=98.66  E-value=6.5e-09  Score=57.93  Aligned_cols=32  Identities=22%  Similarity=0.403  Sum_probs=28.9

Q ss_pred             CCCCCccccccccceecceeEEeCCcccccccc
Q 029230            5 FGGTQQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         5 ~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      .+...++|..|+++|. +..+.|+|+.||++||
T Consensus        14 ~~~r~P~C~~C~~pI~-g~~vtAlgk~WHPEhF   45 (45)
T d2dara2          14 AGKRTPMCAHCNQVIR-GPFLVALGKSWHPEEF   45 (45)
T ss_dssp             TTTCCCBBSSSCCBCC-SCEEEETTEEECTTTC
T ss_pred             CCCCCeeccccCCccc-CceeeecCCccCcCCC
Confidence            3456799999999997 9999999999999998

>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=98.62  E-value=1.5e-08  Score=52.46  Aligned_cols=32  Identities=16%  Similarity=0.368  Sum_probs=29.4

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      +|..|.+++.++.|++.||+|||+.||.++-|
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            58999999999999999999999999998743

>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=98.59  E-value=2.3e-08  Score=51.46  Aligned_cols=34  Identities=26%  Similarity=0.483  Sum_probs=32.4

Q ss_pred             cccCcCCCCCCCCCeeeeCCeeecHHHHHhHhcC
Q 029230          135 FKCSHGGCTISPSNYIAHEGKLYCKHHHIQLFRE  168 (197)
Q Consensus       135 F~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~~  168 (197)
                      |+|+.|.+++-+...+++.|..||+.||.++|+.
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            7899999999999999999999999999999974

>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=98.58  E-value=1e-08  Score=51.26  Aligned_cols=28  Identities=43%  Similarity=0.994  Sum_probs=27.0

Q ss_pred             CCCCCCCceeecCceeeecCcccccccc
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      +.|++|++.|++.|.+.-+++.||..||
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            7899999999999999999999999998

>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=98.57  E-value=1.3e-08  Score=58.16  Aligned_cols=35  Identities=26%  Similarity=0.715  Sum_probs=32.7

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHHhhccC
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTG   72 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~   72 (197)
                      +|..|++.|++....++|+++||+.||.++|+|++
T Consensus         1 KC~~C~k~Lds~t~~ehdg~~YCk~CY~k~fGPKG   35 (49)
T d1b8ta4           1 RCAKCGKSLESTTLADKDGEIYCKGCYAKNFGPKG   35 (49)
T ss_dssp             BCTTTCCBCCSSSEEEETTEEEEHHHHHHHTCCCC
T ss_pred             ChhhcCCccCCCcccccCCcccchhhhhhccCCCc
Confidence            68999999999999999999999999999999665

>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=98.53  E-value=1.7e-08  Score=52.01  Aligned_cols=32  Identities=25%  Similarity=0.595  Sum_probs=29.9

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      .|..|.++|.++.|..+|++|||-.||..+|+
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

>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=98.53  E-value=2.8e-08  Score=50.82  Aligned_cols=32  Identities=31%  Similarity=0.639  Sum_probs=29.5

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecH-HHHHhHhc
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCK-HHHIQLFR  167 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~-~cy~~~~~  167 (197)
                      +|..|++.|..+...++||+|||. +||..+||
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            589999999999999999999995 69999986

>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=98.48  E-value=4.2e-08  Score=48.75  Aligned_cols=30  Identities=27%  Similarity=0.712  Sum_probs=28.4

Q ss_pred             cccCcCCCCCCCCCeeeeCCeeecHHHHHh
Q 029230          135 FKCSHGGCTISPSNYIAHEGKLYCKHHHIQ  164 (197)
Q Consensus       135 F~C~~C~~~l~~~~~~~~dg~~yC~~cy~~  164 (197)
                      |+|+.|++.|.+.....+||.+||+.||.+
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

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

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

Probab=98.47  E-value=3.7e-08  Score=51.32  Aligned_cols=29  Identities=24%  Similarity=0.649  Sum_probs=27.2

Q ss_pred             CCCCCCCCceeecCceeeecCcccccccc
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      +..|++|++.|..++.+.|+++.||.+||
T Consensus         8 ~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           8 PSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             CSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             CccccccchhhhCCceeeeeecceeeeeC
Confidence            36799999999999999999999999998

>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=98.46  E-value=3.8e-08  Score=51.68  Aligned_cols=32  Identities=31%  Similarity=0.724  Sum_probs=28.9

Q ss_pred             CCCCCccccccccceecceeEEeCCcccccccc
Q 029230            5 FGGTQQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         5 ~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      +.....+|..|+++|. +..+.|.|+.||+.||
T Consensus         4 y~~tlEkC~~C~~~I~-driLrA~Gk~yHP~CF   35 (35)
T d2dloa1           4 YVATLEKCATCSQPIL-DRILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCSSCCBCTTTCCBCC-SCCEEETTEEECTTTC
T ss_pred             HHHHHHHHHHhchHHH-HHHHHHhCCCCCCCCC
Confidence            4566789999999998 7889999999999998

>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=98.45  E-value=5e-08  Score=51.24  Aligned_cols=28  Identities=32%  Similarity=0.807  Sum_probs=24.3

Q ss_pred             CCCCCCCCceeecCceeeecCcccccccc
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      ..+|..|+++|.+. .+.|.|+.||+.||
T Consensus         8 lEkC~~C~~~I~dr-iLrA~Gk~yHP~CF   35 (35)
T d2dloa1           8 LEKCATCSQPILDR-ILRAMGKAYHPGCF   35 (35)
T ss_dssp             CCBCTTTCCBCCSC-CEEETTEEECTTTC
T ss_pred             HHHHHHhchHHHHH-HHHHhCCCCCCCCC
Confidence            48999999999743 47899999999998

>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=98.45  E-value=4.1e-08  Score=54.97  Aligned_cols=32  Identities=31%  Similarity=0.800  Sum_probs=29.5

Q ss_pred             CCCCccccccccceecceeEEeCCcccccccc
Q 029230            6 GGTQQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         6 ~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      .++..+|..|++.|+..|.+.++|+.||..||
T Consensus        12 ~g~~~kC~~C~k~VY~~E~~~~~g~~~Hk~CF   43 (43)
T d1b8ta3          12 VGGSDGCPRCGQAVYAAEKVIGAGKSWHKSCF   43 (43)
T ss_dssp             CCCCEECTTTSCEECSSSCEEETTEEECTTTC
T ss_pred             cCCCCcCccCCCEeeHHHHhhcCCCccccCCC
Confidence            34568999999999999999999999999998

>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=98.45  E-value=4.9e-08  Score=55.07  Aligned_cols=36  Identities=31%  Similarity=0.731  Sum_probs=33.2

Q ss_pred             ccccccccccCCCeeecCCeeec-cccHHHHhhccCC
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYC-RPHFDQLFKRTGS   73 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC-~~c~~~~~~~~~~   73 (197)
                      +|..|++.|+++...+++++||| +.||.++|+|++.
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 7799999998763

>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=98.44  E-value=3.4e-08  Score=49.07  Aligned_cols=30  Identities=30%  Similarity=0.831  Sum_probs=28.3

Q ss_pred             cccccccccccCCCeeecCCeeeccccHHH
Q 029230           37 FRCHHCKGTLKLSNFNSFEGVLYCRPHFDQ   66 (197)
Q Consensus        37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~   66 (197)
                      |+|+.|++.|.+.....+||++||+.||.+
T Consensus         1 frca~cgk~lestt~adkdgeiyck~cyak   30 (31)
T d1ibia2           1 FRCAKCGKSLESTTLTEKEGEIYCKGCYAK   30 (31)
T ss_dssp             EECSSSCCEECSSCSEEETTEEECHHHHHH
T ss_pred             CccccccCccccceeeccCCcEEEeeeeec
Confidence            899999999999999999999999999964

>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=98.41  E-value=2.9e-08  Score=49.58  Aligned_cols=29  Identities=38%  Similarity=0.902  Sum_probs=27.6

Q ss_pred             CccccccccceecceeEEeCCcccccccc
Q 029230            9 QQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         9 ~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      ++.|++|++.|++.+.+..+++.||..||
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            47899999999999999999999999998

>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=98.41  E-value=6.1e-08  Score=50.14  Aligned_cols=31  Identities=19%  Similarity=0.563  Sum_probs=28.8

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHHh
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQLF   68 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~   68 (197)
                      +|..|.+++.++.|++.+|+|||+.+|.++.
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            5899999999999999999999999998864

>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=98.41  E-value=6.5e-08  Score=51.45  Aligned_cols=32  Identities=38%  Similarity=0.951  Sum_probs=29.9

Q ss_pred             CCCCccccccccceecceeEEeCCcccccccc
Q 029230            6 GGTQQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         6 ~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      .+...+|..|++.|+..+.+.++|+.||..||
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            45678999999999999999999999999998

>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=98.41  E-value=3.3e-08  Score=50.28  Aligned_cols=27  Identities=22%  Similarity=0.410  Sum_probs=23.6

Q ss_pred             CCCCCCCCceeecCceeeecCccccccc
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSC  134 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~C  134 (197)
                      .++|+.|++||. +..|.|+|+.||+++
T Consensus         5 ~p~C~~C~~PI~-~~~vtAlgk~WHpEH   31 (31)
T d1u5sb1           5 VPICGACRRPIE-GRVVNAMGKQWHVEH   31 (31)
T ss_dssp             CCEETTTTEECC-SCEECCTTSBEETTT
T ss_pred             CcchhhcCCchh-hhHhhhhccccCCCC
Confidence            489999999998 456889999999974

>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=98.40  E-value=4.4e-08  Score=52.30  Aligned_cols=33  Identities=24%  Similarity=0.834  Sum_probs=30.6

Q ss_pred             CCCCCccccccccceecceeEEeCCcccccccc
Q 029230            5 FGGTQQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         5 ~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      .++...+|..|++.|++.+++.++|+.||..||
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            356779999999999999999999999999998

>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=98.39  E-value=5.9e-08  Score=49.11  Aligned_cols=29  Identities=41%  Similarity=0.897  Sum_probs=27.3

Q ss_pred             CccccccccceecceeEEeCCcccccccc
Q 029230            9 QQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         9 ~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      ++.|++|+++|+..|.+..+|+.||..|+
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            48999999999999999999999999985

>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=98.39  E-value=2.1e-07  Score=56.02  Aligned_cols=36  Identities=19%  Similarity=0.547  Sum_probs=33.6

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHHhhccCC
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFKRTGS   73 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~~~~~   73 (197)
                      .|..|++.|+++...++++++||+.||.++|+|++.
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            488999999999999999999999999999999874

>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=98.36  E-value=9.3e-08  Score=48.50  Aligned_cols=32  Identities=31%  Similarity=0.613  Sum_probs=29.9

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      .|+.|+++|.++.|..+|..|||..||.++|+
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

>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=98.34  E-value=1.4e-07  Score=47.71  Aligned_cols=31  Identities=29%  Similarity=0.752  Sum_probs=27.9

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      +|..|++.|. +.|..+||.|||+.||+..|+
T Consensus         1 kC~~C~~vL~-gEYm~kdG~PyCe~DY~~~FG   31 (31)
T d2dj7a1           1 KCQTCSVILT-GEYISKDGVPYCESDYHAQFG   31 (31)
T ss_dssp             BCSSSCCBCS-SCCEEETTEEECTTHHHHHTT
T ss_pred             CccccCcccc-ceeecCCCCcccHHHHHHhcC
Confidence            5899999997 589999999999999999874

>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=98.31  E-value=3.7e-07  Score=46.51  Aligned_cols=32  Identities=13%  Similarity=0.297  Sum_probs=29.7

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      .|..|..+|+...|..+++..||..||+++|+
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            37889999999999999999999999999985

>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=98.31  E-value=1.2e-07  Score=49.41  Aligned_cols=30  Identities=23%  Similarity=0.592  Sum_probs=28.2

Q ss_pred             CCccccccccceecceeEEeCCcccccccc
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      +...|++|++.|..++.+.++++.||.+||
T Consensus         7 g~~~CagCg~eik~gQaL~ALdkqWH~~CF   36 (36)
T d2dj7a2           7 GPSHCAGCKEEIKHGQSLLALDKQWHVSCF   36 (36)
T ss_dssp             SCSCCTTTCCCCSSSCCEEETTEEECTTTC
T ss_pred             CCccccccchhhhCCceeeeeecceeeeeC
Confidence            457899999999999999999999999998

>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=98.29  E-value=1.1e-07  Score=48.32  Aligned_cols=28  Identities=18%  Similarity=0.299  Sum_probs=25.3

Q ss_pred             CCccccccccceecceeEEeCCccccccc
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKAC   36 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~C   36 (197)
                      +.++|+.|+++|. +..+.++|+.||++.
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            4689999999998 799999999999974

>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=98.28  E-value=1.7e-07  Score=48.13  Aligned_cols=33  Identities=30%  Similarity=0.739  Sum_probs=31.4

Q ss_pred             cccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           37 FRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      |+|+.|.+++-+...+++.|..||+.+|.++|+
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            789999999998899999999999999999986

>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=98.28  E-value=1.6e-07  Score=50.45  Aligned_cols=31  Identities=32%  Similarity=0.673  Sum_probs=27.5

Q ss_pred             CCCccccccccceeccee-EEeCCcccccccc
Q 029230            7 GTQQKCMACDKTVYLVDK-LTADNRVYHKACF   37 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~-~~~~g~~~H~~CF   37 (197)
                      ..+++|.+|+++|..+.. |.+.|+.||..||
T Consensus         6 ~~a~~C~~C~k~I~~G~k~veykg~~WHe~CF   37 (37)
T d1x63a1           6 EDSPKCKGCFKAIVAGDQNVEYKGTVWHKDCF   37 (37)
T ss_dssp             CCSCBCSSSCCBCCSSSCEEECSSCEEETTTC
T ss_pred             ccCcccccCCCccCCCCeEeEeCCccchhccC
Confidence            356899999999997755 9999999999998

>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=98.27  E-value=4.6e-07  Score=46.05  Aligned_cols=32  Identities=19%  Similarity=0.408  Sum_probs=29.7

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      .|..|..+|+...|..+++..||.+||+++|+
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            37889999999999999999999999999985

>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=98.26  E-value=1.3e-07  Score=51.56  Aligned_cols=26  Identities=38%  Similarity=0.843  Sum_probs=24.3

Q ss_pred             CCCCCCCceeecCceeeecCccccccc
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSC  134 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~C  134 (197)
                      .+|..|++-|. ++.|.|.+++||++|
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            89999999996 788899999999988

>d1ibia1 g.39.1.3 (A:117-144) Cysteine-rich (intestinal) protein, CRP, CRIP {Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: Cysteine-rich (intestinal) protein, CRP, CRIP
species: Japanese quail (Coturnix coturnix japonica), CRP2 [TaxId: 93934]

Probab=98.22  E-value=2.2e-07  Score=45.51  Aligned_cols=27  Identities=41%  Similarity=0.947  Sum_probs=25.3

Q ss_pred             CCCCCCCceeecCceeeecCccccccc
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSC  134 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~C  134 (197)
                      .+|++|++.|+.+|.|.-.|+.||+.|
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

>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=98.19  E-value=4.3e-07  Score=46.30  Aligned_cols=32  Identities=28%  Similarity=0.771  Sum_probs=29.1

Q ss_pred             ccccccccccCCCeeecCCeeecc-ccHHHHhh
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCR-PHFDQLFK   69 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~-~c~~~~~~   69 (197)
                      +|..|++.|..+...+++|+|||. +||..+|+
T Consensus         1 kCekC~ktL~~G~HaEH~gkPYC~~PCY~aLFG   33 (33)
T d2cu8a2           1 KCERCSKTLTPGGHAEHDGKPFCHKPCYATLFG   33 (33)
T ss_dssp             BCSSSCCBCCTTSCEEETTEEECTTTHHHHHSC
T ss_pred             CchhcccccCCCCccccCCCcCcCcchHHhhcC
Confidence            589999999999999999999996 59998874

>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=98.17  E-value=8.3e-07  Score=45.09  Aligned_cols=32  Identities=25%  Similarity=0.609  Sum_probs=29.3

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      .|+.|+++|....|.+..|.+||+.||.+.|+
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            38899999999999999999999999999874

>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=98.16  E-value=4.6e-07  Score=46.13  Aligned_cols=32  Identities=19%  Similarity=0.596  Sum_probs=29.5

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      .|..|.++|+.++|..+++..||.+||++.|+
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

>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=98.15  E-value=6.2e-07  Score=45.34  Aligned_cols=29  Identities=21%  Similarity=0.416  Sum_probs=26.1

Q ss_pred             CCccccccccceecceeEEeCCccccccc
Q 029230            8 TQQKCMACDKTVYLVDKLTADNRVYHKAC   36 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~~~~~g~~~H~~C   36 (197)
                      ....|++|+++|.+...+.+.++.||..|
T Consensus         2 ~~~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           2 SLLTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             CCBCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             CCcccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            45789999999998888999999999987

>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=98.13  E-value=5.9e-07  Score=45.64  Aligned_cols=32  Identities=28%  Similarity=0.670  Sum_probs=29.5

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      .|..|.++|+.++|..+++..||.+||++.|+
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            37899999999999999999999999999874

>d1rutx3 g.39.1.3 (X:83-113) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=98.13  E-value=7e-07  Score=45.61  Aligned_cols=28  Identities=32%  Similarity=0.809  Sum_probs=25.7

Q ss_pred             CCCCCCCceeecCceee-ecCcccccccc
Q 029230          108 DKCVGCDRTVYPTEKVS-VNGAAYHRSCF  135 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~-~~g~~~H~~CF  135 (197)
                      ..|++|++.|.+.|.|+ +.+..||..||
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            46999999999999875 99999999998

>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=98.12  E-value=6e-07  Score=45.62  Aligned_cols=31  Identities=35%  Similarity=0.884  Sum_probs=28.9

Q ss_pred             cccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           39 CHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        39 C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      |+.|+.+|.+..|++.+|.+||+.||++.|+
T Consensus         2 Ca~C~~sL~d~gFVEE~g~lYCe~Cye~ffA   32 (32)
T d2dara1           2 CAHCKNTMAYIGFVEEKGALYCELCYEKFFA   32 (32)
T ss_dssp             CSSSCCBCSSSCBEESSSCEECHHHHHHHTS
T ss_pred             cccccccHhhcceeeecCcEeHHHHHHHhcC
Confidence            8899999999999999999999999998764

>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=98.11  E-value=6.2e-07  Score=45.08  Aligned_cols=31  Identities=16%  Similarity=0.386  Sum_probs=28.7

Q ss_pred             cCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230          137 CSHGGCTISPSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       137 C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      |-.|.+.|++.....+++.+||+.||.++||
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            6789999999999999999999999999975

>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=8.4e-07  Score=44.84  Aligned_cols=27  Identities=19%  Similarity=0.457  Sum_probs=24.0

Q ss_pred             CCCCCCCceeecCceeeecCccccccc
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSC  134 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~C  134 (197)
                      ..|++|+++|.+.-.+.+.++.||.+|
T Consensus         4 ~~CaGC~~~I~DRflL~a~Dr~WH~~C   30 (30)
T d1j2oa1           4 LTCGGCQQNIGDRYFLKAIDQYWHEDC   30 (30)
T ss_dssp             BCBSSSCSCBCSSEEEECSSSEECTTT
T ss_pred             cccCCCCCcchHHHHHHHHHHHHhcCC
Confidence            679999999987666789999999987

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

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

Probab=98.08  E-value=8e-07  Score=45.09  Aligned_cols=28  Identities=21%  Similarity=0.476  Sum_probs=25.7

Q ss_pred             ccccccccceecceeEEeCCcccccccc
Q 029230           10 QKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus        10 ~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      ..|++|+++|.+...+.+.++.||..|+
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            5799999999988889999999999985

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

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

Probab=98.00  E-value=1.4e-06  Score=44.20  Aligned_cols=28  Identities=18%  Similarity=0.549  Sum_probs=24.7

Q ss_pred             CCCCCCCceeecCceeeecCcccccccc
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      ..|++|+++|.+.-.+.+.++.||..|.
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            5799999999877667899999999984

>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=1.2e-06  Score=42.31  Aligned_cols=26  Identities=27%  Similarity=0.754  Sum_probs=23.7

Q ss_pred             ccccccceeccee-EEeCCcccccccc
Q 029230           12 CMACDKTVYLVDK-LTADNRVYHKACF   37 (197)
Q Consensus        12 C~~C~~~I~~~~~-~~~~g~~~H~~CF   37 (197)
                      |..|.+.|+++.+ +...|..||..||
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            7889999998854 8999999999998

>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=97.95  E-value=1.8e-06  Score=43.98  Aligned_cols=31  Identities=42%  Similarity=0.961  Sum_probs=28.3

Q ss_pred             CCCCCCCCCCceeecCceeeecCcccccccc
Q 029230          105 GTRDKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       105 ~~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      |+..+|..|.+.|+.+|-|.-.|+.||+.||
T Consensus         5 ggg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           5 GGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CCCceeccccceEeeeeeeeecCcccccccC
Confidence            3458999999999999989999999999998

>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=97.94  E-value=1.3e-06  Score=42.14  Aligned_cols=26  Identities=35%  Similarity=0.786  Sum_probs=23.6

Q ss_pred             ccccccceeccee-EEeCCcccccccc
Q 029230           12 CMACDKTVYLVDK-LTADNRVYHKACF   37 (197)
Q Consensus        12 C~~C~~~I~~~~~-~~~~g~~~H~~CF   37 (197)
                      |..|.+.|+++.+ +...|.+||..||
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            7889999998854 8999999999998

>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=97.93  E-value=1.6e-06  Score=42.82  Aligned_cols=26  Identities=27%  Similarity=0.790  Sum_probs=22.4

Q ss_pred             CCCCCceeecC---ceeeecCcccccccc
Q 029230          110 CVGCDRTVYPT---EKVSVNGAAYHRSCF  135 (197)
Q Consensus       110 C~~C~~~I~~~---e~v~~~g~~~H~~CF  135 (197)
                      |++|.+||+.-   ..|.+.++.||.+||
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            78999999853   358999999999998

>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=97.93  E-value=2.5e-06  Score=43.45  Aligned_cols=34  Identities=35%  Similarity=0.875  Sum_probs=30.7

Q ss_pred             CCCCCCccccccccceecceeEEeCCcccccccc
Q 029230            4 PFGGTQQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         4 ~~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      +..++..+|..|.+.|+..+-+..+|++||..||
T Consensus         2 pn~ggg~kcg~c~ktvy~aeevqc~g~sfhk~cf   35 (35)
T d1b8ta1           2 PNWGGGKKCGVCQKAVYFAEEVQCEGSSFHKSCF   35 (35)
T ss_dssp             CCCCCCEECTTTCCEECSSCCEEETTEEECTTTC
T ss_pred             CccCCCceeccccceEeeeeeeeecCcccccccC
Confidence            3456778999999999999999999999999998

>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=97.93  E-value=1.7e-06  Score=41.78  Aligned_cols=26  Identities=31%  Similarity=1.014  Sum_probs=23.6

Q ss_pred             CCCCCceeecCce-eeecCcccccccc
Q 029230          110 CVGCDRTVYPTEK-VSVNGAAYHRSCF  135 (197)
Q Consensus       110 C~~C~~~I~~~e~-v~~~g~~~H~~CF  135 (197)
                      |..|.+.|.++.+ +.+.|..||..||
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            7789999999965 7899999999998

>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=97.88  E-value=2.4e-06  Score=41.16  Aligned_cols=26  Identities=35%  Similarity=0.963  Sum_probs=23.6

Q ss_pred             CCCCCceeecCce-eeecCcccccccc
Q 029230          110 CVGCDRTVYPTEK-VSVNGAAYHRSCF  135 (197)
Q Consensus       110 C~~C~~~I~~~e~-v~~~g~~~H~~CF  135 (197)
                      |..|.+.|.++.+ +...|..||..||
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            7889999999965 7899999999998

>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=97.84  E-value=7.8e-06  Score=40.79  Aligned_cols=29  Identities=17%  Similarity=0.348  Sum_probs=27.1

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHh
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQ  164 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~  164 (197)
                      .|..|.++|.+.+|...++++||-+||..
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=97.83  E-value=3.7e-06  Score=41.46  Aligned_cols=26  Identities=23%  Similarity=0.769  Sum_probs=22.2

Q ss_pred             CCCCCceeecC---ceeeecCcccccccc
Q 029230          110 CVGCDRTVYPT---EKVSVNGAAYHRSCF  135 (197)
Q Consensus       110 C~~C~~~I~~~---e~v~~~g~~~H~~CF  135 (197)
                      |.+|.+||..-   ..|.+.++.||.+||
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            78899999753   358899999999998

>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=97.81  E-value=4.3e-06  Score=41.95  Aligned_cols=31  Identities=16%  Similarity=0.612  Sum_probs=28.2

Q ss_pred             cccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           39 CHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        39 C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      |-.|++.|++....++++++||+.||.+.++
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            7789999999999999999999999988763

>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=97.77  E-value=4.7e-06  Score=41.14  Aligned_cols=26  Identities=23%  Similarity=0.728  Sum_probs=22.7

Q ss_pred             ccccccceec---ceeEEeCCcccccccc
Q 029230           12 CMACDKTVYL---VDKLTADNRVYHKACF   37 (197)
Q Consensus        12 C~~C~~~I~~---~~~~~~~g~~~H~~CF   37 (197)
                      |..|.+||..   ..+|...++.||..||
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            7899999974   3569999999999998

>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=97.77  E-value=4.5e-06  Score=40.73  Aligned_cols=27  Identities=33%  Similarity=0.879  Sum_probs=25.3

Q ss_pred             ccccccccceecceeEEeCCccccccc
Q 029230           10 QKCMACDKTVYLVDKLTADNRVYHKAC   36 (197)
Q Consensus        10 ~~C~~C~~~I~~~~~~~~~g~~~H~~C   36 (197)
                      .+|.+|++.|+..+.+.-.|+.||..|
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

>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=97.74  E-value=5.8e-06  Score=42.98  Aligned_cols=30  Identities=23%  Similarity=0.604  Sum_probs=26.4

Q ss_pred             CCCccccccccceecceeEEeCCcccccccc
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      ..+++|..|+++|. ..-|...++.||.+||
T Consensus         6 kfa~~C~~Ckk~It-~GGvtY~dqpWHkeCF   35 (35)
T d2cuqa2           6 KFAPRCARCSKTLT-QGGVTYRDQPWHRECL   35 (35)
T ss_dssp             CSSCCCTTTCCCCC-SCCEESSSSEECTTTC
T ss_pred             HHHHHHhhcCCccc-cCceeecCCcchhhhC
Confidence            35689999999998 6778899999999998

>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=97.66  E-value=9.9e-06  Score=40.51  Aligned_cols=30  Identities=23%  Similarity=0.568  Sum_probs=27.0

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHH
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQL   67 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~   67 (197)
                      .|..|+..|.++.|+..+.+.||++||-..
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            478899999999999999999999999653

>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=97.66  E-value=1.3e-05  Score=38.64  Aligned_cols=27  Identities=52%  Similarity=1.153  Sum_probs=25.7

Q ss_pred             CCCCCCceeecCceeeecCcccccccc
Q 029230          109 KCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       109 ~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      +|..|.+.|+.+|-|.-.|+.||+.||
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            699999999999989999999999998

>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=97.63  E-value=1.4e-05  Score=39.89  Aligned_cols=29  Identities=24%  Similarity=0.575  Sum_probs=26.9

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHH
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQ   66 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~   66 (197)
                      .|..|.+.|.+..|...++.+||-+||..
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

>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=97.63  E-value=2.3e-05  Score=40.23  Aligned_cols=32  Identities=9%  Similarity=0.231  Sum_probs=28.3

Q ss_pred             ccCcCCCCCCCCCeeee-CCeeecHHHHHhHhc
Q 029230          136 KCSHGGCTISPSNYIAH-EGKLYCKHHHIQLFR  167 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~-dg~~yC~~cy~~~~~  167 (197)
                      .|..|++.|++-.|... ++++||.++|.++|+
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            48889999999899775 699999999999985

>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=97.60  E-value=4.3e-05  Score=37.68  Aligned_cols=32  Identities=22%  Similarity=0.488  Sum_probs=29.5

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhHhc
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      .|+.|+..|..+.|+.++..+||..|...+|+
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            48899999999999999999999999999875

>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=97.59  E-value=1.7e-05  Score=40.78  Aligned_cols=32  Identities=22%  Similarity=0.402  Sum_probs=27.9

Q ss_pred             ccccccccccCCCeeec-CCeeeccccHHHHhh
Q 029230           38 RCHHCKGTLKLSNFNSF-EGVLYCRPHFDQLFK   69 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~-~g~~yC~~c~~~~~~   69 (197)
                      +|..|++.|++..|... ++++||-++|+++|+
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            58899999999999754 789999999999874

>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=97.59  E-value=1.4e-05  Score=38.55  Aligned_cols=28  Identities=43%  Similarity=1.050  Sum_probs=26.3

Q ss_pred             ccccccccceecceeEEeCCcccccccc
Q 029230           10 QKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus        10 ~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      ++|+.|.+.|+..+-+..+|++||..||
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            4799999999999999999999999998

>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=97.57  E-value=1.4e-05  Score=39.30  Aligned_cols=26  Identities=27%  Similarity=0.705  Sum_probs=22.5

Q ss_pred             ccccccceec---ceeEEeCCcccccccc
Q 029230           12 CMACDKTVYL---VDKLTADNRVYHKACF   37 (197)
Q Consensus        12 C~~C~~~I~~---~~~~~~~g~~~H~~CF   37 (197)
                      |..|.+||..   ..++...++.||.+||
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            7889999974   3569999999999998

>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=97.54  E-value=2.9e-05  Score=39.73  Aligned_cols=32  Identities=16%  Similarity=0.314  Sum_probs=28.5

Q ss_pred             CCCCCccccccccceecceeEEeCCcccccccc
Q 029230            5 FGGTQQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         5 ~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      .....+.|.+|+.-|. +..+.+.++.+|++||
T Consensus         4 ~~qklp~CdkCg~GIV-G~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           4 NAQKLPMCDKCGTGIV-GVFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCCCCCSSSCCCCC-SSCEECSSCEECTTTT
T ss_pred             ccccCccccccCCCcE-eEEEEeccccCCCCCC
Confidence            3446799999999998 8999999999999998

>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=97.46  E-value=2.6e-05  Score=39.61  Aligned_cols=29  Identities=31%  Similarity=0.737  Sum_probs=25.8

Q ss_pred             Cccccccccceeccee-EEeCCcccccccc
Q 029230            9 QQKCMACDKTVYLVDK-LTADNRVYHKACF   37 (197)
Q Consensus         9 ~~~C~~C~~~I~~~~~-~~~~g~~~H~~CF   37 (197)
                      ...|++|++.|...+. +.+.+..||..||
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            3579999999998876 5999999999998

>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=97.45  E-value=5.3e-05  Score=37.80  Aligned_cols=30  Identities=20%  Similarity=0.420  Sum_probs=27.2

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhH
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQL  165 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~  165 (197)
                      .|..|+..|.+..|+..+.+.||+.||...
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            488899999999999999999999999753

>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=97.39  E-value=5.6e-05  Score=38.63  Aligned_cols=28  Identities=18%  Similarity=0.395  Sum_probs=24.8

Q ss_pred             CCCCCCCCceeecCceeeecCcccccccc
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      .+.|..|+..|.. -.|.+.++.+|++||
T Consensus         8 lp~CdkCg~GIVG-~~VK~rDk~rHPeCf   35 (35)
T d1x62a2           8 LPMCDKCGTGIVG-VFVKLRDRHRHPECY   35 (35)
T ss_dssp             CCCCSSSCCCCCS-SCEECSSCEECTTTT
T ss_pred             CccccccCCCcEe-EEEEeccccCCCCCC
Confidence            3899999999984 468899999999998

>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=97.38  E-value=3e-05  Score=42.01  Aligned_cols=27  Identities=26%  Similarity=0.725  Sum_probs=25.0

Q ss_pred             CccccccccceecceeEEeCCccccccc
Q 029230            9 QQKCMACDKTVYLVDKLTADNRVYHKAC   36 (197)
Q Consensus         9 ~~~C~~C~~~I~~~~~~~~~g~~~H~~C   36 (197)
                      ..+|..|++.|. +++|.|.++.||+.|
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            368999999997 999999999999998

>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=97.38  E-value=5.8e-05  Score=41.16  Aligned_cols=30  Identities=20%  Similarity=0.454  Sum_probs=27.5

Q ss_pred             CCCccccccccceecceeEEeCCcccccccc
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      ...+.|.+|+.-|. +..+.+.++.+|++||
T Consensus        16 QkLP~CdkCg~GIV-G~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          16 QRMPLCDKCGSGIV-GAVVKARDKYRHPECF   45 (45)
T ss_dssp             CSCCBCTTTCCBCC-SCCEESSSCEECTTTC
T ss_pred             ccCccccccCCCcE-EEEEEeccccCCCCCC
Confidence            35689999999998 8999999999999998

>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=97.37  E-value=4.4e-05  Score=36.53  Aligned_cols=26  Identities=31%  Similarity=0.783  Sum_probs=21.5

Q ss_pred             CCCCCceeecCce-eeecCcccccccc
Q 029230          110 CVGCDRTVYPTEK-VSVNGAAYHRSCF  135 (197)
Q Consensus       110 C~~C~~~I~~~e~-v~~~g~~~H~~CF  135 (197)
                      |.-|.+||..... |...++.||..||
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            7789999964432 7899999999998

>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=97.37  E-value=5.2e-05  Score=37.40  Aligned_cols=32  Identities=22%  Similarity=0.515  Sum_probs=29.1

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      +|+.|.+.+..++|+.++...||..|.+..|+
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            58999999999999999999999999988763

>d1x64a2 g.39.1.3 (A:53-83) PDZ and LIM domain protein 3, PDLIM3 {Mouse (Mus musculus) [TaxId: 10090]}

class: Small proteins
fold: Glucocorticoid receptor-like (DNA-binding domain)
superfamily: Glucocorticoid receptor-like (DNA-binding domain)
family: LIM domain
domain: PDZ and LIM domain protein 3, PDLIM3
species: Mouse (Mus musculus) [TaxId: 10090]

Probab=97.35  E-value=0.00013  Score=36.30  Aligned_cols=30  Identities=27%  Similarity=0.583  Sum_probs=26.9

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhH
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQL  165 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~  165 (197)
                      .|+.|+..|....++..++++||+.|...+
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            489999999998999999999999998764

>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=97.30  E-value=6.9e-05  Score=40.88  Aligned_cols=28  Identities=21%  Similarity=0.423  Sum_probs=24.9

Q ss_pred             CCCCCCCCceeecCceeeecCcccccccc
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      .+.|..|+..|.. -.|.+.++.+|++||
T Consensus        18 LP~CdkCg~GIVG-~~VK~rDK~rHPeCf   45 (45)
T d1x64a1          18 MPLCDKCGSGIVG-AVVKARDKYRHPECF   45 (45)
T ss_dssp             CCBCTTTCCBCCS-CCEESSSCEECTTTC
T ss_pred             CccccccCCCcEE-EEEEeccccCCCCCC
Confidence            4899999999984 468899999999998

>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=97.24  E-value=5.4e-05  Score=37.64  Aligned_cols=29  Identities=28%  Similarity=0.614  Sum_probs=26.1

Q ss_pred             CCCccccccccceecceeEEeCCccccccc
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKAC   36 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~C   36 (197)
                      ++..-|..|.+.|. +.++.+.++.||+.|
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 999999999999988

>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=97.20  E-value=6.5e-05  Score=35.94  Aligned_cols=26  Identities=31%  Similarity=0.800  Sum_probs=21.9

Q ss_pred             ccccccceecce-eEEeCCcccccccc
Q 029230           12 CMACDKTVYLVD-KLTADNRVYHKACF   37 (197)
Q Consensus        12 C~~C~~~I~~~~-~~~~~g~~~H~~CF   37 (197)
                      |.-|.+||..+. -+...++.||..||
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            778999997543 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=97.14  E-value=4e-05  Score=39.19  Aligned_cols=26  Identities=23%  Similarity=0.526  Sum_probs=22.0

Q ss_pred             CCCCCCCceeecCceeeecCccccccc
Q 029230          108 DKCVGCDRTVYPTEKVSVNGAAYHRSC  134 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~v~~~g~~~H~~C  134 (197)
                      ..|.+|...|+ +-.+.|.+.+||++|
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            88999999887 555668889999998

>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=96.95  E-value=0.00024  Score=35.26  Aligned_cols=29  Identities=34%  Similarity=0.669  Sum_probs=25.5

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHH
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQ   66 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~   66 (197)
                      .|+.|+..|....++..++.+||+.+...
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            48999999998888889999999988654

>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=96.90  E-value=0.0003  Score=34.86  Aligned_cols=27  Identities=22%  Similarity=0.607  Sum_probs=23.2

Q ss_pred             CCCCCCCCceeecCceeeecCccccccc
Q 029230          107 RDKCVGCDRTVYPTEKVSVNGAAYHRSC  134 (197)
Q Consensus       107 ~~~C~~C~~~I~~~e~v~~~g~~~H~~C  134 (197)
                      ..-|..|.+-|+ +..+.+.++.||+.|
T Consensus         5 ssgC~~C~~~It-GkVLEAG~khYHP~C   31 (32)
T d1wiga1           5 SSGCDSCEKYIT-GRVLEAGEKHYHPSC   31 (32)
T ss_dssp             CCSCSSSCCCCS-SCCBCCSSCCBCTTT
T ss_pred             cchhhhhhhhhh-hhhhhccccccCCCC
Confidence            367999999998 556789999999987

>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=96.82  E-value=0.00015  Score=36.06  Aligned_cols=30  Identities=20%  Similarity=0.505  Sum_probs=26.5

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhH
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQL  165 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~  165 (197)
                      .|+.|+..|....++..++++||+.|...+
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            489999999888899999999999998765

>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=96.64  E-value=0.00089  Score=32.98  Aligned_cols=29  Identities=24%  Similarity=0.586  Sum_probs=24.6

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhH
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQL  165 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~  165 (197)
                      .|+.|++.|.. .-.+.+|.+||.+|..++
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 567889999999998764

>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=96.63  E-value=0.0004  Score=34.24  Aligned_cols=27  Identities=22%  Similarity=0.493  Sum_probs=25.1

Q ss_pred             ccccccccccCCCeeecCCeeeccccH
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHF   64 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~   64 (197)
                      +|..|-.+|....|..+|++++|..|-
T Consensus         1 RCaKC~hpLA~E~F~aKd~kI~C~Kc~   27 (31)
T d2cupa2           1 RCAKCLHPLANETFVAKDNKILCNKCT   27 (31)
T ss_dssp             CCSSSCCCTTSSCCEEETTEEECHHHH
T ss_pred             CchhhccccccCcccccCCeEeecccc
Confidence            689999999999999999999999885

>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=96.61  E-value=0.00057  Score=32.05  Aligned_cols=26  Identities=31%  Similarity=0.686  Sum_probs=20.9

Q ss_pred             CCCCCceeecC-ceeeecCcccccccc
Q 029230          110 CVGCDRTVYPT-EKVSVNGAAYHRSCF  135 (197)
Q Consensus       110 C~~C~~~I~~~-e~v~~~g~~~H~~CF  135 (197)
                      |.+|++-+... ..|.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            67888877633 348899999999998

>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=96.45  E-value=0.0015  Score=32.13  Aligned_cols=28  Identities=14%  Similarity=0.513  Sum_probs=25.3

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHH
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHI  163 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~  163 (197)
                      +|+.|-.+|..+.|..+|++++|..|-.
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            5888999999999999999999998854

>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=96.43  E-value=0.0003  Score=34.99  Aligned_cols=29  Identities=28%  Similarity=0.562  Sum_probs=25.2

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHH
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQ   66 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~   66 (197)
                      .|+.|+..|....++..++.+||+.+...
T Consensus         1 vC~dCg~NLKqrG~Ffve~~lyCE~HAr~   29 (31)
T d1x62a1           1 VCTDCGTNLKQKGHFFVEDQIYCEKHARE   29 (31)
T ss_dssp             SCSSSCCCHHHHCCEESSSCEECHHHHHH
T ss_pred             CccccccChhhcceEEeccEEehhhhhhh
Confidence            48999999998888889999999988654

>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=96.29  E-value=0.0013  Score=33.31  Aligned_cols=32  Identities=25%  Similarity=0.564  Sum_probs=27.7

Q ss_pred             ccCcCCCCCC--CCCeeeeCCeeecHHHHHhHhc
Q 029230          136 KCSHGGCTIS--PSNYIAHEGKLYCKHHHIQLFR  167 (197)
Q Consensus       136 ~C~~C~~~l~--~~~~~~~dg~~yC~~cy~~~~~  167 (197)
                      +|+-|+..|.  +...+.+.|.++|+.+|.++||
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            5778888886  5678999999999999999986

>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=96.25  E-value=0.0013  Score=33.52  Aligned_cols=29  Identities=21%  Similarity=0.638  Sum_probs=24.4

Q ss_pred             CCccccccccceeccee-EEeCCccccccc
Q 029230            8 TQQKCMACDKTVYLVDK-LTADNRVYHKAC   36 (197)
Q Consensus         8 ~~~~C~~C~~~I~~~~~-~~~~g~~~H~~C   36 (197)
                      ....|.+|+.-..+.+. |...|..||+.|
T Consensus         6 ~~~~C~RC~~gF~p~EkiVNSnGEl~H~qC   35 (35)
T d1g47a1           6 ASATCERCKGGFAPAEKIVNSNGELYHEQC   35 (35)
T ss_dssp             CCCBCSSSCCBCCSTTTCEEETTEEECTTT
T ss_pred             HHHHHHHHccCCCchHHhhcCCCccccccC
Confidence            45789999999887665 788999999987

>d1x6aa2 g.39.1.3 (A:42-75) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=96.23  E-value=0.0029  Score=32.03  Aligned_cols=31  Identities=26%  Similarity=0.533  Sum_probs=25.0

Q ss_pred             cccCcCCCCCCC-CCeeee-CCeeecHHHHHhH
Q 029230          135 FKCSHGGCTISP-SNYIAH-EGKLYCKHHHIQL  165 (197)
Q Consensus       135 F~C~~C~~~l~~-~~~~~~-dg~~yC~~cy~~~  165 (197)
                      |.|..|+.-|.. +.|... ..++||..||.+.
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            789999998875 556554 5899999999875

>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=96.21  E-value=0.0011  Score=31.10  Aligned_cols=26  Identities=35%  Similarity=0.685  Sum_probs=21.6

Q ss_pred             ccccccceec-ceeEEeCCcccccccc
Q 029230           12 CMACDKTVYL-VDKLTADNRVYHKACF   37 (197)
Q Consensus        12 C~~C~~~I~~-~~~~~~~g~~~H~~CF   37 (197)
                      |.+|++.+.. +.-+.++++.||..||
T Consensus         1 cggcgedvvgdgagvvaldrvfhvgcf   27 (27)
T d1x61a1           1 CGGCGEDVVGDGAGVVALDRVFHVGCF   27 (27)
T ss_dssp             CSSSCSCCCSSSCCEECSSSEECTTTC
T ss_pred             CCCcccccccCCcceEEEeeeEEeccC
Confidence            7889988863 3458999999999998

>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=96.07  E-value=0.0015  Score=33.35  Aligned_cols=27  Identities=41%  Similarity=0.859  Sum_probs=24.0

Q ss_pred             CCCCCCCceeecCce-eeecCccccccc
Q 029230          108 DKCVGCDRTVYPTEK-VSVNGAAYHRSC  134 (197)
Q Consensus       108 ~~C~~C~~~I~~~e~-v~~~g~~~H~~C  134 (197)
                      -.|.+|+....+.|. |...|..||..|
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            579999999999987 579999999987

>d1rutx2 g.39.1.3 (X:49-82) LIM only 4 (Lmo4) {Mouse (Mus musculus) [TaxId: 10090]}

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

Probab=95.98  E-value=0.0014  Score=33.21  Aligned_cols=32  Identities=25%  Similarity=0.644  Sum_probs=26.6

Q ss_pred             cccccccccc--CCCeeecCCeeeccccHHHHhh
Q 029230           38 RCHHCKGTLK--LSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        38 ~C~~C~~~L~--~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      +|+-|+..|.  +.+.+.+.|.++|+.+|.++|+
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            4777888886  3467889999999999999984

>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=95.28  E-value=0.0068  Score=29.99  Aligned_cols=30  Identities=30%  Similarity=0.588  Sum_probs=26.9

Q ss_pred             ccccccccccCCCeeecCCeeeccccHHHH
Q 029230           38 RCHHCKGTLKLSNFNSFEGVLYCRPHFDQL   67 (197)
Q Consensus        38 ~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~   67 (197)
                      +|..|...|.+..|+-..|+.+|.+|..+.
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            689999999999999999999999998653

>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=95.22  E-value=0.014  Score=28.87  Aligned_cols=30  Identities=13%  Similarity=0.431  Sum_probs=26.7

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHHHhH
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHHIQL  165 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy~~~  165 (197)
                      +|..|...|..-.|....|+.+|.+|..+.
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            588999999998999999999999998753

>d1x6aa1 g.39.1.3 (A:8-41) Lim domain kinase 2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=95.15  E-value=0.0046  Score=31.32  Aligned_cols=29  Identities=21%  Similarity=0.367  Sum_probs=25.2

Q ss_pred             CCCccccccccceecceeEEeCCccccccc
Q 029230            7 GTQQKCMACDKTVYLVDKLTADNRVYHKAC   36 (197)
Q Consensus         7 ~~~~~C~~C~~~I~~~~~~~~~g~~~H~~C   36 (197)
                      .....|..|...|. +.++.+.+.-||++|
T Consensus         6 kfge~C~~C~~~it-GpvMvAG~~K~HPEC   34 (34)
T d1x6aa1           6 KFGEFCHGCSLLMT-GPFMVAGEFKYHPEC   34 (34)
T ss_dssp             CSSCBCTTTCCBCC-SCCBCCTTCCBCTTS
T ss_pred             HHHHHhhhhHhhcc-cceeeecccccCCCC
Confidence            34578999999886 899999999999998

>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=95.08  E-value=0.0052  Score=32.45  Aligned_cols=28  Identities=21%  Similarity=0.532  Sum_probs=21.3

Q ss_pred             CCCCCCceeecCcee-eecCccccccccc
Q 029230          109 KCVGCDRTVYPTEKV-SVNGAAYHRSCFK  136 (197)
Q Consensus       109 ~C~~C~~~I~~~e~v-~~~g~~~H~~CF~  136 (197)
                      .|++|++....+|-+ ...+..||+.|-.
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            489999998888654 4566789998854

>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=94.98  E-value=0.0077  Score=29.85  Aligned_cols=27  Identities=26%  Similarity=0.701  Sum_probs=22.5

Q ss_pred             ccccccccccCC-CeeecCCeeeccccH
Q 029230           38 RCHHCKGTLKLS-NFNSFEGVLYCRPHF   64 (197)
Q Consensus        38 ~C~~C~~~L~~~-~f~~~~g~~yC~~c~   64 (197)
                      +|+.|...|.++ .|...+|.+||+.+-
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            488899999765 688899999999763

>d2cora1 g.39.1.3 (A:43-73) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=94.63  E-value=0.0075  Score=29.54  Aligned_cols=28  Identities=32%  Similarity=0.816  Sum_probs=22.6

Q ss_pred             cccccccccCCCeeecCCeeeccccHHHH
Q 029230           39 CHHCKGTLKLSNFNSFEGVLYCRPHFDQL   67 (197)
Q Consensus        39 C~~C~~~L~~~~f~~~~g~~yC~~c~~~~   67 (197)
                      |+.|++.|.. .-.+..|++||-+|..++
T Consensus         2 C~~Cgkelta-dArEl~geLyCLpChdKm   29 (31)
T d2cora1           2 CANCGKELTA-DARELKGELYCLPCHDKM   29 (31)
T ss_dssp             CSSSCCBCCT-TCEEETTEEECHHHHHTT
T ss_pred             ccccccccch-hHHHhcCCEEEEeccccc
Confidence            7899999975 345689999999998653

>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=94.53  E-value=0.01  Score=30.17  Aligned_cols=29  Identities=17%  Similarity=0.433  Sum_probs=24.4

Q ss_pred             CCCCCCCCCceeecCceeeecCcccccccc
Q 029230          106 TRDKCVGCDRTVYPTEKVSVNGAAYHRSCF  135 (197)
Q Consensus       106 ~~~~C~~C~~~I~~~e~v~~~g~~~H~~CF  135 (197)
                      +...|..|...|.. +.+.+.|..||+..|
T Consensus         7 Gk~vC~KCh~iIdd-~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           7 GKYICQKCHAIIDE-QPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCBCTTTCCBCCS-CCCCCSSSCCCTTTS
T ss_pred             hhHHHHHHHhhhhc-CcceecCCCCCCCCC
Confidence            34789999998864 568999999999887

>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=94.51  E-value=0.013  Score=29.51  Aligned_cols=31  Identities=23%  Similarity=0.627  Sum_probs=24.7

Q ss_pred             cccccccccccCC-CeeecC-CeeeccccHHHH
Q 029230           37 FRCHHCKGTLKLS-NFNSFE-GVLYCRPHFDQL   67 (197)
Q Consensus        37 F~C~~C~~~L~~~-~f~~~~-g~~yC~~c~~~~   67 (197)
                      |.|..|+.-+.++ +|...+ .++||..||.+.
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            7899999999876 566554 589999999764

>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=93.77  E-value=0.02  Score=28.28  Aligned_cols=26  Identities=23%  Similarity=0.562  Sum_probs=20.8

Q ss_pred             ccCcCCCCCC-CCCeeeeCCeeecHHH
Q 029230          136 KCSHGGCTIS-PSNYIAHEGKLYCKHH  161 (197)
Q Consensus       136 ~C~~C~~~l~-~~~~~~~dg~~yC~~c  161 (197)
                      .|+.|...|. ++.|...+|.+||+.+
T Consensus         1 tC~tC~n~LVPGDRFHyvNG~lfCE~D   27 (33)
T d1rutx4           1 TCSTCRNRLVPGDRFHYINGSLFCEHD   27 (33)
T ss_dssp             BCTTTCCBCCTTCEEEEETTEEEEGGG
T ss_pred             CcccccccccCCceeEEecCEEEEecC
Confidence            4778877775 5778999999999865

>d2cora2 g.39.1.3 (A:8-42) Pinch (particularly interesting new Cys-His) protein {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=93.43  E-value=0.02  Score=29.10  Aligned_cols=32  Identities=25%  Similarity=0.389  Sum_probs=26.4

Q ss_pred             CCCCCccccccccceecceeEEeCCcccccccc
Q 029230            5 FGGTQQKCMACDKTVYLVDKLTADNRVYHKACF   37 (197)
Q Consensus         5 ~~~~~~~C~~C~~~I~~~~~~~~~g~~~H~~CF   37 (197)
                      .+.+.-+|.+|...|. .+-+...|..||+..|
T Consensus         4 ~glGk~vC~KCh~iId-d~pL~Fr~d~YHp~HF   35 (35)
T d2cora2           4 RGLGKYICQKCHAIID-EQPLIFKNDPYHPDHF   35 (35)
T ss_dssp             CCCCCCBCTTTCCBCC-SCCCCCSSSCCCTTTS
T ss_pred             cchhhHHHHHHHhhhh-cCcceecCCCCCCCCC
Confidence            3456678999999996 5778899999999876

>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=93.01  E-value=0.018  Score=30.34  Aligned_cols=28  Identities=18%  Similarity=0.542  Sum_probs=19.8

Q ss_pred             cccccccceecceeE-EeCCccccccccc
Q 029230           11 KCMACDKTVYLVDKL-TADNRVYHKACFR   38 (197)
Q Consensus        11 ~C~~C~~~I~~~~~~-~~~g~~~H~~CF~   38 (197)
                      .|.+|++.+..++-+ ...+..||+.|-.
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            388888888776554 5556679988743

>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=91.92  E-value=0.055  Score=26.67  Aligned_cols=26  Identities=19%  Similarity=0.431  Sum_probs=23.2

Q ss_pred             cccccccccCCCeeecCCeeeccccH
Q 029230           39 CHHCKGTLKLSNFNSFEGVLYCRPHF   64 (197)
Q Consensus        39 C~~C~~~L~~~~f~~~~g~~yC~~c~   64 (197)
                      |..|+.+|.+..|......++|.+|-
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            77899999999999999999999884

>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=90.75  E-value=0.084  Score=33.47  Aligned_cols=34  Identities=15%  Similarity=0.326  Sum_probs=24.4

Q ss_pred             ccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           36 CFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        36 CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      =++|..|...|........=|+.||..|..+.+.
T Consensus        22 ~l~C~IC~~~~~~pv~~~~CgH~fC~~Ci~~~~~   55 (97)
T d1jm7b_          22 LLRCSRCTNILREPVCLGGCEHIFCSNCVSDCIG   55 (97)
T ss_dssp             TTSCSSSCSCCSSCBCCCSSSCCBCTTTGGGGTT
T ss_pred             cCCCccCCchhhcCceeCCCCCchhHHHHHHHHh
Confidence            3688999888875433334589999999876654

>d1x68a2 g.39.1.3 (A:37-70) Four and a half LIM domains protein 5, FHL-5 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=90.03  E-value=0.092  Score=25.82  Aligned_cols=25  Identities=8%  Similarity=0.587  Sum_probs=21.7

Q ss_pred             cCcCCCCCCCCCeeeeCCeeecHHH
Q 029230          137 CSHGGCTISPSNYIAHEGKLYCKHH  161 (197)
Q Consensus       137 C~~C~~~l~~~~~~~~dg~~yC~~c  161 (197)
                      |..|+..|.+..|.-.+..++|..|
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            6678888999899999999999887

>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=89.89  E-value=0.043  Score=27.17  Aligned_cols=28  Identities=29%  Similarity=0.680  Sum_probs=21.6

Q ss_pred             ccCcCCCCCCCCCeee--eCCeeecHHHHH
Q 029230          136 KCSHGGCTISPSNYIA--HEGKLYCKHHHI  163 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~--~dg~~yC~~cy~  163 (197)
                      +|..|..+|-.+.|..  .||.+||..|+.
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            5778888988777654  589999987754

>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=89.18  E-value=0.12  Score=25.42  Aligned_cols=30  Identities=23%  Similarity=0.397  Sum_probs=23.0

Q ss_pred             ccccccccccC--CCeeecCCeeeccccHHHH
Q 029230           38 RCHHCKGTLKL--SNFNSFEGVLYCRPHFDQL   67 (197)
Q Consensus        38 ~C~~C~~~L~~--~~f~~~~g~~yC~~c~~~~   67 (197)
                      .|.-|+..|..  ...+.+.+.++|+.+|.++
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            56777777864  3567789999999999753

>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=88.57  E-value=0.26  Score=25.36  Aligned_cols=19  Identities=32%  Similarity=0.725  Sum_probs=9.4

Q ss_pred             CCCCCceeecCceeeecCc
Q 029230          110 CVGCDRTVYPTEKVSVNGA  128 (197)
Q Consensus       110 C~~C~~~I~~~e~v~~~g~  128 (197)
                      |+.|.++.-++++|++.|+
T Consensus         3 C~vCr~pFP~GDRVTFnGK   21 (40)
T d1v6ga2           3 CAVCRLPFPPGDRVTFNGK   21 (40)
T ss_dssp             CSSSCCCCCSSSCEEEETT
T ss_pred             ccccCCCCCCCCeEEEcCc
Confidence            4455555544555544444

>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=88.29  E-value=0.3  Score=29.55  Aligned_cols=35  Identities=9%  Similarity=0.098  Sum_probs=28.2

Q ss_pred             ccccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           34 KACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        34 ~~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      ++-|.|..|...+.+ .....-|..||..|..+.+.
T Consensus         5 P~~l~CpIc~~l~~d-Pv~~~cGhtfc~~ci~~~l~   39 (80)
T d2c2la2           5 PDYLCGKISFELMRE-PCITPSGITYDRKDIEEHLQ   39 (80)
T ss_dssp             CSTTBCTTTCSBCSS-EEECSSCCEEETTHHHHHHH
T ss_pred             CccccCcCcCchhhh-hcccCCcCeecHHHHHHHHh
Confidence            567999999988875 45567899999999887664

>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=86.89  E-value=0.25  Score=27.85  Aligned_cols=33  Identities=9%  Similarity=0.186  Sum_probs=23.6

Q ss_pred             cccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           37 FRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        37 F~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      +.|..|...+.+.-.....|..||..|..+-+.
T Consensus         1 l~C~Ic~~~~~~Pv~~~~cGh~fc~~cI~~~l~   33 (56)
T d2baya1           1 MLCAISGKVPRRPVLSPKSRTIFEKSLLEQYVK   33 (56)
T ss_dssp             CCCTTTCSCCSSEEEETTTTEEEEHHHHHHHHH
T ss_pred             CCCccCCchHHhcCccCCCCCcccHHHHHHHHh
Confidence            357888887764333345799999999877654

>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=86.09  E-value=0.16  Score=24.48  Aligned_cols=27  Identities=22%  Similarity=0.303  Sum_probs=16.0

Q ss_pred             ccCcCCCCCCCCCeeeeCCeeecHHHH
Q 029230          136 KCSHGGCTISPSNYIAHEGKLYCKHHH  162 (197)
Q Consensus       136 ~C~~C~~~l~~~~~~~~dg~~yC~~cy  162 (197)
                      +|..|+.---...-...+|+|.|++.|
T Consensus         5 rcdvcgeytyeadakllngkpvckpdy   31 (33)
T d2gvia2           5 RCDVCGEYTYEADAKLLNGKPVCKPDY   31 (33)
T ss_dssp             ECTTTCCEEEGGGCEEETTEEECHHHH
T ss_pred             EEeeccceeeccchhhhCCCcccCccc
Confidence            455555422222344568899998887

>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=85.85  E-value=0.28  Score=30.42  Aligned_cols=34  Identities=21%  Similarity=0.370  Sum_probs=26.6

Q ss_pred             cccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           35 ACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        35 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      .-+.|..|...+.. .....=|..||..|..+.+.
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            45889999888864 45556799999999987764

>d1x4la2 g.39.1.3 (A:37-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=85.64  E-value=0.2  Score=23.82  Aligned_cols=27  Identities=19%  Similarity=0.315  Sum_probs=22.6

Q ss_pred             cccccccccCCCeeecCCeeeccccHH
Q 029230           39 CHHCKGTLKLSNFNSFEGVLYCRPHFD   65 (197)
Q Consensus        39 C~~C~~~L~~~~f~~~~g~~yC~~c~~   65 (197)
                      |..|..+|.+..|...-..++|.+|-.
T Consensus         2 c~kcsvslvgrgflterddilc~dcgk   28 (30)
T d1x4la2           2 CKKCSLSLVGRGFLTERDDILCPDCGK   28 (30)
T ss_dssp             CSSSCCBCTTSCCEECSSSEECHHHHH
T ss_pred             cceeeEEEEeeeccccccceeccccCc
Confidence            778899999889988778899988753

>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=84.02  E-value=0.73  Score=27.49  Aligned_cols=34  Identities=21%  Similarity=0.281  Sum_probs=27.0

Q ss_pred             cccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           35 ACFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        35 ~CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      .=|.|..|...+.+ ......|..||..|..+.+.
T Consensus         7 ~~l~CpIc~~~m~d-PV~~~cgh~fc~~ci~~~~~   40 (78)
T d1t1ha_           7 EYFRCPISLELMKD-PVIVSTGQTYERSSIQKWLD   40 (78)
T ss_dssp             SSSSCTTTSCCCSS-EEEETTTEEEEHHHHHHHHT
T ss_pred             ccCCCcCcCchhhC-ceEccCCCcchHHHHHHHHH
Confidence            45899999988875 44567899999999987664

>d1x4la2 g.39.1.3 (A:37-66) Four and a half LIM domains protein 2, FHL2 {Human (Homo sapiens) [TaxId: 9606]}

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

Probab=83.06  E-value=0.56  Score=22.15  Aligned_cols=27  Identities=7%  Similarity=0.374  Sum_probs=22.1

Q ss_pred             cCcCCCCCCCCCeeeeCCeeecHHHHH
Q 029230          137 CSHGGCTISPSNYIAHEGKLYCKHHHI  163 (197)
Q Consensus       137 C~~C~~~l~~~~~~~~dg~~yC~~cy~  163 (197)
                      |..|...|.+..|....+.++|..|-.
T Consensus         2 c~kcsvslvgrgflterddilc~dcgk   28 (30)
T d1x4la2           2 CKKCSLSLVGRGFLTERDDILCPDCGK   28 (30)
T ss_dssp             CSSSCCBCTTSCCEECSSSEECHHHHH
T ss_pred             cceeeEEEEeeeccccccceeccccCc
Confidence            667778888888888888899998854

>d1jm7a_ g.44.1.1 (A:) brca1 RING domain {Human (Homo sapiens) [TaxId: 9606]}

class: Small proteins
fold: RING/U-box
superfamily: RING/U-box
family: RING finger domain, C3HC4
domain: brca1 RING domain
species: Human (Homo sapiens) [TaxId: 9606]

Probab=81.36  E-value=0.79  Score=28.93  Aligned_cols=33  Identities=15%  Similarity=0.368  Sum_probs=24.6

Q ss_pred             ccccccccccccCCCeeecCCeeeccccHHHHhh
Q 029230           36 CFRCHHCKGTLKLSNFNSFEGVLYCRPHFDQLFK   69 (197)
Q Consensus        36 CF~C~~C~~~L~~~~f~~~~g~~yC~~c~~~~~~   69 (197)
                      -+.|..|...+.. .....=|+.||..|..+.+.
T Consensus        21 ~l~CpIC~~~~~~-pv~~~CgH~fC~~Ci~~~~~   53 (103)
T d1jm7a_          21 ILECPICLELIKE-PVSTKCDHIFCKFCMLKLLN   53 (103)
T ss_dssp             HTSCSSSCCCCSS-CCBCTTSCCCCSHHHHHHHH
T ss_pred             CcCCCccCchhCC-eEEcCCCCchhhHHHHHHHH
Confidence            3678888877764 44456789999999887664

>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=80.47  E-value=0.46  Score=24.39  Aligned_cols=29  Identities=14%  Similarity=0.358  Sum_probs=22.4

Q ss_pred             cccCcCCCCCCC-CCeeeeCCeeecHHHHH
Q 029230          135 FKCSHGGCTISP-SNYIAHEGKLYCKHHHI  163 (197)
Q Consensus       135 F~C~~C~~~l~~-~~~~~~dg~~yC~~cy~  163 (197)
                      |+|+.|.+++.. ++....+..-.|..|-.
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            048899999985 45667778899999965